Starting phenix.real_space_refine on Tue Aug 26 13:08:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypk_34003/08_2025/7ypk_34003.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypk_34003/08_2025/7ypk_34003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ypk_34003/08_2025/7ypk_34003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypk_34003/08_2025/7ypk_34003.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypk_34003/08_2025/7ypk_34003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypk_34003/08_2025/7ypk_34003.cif" } resolution = 3.4 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= 0.017 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 12 5.49 5 S 130 5.16 5 C 23219 2.51 5 N 6457 2.21 5 O 6974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36792 Number of models: 1 Model: "" Number of chains: 13 Chain: "S" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6117 Classifications: {'peptide': 779} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 730} Chain: "A" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6117 Classifications: {'peptide': 779} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 730} Chain: "B" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6075 Classifications: {'peptide': 774} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 725} Chain breaks: 1 Chain: "C" Number of atoms: 6035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 6035 Classifications: {'peptide': 769} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 720} Chain breaks: 1 Chain: "D" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6074 Classifications: {'peptide': 774} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 725} Chain breaks: 1 Chain: "E" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6117 Classifications: {'peptide': 779} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 730} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.94, per 1000 atoms: 0.22 Number of scatterers: 36792 At special positions: 0 Unit cell: (164.455, 198.407, 206.895, 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 130 16.00 P 12 15.00 O 6974 8.00 N 6457 7.00 C 23219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8690 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 48 sheets defined 48.4% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 31 through 39 removed outlier: 4.002A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 62 Processing helix chain 'F' and resid 117 through 139 removed outlier: 4.445A pdb=" N VAL F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 157 through 169 removed outlier: 3.765A pdb=" N ASP F 163 " --> pdb=" O ALA F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 Processing helix chain 'F' and resid 184 through 239 Processing helix chain 'F' and resid 243 through 257 Processing helix chain 'F' and resid 259 through 276 removed outlier: 5.566A pdb=" N LYS F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 4.155A pdb=" N TYR F 289 " --> pdb=" O VAL F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 319 removed outlier: 3.659A pdb=" N THR F 311 " --> pdb=" O ASP F 307 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN F 313 " --> pdb=" O ASN F 309 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS F 319 " --> pdb=" O LEU F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 339 removed outlier: 3.757A pdb=" N LEU F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG F 336 " --> pdb=" O TYR F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 removed outlier: 3.732A pdb=" N ALA F 369 " --> pdb=" O GLY F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 391 removed outlier: 3.728A pdb=" N ILE F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 412 removed outlier: 4.267A pdb=" N GLN F 411 " --> pdb=" O HIS F 407 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 443 removed outlier: 4.279A pdb=" N GLU F 441 " --> pdb=" O SER F 437 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 450 Processing helix chain 'F' and resid 478 through 483 Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 505 through 514 Processing helix chain 'F' and resid 523 through 534 Processing helix chain 'F' and resid 540 through 561 Processing helix chain 'F' and resid 573 through 579 Processing helix chain 'F' and resid 630 through 646 removed outlier: 3.601A pdb=" N LYS F 634 " --> pdb=" O GLY F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 661 removed outlier: 3.536A pdb=" N VAL F 661 " --> pdb=" O PHE F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 693 Processing helix chain 'F' and resid 717 through 729 removed outlier: 3.634A pdb=" N ALA F 724 " --> pdb=" O GLU F 720 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA F 725 " --> pdb=" O LYS F 721 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 746 removed outlier: 4.230A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU F 743 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU F 744 " --> pdb=" O ALA F 741 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU F 746 " --> pdb=" O LEU F 743 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 754 Processing helix chain 'F' and resid 761 through 769 removed outlier: 3.778A pdb=" N VAL F 765 " --> pdb=" O ASP F 761 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 767 " --> pdb=" O GLY F 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 38 removed outlier: 3.982A pdb=" N MET A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 117 through 140 removed outlier: 4.195A pdb=" N VAL A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASN A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.870A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 removed outlier: 3.896A pdb=" N LEU A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 162 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 184 through 238 Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.657A pdb=" N GLU A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 removed outlier: 3.591A pdb=" N THR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 4.122A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.549A pdb=" N GLN A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 340 removed outlier: 3.680A pdb=" N ARG A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 removed outlier: 3.827A pdb=" N SER A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 515 removed outlier: 4.072A pdb=" N LYS A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.708A pdb=" N ILE A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 561 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 632 through 647 removed outlier: 3.676A pdb=" N SER A 636 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 680 through 693 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.678A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 725 " --> pdb=" O LYS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 removed outlier: 4.240A pdb=" N ALA A 741 " --> pdb=" O ASP A 738 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 743 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 744 " --> pdb=" O ALA A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.871A pdb=" N LEU A 751 " --> pdb=" O PRO A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 770 Processing helix chain 'B' and resid 27 through 40 removed outlier: 4.043A pdb=" N ARG B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 139 removed outlier: 3.569A pdb=" N LYS B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 143 Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.846A pdb=" N GLN B 148 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 169 removed outlier: 4.210A pdb=" N ILE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.898A pdb=" N LEU B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 256 removed outlier: 3.554A pdb=" N LEU B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 276 removed outlier: 3.592A pdb=" N MET B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.703A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 322 through 339 removed outlier: 4.366A pdb=" N LYS B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ARG B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 373 removed outlier: 3.565A pdb=" N ARG B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.978A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 505 through 515 removed outlier: 3.624A pdb=" N LYS B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.522A pdb=" N LEU B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG B 529 " --> pdb=" O ALA B 525 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 561 Processing helix chain 'B' and resid 572 through 579 removed outlier: 4.417A pdb=" N THR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.716A pdb=" N SER B 636 " --> pdb=" O VAL B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 660 Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 718 through 728 Processing helix chain 'B' and resid 739 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.506A pdb=" N GLU B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 753 " --> pdb=" O GLU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 769 removed outlier: 3.767A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU B 767 " --> pdb=" O GLY B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 117 through 138 removed outlier: 4.306A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 154 removed outlier: 4.012A pdb=" N GLY C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 172 through 182 Processing helix chain 'C' and resid 184 through 238 removed outlier: 3.713A pdb=" N MET C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 237 " --> pdb=" O ILE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 removed outlier: 3.999A pdb=" N ALA C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 259 through 272 removed outlier: 3.755A pdb=" N ARG C 272 " --> pdb=" O LYS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 Processing helix chain 'C' and resid 307 through 319 removed outlier: 4.124A pdb=" N GLU C 317 " --> pdb=" O GLN C 313 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 340 removed outlier: 3.762A pdb=" N LYS C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU C 327 " --> pdb=" O LYS C 323 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG C 336 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN C 337 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 339 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 373 Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.644A pdb=" N MET C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 444 removed outlier: 4.332A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 484 Processing helix chain 'C' and resid 494 through 505 removed outlier: 3.570A pdb=" N ALA C 500 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 514 removed outlier: 3.965A pdb=" N LYS C 509 " --> pdb=" O TYR C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.687A pdb=" N THR C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 561 removed outlier: 3.749A pdb=" N ARG C 545 " --> pdb=" O ARG C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 Processing helix chain 'C' and resid 630 through 647 Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.800A pdb=" N LYS C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 692 removed outlier: 4.023A pdb=" N MET C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 684 " --> pdb=" O GLY C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 729 Processing helix chain 'C' and resid 738 through 746 removed outlier: 4.561A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU C 745 " --> pdb=" O GLN C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 761 through 769 removed outlier: 3.591A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 38 removed outlier: 3.507A pdb=" N LYS D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 136 Processing helix chain 'D' and resid 137 through 143 removed outlier: 3.764A pdb=" N LYS D 140 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D 141 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 168 removed outlier: 4.024A pdb=" N HIS D 168 " --> pdb=" O THR D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 181 removed outlier: 3.515A pdb=" N LYS D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 242 removed outlier: 3.517A pdb=" N LYS D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 260 through 276 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.507A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.741A pdb=" N THR D 311 " --> pdb=" O ASP D 307 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU D 317 " --> pdb=" O GLN D 313 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 339 removed outlier: 3.549A pdb=" N GLU D 327 " --> pdb=" O LYS D 323 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 372 Processing helix chain 'D' and resid 386 through 391 removed outlier: 3.697A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.567A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.608A pdb=" N LYS D 426 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 444 Processing helix chain 'D' and resid 478 through 483 removed outlier: 3.769A pdb=" N ASP D 483 " --> pdb=" O ARG D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.917A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 561 removed outlier: 3.958A pdb=" N GLU D 546 " --> pdb=" O GLY D 542 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU D 547 " --> pdb=" O LEU D 543 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU D 560 " --> pdb=" O LYS D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 579 removed outlier: 3.628A pdb=" N TYR D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 647 Processing helix chain 'D' and resid 657 through 659 No H-bonds generated for 'chain 'D' and resid 657 through 659' Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 718 through 728 Processing helix chain 'D' and resid 738 through 744 removed outlier: 4.360A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 764 through 770 removed outlier: 3.589A pdb=" N LEU D 770 " --> pdb=" O LEU D 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 37 removed outlier: 3.839A pdb=" N VAL E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 40 No H-bonds generated for 'chain 'E' and resid 38 through 40' Processing helix chain 'E' and resid 58 through 60 No H-bonds generated for 'chain 'E' and resid 58 through 60' Processing helix chain 'E' and resid 117 through 136 removed outlier: 3.954A pdb=" N VAL E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.724A pdb=" N LEU E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 182 Processing helix chain 'E' and resid 184 through 238 Processing helix chain 'E' and resid 241 through 256 removed outlier: 4.983A pdb=" N ARG E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LYS E 251 " --> pdb=" O GLU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 271 removed outlier: 3.641A pdb=" N LYS E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP E 271 " --> pdb=" O LEU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.662A pdb=" N GLU E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 322 through 338 Processing helix chain 'E' and resid 361 through 373 removed outlier: 3.800A pdb=" N GLY E 365 " --> pdb=" O LYS E 361 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG E 366 " --> pdb=" O THR E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 412 removed outlier: 3.758A pdb=" N MET E 409 " --> pdb=" O LEU E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 444 removed outlier: 4.045A pdb=" N ALA E 438 " --> pdb=" O ASP E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 478 through 483 removed outlier: 3.731A pdb=" N ASP E 483 " --> pdb=" O ARG E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 515 removed outlier: 3.626A pdb=" N LYS E 509 " --> pdb=" O TYR E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 534 removed outlier: 3.857A pdb=" N ILE E 527 " --> pdb=" O THR E 523 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU E 528 " --> pdb=" O ASP E 524 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG E 529 " --> pdb=" O ALA E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 561 removed outlier: 4.063A pdb=" N ARG E 545 " --> pdb=" O ARG E 541 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 546 " --> pdb=" O GLY E 542 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU E 560 " --> pdb=" O LYS E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 579 removed outlier: 3.931A pdb=" N TYR E 577 " --> pdb=" O ASP E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 647 removed outlier: 3.665A pdb=" N LYS E 634 " --> pdb=" O GLY E 630 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 635 " --> pdb=" O GLU E 631 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER E 636 " --> pdb=" O VAL E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 693 Processing helix chain 'E' and resid 717 through 728 removed outlier: 4.153A pdb=" N LYS E 721 " --> pdb=" O GLY E 717 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS E 726 " --> pdb=" O LEU E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 743 removed outlier: 4.471A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU E 743 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 754 removed outlier: 3.775A pdb=" N GLY E 753 " --> pdb=" O GLU E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 770 removed outlier: 4.060A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E 770 " --> pdb=" O LEU E 766 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.519A pdb=" N ARG F 106 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP F 96 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA F 92 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY F 66 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE F 8 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 20 through 25 removed outlier: 3.775A pdb=" N THR F 21 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL F 86 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN F 83 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET F 75 " --> pdb=" O GLN F 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 376 through 379 removed outlier: 5.745A pdb=" N LEU F 353 " --> pdb=" O ALA F 471 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.521A pdb=" N GLU F 521 " --> pdb=" O ILE F 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 596 through 597 Processing sheet with id=AA6, first strand: chain 'F' and resid 600 through 603 Processing sheet with id=AA7, first strand: chain 'F' and resid 622 through 626 removed outlier: 5.801A pdb=" N LYS F 622 " --> pdb=" O LEU F 663 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL F 665 " --> pdb=" O LYS F 622 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N SER F 624 " --> pdb=" O VAL F 665 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 700 through 701 removed outlier: 6.644A pdb=" N ALA F 701 " --> pdb=" O VAL F 734 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE F 733 " --> pdb=" O LYS F 757 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL F 759 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU F 735 " --> pdb=" O VAL F 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 705 through 706 removed outlier: 4.046A pdb=" N GLU F 705 " --> pdb=" O MET F 713 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.535A pdb=" N PHE A 45 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 47 " --> pdb=" O ILE A 8 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.992A pdb=" N THR A 21 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 86 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 84 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ALA A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N VAL A 86 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS A 72 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.786A pdb=" N HIS A 377 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 420 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 486 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 451 through 452 removed outlier: 3.729A pdb=" N PHE A 451 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR A 460 " --> pdb=" O PHE A 451 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 521 through 522 removed outlier: 7.319A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 596 through 603 removed outlier: 3.993A pdb=" N ALA A 601 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR A 608 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 603 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 615 " --> pdb=" O HIS A 664 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS A 664 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 617 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 700 through 702 removed outlier: 6.276A pdb=" N ALA A 701 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 735 " --> pdb=" O LYS A 757 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 705 through 706 removed outlier: 3.778A pdb=" N GLU A 705 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.720A pdb=" N LEU B 5 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA B 105 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG B 104 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 98 " --> pdb=" O ARG B 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 21 through 22 removed outlier: 4.903A pdb=" N THR B 21 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 86 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA B 88 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL B 70 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA B 90 " --> pdb=" O GLN B 68 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 67 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.573A pdb=" N HIS B 377 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 420 " --> pdb=" O HIS B 377 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU B 353 " --> pdb=" O ALA B 471 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.762A pdb=" N GLU B 521 " --> pdb=" O ILE B 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 596 through 598 Processing sheet with id=AC5, first strand: chain 'B' and resid 601 through 603 Processing sheet with id=AC6, first strand: chain 'B' and resid 622 through 626 Processing sheet with id=AC7, first strand: chain 'B' and resid 700 through 701 removed outlier: 6.422A pdb=" N ALA B 701 " --> pdb=" O VAL B 734 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 705 through 706 removed outlier: 3.840A pdb=" N GLU B 705 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 7 through 9 removed outlier: 3.644A pdb=" N VAL C 47 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS C 72 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N MET C 85 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA C 74 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N GLN C 83 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 469 through 471 removed outlier: 6.545A pdb=" N LEU C 351 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA C 471 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU C 353 " --> pdb=" O ALA C 471 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE C 350 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 488 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 520 through 521 Processing sheet with id=AD3, first strand: chain 'C' and resid 596 through 597 removed outlier: 3.694A pdb=" N ALA C 615 " --> pdb=" O HIS C 664 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS C 664 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 600 through 602 Processing sheet with id=AD5, first strand: chain 'C' and resid 700 through 701 removed outlier: 7.337A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 9 through 10 removed outlier: 3.988A pdb=" N LEU D 10 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY D 66 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN D 68 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA D 90 " --> pdb=" O GLN D 68 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL D 23 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL D 86 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 418 through 421 removed outlier: 6.186A pdb=" N ILE D 419 " --> pdb=" O ILE D 468 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR D 470 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU D 421 " --> pdb=" O THR D 470 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU D 351 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE D 350 " --> pdb=" O GLU D 486 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE D 488 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL D 352 " --> pdb=" O ILE D 488 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 520 through 522 removed outlier: 7.606A pdb=" N GLU D 521 " --> pdb=" O ILE D 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 596 through 602 removed outlier: 3.533A pdb=" N ALA D 597 " --> pdb=" O ILE D 612 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 701 through 702 removed outlier: 6.725A pdb=" N ALA D 701 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE D 733 " --> pdb=" O GLU D 755 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 705 through 706 removed outlier: 3.682A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'E' and resid 23 through 25 removed outlier: 3.570A pdb=" N VAL E 23 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 25 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL E 84 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ALA E 74 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL E 86 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS E 72 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA E 88 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL E 70 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TRP E 65 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA E 48 " --> pdb=" O TRP E 65 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 23 through 25 removed outlier: 3.570A pdb=" N VAL E 23 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 25 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG E 91 " --> pdb=" O SER E 111 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 376 through 379 removed outlier: 4.077A pdb=" N HIS E 377 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU E 420 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE E 419 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR E 470 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU E 421 " --> pdb=" O THR E 470 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU E 486 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL E 352 " --> pdb=" O GLU E 486 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE E 488 " --> pdb=" O VAL E 352 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.862A pdb=" N GLU E 521 " --> pdb=" O ILE E 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'E' and resid 593 through 594 removed outlier: 3.641A pdb=" N GLN E 593 " --> pdb=" O ALA E 696 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 596 through 597 Processing sheet with id=AF1, first strand: chain 'E' and resid 600 through 603 Processing sheet with id=AF2, first strand: chain 'E' and resid 700 through 701 removed outlier: 3.509A pdb=" N VAL E 734 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE E 733 " --> pdb=" O LYS E 757 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL E 759 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU E 735 " --> pdb=" O VAL E 759 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 705 through 706 removed outlier: 4.138A pdb=" N GLU E 705 " --> pdb=" O MET E 713 " (cutoff:3.500A) 1543 hydrogen bonds defined for protein. 4506 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: 7.71 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6361 1.29 - 1.42: 8381 1.42 - 1.55: 22440 1.55 - 1.68: 18 1.68 - 1.82: 260 Bond restraints: 37460 Sorted by residual: bond pdb=" C LEU D 270 " pdb=" O LEU D 270 " ideal model delta sigma weight residual 1.236 1.156 0.080 1.19e-02 7.06e+03 4.54e+01 bond pdb=" C4 ADP F 801 " pdb=" C5 ADP F 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP E 801 " pdb=" C5 ADP E 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 37455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 49537 2.57 - 5.14: 1165 5.14 - 7.72: 84 7.72 - 10.29: 22 10.29 - 12.86: 7 Bond angle restraints: 50815 Sorted by residual: angle pdb=" CA GLY B 606 " pdb=" C GLY B 606 " pdb=" O GLY B 606 " ideal model delta sigma weight residual 122.45 118.23 4.22 7.20e-01 1.93e+00 3.43e+01 angle pdb=" CA GLY E 403 " pdb=" C GLY E 403 " pdb=" O GLY E 403 " ideal model delta sigma weight residual 122.29 118.17 4.12 8.10e-01 1.52e+00 2.59e+01 angle pdb=" N LEU A 381 " pdb=" CA LEU A 381 " pdb=" C LEU A 381 " ideal model delta sigma weight residual 113.01 106.93 6.08 1.20e+00 6.94e-01 2.57e+01 angle pdb=" N LYS F 265 " pdb=" CA LYS F 265 " pdb=" CB LYS F 265 " ideal model delta sigma weight residual 110.01 117.34 -7.33 1.45e+00 4.76e-01 2.56e+01 angle pdb=" CA ARG D 287 " pdb=" C ARG D 287 " pdb=" O ARG D 287 " ideal model delta sigma weight residual 120.82 115.55 5.27 1.05e+00 9.07e-01 2.52e+01 ... (remaining 50810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.58: 22381 28.58 - 57.16: 681 57.16 - 85.75: 48 85.75 - 114.33: 6 114.33 - 142.91: 6 Dihedral angle restraints: 23122 sinusoidal: 9631 harmonic: 13491 Sorted by residual: dihedral pdb=" C5' ADP C 801 " pdb=" O5' ADP C 801 " pdb=" PA ADP C 801 " pdb=" O2A ADP C 801 " ideal model delta sinusoidal sigma weight residual 300.00 157.09 142.91 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" O2A ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PA ADP F 801 " pdb=" PB ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 76.00 -136.00 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C5' ADP B 801 " pdb=" O5' ADP B 801 " pdb=" PA ADP B 801 " pdb=" O2A ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 176.63 123.37 1 2.00e+01 2.50e-03 3.72e+01 ... (remaining 23119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4355 0.056 - 0.112: 1109 0.112 - 0.169: 280 0.169 - 0.225: 53 0.225 - 0.281: 6 Chirality restraints: 5803 Sorted by residual: chirality pdb=" CB VAL D 213 " pdb=" CA VAL D 213 " pdb=" CG1 VAL D 213 " pdb=" CG2 VAL D 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ARG B 391 " pdb=" N ARG B 391 " pdb=" C ARG B 391 " pdb=" CB ARG B 391 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE F 424 " pdb=" N ILE F 424 " pdb=" C ILE F 424 " pdb=" CB ILE F 424 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 5800 not shown) Planarity restraints: 6590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 213 " 0.015 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C VAL D 213 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL D 213 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS D 214 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 258 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C MET F 258 " -0.052 2.00e-02 2.50e+03 pdb=" O MET F 258 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO F 259 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 243 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C LEU A 243 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU A 243 " 0.018 2.00e-02 2.50e+03 pdb=" N SER A 244 " 0.017 2.00e-02 2.50e+03 ... (remaining 6587 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3339 2.74 - 3.28: 39531 3.28 - 3.82: 62769 3.82 - 4.36: 74343 4.36 - 4.90: 119514 Nonbonded interactions: 299496 Sorted by model distance: nonbonded pdb=" OH TYR F 534 " pdb=" O GLY F 579 " model vdw 2.204 3.040 nonbonded pdb=" NE ARG E 374 " pdb=" O ASN E 416 " model vdw 2.232 3.120 nonbonded pdb=" NH2 ARG F 541 " pdb=" OD1 ASP A 444 " model vdw 2.239 3.120 nonbonded pdb=" O TYR A 63 " pdb=" OH TYR A 97 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR E 603 " pdb=" O GLY E 606 " model vdw 2.248 3.040 ... (remaining 299491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 424 or resid 435 through 801)) selection = (chain 'B' and (resid 2 through 424 or resid 435 through 801)) selection = chain 'C' selection = (chain 'D' and (resid 2 through 424 or resid 435 through 801)) selection = (chain 'E' and (resid 2 through 424 or resid 435 through 801)) selection = (chain 'F' and (resid 2 through 424 or resid 435 through 801)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.570 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 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 : 0.006 0.109 37460 Z= 0.396 Angle : 0.880 12.860 50815 Z= 0.574 Chirality : 0.056 0.281 5803 Planarity : 0.004 0.050 6590 Dihedral : 13.089 142.909 14432 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.30 % Rotamer: Outliers : 0.46 % Allowed : 2.00 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -0.90 (0.12), residues: 4636 helix: 0.12 (0.12), residues: 1985 sheet: -0.22 (0.23), residues: 493 loop : -1.33 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 385 TYR 0.021 0.001 TYR C 225 PHE 0.018 0.001 PHE A 466 TRP 0.016 0.001 TRP A 563 HIS 0.004 0.001 HIS C 393 Details of bonding type rmsd covalent geometry : bond 0.00564 (37460) covalent geometry : angle 0.87970 (50815) hydrogen bonds : bond 0.17744 ( 1542) hydrogen bonds : angle 7.08080 ( 4506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 324 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 328 ARG cc_start: 0.7173 (tpt170) cc_final: 0.5549 (tpt170) REVERT: A 258 MET cc_start: 0.5783 (mpp) cc_final: 0.4589 (mpp) REVERT: A 427 MET cc_start: 0.5910 (mmm) cc_final: 0.5449 (tmm) REVERT: A 516 MET cc_start: 0.8300 (ppp) cc_final: 0.7659 (ppp) REVERT: A 683 MET cc_start: 0.8565 (mtm) cc_final: 0.8173 (mtm) REVERT: C 309 ASN cc_start: 0.8796 (m-40) cc_final: 0.8569 (m-40) REVERT: C 516 MET cc_start: 0.5546 (ppp) cc_final: 0.5182 (ppp) REVERT: D 260 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8411 (tm-30) REVERT: D 409 MET cc_start: 0.4971 (tpt) cc_final: 0.4477 (tpt) REVERT: D 698 MET cc_start: 0.7482 (mpp) cc_final: 0.6891 (mpp) outliers start: 18 outliers final: 4 residues processed: 340 average time/residue: 0.1968 time to fit residues: 112.5210 Evaluate side-chains 258 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 254 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain E residue 665 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 0.0870 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 50.0000 overall best weight: 3.5966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 GLN F 313 GLN ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN F 510 GLN F 664 HIS A 138 ASN A 727 GLN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS D 220 ASN D 346 ASN ** D 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.166871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.120583 restraints weight = 183569.748| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 11.61 r_work: 0.3795 rms_B_bonded: 10.85 restraints_weight: 2.0000 r_work: 0.3890 rms_B_bonded: 8.13 restraints_weight: 4.0000 r_work: 0.4060 rms_B_bonded: 5.40 restraints_weight: 8.0000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 37460 Z= 0.220 Angle : 0.708 11.214 50815 Z= 0.347 Chirality : 0.045 0.208 5803 Planarity : 0.005 0.056 6590 Dihedral : 6.750 146.839 5208 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.36 % Rotamer: Outliers : 1.15 % Allowed : 8.42 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -0.78 (0.12), residues: 4636 helix: 0.33 (0.11), residues: 2026 sheet: -0.59 (0.23), residues: 484 loop : -1.28 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 484 TYR 0.020 0.002 TYR D 289 PHE 0.044 0.002 PHE D 203 TRP 0.014 0.001 TRP C 298 HIS 0.008 0.001 HIS F 664 Details of bonding type rmsd covalent geometry : bond 0.00488 (37460) covalent geometry : angle 0.70803 (50815) hydrogen bonds : bond 0.04959 ( 1542) hydrogen bonds : angle 5.44254 ( 4506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 713 MET cc_start: 0.8628 (mpp) cc_final: 0.8339 (mpp) REVERT: A 372 MET cc_start: 0.7698 (pmm) cc_final: 0.7463 (pmm) REVERT: A 451 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.5815 (m-10) REVERT: A 505 TYR cc_start: 0.7750 (m-10) cc_final: 0.7539 (m-10) REVERT: A 516 MET cc_start: 0.8529 (ppp) cc_final: 0.8063 (ppp) REVERT: A 663 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8128 (tp) REVERT: B 633 MET cc_start: 0.8091 (mpp) cc_final: 0.7313 (mpp) REVERT: C 276 MET cc_start: 0.5910 (mtm) cc_final: 0.5142 (mtt) REVERT: C 702 MET cc_start: 0.6175 (mmt) cc_final: 0.5798 (mmt) REVERT: D 262 VAL cc_start: 0.4492 (OUTLIER) cc_final: 0.3791 (p) REVERT: D 409 MET cc_start: 0.6094 (tpt) cc_final: 0.5400 (tpt) REVERT: D 683 MET cc_start: 0.8445 (mpp) cc_final: 0.8085 (mpt) REVERT: D 698 MET cc_start: 0.7500 (mpp) cc_final: 0.7244 (mpp) REVERT: E 457 ASP cc_start: 0.9220 (p0) cc_final: 0.8988 (p0) REVERT: E 516 MET cc_start: 0.7946 (ppp) cc_final: 0.7605 (ppp) outliers start: 45 outliers final: 21 residues processed: 295 average time/residue: 0.1937 time to fit residues: 98.2424 Evaluate side-chains 256 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 758 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 286 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 391 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 460 optimal weight: 1.9990 chunk 373 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 418 optimal weight: 7.9990 chunk 297 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 407 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 666 HIS ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN C 319 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 GLN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 HIS E 337 GLN E 411 GLN E 666 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.150252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.091420 restraints weight = 84785.695| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 6.71 r_work: 0.3763 rms_B_bonded: 6.56 restraints_weight: 2.0000 r_work: 0.3842 rms_B_bonded: 6.16 restraints_weight: 4.0000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.177 37460 Z= 0.263 Angle : 0.751 13.784 50815 Z= 0.369 Chirality : 0.046 0.188 5803 Planarity : 0.005 0.056 6590 Dihedral : 6.880 159.860 5208 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.13 % Rotamer: Outliers : 2.20 % Allowed : 12.67 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -0.91 (0.12), residues: 4636 helix: 0.29 (0.12), residues: 2020 sheet: -0.88 (0.23), residues: 522 loop : -1.37 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 391 TYR 0.017 0.002 TYR B 658 PHE 0.033 0.002 PHE D 203 TRP 0.012 0.002 TRP B 602 HIS 0.009 0.002 HIS C 664 Details of bonding type rmsd covalent geometry : bond 0.00581 (37460) covalent geometry : angle 0.75123 (50815) hydrogen bonds : bond 0.04776 ( 1542) hydrogen bonds : angle 5.36581 ( 4506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 239 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 275 ARG cc_start: 0.7483 (mmm160) cc_final: 0.7100 (mmm160) REVERT: F 409 MET cc_start: 0.8611 (mtp) cc_final: 0.8271 (mtm) REVERT: F 439 MET cc_start: 0.9203 (mmm) cc_final: 0.8748 (mmm) REVERT: F 713 MET cc_start: 0.8889 (mpp) cc_final: 0.8584 (mpp) REVERT: A 505 TYR cc_start: 0.7928 (m-10) cc_final: 0.7669 (m-10) REVERT: A 516 MET cc_start: 0.8530 (ppp) cc_final: 0.8104 (ppp) REVERT: A 563 TRP cc_start: 0.3654 (p90) cc_final: 0.3078 (p90) REVERT: A 663 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8619 (tp) REVERT: B 260 GLU cc_start: 0.8963 (pm20) cc_final: 0.8651 (mm-30) REVERT: B 347 LYS cc_start: 0.8967 (mptt) cc_final: 0.8764 (mmtt) REVERT: B 485 MET cc_start: 0.7178 (pmm) cc_final: 0.6891 (pmm) REVERT: B 698 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7334 (mmm) REVERT: C 276 MET cc_start: 0.5865 (mtm) cc_final: 0.4950 (mtt) REVERT: C 596 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8613 (t) REVERT: C 702 MET cc_start: 0.7043 (mmt) cc_final: 0.6826 (mmt) REVERT: D 409 MET cc_start: 0.5657 (tpt) cc_final: 0.4786 (tpt) REVERT: D 683 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8315 (mpt) outliers start: 86 outliers final: 43 residues processed: 305 average time/residue: 0.1884 time to fit residues: 98.4562 Evaluate side-chains 273 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 758 LEU Chi-restraints excluded: chain E residue 779 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 357 optimal weight: 0.0970 chunk 277 optimal weight: 9.9990 chunk 432 optimal weight: 0.0870 chunk 117 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 371 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 431 optimal weight: 2.9990 chunk 256 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 393 HIS ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS C 495 ASN C 499 GLN ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.159088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.091951 restraints weight = 100685.270| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 6.16 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37460 Z= 0.127 Angle : 0.636 12.248 50815 Z= 0.304 Chirality : 0.043 0.224 5803 Planarity : 0.004 0.058 6590 Dihedral : 6.404 147.717 5208 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.66 % Favored : 95.30 % Rotamer: Outliers : 2.05 % Allowed : 14.39 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -0.62 (0.12), residues: 4636 helix: 0.49 (0.12), residues: 2041 sheet: -0.69 (0.23), residues: 515 loop : -1.21 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 378 TYR 0.018 0.001 TYR B 460 PHE 0.023 0.001 PHE D 203 TRP 0.012 0.001 TRP E 298 HIS 0.007 0.001 HIS E 664 Details of bonding type rmsd covalent geometry : bond 0.00283 (37460) covalent geometry : angle 0.63642 (50815) hydrogen bonds : bond 0.03936 ( 1542) hydrogen bonds : angle 4.97646 ( 4506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 258 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 372 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7648 (mpp) REVERT: F 409 MET cc_start: 0.8460 (mtp) cc_final: 0.8158 (mtm) REVERT: F 426 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7804 (mtpt) REVERT: F 439 MET cc_start: 0.9226 (mmm) cc_final: 0.8789 (mmm) REVERT: F 713 MET cc_start: 0.8633 (mpp) cc_final: 0.8316 (mpp) REVERT: A 505 TYR cc_start: 0.7655 (m-10) cc_final: 0.7359 (m-10) REVERT: A 659 ASN cc_start: 0.6686 (m-40) cc_final: 0.6328 (m-40) REVERT: A 663 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8413 (tp) REVERT: B 260 GLU cc_start: 0.8940 (pm20) cc_final: 0.8645 (mm-30) REVERT: B 485 MET cc_start: 0.6802 (pmm) cc_final: 0.6517 (pmm) REVERT: B 633 MET cc_start: 0.8163 (mpp) cc_final: 0.7848 (mpp) REVERT: B 698 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7467 (mmm) REVERT: B 713 MET cc_start: 0.8466 (mmm) cc_final: 0.8080 (mpp) REVERT: C 276 MET cc_start: 0.5706 (mtm) cc_final: 0.5064 (mtt) REVERT: C 516 MET cc_start: 0.5358 (ppp) cc_final: 0.4958 (ppp) REVERT: D 235 LYS cc_start: 0.4250 (OUTLIER) cc_final: 0.1807 (tttm) REVERT: D 409 MET cc_start: 0.5762 (tpt) cc_final: 0.5022 (tpt) REVERT: E 613 GLU cc_start: 0.6693 (mp0) cc_final: 0.6371 (mm-30) outliers start: 80 outliers final: 42 residues processed: 314 average time/residue: 0.1793 time to fit residues: 96.7407 Evaluate side-chains 277 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 665 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 136 optimal weight: 0.9990 chunk 397 optimal weight: 40.0000 chunk 353 optimal weight: 6.9990 chunk 259 optimal weight: 30.0000 chunk 322 optimal weight: 0.2980 chunk 263 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 HIS ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 HIS ** D 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.153559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.4181 r_free = 0.4181 target = 0.088607 restraints weight = 90439.187| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 6.26 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 37460 Z= 0.197 Angle : 0.680 12.165 50815 Z= 0.328 Chirality : 0.044 0.254 5803 Planarity : 0.005 0.133 6590 Dihedral : 6.408 141.465 5208 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 2.64 % Allowed : 15.34 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -0.67 (0.12), residues: 4636 helix: 0.52 (0.12), residues: 2032 sheet: -0.85 (0.22), residues: 542 loop : -1.27 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 328 TYR 0.016 0.002 TYR B 460 PHE 0.022 0.002 PHE D 657 TRP 0.018 0.001 TRP D 563 HIS 0.007 0.001 HIS C 664 Details of bonding type rmsd covalent geometry : bond 0.00442 (37460) covalent geometry : angle 0.68049 (50815) hydrogen bonds : bond 0.03988 ( 1542) hydrogen bonds : angle 5.02287 ( 4506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 230 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 275 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7473 (mmm160) REVERT: F 364 LEU cc_start: 0.5498 (OUTLIER) cc_final: 0.5236 (mm) REVERT: F 372 MET cc_start: 0.8030 (mpp) cc_final: 0.7625 (mpp) REVERT: F 426 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7842 (mtpt) REVERT: F 439 MET cc_start: 0.9276 (mmm) cc_final: 0.8796 (mmm) REVERT: F 713 MET cc_start: 0.8669 (mpp) cc_final: 0.8406 (mpp) REVERT: A 217 MET cc_start: 0.2988 (tpt) cc_final: 0.2579 (ttm) REVERT: A 505 TYR cc_start: 0.7828 (m-10) cc_final: 0.7521 (m-10) REVERT: A 563 TRP cc_start: 0.3373 (p90) cc_final: 0.3049 (p90) REVERT: A 663 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8553 (tp) REVERT: B 260 GLU cc_start: 0.8962 (pm20) cc_final: 0.8640 (mm-30) REVERT: B 372 MET cc_start: 0.8323 (mtt) cc_final: 0.7972 (mpp) REVERT: B 485 MET cc_start: 0.6937 (pmm) cc_final: 0.6586 (pmm) REVERT: B 698 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7312 (mmm) REVERT: C 276 MET cc_start: 0.5845 (mtm) cc_final: 0.5112 (mtt) REVERT: C 516 MET cc_start: 0.5827 (ppp) cc_final: 0.5506 (ppp) REVERT: C 596 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8517 (t) REVERT: D 235 LYS cc_start: 0.3784 (OUTLIER) cc_final: 0.1042 (tttm) REVERT: D 409 MET cc_start: 0.5613 (tpt) cc_final: 0.4830 (tpt) REVERT: D 580 ILE cc_start: 0.8526 (mm) cc_final: 0.8174 (tt) REVERT: D 683 MET cc_start: 0.8463 (mpt) cc_final: 0.8246 (mpt) outliers start: 103 outliers final: 66 residues processed: 308 average time/residue: 0.1847 time to fit residues: 98.9255 Evaluate side-chains 295 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 224 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 758 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 779 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 204 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 313 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 453 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 HIS ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.155033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.090480 restraints weight = 91785.933| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 6.10 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 37460 Z= 0.149 Angle : 0.651 11.928 50815 Z= 0.309 Chirality : 0.043 0.322 5803 Planarity : 0.004 0.092 6590 Dihedral : 6.174 126.291 5205 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 2.56 % Allowed : 16.18 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -0.56 (0.13), residues: 4636 helix: 0.63 (0.12), residues: 2036 sheet: -0.83 (0.23), residues: 537 loop : -1.21 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 250 TYR 0.026 0.001 TYR F 224 PHE 0.019 0.001 PHE D 203 TRP 0.011 0.001 TRP E 298 HIS 0.005 0.001 HIS C 666 Details of bonding type rmsd covalent geometry : bond 0.00338 (37460) covalent geometry : angle 0.65117 (50815) hydrogen bonds : bond 0.03727 ( 1542) hydrogen bonds : angle 4.88182 ( 4506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 238 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 275 ARG cc_start: 0.8149 (mmm160) cc_final: 0.7754 (mmm160) REVERT: F 364 LEU cc_start: 0.5559 (OUTLIER) cc_final: 0.5299 (mm) REVERT: F 372 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7653 (mpp) REVERT: F 426 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7828 (mtpt) REVERT: F 439 MET cc_start: 0.9217 (mmm) cc_final: 0.8744 (mmm) REVERT: F 713 MET cc_start: 0.8676 (mpp) cc_final: 0.8321 (mpp) REVERT: A 342 LEU cc_start: 0.3363 (OUTLIER) cc_final: 0.3052 (mp) REVERT: A 505 TYR cc_start: 0.7721 (m-10) cc_final: 0.7448 (m-10) REVERT: A 663 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8518 (tp) REVERT: A 713 MET cc_start: 0.8591 (mpp) cc_final: 0.8390 (mpp) REVERT: B 260 GLU cc_start: 0.8935 (pm20) cc_final: 0.8667 (mm-30) REVERT: B 485 MET cc_start: 0.7117 (pmm) cc_final: 0.6809 (pmm) REVERT: B 496 MET cc_start: 0.8325 (mpp) cc_final: 0.8074 (mpp) REVERT: B 633 MET cc_start: 0.8133 (mpp) cc_final: 0.7717 (mpp) REVERT: B 698 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7316 (mmm) REVERT: B 713 MET cc_start: 0.8469 (mmm) cc_final: 0.8067 (mpp) REVERT: B 776 MET cc_start: 0.7616 (ppp) cc_final: 0.7065 (ppp) REVERT: C 276 MET cc_start: 0.5912 (mtm) cc_final: 0.5122 (mtt) REVERT: C 516 MET cc_start: 0.5638 (ppp) cc_final: 0.5229 (ppp) REVERT: C 596 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8392 (t) REVERT: C 702 MET cc_start: 0.6191 (mmt) cc_final: 0.5664 (mmt) REVERT: D 235 LYS cc_start: 0.4238 (OUTLIER) cc_final: 0.3748 (mmtm) REVERT: D 409 MET cc_start: 0.5610 (tpt) cc_final: 0.4828 (tpt) REVERT: D 496 MET cc_start: 0.8330 (mmt) cc_final: 0.8055 (mpp) REVERT: D 683 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8110 (mpt) REVERT: E 217 MET cc_start: -0.1171 (ppp) cc_final: -0.1457 (pmm) REVERT: E 258 MET cc_start: 0.6543 (mpp) cc_final: 0.5846 (mpp) REVERT: E 427 MET cc_start: 0.6092 (tpp) cc_final: 0.5824 (tpp) REVERT: E 531 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7923 (tp) REVERT: E 613 GLU cc_start: 0.6692 (mp0) cc_final: 0.6374 (mm-30) outliers start: 100 outliers final: 65 residues processed: 313 average time/residue: 0.1789 time to fit residues: 95.5667 Evaluate side-chains 304 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 230 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 665 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 25 optimal weight: 6.9990 chunk 362 optimal weight: 9.9990 chunk 11 optimal weight: 40.0000 chunk 377 optimal weight: 0.8980 chunk 434 optimal weight: 0.9980 chunk 246 optimal weight: 40.0000 chunk 297 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 419 optimal weight: 4.9990 chunk 433 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS B 220 ASN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 742 GLN D 731 HIS ** D 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.149155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.089461 restraints weight = 83563.064| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 6.19 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 37460 Z= 0.225 Angle : 0.722 12.182 50815 Z= 0.346 Chirality : 0.045 0.193 5803 Planarity : 0.005 0.077 6590 Dihedral : 6.380 119.665 5205 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.30 % Favored : 93.66 % Rotamer: Outliers : 2.94 % Allowed : 16.97 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.36 % 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 aren not related in a simple way. whole: -0.72 (0.13), residues: 4636 helix: 0.52 (0.12), residues: 2033 sheet: -1.04 (0.22), residues: 550 loop : -1.29 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 366 TYR 0.044 0.002 TYR F 224 PHE 0.020 0.002 PHE B 203 TRP 0.011 0.002 TRP F 292 HIS 0.009 0.001 HIS E 666 Details of bonding type rmsd covalent geometry : bond 0.00506 (37460) covalent geometry : angle 0.72249 (50815) hydrogen bonds : bond 0.04018 ( 1542) hydrogen bonds : angle 5.03147 ( 4506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 230 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 217 MET cc_start: 0.7496 (ppp) cc_final: 0.7273 (tmm) REVERT: F 364 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5435 (mm) REVERT: F 372 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.6653 (mpt) REVERT: F 426 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7817 (mtpt) REVERT: F 439 MET cc_start: 0.9266 (mmm) cc_final: 0.8778 (mmm) REVERT: F 648 THR cc_start: 0.8952 (p) cc_final: 0.8683 (t) REVERT: F 713 MET cc_start: 0.8759 (mpp) cc_final: 0.8389 (mpp) REVERT: A 217 MET cc_start: 0.3055 (tpt) cc_final: 0.2516 (mtp) REVERT: A 342 LEU cc_start: 0.3353 (OUTLIER) cc_final: 0.3026 (mp) REVERT: A 485 MET cc_start: 0.6447 (OUTLIER) cc_final: 0.5973 (mmt) REVERT: A 505 TYR cc_start: 0.7717 (m-10) cc_final: 0.7487 (m-10) REVERT: A 516 MET cc_start: 0.8753 (ppp) cc_final: 0.7862 (ppp) REVERT: A 663 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8547 (tp) REVERT: A 713 MET cc_start: 0.8552 (mpp) cc_final: 0.8336 (mpp) REVERT: B 260 GLU cc_start: 0.8946 (pm20) cc_final: 0.8694 (mm-30) REVERT: B 485 MET cc_start: 0.7233 (pmm) cc_final: 0.6909 (pmm) REVERT: B 698 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7330 (mmm) REVERT: C 276 MET cc_start: 0.5814 (mtm) cc_final: 0.4927 (mtt) REVERT: C 372 MET cc_start: 0.8219 (tmm) cc_final: 0.7960 (tmm) REVERT: C 516 MET cc_start: 0.5985 (ppp) cc_final: 0.5665 (ppp) REVERT: C 596 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8541 (t) REVERT: D 235 LYS cc_start: 0.4042 (OUTLIER) cc_final: 0.1030 (tttm) REVERT: D 345 ARG cc_start: 0.7021 (mmt180) cc_final: 0.6728 (mmt-90) REVERT: D 409 MET cc_start: 0.5778 (tpt) cc_final: 0.5573 (tpt) REVERT: D 496 MET cc_start: 0.8463 (mmt) cc_final: 0.8261 (mmt) REVERT: D 683 MET cc_start: 0.8601 (mpt) cc_final: 0.8263 (mpt) REVERT: E 217 MET cc_start: -0.1192 (ppp) cc_final: -0.1483 (pmm) REVERT: E 258 MET cc_start: 0.6226 (mpp) cc_final: 0.5978 (mpp) REVERT: E 276 MET cc_start: -0.0140 (mmp) cc_final: -0.0414 (mmp) REVERT: E 516 MET cc_start: 0.8186 (ppp) cc_final: 0.7958 (ppp) REVERT: E 531 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7942 (tp) outliers start: 115 outliers final: 77 residues processed: 323 average time/residue: 0.1834 time to fit residues: 102.0610 Evaluate side-chains 308 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 222 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 657 PHE Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 758 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 779 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 0.0010 chunk 460 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 280 optimal weight: 8.9990 chunk 156 optimal weight: 0.0030 chunk 189 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 170 optimal weight: 0.0370 chunk 160 optimal weight: 4.9990 overall best weight: 0.8076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 ASN C 373 ASN C 472 ASN C 628 GLN ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN C 742 GLN D 731 HIS ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.156336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.4203 r_free = 0.4203 target = 0.089745 restraints weight = 91045.551| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 5.98 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 37460 Z= 0.121 Angle : 0.650 11.127 50815 Z= 0.307 Chirality : 0.044 0.334 5803 Planarity : 0.004 0.071 6590 Dihedral : 5.987 111.503 5205 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.25 % Rotamer: Outliers : 2.15 % Allowed : 17.82 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -0.48 (0.13), residues: 4636 helix: 0.69 (0.12), residues: 2030 sheet: -0.86 (0.23), residues: 539 loop : -1.13 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 275 TYR 0.045 0.001 TYR F 224 PHE 0.021 0.001 PHE B 203 TRP 0.023 0.001 TRP E 298 HIS 0.005 0.001 HIS C 393 Details of bonding type rmsd covalent geometry : bond 0.00272 (37460) covalent geometry : angle 0.65026 (50815) hydrogen bonds : bond 0.03512 ( 1542) hydrogen bonds : angle 4.78541 ( 4506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 247 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 372 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.6681 (mpt) REVERT: F 426 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7717 (mtpt) REVERT: F 556 LYS cc_start: 0.8034 (pttt) cc_final: 0.7750 (tptt) REVERT: F 633 MET cc_start: 0.8007 (mpp) cc_final: 0.7779 (mpp) REVERT: F 648 THR cc_start: 0.8898 (p) cc_final: 0.8662 (t) REVERT: F 713 MET cc_start: 0.8670 (mpp) cc_final: 0.8288 (mpp) REVERT: A 505 TYR cc_start: 0.7755 (m-10) cc_final: 0.7456 (m-10) REVERT: A 563 TRP cc_start: 0.3140 (p90) cc_final: 0.2882 (p90) REVERT: A 663 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8484 (tp) REVERT: B 260 GLU cc_start: 0.8969 (pm20) cc_final: 0.8664 (mm-30) REVERT: B 485 MET cc_start: 0.7225 (pmm) cc_final: 0.6924 (pmm) REVERT: B 702 MET cc_start: 0.5661 (mmt) cc_final: 0.4786 (mmt) REVERT: B 713 MET cc_start: 0.8364 (mmm) cc_final: 0.7725 (mpp) REVERT: C 276 MET cc_start: 0.6034 (mtm) cc_final: 0.5258 (mtt) REVERT: C 372 MET cc_start: 0.8164 (tmm) cc_final: 0.7951 (tmm) REVERT: C 516 MET cc_start: 0.6395 (ppp) cc_final: 0.5862 (ppp) REVERT: C 596 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8365 (t) REVERT: D 217 MET cc_start: 0.2286 (ttm) cc_final: 0.2078 (tpp) REVERT: D 235 LYS cc_start: 0.3574 (OUTLIER) cc_final: 0.0475 (tttm) REVERT: D 345 ARG cc_start: 0.7075 (mmt180) cc_final: 0.6734 (mmt-90) REVERT: D 409 MET cc_start: 0.5763 (tpt) cc_final: 0.5080 (tpt) REVERT: D 496 MET cc_start: 0.8366 (mmt) cc_final: 0.8137 (mmt) REVERT: D 683 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8141 (mpt) REVERT: E 217 MET cc_start: -0.1199 (ppp) cc_final: -0.1506 (pmm) REVERT: E 258 MET cc_start: 0.5735 (mpp) cc_final: 0.5389 (mpp) REVERT: E 426 LYS cc_start: 0.7756 (mmtm) cc_final: 0.7489 (mmtt) REVERT: E 531 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7970 (tp) outliers start: 84 outliers final: 56 residues processed: 310 average time/residue: 0.1890 time to fit residues: 99.6341 Evaluate side-chains 295 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 233 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 665 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 17 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 296 optimal weight: 0.0770 chunk 279 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 238 optimal weight: 50.0000 chunk 137 optimal weight: 0.6980 chunk 389 optimal weight: 9.9990 chunk 378 optimal weight: 0.0870 chunk 457 optimal weight: 0.9980 overall best weight: 0.9718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 ASN C 666 HIS C 742 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.157237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.090665 restraints weight = 90879.172| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 6.13 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37460 Z= 0.120 Angle : 0.648 10.924 50815 Z= 0.305 Chirality : 0.043 0.282 5803 Planarity : 0.004 0.071 6590 Dihedral : 5.809 108.711 5205 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.74 % Rotamer: Outliers : 2.10 % Allowed : 18.07 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -0.33 (0.13), residues: 4636 helix: 0.82 (0.12), residues: 2023 sheet: -0.70 (0.23), residues: 547 loop : -1.10 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 275 TYR 0.043 0.001 TYR F 224 PHE 0.024 0.001 PHE B 203 TRP 0.031 0.001 TRP F 602 HIS 0.005 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00273 (37460) covalent geometry : angle 0.64754 (50815) hydrogen bonds : bond 0.03400 ( 1542) hydrogen bonds : angle 4.68918 ( 4506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 244 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 364 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4965 (mm) REVERT: F 372 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.6757 (mpt) REVERT: F 426 LYS cc_start: 0.8309 (mtpt) cc_final: 0.7962 (mtpt) REVERT: F 648 THR cc_start: 0.8837 (p) cc_final: 0.8606 (t) REVERT: F 713 MET cc_start: 0.8620 (mpp) cc_final: 0.8284 (mpp) REVERT: A 217 MET cc_start: 0.2810 (tpt) cc_final: 0.2293 (ttm) REVERT: A 505 TYR cc_start: 0.7701 (m-10) cc_final: 0.7421 (m-10) REVERT: A 663 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8514 (tp) REVERT: B 260 GLU cc_start: 0.8944 (pm20) cc_final: 0.8671 (mm-30) REVERT: B 372 MET cc_start: 0.8337 (mtt) cc_final: 0.8013 (mpp) REVERT: B 485 MET cc_start: 0.7124 (pmm) cc_final: 0.6864 (pmm) REVERT: B 713 MET cc_start: 0.8378 (mmm) cc_final: 0.7741 (mpp) REVERT: C 276 MET cc_start: 0.6250 (mtm) cc_final: 0.5571 (mtt) REVERT: C 372 MET cc_start: 0.8108 (tmm) cc_final: 0.7890 (tmm) REVERT: C 401 MET cc_start: 0.7149 (ppp) cc_final: 0.6916 (ppp) REVERT: C 516 MET cc_start: 0.6376 (ppp) cc_final: 0.5815 (ppp) REVERT: C 596 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8320 (t) REVERT: D 217 MET cc_start: 0.2313 (ttm) cc_final: 0.2098 (tpp) REVERT: D 235 LYS cc_start: 0.3745 (OUTLIER) cc_final: 0.3243 (mmtm) REVERT: D 345 ARG cc_start: 0.7056 (mmt180) cc_final: 0.6692 (mmt-90) REVERT: D 409 MET cc_start: 0.5608 (tpt) cc_final: 0.4939 (tpt) REVERT: D 496 MET cc_start: 0.8323 (mmt) cc_final: 0.8082 (mmt) REVERT: D 683 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8072 (mpt) REVERT: E 217 MET cc_start: -0.1203 (ppp) cc_final: -0.1515 (pmm) REVERT: E 250 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7377 (mmt180) REVERT: E 426 LYS cc_start: 0.7774 (mmtm) cc_final: 0.7510 (mmtt) REVERT: E 531 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7937 (tp) outliers start: 82 outliers final: 55 residues processed: 310 average time/residue: 0.2224 time to fit residues: 117.2270 Evaluate side-chains 301 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 238 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 602 TRP Chi-restraints excluded: chain F residue 657 PHE Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 289 TYR Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 665 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 170 optimal weight: 6.9990 chunk 382 optimal weight: 2.9990 chunk 394 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 405 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 413 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 HIS ** D 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.151708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.090331 restraints weight = 82303.216| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 6.06 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 37460 Z= 0.189 Angle : 0.701 12.313 50815 Z= 0.333 Chirality : 0.044 0.269 5803 Planarity : 0.005 0.072 6590 Dihedral : 5.991 113.460 5205 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 1.92 % Allowed : 18.54 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % Twisted Proline : 0.36 % 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 aren not related in a simple way. whole: -0.44 (0.13), residues: 4636 helix: 0.73 (0.12), residues: 2025 sheet: -0.78 (0.23), residues: 553 loop : -1.14 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 345 TYR 0.045 0.002 TYR F 224 PHE 0.025 0.002 PHE B 203 TRP 0.013 0.001 TRP E 298 HIS 0.007 0.001 HIS E 666 Details of bonding type rmsd covalent geometry : bond 0.00427 (37460) covalent geometry : angle 0.70129 (50815) hydrogen bonds : bond 0.03704 ( 1542) hydrogen bonds : angle 4.81484 ( 4506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 233 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 364 LEU cc_start: 0.5722 (OUTLIER) cc_final: 0.5493 (mm) REVERT: F 372 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.6630 (mpt) REVERT: F 426 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7840 (mtpt) REVERT: F 556 LYS cc_start: 0.8028 (pttt) cc_final: 0.7754 (tptm) REVERT: F 648 THR cc_start: 0.8991 (p) cc_final: 0.8752 (t) REVERT: F 713 MET cc_start: 0.8739 (mpp) cc_final: 0.8327 (mpp) REVERT: A 366 ARG cc_start: 0.8237 (ptp-110) cc_final: 0.7903 (mtm-85) REVERT: A 663 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8555 (tp) REVERT: B 260 GLU cc_start: 0.8947 (pm20) cc_final: 0.8702 (mm-30) REVERT: B 372 MET cc_start: 0.8331 (mtt) cc_final: 0.8073 (mpp) REVERT: C 276 MET cc_start: 0.5966 (mtm) cc_final: 0.5064 (mtt) REVERT: C 372 MET cc_start: 0.8118 (tmm) cc_final: 0.7832 (tmm) REVERT: C 401 MET cc_start: 0.7398 (ppp) cc_final: 0.7176 (ppp) REVERT: C 516 MET cc_start: 0.6245 (ppp) cc_final: 0.5865 (ppp) REVERT: C 596 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8474 (t) REVERT: D 217 MET cc_start: 0.2410 (ttm) cc_final: 0.2204 (tpp) REVERT: D 345 ARG cc_start: 0.7075 (mmt180) cc_final: 0.6747 (mmt-90) REVERT: D 409 MET cc_start: 0.5883 (tpt) cc_final: 0.5182 (tpt) REVERT: D 683 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8166 (mpt) REVERT: E 217 MET cc_start: -0.1171 (ppp) cc_final: -0.1474 (pmm) REVERT: E 258 MET cc_start: 0.5552 (mpp) cc_final: 0.5094 (mmm) REVERT: E 317 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8147 (pp20) REVERT: E 531 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7892 (tp) outliers start: 75 outliers final: 62 residues processed: 289 average time/residue: 0.2208 time to fit residues: 108.3682 Evaluate side-chains 298 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 230 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 485 MET Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 657 PHE Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 289 TYR Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 363 optimal weight: 0.7980 chunk 334 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 164 optimal weight: 30.0000 chunk 331 optimal weight: 8.9990 chunk 223 optimal weight: 0.0770 chunk 186 optimal weight: 3.9990 chunk 439 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 chunk 125 optimal weight: 0.9980 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 HIS ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.155404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4192 r_free = 0.4192 target = 0.088602 restraints weight = 90360.872| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 5.99 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 37460 Z= 0.133 Angle : 0.671 11.970 50815 Z= 0.315 Chirality : 0.043 0.278 5803 Planarity : 0.004 0.071 6590 Dihedral : 5.871 110.567 5205 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.39 % Favored : 94.59 % Rotamer: Outliers : 1.87 % Allowed : 18.56 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.18 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -0.35 (0.13), residues: 4636 helix: 0.81 (0.12), residues: 2015 sheet: -0.72 (0.23), residues: 541 loop : -1.10 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 345 TYR 0.045 0.001 TYR F 224 PHE 0.025 0.001 PHE B 203 TRP 0.019 0.001 TRP E 298 HIS 0.005 0.001 HIS F 664 Details of bonding type rmsd covalent geometry : bond 0.00304 (37460) covalent geometry : angle 0.67100 (50815) hydrogen bonds : bond 0.03462 ( 1542) hydrogen bonds : angle 4.69942 ( 4506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18937.07 seconds wall clock time: 321 minutes 25.14 seconds (19285.14 seconds total)