Starting phenix.real_space_refine on Thu Jul 2 17:45:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yiu_33864/07_2026/7yiu_33864.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yiu_33864/07_2026/7yiu_33864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yiu_33864/07_2026/7yiu_33864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yiu_33864/07_2026/7yiu_33864.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yiu_33864/07_2026/7yiu_33864.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yiu_33864/07_2026/7yiu_33864.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yiu_33864/07_2026/7yiu_33864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yiu_33864/07_2026/7yiu_33864.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 52 5.16 5 C 5994 2.51 5 N 1561 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9285 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3940 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 481} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 341 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'TRP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1236 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 411 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "A" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3285 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'6CM': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 1.56, per 1000 atoms: 0.17 Number of scatterers: 9285 At special positions: 0 Unit cell: (91.8, 85.32, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 1 15.00 O 1677 8.00 N 1561 7.00 C 5994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 220.4 milliseconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 46.9% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 67 through 73 removed outlier: 3.508A pdb=" N LEU B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 90 removed outlier: 3.751A pdb=" N GLY B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 88 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 105 through 109 removed outlier: 4.026A pdb=" N LYS B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 134 removed outlier: 3.599A pdb=" N ASN B 133 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP B 134 " --> pdb=" O ARG B 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 130 through 134' Processing helix chain 'B' and resid 177 through 181 removed outlier: 4.232A pdb=" N PHE B 181 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 228 removed outlier: 3.717A pdb=" N GLU B 220 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 244 removed outlier: 4.022A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.630A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.643A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.660A pdb=" N TYR B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 removed outlier: 3.799A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.524A pdb=" N GLN B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET B 427 " --> pdb=" O MET B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.633A pdb=" N CYS B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B 445 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 490 removed outlier: 3.840A pdb=" N ILE B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 487 " --> pdb=" O GLY B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 535 Processing helix chain 'E' and resid 10 through 16 removed outlier: 3.647A pdb=" N VAL E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 removed outlier: 3.543A pdb=" N LEU E 27 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP E 34 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 19 removed outlier: 3.619A pdb=" N SER D 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.607A pdb=" N ILE D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 66 removed outlier: 3.672A pdb=" N ASN D 53 " --> pdb=" O TRP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 96 through 116 removed outlier: 3.595A pdb=" N PHE D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Proline residue: D 106 - end of helix removed outlier: 3.531A pdb=" N THR D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 136 removed outlier: 3.569A pdb=" N ASN D 127 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL D 129 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 3.728A pdb=" N HIS D 143 " --> pdb=" O PRO D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'C' and resid 10 through 14 Processing helix chain 'C' and resid 14 through 24 removed outlier: 3.694A pdb=" N THR C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.636A pdb=" N VAL C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 3.708A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.811A pdb=" N GLU A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.847A pdb=" N ALA A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.583A pdb=" N ASP A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.722A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 227 removed outlier: 3.642A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.664A pdb=" N ARG A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.524A pdb=" N LEU A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.894A pdb=" N ILE A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.673A pdb=" N ALA A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.708A pdb=" N PHE A 363 " --> pdb=" O PRO A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.564A pdb=" N GLU A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.747A pdb=" N ASN A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.530A pdb=" N THR A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'B' and resid 146 through 152 removed outlier: 6.205A pdb=" N VAL B 146 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY B 169 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASN B 165 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLN B 152 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR B 163 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.703A pdb=" N LEU B 341 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET B 374 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU B 343 " --> pdb=" O MET B 374 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N THR B 376 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 259 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 470 through 472 removed outlier: 3.838A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.763A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.611A pdb=" N GLY A 316 " --> pdb=" O TYR A 164 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASN A 306 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 383 through 386 removed outlier: 3.520A pdb=" N VAL A 386 " --> pdb=" O HIS A 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 427 through 428 removed outlier: 4.487A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2778 1.33 - 1.45: 1310 1.45 - 1.57: 5308 1.57 - 1.69: 1 1.69 - 1.81: 87 Bond restraints: 9484 Sorted by residual: bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.485 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.482 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C PHE B 498 " pdb=" O PHE B 498 " ideal model delta sigma weight residual 1.244 1.212 0.032 9.10e-03 1.21e+04 1.21e+01 bond pdb=" CA ASN B 120 " pdb=" CB ASN B 120 " ideal model delta sigma weight residual 1.532 1.565 -0.032 1.53e-02 4.27e+03 4.51e+00 ... (remaining 9479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 12067 2.10 - 4.20: 651 4.20 - 6.30: 83 6.30 - 8.40: 14 8.40 - 10.50: 4 Bond angle restraints: 12819 Sorted by residual: angle pdb=" N LYS B 168 " pdb=" CA LYS B 168 " pdb=" C LYS B 168 " ideal model delta sigma weight residual 111.02 119.68 -8.66 1.22e+00 6.72e-01 5.04e+01 angle pdb=" N GLY B 497 " pdb=" CA GLY B 497 " pdb=" C GLY B 497 " ideal model delta sigma weight residual 112.60 121.63 -9.03 1.43e+00 4.89e-01 3.98e+01 angle pdb=" N PRO A 78 " pdb=" CA PRO A 78 " pdb=" CB PRO A 78 " ideal model delta sigma weight residual 103.33 110.19 -6.86 1.10e+00 8.26e-01 3.89e+01 angle pdb=" C GLN B 300 " pdb=" N PRO B 301 " pdb=" CA PRO B 301 " ideal model delta sigma weight residual 119.84 127.47 -7.63 1.25e+00 6.40e-01 3.73e+01 angle pdb=" N MET B 456 " pdb=" CA MET B 456 " pdb=" C MET B 456 " ideal model delta sigma weight residual 113.41 106.08 7.33 1.22e+00 6.72e-01 3.61e+01 ... (remaining 12814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4760 17.64 - 35.28: 544 35.28 - 52.91: 273 52.91 - 70.55: 83 70.55 - 88.19: 10 Dihedral angle restraints: 5670 sinusoidal: 2294 harmonic: 3376 Sorted by residual: dihedral pdb=" C ASN B 120 " pdb=" N ASN B 120 " pdb=" CA ASN B 120 " pdb=" CB ASN B 120 " ideal model delta harmonic sigma weight residual -122.60 -137.95 15.35 0 2.50e+00 1.60e-01 3.77e+01 dihedral pdb=" N ASN B 120 " pdb=" C ASN B 120 " pdb=" CA ASN B 120 " pdb=" CB ASN B 120 " ideal model delta harmonic sigma weight residual 122.80 136.47 -13.67 0 2.50e+00 1.60e-01 2.99e+01 dihedral pdb=" N LEU A 111 " pdb=" C LEU A 111 " pdb=" CA LEU A 111 " pdb=" CB LEU A 111 " ideal model delta harmonic sigma weight residual 122.80 133.25 -10.45 0 2.50e+00 1.60e-01 1.75e+01 ... (remaining 5667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1248 0.098 - 0.196: 163 0.196 - 0.294: 14 0.294 - 0.392: 3 0.392 - 0.490: 2 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CA ASN B 120 " pdb=" N ASN B 120 " pdb=" C ASN B 120 " pdb=" CB ASN B 120 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" CA LEU A 111 " pdb=" N LEU A 111 " pdb=" C LEU A 111 " pdb=" CB LEU A 111 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CA LYS B 168 " pdb=" N LYS B 168 " pdb=" C LYS B 168 " pdb=" CB LYS B 168 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 1427 not shown) Planarity restraints: 1622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 6CM D 801 " -0.084 2.00e-02 2.50e+03 2.81e-01 9.90e+02 pdb=" C2 6CM D 801 " 0.331 2.00e-02 2.50e+03 pdb=" C20 6CM D 801 " 0.171 2.00e-02 2.50e+03 pdb=" N2 6CM D 801 " -0.495 2.00e-02 2.50e+03 pdb=" O19 6CM D 801 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.059 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO B 502 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 501 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C THR B 501 " -0.036 2.00e-02 2.50e+03 pdb=" O THR B 501 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 502 " 0.012 2.00e-02 2.50e+03 ... (remaining 1619 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 32 2.53 - 3.12: 6263 3.12 - 3.71: 13016 3.71 - 4.31: 20001 4.31 - 4.90: 33819 Nonbonded interactions: 73131 Sorted by model distance: nonbonded pdb=" O THR B 66 " pdb=" NH1 ARG D 20 " model vdw 1.932 3.120 nonbonded pdb=" NH2 ARG A 151 " pdb=" OD1 ASN A 354 " model vdw 1.966 3.120 nonbonded pdb=" OH TYR A 128 " pdb=" OD1 ASP A 143 " model vdw 1.991 3.040 nonbonded pdb=" O LEU B 473 " pdb=" O SER B 506 " model vdw 2.002 3.040 nonbonded pdb=" O ALA B 201 " pdb=" OG SER B 412 " model vdw 2.011 3.040 ... (remaining 73126 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=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 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 : 0.008 0.355 9485 Z= 0.541 Angle : 1.076 10.505 12819 Z= 0.718 Chirality : 0.070 0.490 1430 Planarity : 0.009 0.281 1622 Dihedral : 19.600 88.187 3510 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 1.21 % Allowed : 6.49 % Favored : 92.30 % Rotamer: Outliers : 16.13 % Allowed : 10.14 % Favored : 73.73 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.83 (0.20), residues: 1156 helix: -4.19 (0.14), residues: 506 sheet: -1.58 (0.44), residues: 123 loop : -2.41 (0.24), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 233 TYR 0.021 0.002 TYR A 166 PHE 0.025 0.002 PHE A 138 TRP 0.011 0.002 TRP C 32 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.40 ( 9484) covalent geometry : angle 1.07560 / 0.72 (12819) hydrogen bonds : bond 0.34533 / 22.97 ( 289) hydrogen bonds : angle 10.26452 / 6.95 ( 816) Misc. bond : bond 0.35539 / 18.70 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 127 time to evaluate : 0.261 Fit side-chains REVERT: B 57 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7011 (ptp-170) REVERT: B 68 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8862 (tpt) REVERT: B 92 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8212 (ptt180) REVERT: B 111 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.9016 (m-80) REVERT: B 150 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: B 165 ASN cc_start: 0.7755 (p0) cc_final: 0.7172 (p0) REVERT: B 190 GLU cc_start: 0.8005 (tt0) cc_final: 0.7755 (tp30) REVERT: B 197 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: B 271 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8267 (mtt-85) REVERT: B 305 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.8053 (mmt-90) REVERT: B 423 MET cc_start: 0.9117 (ttp) cc_final: 0.8830 (ttp) REVERT: B 463 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8517 (t0) REVERT: B 475 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.7463 (mtt) REVERT: B 521 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8935 (mp) REVERT: B 543 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6294 (ttm170) REVERT: E 10 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6475 (tm) REVERT: E 13 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7475 (mtp) REVERT: E 15 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7294 (tt0) REVERT: E 37 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6944 (tpt-90) REVERT: E 42 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7752 (mttm) REVERT: D 152 LYS cc_start: 0.8898 (tptm) cc_final: 0.8529 (tmtm) REVERT: C 12 GLN cc_start: 0.7805 (tt0) cc_final: 0.7553 (tt0) REVERT: C 53 TYR cc_start: 0.7671 (t80) cc_final: 0.7449 (t80) REVERT: A 77 HIS cc_start: 0.6181 (OUTLIER) cc_final: 0.5604 (m90) REVERT: A 236 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7727 (mtt180) REVERT: A 249 MET cc_start: 0.8678 (ttm) cc_final: 0.8459 (ttt) REVERT: A 268 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8861 (mmtp) REVERT: A 287 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8441 (mtt180) REVERT: A 368 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8336 (pp20) REVERT: A 375 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8637 (tttm) REVERT: A 407 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: A 419 CYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8107 (m) REVERT: A 427 THR cc_start: 0.8972 (p) cc_final: 0.8658 (t) REVERT: A 464 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9009 (mt) outliers start: 159 outliers final: 79 residues processed: 251 average time/residue: 0.4912 time to fit residues: 131.0906 Evaluate side-chains 211 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 109 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.0050 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 108 GLN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS D 94 GLN C 38 ASN A 285 HIS A 407 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.105575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.087709 restraints weight = 12329.370| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.55 r_work: 0.2757 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9485 Z= 0.135 Angle : 0.620 10.190 12819 Z= 0.333 Chirality : 0.045 0.189 1430 Planarity : 0.005 0.062 1622 Dihedral : 13.634 77.334 1546 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 7.30 % Allowed : 17.85 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.22), residues: 1156 helix: -2.63 (0.19), residues: 521 sheet: -1.15 (0.45), residues: 122 loop : -2.10 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.013 0.001 TYR C 50 PHE 0.015 0.001 PHE B 121 TRP 0.012 0.001 TRP C 10 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 9484) covalent geometry : angle 0.61984 / 0.33 (12819) hydrogen bonds : bond 0.05485 / 3.63 ( 289) hydrogen bonds : angle 5.37649 / 3.63 ( 816) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 115 time to evaluate : 0.283 Fit side-chains REVERT: B 50 GLN cc_start: 0.5656 (OUTLIER) cc_final: 0.5000 (pm20) REVERT: B 57 ARG cc_start: 0.7559 (mtm110) cc_final: 0.6693 (ptp-170) REVERT: B 150 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: B 165 ASN cc_start: 0.7747 (p0) cc_final: 0.7317 (p0) REVERT: B 183 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7983 (ptt90) REVERT: B 190 GLU cc_start: 0.8728 (tt0) cc_final: 0.8115 (tp30) REVERT: B 197 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 198 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8303 (pp20) REVERT: B 434 LEU cc_start: 0.7872 (mm) cc_final: 0.7017 (tt) REVERT: B 440 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8298 (pp30) REVERT: B 454 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8988 (tppp) REVERT: E 13 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7668 (mtp) REVERT: E 18 TYR cc_start: 0.4320 (OUTLIER) cc_final: 0.4091 (t80) REVERT: D 58 MET cc_start: 0.8056 (ttp) cc_final: 0.7586 (tpt) REVERT: D 122 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8416 (tp) REVERT: D 152 LYS cc_start: 0.8948 (tptm) cc_final: 0.8559 (tmtm) REVERT: A 77 HIS cc_start: 0.6344 (OUTLIER) cc_final: 0.5691 (m90) REVERT: A 203 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7607 (mmt-90) REVERT: A 360 PRO cc_start: 0.8945 (Cg_endo) cc_final: 0.8614 (Cg_exo) REVERT: A 368 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8587 (pp20) REVERT: A 427 THR cc_start: 0.9042 (p) cc_final: 0.8716 (t) REVERT: A 464 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8754 (mt) outliers start: 72 outliers final: 41 residues processed: 170 average time/residue: 0.5113 time to fit residues: 92.7817 Evaluate side-chains 160 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 106 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 0.0470 chunk 11 optimal weight: 0.7980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 141 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.106987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.089077 restraints weight = 12293.311| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.56 r_work: 0.2776 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9485 Z= 0.107 Angle : 0.529 8.376 12819 Z= 0.281 Chirality : 0.043 0.187 1430 Planarity : 0.004 0.035 1622 Dihedral : 10.504 59.696 1416 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.27 % Allowed : 20.18 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.24), residues: 1156 helix: -1.29 (0.22), residues: 521 sheet: -0.92 (0.46), residues: 124 loop : -1.95 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 99 TYR 0.009 0.001 TYR A 166 PHE 0.015 0.001 PHE B 121 TRP 0.009 0.001 TRP B 134 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 9484) covalent geometry : angle 0.52926 / 0.28 (12819) hydrogen bonds : bond 0.04075 / 2.68 ( 289) hydrogen bonds : angle 4.60808 / 3.09 ( 816) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 0.314 Fit side-chains REVERT: B 57 ARG cc_start: 0.7563 (mtm110) cc_final: 0.6699 (ptp-170) REVERT: B 106 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: B 126 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 183 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7983 (ptt90) REVERT: B 190 GLU cc_start: 0.8724 (tt0) cc_final: 0.8081 (tp30) REVERT: B 197 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7901 (tm-30) REVERT: B 198 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8310 (pp20) REVERT: B 291 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8631 (mt) REVERT: B 434 LEU cc_start: 0.8128 (mm) cc_final: 0.7158 (tt) REVERT: B 440 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8248 (pp30) REVERT: E 18 TYR cc_start: 0.4327 (OUTLIER) cc_final: 0.4065 (t80) REVERT: D 58 MET cc_start: 0.8101 (ttp) cc_final: 0.7567 (tpt) REVERT: D 122 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8452 (tp) REVERT: D 152 LYS cc_start: 0.8950 (tptm) cc_final: 0.8622 (tmtm) REVERT: A 62 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: A 223 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8420 (mt-10) REVERT: A 360 PRO cc_start: 0.8872 (Cg_endo) cc_final: 0.8613 (Cg_exo) REVERT: A 368 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8645 (pp20) REVERT: A 423 SER cc_start: 0.8351 (m) cc_final: 0.8061 (t) REVERT: A 427 THR cc_start: 0.8999 (p) cc_final: 0.8695 (t) REVERT: A 464 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8642 (mt) outliers start: 52 outliers final: 23 residues processed: 159 average time/residue: 0.5412 time to fit residues: 91.6554 Evaluate side-chains 148 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 105 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 102 optimal weight: 0.0870 chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 ASN D 11 ASN D 141 GLN A 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.089409 restraints weight = 12429.224| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.57 r_work: 0.2780 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9485 Z= 0.103 Angle : 0.511 8.246 12819 Z= 0.270 Chirality : 0.043 0.181 1430 Planarity : 0.004 0.039 1622 Dihedral : 8.304 59.174 1363 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.06 % Allowed : 22.21 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.24), residues: 1156 helix: -0.64 (0.23), residues: 526 sheet: -0.84 (0.47), residues: 124 loop : -1.87 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.009 0.001 TYR B 235 PHE 0.013 0.001 PHE B 121 TRP 0.007 0.001 TRP B 94 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 9484) covalent geometry : angle 0.51122 / 0.27 (12819) hydrogen bonds : bond 0.03650 / 2.40 ( 289) hydrogen bonds : angle 4.38491 / 2.94 ( 816) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 0.350 Fit side-chains REVERT: B 93 TYR cc_start: 0.6363 (m-80) cc_final: 0.5758 (m-10) REVERT: B 106 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: B 126 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8427 (mp) REVERT: B 185 THR cc_start: 0.8350 (p) cc_final: 0.8059 (t) REVERT: B 190 GLU cc_start: 0.8703 (tt0) cc_final: 0.8127 (tp30) REVERT: B 197 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: B 198 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8353 (pp20) REVERT: B 291 LEU cc_start: 0.8870 (tp) cc_final: 0.8585 (mt) REVERT: B 440 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8215 (pp30) REVERT: E 13 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7700 (OUTLIER) REVERT: E 18 TYR cc_start: 0.4438 (OUTLIER) cc_final: 0.4166 (t80) REVERT: D 58 MET cc_start: 0.8121 (ttp) cc_final: 0.7555 (tpt) REVERT: D 122 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8418 (tp) REVERT: D 152 LYS cc_start: 0.8962 (tptm) cc_final: 0.8646 (tmtm) REVERT: A 62 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: A 223 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 277 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8966 (mp) REVERT: A 360 PRO cc_start: 0.8836 (Cg_endo) cc_final: 0.8611 (Cg_exo) REVERT: A 367 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8691 (ptmt) REVERT: A 368 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8616 (pp20) REVERT: A 423 SER cc_start: 0.8243 (m) cc_final: 0.7968 (t) REVERT: A 427 THR cc_start: 0.8990 (p) cc_final: 0.8721 (t) REVERT: A 464 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8649 (mt) outliers start: 40 outliers final: 17 residues processed: 141 average time/residue: 0.5216 time to fit residues: 78.4133 Evaluate side-chains 135 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 99 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 11 ASN D 141 GLN A 77 HIS A 83 ASN A 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.081625 restraints weight = 12455.758| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 1.69 r_work: 0.2649 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9485 Z= 0.281 Angle : 0.711 9.102 12819 Z= 0.366 Chirality : 0.051 0.203 1430 Planarity : 0.005 0.052 1622 Dihedral : 8.500 58.698 1348 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 5.07 % Allowed : 21.81 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.24), residues: 1156 helix: -0.86 (0.22), residues: 532 sheet: -0.98 (0.47), residues: 122 loop : -1.89 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 181 TYR 0.019 0.002 TYR B 342 PHE 0.025 0.002 PHE A 138 TRP 0.008 0.002 TRP B 134 HIS 0.005 0.001 HIS B 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.28 ( 9484) covalent geometry : angle 0.71089 / 0.37 (12819) hydrogen bonds : bond 0.06124 / 4.03 ( 289) hydrogen bonds : angle 4.73993 / 3.18 ( 816) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 108 time to evaluate : 0.283 Fit side-chains REVERT: B 57 ARG cc_start: 0.7622 (mtm110) cc_final: 0.6748 (ptp-170) REVERT: B 93 TYR cc_start: 0.6463 (m-80) cc_final: 0.5964 (m-10) REVERT: B 106 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: B 190 GLU cc_start: 0.8804 (tt0) cc_final: 0.8175 (tp30) REVERT: B 197 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8023 (tm-30) REVERT: B 198 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8353 (pt0) REVERT: B 440 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8298 (pp30) REVERT: E 13 MET cc_start: 0.8022 (mtp) cc_final: 0.7705 (mtt) REVERT: E 18 TYR cc_start: 0.4412 (OUTLIER) cc_final: 0.4194 (t80) REVERT: E 42 LYS cc_start: 0.8307 (ptmm) cc_final: 0.8037 (mmtm) REVERT: D 122 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8477 (tp) REVERT: A 62 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: A 277 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8974 (mp) REVERT: A 367 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8368 (ptpp) REVERT: A 368 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8720 (pp20) REVERT: A 405 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7188 (ttt90) REVERT: A 464 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8738 (mt) outliers start: 50 outliers final: 24 residues processed: 146 average time/residue: 0.5335 time to fit residues: 82.7942 Evaluate side-chains 139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS A 83 ASN A 296 ASN A 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.104705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.086731 restraints weight = 12383.482| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.56 r_work: 0.2736 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9485 Z= 0.111 Angle : 0.534 7.829 12819 Z= 0.280 Chirality : 0.043 0.186 1430 Planarity : 0.004 0.045 1622 Dihedral : 8.056 59.749 1348 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.06 % Allowed : 23.23 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.24), residues: 1156 helix: -0.35 (0.23), residues: 533 sheet: -0.91 (0.47), residues: 124 loop : -1.80 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 99 TYR 0.010 0.001 TYR B 235 PHE 0.012 0.001 PHE A 138 TRP 0.010 0.001 TRP B 134 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 9484) covalent geometry : angle 0.53396 / 0.28 (12819) hydrogen bonds : bond 0.03962 / 2.59 ( 289) hydrogen bonds : angle 4.43465 / 2.98 ( 816) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.308 Fit side-chains REVERT: B 93 TYR cc_start: 0.6539 (m-80) cc_final: 0.6046 (m-10) REVERT: B 106 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: B 185 THR cc_start: 0.8312 (p) cc_final: 0.8047 (t) REVERT: B 190 GLU cc_start: 0.8728 (tt0) cc_final: 0.8160 (tp30) REVERT: B 197 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: B 198 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8386 (pp20) REVERT: B 291 LEU cc_start: 0.9056 (tp) cc_final: 0.8854 (mt) REVERT: E 13 MET cc_start: 0.8218 (mtp) cc_final: 0.7832 (mtt) REVERT: E 18 TYR cc_start: 0.4456 (OUTLIER) cc_final: 0.4198 (t80) REVERT: D 58 MET cc_start: 0.8061 (ttp) cc_final: 0.7507 (tpt) REVERT: D 152 LYS cc_start: 0.8952 (tptm) cc_final: 0.8539 (tmtm) REVERT: A 58 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: A 62 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: A 277 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8905 (mp) REVERT: A 360 PRO cc_start: 0.8893 (Cg_endo) cc_final: 0.8613 (Cg_exo) REVERT: A 367 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8229 (ptpp) REVERT: A 368 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8633 (pp20) REVERT: A 423 SER cc_start: 0.8322 (m) cc_final: 0.8022 (t) REVERT: A 464 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8695 (mt) outliers start: 40 outliers final: 18 residues processed: 138 average time/residue: 0.5549 time to fit residues: 81.5072 Evaluate side-chains 131 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS A 83 ASN A 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.102261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.083531 restraints weight = 12419.722| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.69 r_work: 0.2681 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9485 Z= 0.177 Angle : 0.597 8.203 12819 Z= 0.310 Chirality : 0.046 0.191 1430 Planarity : 0.004 0.049 1622 Dihedral : 7.906 59.119 1343 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.87 % Allowed : 21.91 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.24), residues: 1156 helix: -0.22 (0.23), residues: 531 sheet: -0.92 (0.47), residues: 124 loop : -1.79 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 99 TYR 0.014 0.002 TYR B 342 PHE 0.019 0.002 PHE A 138 TRP 0.008 0.001 TRP B 134 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 9484) covalent geometry : angle 0.59700 / 0.31 (12819) hydrogen bonds : bond 0.04801 / 3.13 ( 289) hydrogen bonds : angle 4.49680 / 3.01 ( 816) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 103 time to evaluate : 0.371 Fit side-chains REVERT: B 93 TYR cc_start: 0.6616 (m-80) cc_final: 0.6086 (m-10) REVERT: B 106 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: B 190 GLU cc_start: 0.8785 (tt0) cc_final: 0.8188 (tp30) REVERT: B 197 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: B 198 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8407 (pp20) REVERT: B 252 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8527 (tttm) REVERT: B 291 LEU cc_start: 0.9125 (tp) cc_final: 0.8916 (mt) REVERT: E 13 MET cc_start: 0.8184 (mtp) cc_final: 0.7815 (mtt) REVERT: E 18 TYR cc_start: 0.4501 (OUTLIER) cc_final: 0.4279 (t80) REVERT: D 58 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7935 (ttp) REVERT: A 52 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6952 (mm) REVERT: A 62 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: A 277 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8958 (mp) REVERT: A 360 PRO cc_start: 0.8922 (Cg_endo) cc_final: 0.8623 (Cg_exo) REVERT: A 367 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8317 (ptpp) REVERT: A 368 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8679 (pp20) REVERT: A 423 SER cc_start: 0.8326 (m) cc_final: 0.8000 (t) REVERT: A 464 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8643 (mt) outliers start: 48 outliers final: 24 residues processed: 140 average time/residue: 0.5499 time to fit residues: 82.0548 Evaluate side-chains 136 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS A 83 ASN A 296 ASN A 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.104184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.086187 restraints weight = 12261.388| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.56 r_work: 0.2722 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9485 Z= 0.128 Angle : 0.551 9.375 12819 Z= 0.286 Chirality : 0.044 0.186 1430 Planarity : 0.004 0.048 1622 Dihedral : 7.704 59.947 1343 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.06 % Allowed : 23.02 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.25), residues: 1156 helix: 0.03 (0.23), residues: 538 sheet: -0.90 (0.48), residues: 123 loop : -1.75 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 99 TYR 0.010 0.001 TYR B 342 PHE 0.014 0.001 PHE A 138 TRP 0.010 0.001 TRP B 134 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9484) covalent geometry : angle 0.55109 / 0.29 (12819) hydrogen bonds : bond 0.04107 / 2.69 ( 289) hydrogen bonds : angle 4.38864 / 2.94 ( 816) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 0.356 Fit side-chains REVERT: B 93 TYR cc_start: 0.6515 (m-80) cc_final: 0.6037 (m-10) REVERT: B 106 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: B 185 THR cc_start: 0.8302 (p) cc_final: 0.8038 (t) REVERT: B 190 GLU cc_start: 0.8706 (tt0) cc_final: 0.8151 (tp30) REVERT: B 197 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: B 198 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8392 (pp20) REVERT: B 252 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8500 (tttm) REVERT: B 291 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8861 (mt) REVERT: B 444 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8242 (mt-10) REVERT: E 13 MET cc_start: 0.8162 (mtp) cc_final: 0.7752 (mtt) REVERT: E 18 TYR cc_start: 0.4456 (OUTLIER) cc_final: 0.4225 (t80) REVERT: D 58 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7728 (ttp) REVERT: D 60 MET cc_start: 0.9031 (ttt) cc_final: 0.8776 (ttt) REVERT: D 152 LYS cc_start: 0.8975 (tptm) cc_final: 0.8569 (tmtm) REVERT: A 52 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6901 (mm) REVERT: A 58 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: A 62 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: A 277 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8939 (mp) REVERT: A 360 PRO cc_start: 0.8896 (Cg_endo) cc_final: 0.8615 (Cg_exo) REVERT: A 367 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8254 (ptpp) REVERT: A 368 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8620 (pp20) REVERT: A 423 SER cc_start: 0.8262 (m) cc_final: 0.7946 (t) REVERT: A 454 GLU cc_start: 0.7448 (tt0) cc_final: 0.7216 (mt-10) REVERT: A 464 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8700 (mt) outliers start: 40 outliers final: 22 residues processed: 134 average time/residue: 0.5648 time to fit residues: 80.4118 Evaluate side-chains 137 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 107 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 11 ASN A 83 ASN A 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.105700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.087726 restraints weight = 12243.137| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.56 r_work: 0.2750 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9485 Z= 0.106 Angle : 0.521 12.057 12819 Z= 0.269 Chirality : 0.043 0.181 1430 Planarity : 0.004 0.045 1622 Dihedral : 7.326 58.642 1343 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.06 % Allowed : 23.12 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1156 helix: 0.40 (0.23), residues: 539 sheet: -0.84 (0.48), residues: 123 loop : -1.68 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 124 TYR 0.009 0.001 TYR B 342 PHE 0.011 0.001 PHE A 209 TRP 0.010 0.001 TRP B 134 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9484) covalent geometry : angle 0.52149 / 0.27 (12819) hydrogen bonds : bond 0.03570 / 2.34 ( 289) hydrogen bonds : angle 4.25585 / 2.85 ( 816) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.304 Fit side-chains REVERT: B 93 TYR cc_start: 0.6529 (m-80) cc_final: 0.6045 (m-10) REVERT: B 106 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: B 126 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 185 THR cc_start: 0.8286 (p) cc_final: 0.8030 (t) REVERT: B 190 GLU cc_start: 0.8648 (tt0) cc_final: 0.8066 (tp30) REVERT: B 197 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: B 198 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7950 (pp20) REVERT: B 252 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8494 (tttm) REVERT: B 291 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8812 (mt) REVERT: E 13 MET cc_start: 0.8155 (mtp) cc_final: 0.7745 (mtt) REVERT: E 18 TYR cc_start: 0.4429 (OUTLIER) cc_final: 0.4209 (t80) REVERT: D 60 MET cc_start: 0.9025 (ttt) cc_final: 0.8778 (ttt) REVERT: D 152 LYS cc_start: 0.8972 (tptm) cc_final: 0.8559 (tmtm) REVERT: A 52 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6889 (mm) REVERT: A 58 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: A 62 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: A 277 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8938 (mp) REVERT: A 360 PRO cc_start: 0.8875 (Cg_endo) cc_final: 0.8622 (Cg_exo) REVERT: A 367 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8559 (ptmt) REVERT: A 368 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8604 (pp20) REVERT: A 454 GLU cc_start: 0.7402 (tt0) cc_final: 0.7196 (mt-10) REVERT: A 464 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8627 (mt) outliers start: 40 outliers final: 19 residues processed: 138 average time/residue: 0.5921 time to fit residues: 86.9386 Evaluate side-chains 135 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 63 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 108 GLN A 83 ASN A 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.106893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.088962 restraints weight = 12248.750| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.56 r_work: 0.2760 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9485 Z= 0.101 Angle : 0.504 7.634 12819 Z= 0.264 Chirality : 0.043 0.182 1430 Planarity : 0.004 0.044 1622 Dihedral : 6.991 58.264 1340 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.75 % Allowed : 23.33 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.25), residues: 1156 helix: 0.65 (0.24), residues: 539 sheet: -0.84 (0.48), residues: 125 loop : -1.57 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 124 TYR 0.009 0.001 TYR B 235 PHE 0.011 0.001 PHE A 209 TRP 0.009 0.001 TRP B 134 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 9484) covalent geometry : angle 0.50394 / 0.26 (12819) hydrogen bonds : bond 0.03474 / 2.28 ( 289) hydrogen bonds : angle 4.17587 / 2.79 ( 816) Misc. bond : bond 0.00005 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.356 Fit side-chains REVERT: B 93 TYR cc_start: 0.6479 (m-80) cc_final: 0.6002 (m-10) REVERT: B 106 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: B 126 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8534 (mp) REVERT: B 185 THR cc_start: 0.8330 (p) cc_final: 0.8084 (t) REVERT: B 190 GLU cc_start: 0.8611 (tt0) cc_final: 0.8065 (tp30) REVERT: B 197 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: B 198 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7987 (pp20) REVERT: B 252 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8464 (tttm) REVERT: B 291 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8737 (mt) REVERT: E 13 MET cc_start: 0.8127 (mtp) cc_final: 0.7736 (mtt) REVERT: D 60 MET cc_start: 0.8935 (ttt) cc_final: 0.8728 (ttt) REVERT: D 152 LYS cc_start: 0.8957 (tptm) cc_final: 0.8600 (tmtm) REVERT: C 29 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.7780 (mp) REVERT: A 58 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: A 62 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: A 277 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8924 (mp) REVERT: A 360 PRO cc_start: 0.8850 (Cg_endo) cc_final: 0.8642 (Cg_exo) REVERT: A 367 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8580 (ptmt) REVERT: A 368 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8570 (pp20) REVERT: A 427 THR cc_start: 0.9029 (p) cc_final: 0.8729 (t) REVERT: A 464 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8608 (mt) outliers start: 37 outliers final: 17 residues processed: 130 average time/residue: 0.6256 time to fit residues: 86.3380 Evaluate side-chains 130 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 108 GLN D 11 ASN A 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.105316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.087263 restraints weight = 12143.246| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.56 r_work: 0.2743 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9485 Z= 0.119 Angle : 0.530 7.533 12819 Z= 0.275 Chirality : 0.044 0.184 1430 Planarity : 0.004 0.046 1622 Dihedral : 6.721 58.226 1333 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.45 % Allowed : 23.83 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.25), residues: 1156 helix: 0.68 (0.23), residues: 539 sheet: -0.77 (0.48), residues: 123 loop : -1.59 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 271 TYR 0.011 0.001 TYR B 342 PHE 0.013 0.001 PHE A 138 TRP 0.008 0.001 TRP C 32 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 9484) covalent geometry : angle 0.52988 / 0.28 (12819) hydrogen bonds : bond 0.03847 / 2.52 ( 289) hydrogen bonds : angle 4.22349 / 2.82 ( 816) Misc. bond : bond 0.00002 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2850.22 seconds wall clock time: 49 minutes 19.91 seconds (2959.91 seconds total)