Starting phenix.real_space_refine on Tue Mar 3 21:47:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m1h_30047/03_2026/6m1h_30047.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m1h_30047/03_2026/6m1h_30047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m1h_30047/03_2026/6m1h_30047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m1h_30047/03_2026/6m1h_30047.map" model { file = "/net/cci-nas-00/data/ceres_data/6m1h_30047/03_2026/6m1h_30047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m1h_30047/03_2026/6m1h_30047.cif" } resolution = 3.6 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= 0.000 sd= 0.003 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 63 5.16 5 C 5745 2.51 5 N 1563 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2765 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 476 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "C" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2595 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1803 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 209} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.43, per 1000 atoms: 0.27 Number of scatterers: 9036 At special positions: 0 Unit cell: (102.554, 106.918, 153.831, 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 63 16.00 O 1665 8.00 N 1563 7.00 C 5745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 118 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 5 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 107 " distance=2.02 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: 0.87 Conformation dependent library (CDL) restraints added in 415.5 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 37.9% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.722A pdb=" N ALA A 133 " --> pdb=" O HIS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 178 removed outlier: 3.630A pdb=" N LEU A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 205 removed outlier: 3.648A pdb=" N HIS A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 removed outlier: 3.910A pdb=" N HIS A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 253 removed outlier: 4.168A pdb=" N ALA A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.642A pdb=" N PHE A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 290 removed outlier: 3.576A pdb=" N LEU A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 336 removed outlier: 3.716A pdb=" N ILE A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix removed outlier: 3.510A pdb=" N PHE A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 363 Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 366 through 372 Processing helix chain 'A' and resid 381 through 391 removed outlier: 4.187A pdb=" N LEU A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.527A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 removed outlier: 4.363A pdb=" N ARG A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 31 removed outlier: 3.521A pdb=" N ASP B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.608A pdb=" N LYS B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'D' and resid 7 through 13 removed outlier: 4.094A pdb=" N GLN D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 24 removed outlier: 4.081A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 4.024A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 23 removed outlier: 4.096A pdb=" N ALA E 21 " --> pdb=" O GLN E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 26 No H-bonds generated for 'chain 'E' and resid 24 through 26' Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.741A pdb=" N ILE E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 14 Processing helix chain 'F' and resid 15 through 37 removed outlier: 3.959A pdb=" N ARG F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS F 25 " --> pdb=" O GLU F 21 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS F 32 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP F 33 " --> pdb=" O GLN F 29 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN F 35 " --> pdb=" O GLN F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 removed outlier: 3.886A pdb=" N LYS F 271 " --> pdb=" O GLN F 267 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU F 272 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 312 Processing helix chain 'F' and resid 313 through 318 removed outlier: 3.554A pdb=" N ALA F 316 " --> pdb=" O PRO F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 350 removed outlier: 3.613A pdb=" N LYS F 338 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE F 341 " --> pdb=" O ALA F 337 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP F 343 " --> pdb=" O TYR F 339 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU F 346 " --> pdb=" O ARG F 342 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 348 " --> pdb=" O GLU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 391 removed outlier: 4.520A pdb=" N ASP F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG F 380 " --> pdb=" O PHE F 376 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE F 382 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS F 387 " --> pdb=" O ILE F 383 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 76 removed outlier: 3.723A pdb=" N GLU A 71 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS A 118 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 73 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.650A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.606A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 37 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N MET C 34 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.696A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 46 through 51 removed outlier: 6.966A pdb=" N ILE E 338 " --> pdb=" O ARG E 48 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR E 50 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU E 336 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS E 317 " --> pdb=" O GLY E 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 58 through 63 removed outlier: 3.562A pdb=" N ALA E 60 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER E 74 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU E 79 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA E 92 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 81 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 100 through 105 removed outlier: 6.370A pdb=" N CYS E 121 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU E 138 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE E 123 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG E 134 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 149 through 151 removed outlier: 3.935A pdb=" N ILE E 157 " --> pdb=" O TRP E 169 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA E 167 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN E 175 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 187 through 192 removed outlier: 3.528A pdb=" N SER E 189 " --> pdb=" O GLY E 202 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL E 200 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 201 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS E 209 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 229 through 234 removed outlier: 6.845A pdb=" N GLY E 244 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE E 232 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA E 242 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE E 234 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA E 240 " --> pdb=" O PHE E 234 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE E 241 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET E 262 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP E 254 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU E 260 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 273 through 278 removed outlier: 4.194A pdb=" N SER E 275 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP E 298 " --> pdb=" O ARG E 304 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ARG E 304 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 210 through 214 removed outlier: 3.628A pdb=" N PHE F 212 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 45 " --> pdb=" O PHE F 222 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG F 42 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE F 245 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU F 44 " --> pdb=" O ILE F 245 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL F 247 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU F 46 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE F 244 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE F 290 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE F 246 " --> pdb=" O PHE F 290 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 882 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: 1.46 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2920 1.34 - 1.46: 2132 1.46 - 1.58: 4097 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 9235 Sorted by residual: bond pdb=" N VAL A 368 " pdb=" CA VAL A 368 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.04e+00 bond pdb=" N THR A 367 " pdb=" CA THR A 367 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.87e+00 bond pdb=" N THR A 355 " pdb=" CA THR A 355 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.85e+00 bond pdb=" N PHE A 371 " pdb=" CA PHE A 371 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.97e+00 bond pdb=" N LEU A 35 " pdb=" CA LEU A 35 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.86e+00 ... (remaining 9230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 12217 2.65 - 5.30: 258 5.30 - 7.95: 22 7.95 - 10.59: 4 10.59 - 13.24: 2 Bond angle restraints: 12503 Sorted by residual: angle pdb=" N ILE F 372 " pdb=" CA ILE F 372 " pdb=" C ILE F 372 " ideal model delta sigma weight residual 111.62 105.62 6.00 7.90e-01 1.60e+00 5.76e+01 angle pdb=" N ILE F 56 " pdb=" CA ILE F 56 " pdb=" C ILE F 56 " ideal model delta sigma weight residual 111.77 105.90 5.87 1.04e+00 9.25e-01 3.18e+01 angle pdb=" N VAL F 57 " pdb=" CA VAL F 57 " pdb=" C VAL F 57 " ideal model delta sigma weight residual 111.91 107.45 4.46 8.90e-01 1.26e+00 2.51e+01 angle pdb=" C ASP E 195 " pdb=" N THR E 196 " pdb=" CA THR E 196 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" N LYS B 56 " pdb=" CA LYS B 56 " pdb=" C LYS B 56 " ideal model delta sigma weight residual 113.28 108.06 5.22 1.22e+00 6.72e-01 1.83e+01 ... (remaining 12498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 4789 17.33 - 34.67: 551 34.67 - 52.00: 108 52.00 - 69.34: 17 69.34 - 86.67: 10 Dihedral angle restraints: 5475 sinusoidal: 2166 harmonic: 3309 Sorted by residual: dihedral pdb=" CA ARG A 177 " pdb=" C ARG A 177 " pdb=" N PHE A 178 " pdb=" CA PHE A 178 " ideal model delta harmonic sigma weight residual -180.00 -137.40 -42.60 0 5.00e+00 4.00e-02 7.26e+01 dihedral pdb=" CB CYS A 226 " pdb=" SG CYS A 226 " pdb=" SG CYS A 296 " pdb=" CB CYS A 296 " ideal model delta sinusoidal sigma weight residual 93.00 19.71 73.29 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CA ASP E 312 " pdb=" C ASP E 312 " pdb=" N ASN E 313 " pdb=" CA ASN E 313 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 5472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 995 0.059 - 0.118: 307 0.118 - 0.177: 67 0.177 - 0.236: 10 0.236 - 0.295: 1 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CB ILE C 70 " pdb=" CA ILE C 70 " pdb=" CG1 ILE C 70 " pdb=" CG2 ILE C 70 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB THR C 91 " pdb=" CA THR C 91 " pdb=" OG1 THR C 91 " pdb=" CG2 THR C 91 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE E 232 " pdb=" CA ILE E 232 " pdb=" CG1 ILE E 232 " pdb=" CG2 ILE E 232 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1377 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 276 " 0.050 5.00e-02 4.00e+02 7.47e-02 8.93e+00 pdb=" N PRO A 277 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 235 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO E 236 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 101 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.46e+00 pdb=" N PRO C 102 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " -0.035 5.00e-02 4.00e+02 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 43 2.41 - 3.03: 4970 3.03 - 3.65: 13930 3.65 - 4.28: 20265 4.28 - 4.90: 32966 Nonbonded interactions: 72174 Sorted by model distance: nonbonded pdb=" CD2 PHE A 369 " pdb=" CG GLU A 385 " model vdw 1.782 3.740 nonbonded pdb=" CE2 PHE A 369 " pdb=" CG GLU A 385 " model vdw 1.855 3.740 nonbonded pdb=" CE2 PHE A 369 " pdb=" CB GLU A 385 " model vdw 2.060 3.740 nonbonded pdb=" CA GLN A 31 " pdb=" SG CYS A 34 " model vdw 2.171 3.830 nonbonded pdb=" OG SER E 331 " pdb=" OD1 ASP E 333 " model vdw 2.227 3.040 ... (remaining 72169 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.410 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.007 0.063 9242 Z= 0.345 Angle : 0.959 13.242 12517 Z= 0.557 Chirality : 0.059 0.295 1380 Planarity : 0.007 0.075 1597 Dihedral : 15.336 86.669 3312 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.21 % Allowed : 12.45 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.70 (0.21), residues: 1115 helix: -3.94 (0.16), residues: 387 sheet: -2.34 (0.32), residues: 223 loop : -2.66 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 22 TYR 0.034 0.002 TYR E 59 PHE 0.025 0.003 PHE F 363 TRP 0.019 0.003 TRP A 306 HIS 0.012 0.002 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00721 ( 9235) covalent geometry : angle 0.95687 (12503) SS BOND : bond 0.00518 ( 7) SS BOND : angle 2.25737 ( 14) hydrogen bonds : bond 0.31416 ( 317) hydrogen bonds : angle 10.74405 ( 882) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.5849 (m100) cc_final: 0.5121 (m100) REVERT: A 232 PHE cc_start: 0.8849 (t80) cc_final: 0.8546 (t80) REVERT: B 16 LYS cc_start: 0.9072 (mttm) cc_final: 0.8800 (mtpp) REVERT: B 37 MET cc_start: 0.6953 (tpp) cc_final: 0.6285 (tpt) REVERT: B 55 LYS cc_start: 0.9301 (mmmt) cc_final: 0.9098 (mmmt) REVERT: C 73 ASP cc_start: 0.6762 (t0) cc_final: 0.5173 (t0) REVERT: C 90 ASP cc_start: 0.8441 (m-30) cc_final: 0.8083 (m-30) REVERT: E 58 ILE cc_start: 0.9319 (mt) cc_final: 0.8672 (tt) REVERT: E 118 ASP cc_start: 0.8535 (p0) cc_final: 0.8001 (p0) REVERT: E 120 ILE cc_start: 0.8987 (mt) cc_final: 0.8697 (mm) REVERT: E 297 TRP cc_start: 0.8316 (m100) cc_final: 0.7172 (m100) REVERT: F 35 GLN cc_start: 0.7602 (pp30) cc_final: 0.7373 (pp30) REVERT: F 222 PHE cc_start: 0.7446 (m-80) cc_final: 0.7119 (m-10) outliers start: 2 outliers final: 1 residues processed: 236 average time/residue: 0.1193 time to fit residues: 37.1523 Evaluate side-chains 179 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 234 HIS A 240 ASN A 404 ASN ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS E 340 ASN F 41 HIS F 220 HIS F 279 ASN F 377 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.115922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.092320 restraints weight = 24563.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094689 restraints weight = 12489.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.096305 restraints weight = 8377.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.097153 restraints weight = 6588.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.097807 restraints weight = 5770.693| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9242 Z= 0.119 Angle : 0.599 6.920 12517 Z= 0.324 Chirality : 0.043 0.171 1380 Planarity : 0.005 0.051 1597 Dihedral : 5.601 33.005 1237 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.26 % Allowed : 14.81 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.57 (0.22), residues: 1115 helix: -2.54 (0.21), residues: 397 sheet: -1.93 (0.31), residues: 238 loop : -2.28 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 347 TYR 0.026 0.001 TYR A 157 PHE 0.014 0.001 PHE C 103 TRP 0.015 0.002 TRP A 306 HIS 0.010 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9235) covalent geometry : angle 0.59753 (12503) SS BOND : bond 0.01052 ( 7) SS BOND : angle 1.31524 ( 14) hydrogen bonds : bond 0.04316 ( 317) hydrogen bonds : angle 5.67222 ( 882) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.5671 (m100) cc_final: 0.4997 (m100) REVERT: A 210 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8244 (pt) REVERT: B 16 LYS cc_start: 0.9147 (mttm) cc_final: 0.8943 (mtpp) REVERT: B 20 HIS cc_start: 0.8949 (t-90) cc_final: 0.8712 (t70) REVERT: B 29 GLN cc_start: 0.9393 (tp-100) cc_final: 0.8956 (tp-100) REVERT: B 47 VAL cc_start: 0.9060 (t) cc_final: 0.8667 (p) REVERT: B 48 PHE cc_start: 0.8891 (t80) cc_final: 0.8613 (t80) REVERT: B 52 MET cc_start: 0.8870 (mmm) cc_final: 0.8645 (mmm) REVERT: C 18 LEU cc_start: 0.8314 (tp) cc_final: 0.7700 (tp) REVERT: C 39 GLN cc_start: 0.7404 (tt0) cc_final: 0.7061 (tp40) REVERT: C 53 GLN cc_start: 0.6802 (OUTLIER) cc_final: 0.6599 (mm110) REVERT: C 73 ASP cc_start: 0.7019 (t0) cc_final: 0.6552 (t0) REVERT: C 80 TYR cc_start: 0.7490 (m-80) cc_final: 0.7017 (m-80) REVERT: C 83 MET cc_start: 0.7305 (mpp) cc_final: 0.6953 (mpp) REVERT: C 95 TYR cc_start: 0.7991 (m-80) cc_final: 0.7767 (m-10) REVERT: D 18 GLN cc_start: 0.7125 (mp10) cc_final: 0.6537 (mp10) REVERT: D 32 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.9005 (ptpp) REVERT: E 58 ILE cc_start: 0.9355 (mt) cc_final: 0.8645 (tt) REVERT: E 118 ASP cc_start: 0.8338 (p0) cc_final: 0.8008 (p0) REVERT: F 360 TYR cc_start: 0.8102 (m-80) cc_final: 0.7876 (m-80) outliers start: 22 outliers final: 7 residues processed: 234 average time/residue: 0.0932 time to fit residues: 30.2195 Evaluate side-chains 189 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 0.0070 chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 0.0000 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN F 41 HIS ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.117529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.093792 restraints weight = 24724.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.096175 restraints weight = 12553.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.097818 restraints weight = 8457.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.098679 restraints weight = 6663.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.099395 restraints weight = 5848.714| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9242 Z= 0.106 Angle : 0.579 10.939 12517 Z= 0.305 Chirality : 0.042 0.160 1380 Planarity : 0.004 0.037 1597 Dihedral : 4.870 27.983 1235 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.57 % Allowed : 18.31 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.23), residues: 1115 helix: -1.71 (0.23), residues: 406 sheet: -1.59 (0.32), residues: 219 loop : -1.90 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 105 TYR 0.022 0.001 TYR A 157 PHE 0.028 0.001 PHE F 363 TRP 0.013 0.001 TRP A 243 HIS 0.009 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9235) covalent geometry : angle 0.57666 (12503) SS BOND : bond 0.00171 ( 7) SS BOND : angle 1.64747 ( 14) hydrogen bonds : bond 0.03631 ( 317) hydrogen bonds : angle 4.99406 ( 882) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.5561 (m100) cc_final: 0.4581 (m100) REVERT: A 214 GLN cc_start: 0.7611 (mm110) cc_final: 0.7355 (mm-40) REVERT: A 241 TYR cc_start: 0.8891 (m-80) cc_final: 0.8659 (m-80) REVERT: A 306 TRP cc_start: 0.7642 (OUTLIER) cc_final: 0.6780 (t60) REVERT: C 18 LEU cc_start: 0.8294 (tp) cc_final: 0.7494 (mt) REVERT: C 34 MET cc_start: 0.7915 (mmm) cc_final: 0.7647 (mmm) REVERT: C 78 THR cc_start: 0.8138 (p) cc_final: 0.7750 (p) REVERT: C 83 MET cc_start: 0.7423 (mpp) cc_final: 0.7191 (mpp) REVERT: C 95 TYR cc_start: 0.7984 (m-80) cc_final: 0.7774 (m-10) REVERT: D 21 MET cc_start: 0.7656 (mpp) cc_final: 0.7369 (mpp) REVERT: E 58 ILE cc_start: 0.9321 (mt) cc_final: 0.8591 (tt) REVERT: E 61 MET cc_start: 0.8542 (ppp) cc_final: 0.8098 (ppp) REVERT: E 118 ASP cc_start: 0.8337 (p0) cc_final: 0.8101 (p0) REVERT: F 272 LEU cc_start: 0.9336 (tp) cc_final: 0.9098 (tt) REVERT: F 360 TYR cc_start: 0.8037 (m-80) cc_final: 0.7732 (m-80) outliers start: 25 outliers final: 15 residues processed: 234 average time/residue: 0.0909 time to fit residues: 29.4217 Evaluate side-chains 201 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS F 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.113603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089410 restraints weight = 25361.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091767 restraints weight = 13244.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.093344 restraints weight = 9017.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.094293 restraints weight = 7173.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.094756 restraints weight = 6266.377| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9242 Z= 0.178 Angle : 0.610 9.242 12517 Z= 0.328 Chirality : 0.044 0.164 1380 Planarity : 0.004 0.041 1597 Dihedral : 5.109 30.855 1235 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.81 % Allowed : 18.72 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.51 (0.24), residues: 1115 helix: -1.35 (0.23), residues: 406 sheet: -1.42 (0.32), residues: 235 loop : -1.94 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 219 TYR 0.023 0.002 TYR A 149 PHE 0.024 0.002 PHE F 363 TRP 0.016 0.002 TRP A 243 HIS 0.009 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9235) covalent geometry : angle 0.60822 (12503) SS BOND : bond 0.00682 ( 7) SS BOND : angle 1.62198 ( 14) hydrogen bonds : bond 0.03700 ( 317) hydrogen bonds : angle 5.00917 ( 882) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.5650 (m100) cc_final: 0.4758 (m100) REVERT: A 214 GLN cc_start: 0.7655 (mm110) cc_final: 0.7395 (mm-40) REVERT: A 241 TYR cc_start: 0.9074 (m-80) cc_final: 0.8787 (m-80) REVERT: A 306 TRP cc_start: 0.7645 (OUTLIER) cc_final: 0.6644 (t60) REVERT: C 32 TYR cc_start: 0.8084 (m-80) cc_final: 0.7843 (m-80) REVERT: C 78 THR cc_start: 0.7458 (p) cc_final: 0.7187 (p) REVERT: C 83 MET cc_start: 0.7558 (mpp) cc_final: 0.7272 (mpp) REVERT: C 95 TYR cc_start: 0.7885 (m-80) cc_final: 0.7658 (m-10) REVERT: E 58 ILE cc_start: 0.9406 (mt) cc_final: 0.8707 (tt) REVERT: E 118 ASP cc_start: 0.8328 (p0) cc_final: 0.8124 (p0) REVERT: E 188 MET cc_start: 0.7938 (mmm) cc_final: 0.7659 (mmp) REVERT: F 235 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8827 (tt) REVERT: F 272 LEU cc_start: 0.9380 (tp) cc_final: 0.9149 (tt) REVERT: F 360 TYR cc_start: 0.8005 (m-80) cc_final: 0.7754 (m-80) outliers start: 37 outliers final: 24 residues processed: 211 average time/residue: 0.0932 time to fit residues: 27.4364 Evaluate side-chains 203 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN D 18 GLN ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 GLN F 41 HIS ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.114981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090886 restraints weight = 25014.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.093248 restraints weight = 12962.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094816 restraints weight = 8842.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.095616 restraints weight = 7037.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096296 restraints weight = 6217.399| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9242 Z= 0.128 Angle : 0.585 11.399 12517 Z= 0.307 Chirality : 0.043 0.169 1380 Planarity : 0.004 0.041 1597 Dihedral : 4.839 27.248 1235 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.81 % Allowed : 19.55 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.24 (0.24), residues: 1115 helix: -1.16 (0.24), residues: 412 sheet: -1.20 (0.33), residues: 235 loop : -1.79 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 342 TYR 0.017 0.001 TYR A 149 PHE 0.020 0.001 PHE F 363 TRP 0.014 0.001 TRP A 243 HIS 0.008 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9235) covalent geometry : angle 0.58399 (12503) SS BOND : bond 0.00386 ( 7) SS BOND : angle 1.37760 ( 14) hydrogen bonds : bond 0.03324 ( 317) hydrogen bonds : angle 4.78757 ( 882) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.5613 (m100) cc_final: 0.4734 (m100) REVERT: A 214 GLN cc_start: 0.7730 (mm110) cc_final: 0.7336 (mm-40) REVERT: A 241 TYR cc_start: 0.8997 (m-80) cc_final: 0.8682 (m-80) REVERT: A 306 TRP cc_start: 0.7588 (OUTLIER) cc_final: 0.6639 (t60) REVERT: C 32 TYR cc_start: 0.7968 (m-80) cc_final: 0.7711 (m-80) REVERT: C 53 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6022 (mp10) REVERT: C 78 THR cc_start: 0.7404 (p) cc_final: 0.6947 (m) REVERT: C 83 MET cc_start: 0.7458 (mpp) cc_final: 0.7257 (mpp) REVERT: E 58 ILE cc_start: 0.9379 (mt) cc_final: 0.8644 (tt) REVERT: E 264 TYR cc_start: 0.6962 (m-80) cc_final: 0.6656 (m-80) REVERT: F 342 ARG cc_start: 0.8737 (ttp80) cc_final: 0.8522 (ttp80) outliers start: 37 outliers final: 23 residues processed: 218 average time/residue: 0.0882 time to fit residues: 26.9675 Evaluate side-chains 207 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 22 optimal weight: 10.0000 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS ** F 362 HIS ** 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 = 0.3836 r_free = 0.3836 target = 0.115142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.091159 restraints weight = 25302.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.093610 restraints weight = 13106.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.095172 restraints weight = 8868.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096070 restraints weight = 7038.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.096681 restraints weight = 6170.190| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9242 Z= 0.127 Angle : 0.587 11.333 12517 Z= 0.306 Chirality : 0.043 0.176 1380 Planarity : 0.004 0.041 1597 Dihedral : 4.796 26.970 1235 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.12 % Allowed : 20.78 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.03 (0.24), residues: 1115 helix: -0.95 (0.24), residues: 413 sheet: -1.15 (0.33), residues: 233 loop : -1.68 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 342 TYR 0.017 0.001 TYR A 149 PHE 0.024 0.001 PHE C 103 TRP 0.013 0.001 TRP A 297 HIS 0.007 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9235) covalent geometry : angle 0.58530 (12503) SS BOND : bond 0.00315 ( 7) SS BOND : angle 1.33273 ( 14) hydrogen bonds : bond 0.03272 ( 317) hydrogen bonds : angle 4.70454 ( 882) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.5577 (m100) cc_final: 0.4724 (m100) REVERT: A 214 GLN cc_start: 0.7688 (mm110) cc_final: 0.7279 (mm110) REVERT: A 241 TYR cc_start: 0.9046 (m-80) cc_final: 0.8727 (m-80) REVERT: A 306 TRP cc_start: 0.7644 (OUTLIER) cc_final: 0.6783 (t60) REVERT: B 48 PHE cc_start: 0.8950 (t80) cc_final: 0.8736 (t80) REVERT: B 49 LYS cc_start: 0.8642 (tttp) cc_final: 0.8375 (ttpp) REVERT: C 32 TYR cc_start: 0.7851 (m-80) cc_final: 0.7638 (m-80) REVERT: C 53 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6070 (mp10) REVERT: C 83 MET cc_start: 0.7412 (mpp) cc_final: 0.7173 (mpp) REVERT: E 58 ILE cc_start: 0.9401 (mt) cc_final: 0.8892 (tt) REVERT: E 105 TYR cc_start: 0.7782 (t80) cc_final: 0.7462 (t80) REVERT: E 188 MET cc_start: 0.7924 (mmp) cc_final: 0.7722 (mmp) REVERT: E 264 TYR cc_start: 0.7064 (m-80) cc_final: 0.6732 (m-80) outliers start: 40 outliers final: 29 residues processed: 217 average time/residue: 0.0979 time to fit residues: 29.3522 Evaluate side-chains 214 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.116397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.092429 restraints weight = 25184.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.094890 restraints weight = 12962.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096485 restraints weight = 8749.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097283 restraints weight = 6937.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.097957 restraints weight = 6137.268| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9242 Z= 0.108 Angle : 0.573 10.146 12517 Z= 0.298 Chirality : 0.042 0.152 1380 Planarity : 0.004 0.040 1597 Dihedral : 4.570 25.440 1235 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.60 % Allowed : 21.50 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.25), residues: 1115 helix: -0.71 (0.25), residues: 410 sheet: -1.00 (0.34), residues: 231 loop : -1.63 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 105 TYR 0.016 0.001 TYR A 149 PHE 0.018 0.001 PHE A 259 TRP 0.011 0.001 TRP A 243 HIS 0.007 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9235) covalent geometry : angle 0.57215 (12503) SS BOND : bond 0.00264 ( 7) SS BOND : angle 1.07397 ( 14) hydrogen bonds : bond 0.03038 ( 317) hydrogen bonds : angle 4.52688 ( 882) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.5537 (m100) cc_final: 0.4601 (m100) REVERT: A 210 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7719 (pt) REVERT: A 214 GLN cc_start: 0.7785 (mm110) cc_final: 0.7358 (mm110) REVERT: A 241 TYR cc_start: 0.8998 (m-80) cc_final: 0.8655 (m-80) REVERT: A 306 TRP cc_start: 0.7639 (OUTLIER) cc_final: 0.6787 (t60) REVERT: B 49 LYS cc_start: 0.8665 (tttp) cc_final: 0.8368 (ttpp) REVERT: C 53 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6114 (mp10) REVERT: E 58 ILE cc_start: 0.9396 (mt) cc_final: 0.8609 (tt) REVERT: E 105 TYR cc_start: 0.7646 (t80) cc_final: 0.7397 (t80) REVERT: E 264 TYR cc_start: 0.6834 (m-80) cc_final: 0.6516 (m-80) REVERT: F 271 LYS cc_start: 0.9026 (mmmt) cc_final: 0.8798 (mmtt) REVERT: F 360 TYR cc_start: 0.8041 (m-80) cc_final: 0.7804 (m-80) outliers start: 35 outliers final: 23 residues processed: 219 average time/residue: 0.0917 time to fit residues: 27.9740 Evaluate side-chains 217 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS F 267 GLN F 292 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.112901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088680 restraints weight = 25141.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.090982 restraints weight = 13205.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.092486 restraints weight = 9051.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093325 restraints weight = 7238.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.093969 restraints weight = 6371.686| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9242 Z= 0.212 Angle : 0.682 11.095 12517 Z= 0.356 Chirality : 0.046 0.203 1380 Planarity : 0.004 0.052 1597 Dihedral : 5.100 30.479 1235 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.22 % Allowed : 22.22 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.25), residues: 1115 helix: -0.77 (0.24), residues: 404 sheet: -0.97 (0.34), residues: 236 loop : -1.72 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 342 TYR 0.019 0.002 TYR A 157 PHE 0.023 0.002 PHE C 103 TRP 0.027 0.002 TRP A 243 HIS 0.007 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 9235) covalent geometry : angle 0.68051 (12503) SS BOND : bond 0.00430 ( 7) SS BOND : angle 1.48628 ( 14) hydrogen bonds : bond 0.03692 ( 317) hydrogen bonds : angle 4.94195 ( 882) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7836 (pt) REVERT: A 214 GLN cc_start: 0.7840 (mm110) cc_final: 0.7408 (mm110) REVERT: A 241 TYR cc_start: 0.9108 (m-80) cc_final: 0.8791 (m-80) REVERT: A 306 TRP cc_start: 0.7807 (OUTLIER) cc_final: 0.7021 (t60) REVERT: B 49 LYS cc_start: 0.8687 (tttp) cc_final: 0.8429 (ttpp) REVERT: C 53 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6324 (mp10) REVERT: E 58 ILE cc_start: 0.9414 (mt) cc_final: 0.8954 (tt) REVERT: E 105 TYR cc_start: 0.8006 (t80) cc_final: 0.7597 (t80) REVERT: E 225 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7376 (t-90) REVERT: E 264 TYR cc_start: 0.6964 (m-80) cc_final: 0.6635 (m-80) REVERT: F 271 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8901 (mmtt) REVERT: F 360 TYR cc_start: 0.8099 (m-80) cc_final: 0.7755 (m-80) outliers start: 41 outliers final: 29 residues processed: 212 average time/residue: 0.0962 time to fit residues: 27.8702 Evaluate side-chains 214 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 225 HIS Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS F 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.113610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089379 restraints weight = 24959.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091722 restraints weight = 13030.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.093228 restraints weight = 8899.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.094188 restraints weight = 7090.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094612 restraints weight = 6200.374| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9242 Z= 0.183 Angle : 0.667 12.762 12517 Z= 0.347 Chirality : 0.046 0.210 1380 Planarity : 0.004 0.045 1597 Dihedral : 5.080 28.958 1235 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.60 % Allowed : 22.84 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.25), residues: 1115 helix: -0.70 (0.25), residues: 397 sheet: -0.91 (0.34), residues: 233 loop : -1.67 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 27 TYR 0.021 0.002 TYR A 157 PHE 0.027 0.002 PHE C 103 TRP 0.027 0.002 TRP A 243 HIS 0.007 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9235) covalent geometry : angle 0.66598 (12503) SS BOND : bond 0.00357 ( 7) SS BOND : angle 1.47468 ( 14) hydrogen bonds : bond 0.03542 ( 317) hydrogen bonds : angle 4.94854 ( 882) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7855 (pt) REVERT: A 214 GLN cc_start: 0.7835 (mm110) cc_final: 0.7347 (mm110) REVERT: A 241 TYR cc_start: 0.9098 (m-80) cc_final: 0.8764 (m-80) REVERT: A 306 TRP cc_start: 0.7832 (OUTLIER) cc_final: 0.7050 (t60) REVERT: B 49 LYS cc_start: 0.8694 (tttp) cc_final: 0.8438 (ttpp) REVERT: C 18 LEU cc_start: 0.7771 (tt) cc_final: 0.7271 (tt) REVERT: C 53 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6172 (mp10) REVERT: C 73 ASP cc_start: 0.7186 (p0) cc_final: 0.6425 (p0) REVERT: E 58 ILE cc_start: 0.9409 (mt) cc_final: 0.8947 (tt) REVERT: E 105 TYR cc_start: 0.7933 (t80) cc_final: 0.7558 (t80) REVERT: E 225 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7337 (t-90) REVERT: E 264 TYR cc_start: 0.7031 (m-80) cc_final: 0.6747 (m-80) REVERT: F 271 LYS cc_start: 0.9062 (mmmt) cc_final: 0.8852 (mmtt) REVERT: F 360 TYR cc_start: 0.8008 (m-80) cc_final: 0.7639 (m-80) outliers start: 35 outliers final: 28 residues processed: 205 average time/residue: 0.0866 time to fit residues: 24.7993 Evaluate side-chains 214 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 225 HIS Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS F 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.114718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090549 restraints weight = 24767.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092881 restraints weight = 12945.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.094402 restraints weight = 8864.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.095168 restraints weight = 7091.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095826 restraints weight = 6280.641| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9242 Z= 0.146 Angle : 0.653 12.449 12517 Z= 0.339 Chirality : 0.045 0.218 1380 Planarity : 0.004 0.040 1597 Dihedral : 4.916 27.247 1235 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.50 % Allowed : 23.77 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.25), residues: 1115 helix: -0.64 (0.25), residues: 403 sheet: -0.84 (0.35), residues: 233 loop : -1.60 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 197 TYR 0.019 0.001 TYR A 157 PHE 0.027 0.001 PHE C 103 TRP 0.026 0.001 TRP A 243 HIS 0.007 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9235) covalent geometry : angle 0.65147 (12503) SS BOND : bond 0.00359 ( 7) SS BOND : angle 1.49725 ( 14) hydrogen bonds : bond 0.03418 ( 317) hydrogen bonds : angle 4.88885 ( 882) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7802 (pt) REVERT: A 214 GLN cc_start: 0.7829 (mm110) cc_final: 0.7386 (mm110) REVERT: A 241 TYR cc_start: 0.9066 (m-80) cc_final: 0.8715 (m-80) REVERT: A 306 TRP cc_start: 0.7819 (OUTLIER) cc_final: 0.7075 (t60) REVERT: B 25 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8612 (tp40) REVERT: B 49 LYS cc_start: 0.8696 (tttp) cc_final: 0.8412 (ttpp) REVERT: C 18 LEU cc_start: 0.7564 (tt) cc_final: 0.6823 (tt) REVERT: C 53 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6104 (mp10) REVERT: C 87 LYS cc_start: 0.8123 (tptp) cc_final: 0.7750 (tptp) REVERT: E 58 ILE cc_start: 0.9400 (mt) cc_final: 0.8924 (tt) REVERT: E 105 TYR cc_start: 0.7930 (t80) cc_final: 0.7573 (t80) REVERT: E 225 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.7500 (t-90) REVERT: E 264 TYR cc_start: 0.6981 (m-80) cc_final: 0.6722 (m-80) REVERT: F 271 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8843 (mmtt) REVERT: F 360 TYR cc_start: 0.7984 (m-80) cc_final: 0.7624 (m-80) outliers start: 34 outliers final: 24 residues processed: 206 average time/residue: 0.0964 time to fit residues: 27.4090 Evaluate side-chains 206 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 225 HIS Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.114648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.090534 restraints weight = 24748.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092878 restraints weight = 12909.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.094388 restraints weight = 8817.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095328 restraints weight = 7046.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095772 restraints weight = 6168.483| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9242 Z= 0.153 Angle : 0.659 12.241 12517 Z= 0.342 Chirality : 0.045 0.213 1380 Planarity : 0.004 0.041 1597 Dihedral : 4.904 27.229 1235 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.50 % Allowed : 23.35 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.25), residues: 1115 helix: -0.63 (0.25), residues: 401 sheet: -0.89 (0.35), residues: 229 loop : -1.58 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 105 TYR 0.020 0.001 TYR A 157 PHE 0.028 0.002 PHE C 103 TRP 0.025 0.001 TRP A 243 HIS 0.007 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9235) covalent geometry : angle 0.65736 (12503) SS BOND : bond 0.00400 ( 7) SS BOND : angle 1.43227 ( 14) hydrogen bonds : bond 0.03412 ( 317) hydrogen bonds : angle 4.82402 ( 882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.94 seconds wall clock time: 31 minutes 6.16 seconds (1866.16 seconds total)