Starting phenix.real_space_refine on Thu Mar 13 12:01:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m1h_30047/03_2025/6m1h_30047.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m1h_30047/03_2025/6m1h_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_2025/6m1h_30047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m1h_30047/03_2025/6m1h_30047.map" model { file = "/net/cci-nas-00/data/ceres_data/6m1h_30047/03_2025/6m1h_30047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m1h_30047/03_2025/6m1h_30047.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'HIS: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: 5.45, per 1000 atoms: 0.60 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: 2.16 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.94 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: 2.25 Time building geometry restraints manager: 2.57 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: 0.310 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.360 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.130 ------------------------------------------------------------------------------- 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 9235 Z= 0.471 Angle : 0.957 13.242 12503 Z= 0.556 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.003 TRP A 306 HIS 0.012 0.002 HIS A 218 PHE 0.025 0.003 PHE F 363 TYR 0.034 0.002 TYR E 59 ARG 0.007 0.001 ARG E 22 *********************** 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 : 1.036 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: 0.2545 time to fit residues: 78.9312 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 : 0.996 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.115675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092081 restraints weight = 24332.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094391 restraints weight = 12441.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.096008 restraints weight = 8391.142| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9235 Z= 0.172 Angle : 0.595 6.744 12503 Z= 0.323 Chirality : 0.043 0.169 1380 Planarity : 0.005 0.052 1597 Dihedral : 5.604 33.128 1237 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.47 % Allowed : 15.33 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.22), residues: 1115 helix: -2.54 (0.21), residues: 394 sheet: -1.93 (0.31), residues: 238 loop : -2.24 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 306 HIS 0.010 0.001 HIS A 218 PHE 0.013 0.001 PHE A 260 TYR 0.025 0.001 TYR A 157 ARG 0.008 0.001 ARG F 347 *********************** 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: 24 poor density : 222 time to evaluate : 1.169 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: 0.5605 (m100) cc_final: 0.4956 (m100) REVERT: A 210 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8255 (pt) REVERT: A 230 MET cc_start: 0.8085 (tpt) cc_final: 0.7877 (mmm) REVERT: B 16 LYS cc_start: 0.9146 (mttm) cc_final: 0.8945 (mtpp) REVERT: B 20 HIS cc_start: 0.8946 (t-90) cc_final: 0.8708 (t70) REVERT: B 29 GLN cc_start: 0.9388 (tp-100) cc_final: 0.8957 (tp-100) REVERT: B 47 VAL cc_start: 0.9050 (t) cc_final: 0.8666 (p) REVERT: B 48 PHE cc_start: 0.8878 (t80) cc_final: 0.8587 (t80) REVERT: B 52 MET cc_start: 0.8878 (mmm) cc_final: 0.8650 (mmm) REVERT: C 18 LEU cc_start: 0.8345 (tp) cc_final: 0.7733 (tp) REVERT: C 39 GLN cc_start: 0.7364 (tt0) cc_final: 0.6995 (tp40) REVERT: C 53 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.6632 (mm110) REVERT: C 73 ASP cc_start: 0.7096 (t0) cc_final: 0.6588 (t0) REVERT: C 80 TYR cc_start: 0.7589 (m-80) cc_final: 0.7165 (m-80) REVERT: C 83 MET cc_start: 0.7389 (mpp) cc_final: 0.7003 (mpp) REVERT: C 95 TYR cc_start: 0.8027 (m-80) cc_final: 0.7789 (m-10) REVERT: D 18 GLN cc_start: 0.7179 (mp10) cc_final: 0.6600 (mp10) REVERT: D 32 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.9018 (ptpp) REVERT: E 58 ILE cc_start: 0.9361 (mt) cc_final: 0.8656 (tt) REVERT: E 118 ASP cc_start: 0.8399 (p0) cc_final: 0.8062 (p0) outliers start: 24 outliers final: 7 residues processed: 233 average time/residue: 0.2131 time to fit residues: 67.9998 Evaluate side-chains 187 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 65 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN ** 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 = 0.3856 r_free = 0.3856 target = 0.116572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.092650 restraints weight = 24841.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.095085 restraints weight = 12728.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.096719 restraints weight = 8545.191| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9235 Z= 0.165 Angle : 0.580 10.348 12503 Z= 0.309 Chirality : 0.042 0.158 1380 Planarity : 0.004 0.039 1597 Dihedral : 5.021 29.208 1235 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.47 % Allowed : 17.90 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.23), residues: 1115 helix: -1.77 (0.23), residues: 404 sheet: -1.50 (0.32), residues: 227 loop : -2.02 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 243 HIS 0.009 0.001 HIS A 218 PHE 0.028 0.001 PHE F 363 TYR 0.022 0.001 TYR A 157 ARG 0.006 0.000 ARG C 105 *********************** 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 235 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 1.000 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: 0.5595 (m100) cc_final: 0.4616 (m100) REVERT: A 232 PHE cc_start: 0.8580 (t80) cc_final: 0.8160 (t80) REVERT: A 306 TRP cc_start: 0.7611 (OUTLIER) cc_final: 0.6722 (t60) REVERT: B 29 GLN cc_start: 0.9387 (tp-100) cc_final: 0.9176 (tp-100) REVERT: C 18 LEU cc_start: 0.8313 (tp) cc_final: 0.7856 (tp) REVERT: C 34 MET cc_start: 0.7968 (mmm) cc_final: 0.7700 (mmm) REVERT: C 73 ASP cc_start: 0.7512 (t0) cc_final: 0.7287 (t0) REVERT: C 83 MET cc_start: 0.7525 (mpp) cc_final: 0.7266 (mpp) REVERT: C 95 TYR cc_start: 0.8023 (m-80) cc_final: 0.7782 (m-10) REVERT: D 21 MET cc_start: 0.7591 (mpp) cc_final: 0.7299 (mpp) REVERT: D 27 ARG cc_start: 0.6937 (mmt180) cc_final: 0.6736 (mmt180) REVERT: E 58 ILE cc_start: 0.9342 (mt) cc_final: 0.8606 (tt) REVERT: E 118 ASP cc_start: 0.8379 (p0) cc_final: 0.8119 (p0) REVERT: F 218 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8556 (p0) REVERT: F 272 LEU cc_start: 0.9361 (tp) cc_final: 0.9085 (tt) REVERT: F 360 TYR cc_start: 0.8145 (m-80) cc_final: 0.7677 (m-80) outliers start: 24 outliers final: 14 residues processed: 224 average time/residue: 0.2163 time to fit residues: 66.0908 Evaluate side-chains 199 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 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 274 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 218 ASN 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 82 optimal weight: 9.9990 chunk 76 optimal weight: 0.4980 chunk 42 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 62 optimal weight: 0.0010 chunk 36 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.4990 ------------------------------------------------------------------------------- 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** D 18 GLN ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** 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 = 0.3835 r_free = 0.3835 target = 0.115184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091142 restraints weight = 24657.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093568 restraints weight = 12757.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.095123 restraints weight = 8622.665| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9235 Z= 0.193 Angle : 0.575 10.036 12503 Z= 0.307 Chirality : 0.043 0.167 1380 Planarity : 0.004 0.040 1597 Dihedral : 4.894 28.101 1235 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.70 % Allowed : 18.93 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.24), residues: 1115 helix: -1.33 (0.24), residues: 403 sheet: -1.38 (0.33), residues: 228 loop : -1.87 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 243 HIS 0.009 0.001 HIS A 218 PHE 0.020 0.001 PHE F 363 TYR 0.027 0.001 TYR A 149 ARG 0.006 0.000 ARG C 105 *********************** 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 226 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 1.086 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: 0.5611 (m100) cc_final: 0.4657 (m100) REVERT: A 214 GLN cc_start: 0.7683 (mm110) cc_final: 0.7313 (mm110) REVERT: A 241 TYR cc_start: 0.9006 (m-80) cc_final: 0.8761 (m-80) REVERT: A 306 TRP cc_start: 0.7532 (OUTLIER) cc_final: 0.6619 (t60) REVERT: B 15 GLN cc_start: 0.8692 (mm110) cc_final: 0.8476 (mm110) REVERT: C 80 TYR cc_start: 0.7233 (m-80) cc_final: 0.6972 (m-80) REVERT: C 83 MET cc_start: 0.7523 (mpp) cc_final: 0.7271 (mpp) REVERT: C 95 TYR cc_start: 0.7809 (m-80) cc_final: 0.7608 (m-10) REVERT: D 18 GLN cc_start: 0.7413 (mm110) cc_final: 0.7139 (mm-40) REVERT: E 58 ILE cc_start: 0.9357 (mt) cc_final: 0.8641 (tt) REVERT: E 61 MET cc_start: 0.8691 (ppp) cc_final: 0.8187 (ppp) REVERT: E 118 ASP cc_start: 0.8286 (p0) cc_final: 0.8068 (p0) REVERT: F 360 TYR cc_start: 0.8045 (m-80) cc_final: 0.7649 (m-80) outliers start: 36 outliers final: 23 residues processed: 209 average time/residue: 0.2147 time to fit residues: 62.1482 Evaluate side-chains 200 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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 71 SER 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 138 GLU 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 325 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 0.0870 chunk 5 optimal weight: 40.0000 chunk 51 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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 E 225 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.116095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.092117 restraints weight = 24783.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094475 restraints weight = 12841.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096104 restraints weight = 8748.893| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9235 Z= 0.168 Angle : 0.571 9.524 12503 Z= 0.297 Chirality : 0.042 0.167 1380 Planarity : 0.004 0.044 1597 Dihedral : 4.657 25.745 1235 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.70 % Allowed : 18.72 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.24), residues: 1115 helix: -1.01 (0.24), residues: 405 sheet: -1.25 (0.34), residues: 230 loop : -1.75 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 243 HIS 0.008 0.001 HIS A 218 PHE 0.013 0.001 PHE C 103 TYR 0.021 0.001 TYR A 149 ARG 0.008 0.000 ARG E 219 *********************** 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 236 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.977 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: 0.5582 (m100) cc_final: 0.4666 (m100) REVERT: A 214 GLN cc_start: 0.7795 (mm110) cc_final: 0.7400 (mm110) REVERT: A 241 TYR cc_start: 0.9001 (m-80) cc_final: 0.8768 (m-80) REVERT: A 306 TRP cc_start: 0.7622 (OUTLIER) cc_final: 0.6775 (t60) REVERT: C 80 TYR cc_start: 0.7171 (m-80) cc_final: 0.6900 (m-80) REVERT: D 18 GLN cc_start: 0.7575 (mm110) cc_final: 0.7374 (mm-40) REVERT: E 58 ILE cc_start: 0.9384 (mt) cc_final: 0.8632 (tt) REVERT: E 118 ASP cc_start: 0.8249 (p0) cc_final: 0.8043 (p0) REVERT: F 342 ARG cc_start: 0.8730 (ttp80) cc_final: 0.8498 (ttp80) REVERT: F 360 TYR cc_start: 0.8049 (m-80) cc_final: 0.7700 (m-80) outliers start: 36 outliers final: 24 residues processed: 220 average time/residue: 0.2052 time to fit residues: 62.4176 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 : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 PHE 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 138 GLU Chi-restraints excluded: chain E residue 164 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 270 LEU Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.115798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.092365 restraints weight = 24912.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094776 restraints weight = 12692.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.096375 restraints weight = 8529.136| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9235 Z= 0.175 Angle : 0.585 9.554 12503 Z= 0.303 Chirality : 0.043 0.181 1380 Planarity : 0.004 0.042 1597 Dihedral : 4.601 25.718 1235 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.29 % Allowed : 21.50 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.25), residues: 1115 helix: -0.91 (0.24), residues: 412 sheet: -1.03 (0.35), residues: 229 loop : -1.66 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 243 HIS 0.007 0.001 HIS A 218 PHE 0.024 0.001 PHE C 103 TYR 0.020 0.001 TYR A 149 ARG 0.006 0.000 ARG E 219 *********************** 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 231 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 1.021 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: 0.5596 (m100) cc_final: 0.4674 (m100) REVERT: A 214 GLN cc_start: 0.7836 (mm110) cc_final: 0.7437 (mm110) REVERT: A 241 TYR cc_start: 0.9004 (m-80) cc_final: 0.8739 (m-80) REVERT: A 267 TYR cc_start: 0.7349 (t80) cc_final: 0.7071 (t80) REVERT: A 306 TRP cc_start: 0.7680 (OUTLIER) cc_final: 0.6880 (t60) REVERT: C 18 LEU cc_start: 0.8147 (tp) cc_final: 0.7933 (tt) REVERT: C 32 TYR cc_start: 0.7803 (m-80) cc_final: 0.7539 (m-80) REVERT: C 53 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6141 (mp10) REVERT: C 79 LEU cc_start: 0.8487 (tp) cc_final: 0.8255 (tp) REVERT: E 58 ILE cc_start: 0.9403 (mt) cc_final: 0.8625 (tt) REVERT: E 105 TYR cc_start: 0.7676 (t80) cc_final: 0.7414 (t80) REVERT: E 264 TYR cc_start: 0.6950 (m-80) cc_final: 0.6633 (m-80) REVERT: F 271 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8796 (mmtt) REVERT: F 360 TYR cc_start: 0.7986 (m-80) cc_final: 0.7717 (m-80) outliers start: 32 outliers final: 24 residues processed: 216 average time/residue: 0.2096 time to fit residues: 62.5704 Evaluate side-chains 216 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 210 LEU 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 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 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 270 LEU 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 93 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 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 = 0.3862 r_free = 0.3862 target = 0.116757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.092834 restraints weight = 25181.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.095327 restraints weight = 12965.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.096925 restraints weight = 8736.035| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9235 Z= 0.157 Angle : 0.568 9.728 12503 Z= 0.296 Chirality : 0.042 0.143 1380 Planarity : 0.003 0.041 1597 Dihedral : 4.462 23.983 1235 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.91 % Allowed : 21.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.25), residues: 1115 helix: -0.63 (0.25), residues: 408 sheet: -0.98 (0.35), residues: 229 loop : -1.58 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 243 HIS 0.007 0.001 HIS A 218 PHE 0.015 0.001 PHE A 259 TYR 0.018 0.001 TYR A 157 ARG 0.006 0.000 ARG F 342 *********************** 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 251 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 1.149 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: 0.5560 (m100) cc_final: 0.4647 (m100) REVERT: A 214 GLN cc_start: 0.7774 (mm110) cc_final: 0.7351 (mm110) REVERT: A 241 TYR cc_start: 0.8997 (m-80) cc_final: 0.8720 (m-80) REVERT: A 267 TYR cc_start: 0.7320 (t80) cc_final: 0.6942 (t80) REVERT: A 306 TRP cc_start: 0.7611 (OUTLIER) cc_final: 0.6790 (t60) REVERT: B 25 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8658 (tp40) REVERT: C 53 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6201 (mp10) REVERT: C 87 LYS cc_start: 0.7931 (tptp) cc_final: 0.7579 (tptp) REVERT: E 58 ILE cc_start: 0.9423 (mt) cc_final: 0.8614 (tt) REVERT: E 105 TYR cc_start: 0.7634 (t80) cc_final: 0.7396 (t80) REVERT: E 264 TYR cc_start: 0.6845 (m-80) cc_final: 0.6505 (m-80) REVERT: F 271 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8762 (mmtt) REVERT: F 360 TYR cc_start: 0.7908 (m-80) cc_final: 0.7655 (m-80) outliers start: 38 outliers final: 27 residues processed: 231 average time/residue: 0.2194 time to fit residues: 68.9885 Evaluate side-chains 222 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 PHE 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 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 D residue 32 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 158 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 320 VAL Chi-restraints excluded: chain E residue 334 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 0.0050 overall best weight: 5.4002 ------------------------------------------------------------------------------- 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** E 142 HIS ** 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 = 0.3754 r_free = 0.3754 target = 0.110200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.086261 restraints weight = 25578.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.088502 restraints weight = 13380.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.089997 restraints weight = 9162.531| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 9235 Z= 0.502 Angle : 0.808 9.835 12503 Z= 0.430 Chirality : 0.051 0.206 1380 Planarity : 0.005 0.047 1597 Dihedral : 5.763 33.991 1235 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.73 % Allowed : 22.33 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.24), residues: 1115 helix: -1.03 (0.24), residues: 392 sheet: -1.11 (0.34), residues: 238 loop : -1.82 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 268 HIS 0.008 0.002 HIS E 225 PHE 0.025 0.003 PHE F 376 TYR 0.019 0.002 TYR A 149 ARG 0.007 0.001 ARG A 379 *********************** 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 222 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 TYR cc_start: 0.9176 (m-80) cc_final: 0.8891 (m-80) REVERT: A 306 TRP cc_start: 0.7912 (OUTLIER) cc_final: 0.7060 (t60) REVERT: C 32 TYR cc_start: 0.8352 (m-80) cc_final: 0.7952 (m-80) REVERT: C 34 MET cc_start: 0.7844 (mmm) cc_final: 0.7619 (mmm) REVERT: C 53 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6090 (mp10) REVERT: E 58 ILE cc_start: 0.9351 (mt) cc_final: 0.9113 (tt) REVERT: E 124 TYR cc_start: 0.7996 (m-80) cc_final: 0.7663 (m-80) REVERT: E 225 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.6827 (t-90) REVERT: E 264 TYR cc_start: 0.7091 (m-80) cc_final: 0.6774 (m-80) REVERT: F 360 TYR cc_start: 0.8051 (m-80) cc_final: 0.7795 (m-80) outliers start: 46 outliers final: 33 residues processed: 203 average time/residue: 0.2750 time to fit residues: 76.0279 Evaluate side-chains 202 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 A residue 411 ILE 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 18 LEU 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 138 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 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 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 270 LEU 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 33 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS F 292 ASN ** 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 = 0.3839 r_free = 0.3839 target = 0.115627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.091462 restraints weight = 24935.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.093796 restraints weight = 12934.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095240 restraints weight = 8863.238| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9235 Z= 0.175 Angle : 0.634 12.570 12503 Z= 0.329 Chirality : 0.044 0.209 1380 Planarity : 0.004 0.041 1597 Dihedral : 4.935 31.722 1235 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.29 % Allowed : 23.25 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.25), residues: 1115 helix: -0.65 (0.25), residues: 398 sheet: -1.02 (0.34), residues: 235 loop : -1.57 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 243 HIS 0.007 0.001 HIS A 218 PHE 0.028 0.001 PHE C 103 TYR 0.018 0.001 TYR A 157 ARG 0.006 0.000 ARG C 105 *********************** 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 229 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.998 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 241 TYR cc_start: 0.9013 (m-80) cc_final: 0.8718 (m-80) REVERT: A 306 TRP cc_start: 0.7745 (OUTLIER) cc_final: 0.7017 (t60) REVERT: B 49 LYS cc_start: 0.8559 (tttp) cc_final: 0.8345 (ttpp) REVERT: C 53 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6021 (mp10) REVERT: C 87 LYS cc_start: 0.8105 (tptp) cc_final: 0.7696 (tptp) REVERT: E 58 ILE cc_start: 0.9376 (mt) cc_final: 0.8901 (tt) REVERT: E 105 TYR cc_start: 0.7854 (t80) cc_final: 0.7483 (t80) REVERT: E 225 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7074 (t-90) REVERT: F 360 TYR cc_start: 0.7915 (m-80) cc_final: 0.7606 (m-80) outliers start: 32 outliers final: 24 residues processed: 213 average time/residue: 0.2271 time to fit residues: 66.0669 Evaluate side-chains 216 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 C residue 53 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 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 138 GLU 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 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 88 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 97 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.0060 chunk 101 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.4202 ------------------------------------------------------------------------------- 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** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS F 236 GLN ** 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 = 0.3808 r_free = 0.3808 target = 0.113510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089838 restraints weight = 25001.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.092191 restraints weight = 12855.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.093670 restraints weight = 8684.442| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9235 Z= 0.265 Angle : 0.688 12.642 12503 Z= 0.355 Chirality : 0.046 0.213 1380 Planarity : 0.004 0.042 1597 Dihedral : 5.075 28.669 1235 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.98 % Allowed : 24.49 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.25), residues: 1115 helix: -0.70 (0.25), residues: 394 sheet: -1.05 (0.34), residues: 239 loop : -1.59 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 297 HIS 0.007 0.001 HIS A 218 PHE 0.027 0.002 PHE C 103 TYR 0.017 0.002 TYR A 157 ARG 0.004 0.000 ARG A 350 ********************** 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 210 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 TYR cc_start: 0.9076 (m-80) cc_final: 0.8767 (m-80) REVERT: A 306 TRP cc_start: 0.7856 (OUTLIER) cc_final: 0.7055 (t60) REVERT: A 419 LYS cc_start: 0.3712 (mmtm) cc_final: 0.3431 (mmtt) REVERT: B 41 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7320 (tt0) REVERT: C 32 TYR cc_start: 0.7987 (m-80) cc_final: 0.7751 (m-10) REVERT: C 53 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6101 (mp10) REVERT: E 22 ARG cc_start: 0.8057 (ttm170) cc_final: 0.7756 (ttm170) REVERT: E 58 ILE cc_start: 0.9415 (mt) cc_final: 0.8973 (tt) REVERT: E 105 TYR cc_start: 0.7955 (t80) cc_final: 0.7594 (t80) REVERT: E 225 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7020 (t-90) REVERT: F 360 TYR cc_start: 0.7949 (m-80) cc_final: 0.7718 (m-80) outliers start: 29 outliers final: 25 residues processed: 196 average time/residue: 0.2335 time to fit residues: 62.7841 Evaluate side-chains 206 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 C residue 53 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 51 LEU 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 138 GLU 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 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 2 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS F 292 ASN ** 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 = 0.3823 r_free = 0.3823 target = 0.114581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090505 restraints weight = 24997.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.092840 restraints weight = 12980.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.094349 restraints weight = 8837.618| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9235 Z= 0.227 Angle : 0.682 16.279 12503 Z= 0.348 Chirality : 0.045 0.207 1380 Planarity : 0.004 0.039 1597 Dihedral : 4.959 26.794 1235 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.98 % Allowed : 24.79 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.25), residues: 1115 helix: -0.56 (0.25), residues: 391 sheet: -1.05 (0.34), residues: 241 loop : -1.58 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 297 HIS 0.007 0.001 HIS A 218 PHE 0.027 0.002 PHE C 103 TYR 0.018 0.001 TYR A 157 ARG 0.005 0.000 ARG A 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3241.55 seconds wall clock time: 57 minutes 37.71 seconds (3457.71 seconds total)