Starting phenix.real_space_refine on Sat Jul 26 21:55:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m1h_30047/07_2025/6m1h_30047.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m1h_30047/07_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_30047/07_2025/6m1h_30047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m1h_30047/07_2025/6m1h_30047.map" model { file = "/net/cci-nas-00/data/ceres_data/6m1h_30047/07_2025/6m1h_30047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m1h_30047/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.13, per 1000 atoms: 0.57 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: 2.08 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: 1.00 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: 2.56 Time building geometry restraints manager: 2.50 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: 0.370 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.790 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9242 Z= 0.345 Angle : 0.959 13.242 12517 Z= 0.557 Chirality : 0.059 0.295 1380 Planarity : 0.007 0.075 1597 Dihedral : 15.336 86.669 3312 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.21 % Allowed : 12.45 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.31416 ( 317) hydrogen bonds : angle 10.74405 ( 882) SS BOND : bond 0.00518 ( 7) SS BOND : angle 2.25737 ( 14) covalent geometry : bond 0.00721 ( 9235) covalent geometry : angle 0.95687 (12503) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 0.990 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: 0.2507 time to fit residues: 77.7744 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 : 1.022 ------------------------------------------------------------------------------- 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 9242 Z= 0.124 Angle : 0.596 6.744 12517 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 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 317) hydrogen bonds : angle 5.66404 ( 882) SS BOND : bond 0.00299 ( 7) SS BOND : angle 1.26453 ( 14) covalent geometry : bond 0.00262 ( 9235) covalent geometry : angle 0.59499 (12503) *********************** 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 : 1.080 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: 0.2216 time to fit residues: 70.9862 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 : 0.979 ------------------------------------------------------------------------------- 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 9242 Z= 0.112 Angle : 0.583 10.348 12517 Z= 0.310 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 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 317) hydrogen bonds : angle 5.08679 ( 882) SS BOND : bond 0.00490 ( 7) SS BOND : angle 1.82923 ( 14) covalent geometry : bond 0.00251 ( 9235) covalent geometry : angle 0.58015 (12503) *********************** 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 : 1.141 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: 0.2167 time to fit residues: 66.4093 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 : 1.045 ------------------------------------------------------------------------------- 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 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 9242 Z= 0.131 Angle : 0.576 10.036 12517 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 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 317) hydrogen bonds : angle 4.85630 ( 882) SS BOND : bond 0.00251 ( 7) SS BOND : angle 1.32190 ( 14) covalent geometry : bond 0.00296 ( 9235) covalent geometry : angle 0.57485 (12503) *********************** 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 : 0.961 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: 0.2198 time to fit residues: 63.5203 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 : 1.042 ------------------------------------------------------------------------------- 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: 30.0000 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 9242 Z= 0.114 Angle : 0.572 9.524 12517 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 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 317) hydrogen bonds : angle 4.71160 ( 882) SS BOND : bond 0.00317 ( 7) SS BOND : angle 1.41056 ( 14) covalent geometry : bond 0.00257 ( 9235) covalent geometry : angle 0.57079 (12503) *********************** 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 : 1.009 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: 0.2017 time to fit residues: 61.6097 Evaluate side-chains 207 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 9242 Z= 0.119 Angle : 0.586 9.554 12517 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 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 317) hydrogen bonds : angle 4.71454 ( 882) SS BOND : bond 0.00334 ( 7) SS BOND : angle 1.40243 ( 14) covalent geometry : bond 0.00268 ( 9235) covalent geometry : angle 0.58475 (12503) *********************** 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 : 0.954 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: 0.2030 time to fit residues: 60.6248 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 : 1.076 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.116154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.092310 restraints weight = 25154.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094770 restraints weight = 12926.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.096250 restraints weight = 8740.736| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9242 Z= 0.114 Angle : 0.573 9.786 12517 Z= 0.300 Chirality : 0.042 0.144 1380 Planarity : 0.003 0.041 1597 Dihedral : 4.519 24.668 1235 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.81 % Allowed : 21.30 % 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: -0.61 (0.25), residues: 403 sheet: -0.94 (0.35), residues: 227 loop : -1.61 (0.29), residues: 485 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 0.014 0.001 PHE A 259 TYR 0.018 0.001 TYR A 157 ARG 0.006 0.000 ARG F 342 Details of bonding type rmsd hydrogen bonds : bond 0.03079 ( 317) hydrogen bonds : angle 4.55733 ( 882) SS BOND : bond 0.00371 ( 7) SS BOND : angle 1.25373 ( 14) covalent geometry : bond 0.00258 ( 9235) covalent geometry : angle 0.57216 (12503) *********************** 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 242 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 1.132 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: 0.5563 (m100) cc_final: 0.4669 (m100) REVERT: A 214 GLN cc_start: 0.7805 (mm110) cc_final: 0.7362 (mm110) REVERT: A 241 TYR cc_start: 0.9002 (m-80) cc_final: 0.8702 (m-80) REVERT: A 267 TYR cc_start: 0.7319 (t80) cc_final: 0.6925 (t80) REVERT: A 306 TRP cc_start: 0.7674 (OUTLIER) cc_final: 0.6973 (t60) REVERT: C 53 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6243 (mp10) REVERT: E 58 ILE cc_start: 0.9405 (mt) cc_final: 0.8618 (tt) REVERT: E 105 TYR cc_start: 0.7668 (t80) cc_final: 0.7448 (t80) REVERT: E 264 TYR cc_start: 0.6885 (m-80) cc_final: 0.6542 (m-80) REVERT: F 271 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8785 (mmtt) REVERT: F 360 TYR cc_start: 0.7928 (m-80) cc_final: 0.7676 (m-80) outliers start: 37 outliers final: 28 residues processed: 224 average time/residue: 0.2168 time to fit residues: 66.8063 Evaluate side-chains 219 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 95 optimal weight: 0.3980 chunk 102 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 94 optimal weight: 0.3980 chunk 48 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 41 HIS F 236 GLN 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 = 0.3795 r_free = 0.3795 target = 0.112652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.088588 restraints weight = 25400.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.090910 restraints weight = 13284.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.092338 restraints weight = 9069.661| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9242 Z= 0.221 Angle : 0.687 9.693 12517 Z= 0.361 Chirality : 0.046 0.196 1380 Planarity : 0.004 0.043 1597 Dihedral : 5.107 29.430 1235 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.12 % Allowed : 22.84 % Favored : 73.05 % 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: -1.82 (0.25), residues: 1115 helix: -0.71 (0.25), residues: 398 sheet: -0.95 (0.34), residues: 236 loop : -1.66 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 243 HIS 0.007 0.001 HIS A 218 PHE 0.023 0.002 PHE C 103 TYR 0.018 0.002 TYR A 149 ARG 0.006 0.001 ARG F 342 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 317) hydrogen bonds : angle 5.02373 ( 882) SS BOND : bond 0.00374 ( 7) SS BOND : angle 1.61028 ( 14) covalent geometry : bond 0.00495 ( 9235) covalent geometry : angle 0.68538 (12503) *********************** 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: 40 poor density : 182 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLN cc_start: 0.7930 (mm110) cc_final: 0.7493 (mm110) REVERT: A 241 TYR cc_start: 0.9101 (m-80) cc_final: 0.8826 (m-80) REVERT: A 306 TRP cc_start: 0.7769 (OUTLIER) cc_final: 0.6973 (t60) REVERT: B 49 LYS cc_start: 0.8616 (tttp) cc_final: 0.8300 (ttpp) REVERT: C 34 MET cc_start: 0.7820 (mmm) cc_final: 0.7573 (mmm) REVERT: C 53 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6322 (mp10) REVERT: D 27 ARG cc_start: 0.6985 (mmt180) cc_final: 0.6733 (mmt180) REVERT: E 22 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7689 (ttm170) REVERT: E 58 ILE cc_start: 0.9411 (mt) cc_final: 0.8957 (tt) REVERT: E 105 TYR cc_start: 0.7995 (t80) cc_final: 0.7581 (t80) REVERT: E 225 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.7009 (t-90) REVERT: E 264 TYR cc_start: 0.7070 (m-80) cc_final: 0.6741 (m-80) REVERT: F 271 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8841 (mmtt) REVERT: F 360 TYR cc_start: 0.7978 (m-80) cc_final: 0.7660 (m-80) outliers start: 40 outliers final: 29 residues processed: 206 average time/residue: 0.2204 time to fit residues: 62.3312 Evaluate side-chains 209 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 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 125 THR 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 157 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 225 HIS Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 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: 0.7980 chunk 95 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 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 = 0.3824 r_free = 0.3824 target = 0.114545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090523 restraints weight = 24968.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.092895 restraints weight = 13053.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094404 restraints weight = 8882.971| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9242 Z= 0.143 Angle : 0.633 12.173 12517 Z= 0.328 Chirality : 0.044 0.179 1380 Planarity : 0.004 0.040 1597 Dihedral : 4.847 26.259 1235 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.70 % Allowed : 22.94 % Favored : 73.35 % 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: -1.64 (0.25), residues: 1115 helix: -0.52 (0.25), residues: 395 sheet: -0.86 (0.35), residues: 231 loop : -1.58 (0.29), residues: 489 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 0.026 0.001 PHE C 103 TYR 0.018 0.001 TYR A 157 ARG 0.006 0.000 ARG F 342 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 317) hydrogen bonds : angle 4.79538 ( 882) SS BOND : bond 0.00384 ( 7) SS BOND : angle 1.34342 ( 14) covalent geometry : bond 0.00326 ( 9235) covalent geometry : angle 0.63171 (12503) *********************** 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 226 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.983 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 214 GLN cc_start: 0.7860 (mm110) cc_final: 0.7398 (mm110) REVERT: A 241 TYR cc_start: 0.9048 (m-80) cc_final: 0.8787 (m-80) REVERT: A 306 TRP cc_start: 0.7790 (OUTLIER) cc_final: 0.7082 (t60) REVERT: B 25 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8590 (tp40) REVERT: B 49 LYS cc_start: 0.8644 (tttp) cc_final: 0.8389 (ttpp) REVERT: C 53 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6172 (mp10) REVERT: C 87 LYS cc_start: 0.8165 (tptp) cc_final: 0.7806 (tptp) REVERT: E 58 ILE cc_start: 0.9386 (mt) cc_final: 0.8903 (tt) REVERT: E 105 TYR cc_start: 0.7867 (t80) cc_final: 0.7478 (t80) REVERT: E 225 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.6948 (t-90) REVERT: E 264 TYR cc_start: 0.6932 (m-80) cc_final: 0.6642 (m-80) REVERT: F 271 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8796 (mmtt) REVERT: F 360 TYR cc_start: 0.7939 (m-80) cc_final: 0.7682 (m-80) outliers start: 36 outliers final: 29 residues processed: 209 average time/residue: 0.2244 time to fit residues: 64.2644 Evaluate side-chains 219 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 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 164 THR Chi-restraints excluded: chain E residue 225 HIS Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 7 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.4924 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.115260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.091254 restraints weight = 25105.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.093613 restraints weight = 13000.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095127 restraints weight = 8861.154| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9242 Z= 0.132 Angle : 0.641 12.162 12517 Z= 0.329 Chirality : 0.044 0.195 1380 Planarity : 0.003 0.040 1597 Dihedral : 4.721 25.329 1235 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.40 % Allowed : 23.87 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.55 (0.25), residues: 1115 helix: -0.37 (0.25), residues: 392 sheet: -0.88 (0.34), residues: 234 loop : -1.56 (0.28), residues: 489 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 0.027 0.001 PHE C 103 TYR 0.017 0.001 TYR A 157 ARG 0.004 0.000 ARG F 342 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 317) hydrogen bonds : angle 4.82562 ( 882) SS BOND : bond 0.00467 ( 7) SS BOND : angle 1.48336 ( 14) covalent geometry : bond 0.00299 ( 9235) covalent geometry : angle 0.63934 (12503) ********************** 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 222 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.994 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 214 GLN cc_start: 0.7954 (mm110) cc_final: 0.7509 (mm110) REVERT: A 241 TYR cc_start: 0.9041 (m-80) cc_final: 0.8784 (m-80) REVERT: A 306 TRP cc_start: 0.7730 (OUTLIER) cc_final: 0.7110 (t60) REVERT: B 49 LYS cc_start: 0.8685 (tttp) cc_final: 0.8420 (ttpp) REVERT: C 53 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6147 (mp10) REVERT: C 87 LYS cc_start: 0.8136 (tptp) cc_final: 0.7776 (tptp) REVERT: E 58 ILE cc_start: 0.9388 (mt) cc_final: 0.8895 (tt) REVERT: E 105 TYR cc_start: 0.7811 (t80) cc_final: 0.7462 (t80) REVERT: E 225 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.6906 (t-90) REVERT: E 264 TYR cc_start: 0.6939 (m-80) cc_final: 0.6656 (m-80) REVERT: F 271 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8810 (mmtt) REVERT: F 360 TYR cc_start: 0.7937 (m-80) cc_final: 0.7695 (m-80) outliers start: 33 outliers final: 29 residues processed: 207 average time/residue: 0.2155 time to fit residues: 60.6419 Evaluate side-chains 215 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 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 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 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 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 = 0.3809 r_free = 0.3809 target = 0.113606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.089457 restraints weight = 25163.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.091759 restraints weight = 13223.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.093250 restraints weight = 9078.432| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9242 Z= 0.189 Angle : 0.692 14.771 12517 Z= 0.356 Chirality : 0.046 0.197 1380 Planarity : 0.004 0.039 1597 Dihedral : 4.999 27.716 1235 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.60 % Allowed : 23.97 % Favored : 72.43 % 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: -1.74 (0.25), residues: 1115 helix: -0.57 (0.25), residues: 399 sheet: -1.03 (0.34), residues: 241 loop : -1.61 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 297 HIS 0.007 0.001 HIS A 218 PHE 0.028 0.002 PHE C 103 TYR 0.018 0.002 TYR A 157 ARG 0.004 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 317) hydrogen bonds : angle 4.97740 ( 882) SS BOND : bond 0.00373 ( 7) SS BOND : angle 1.57425 ( 14) covalent geometry : bond 0.00427 ( 9235) covalent geometry : angle 0.69014 (12503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3400.92 seconds wall clock time: 59 minutes 50.22 seconds (3590.22 seconds total)