Starting phenix.real_space_refine on Mon Jul 6 16:57:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fd5_31535/07_2026/7fd5_31535.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fd5_31535/07_2026/7fd5_31535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fd5_31535/07_2026/7fd5_31535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fd5_31535/07_2026/7fd5_31535.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fd5_31535/07_2026/7fd5_31535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fd5_31535/07_2026/7fd5_31535.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fd5_31535/07_2026/7fd5_31535.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fd5_31535/07_2026/7fd5_31535.cif" } resolution = 2.4 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= 0.004 sd= 0.144 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 S 135 5.16 5 B 6 2.79 5 C 23460 2.51 5 N 6514 2.21 5 O 7049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37179 Number of models: 1 Model: "" Number of chains: 13 Chain: "F" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "B" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "D" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "C" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "E" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "A" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 730} Chain: "S" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 111 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.30, per 1000 atoms: 0.25 Number of scatterers: 37179 At special positions: 0 Unit cell: (191.06, 188.6, 199.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 135 16.00 P 15 15.00 O 7049 8.00 N 6514 7.00 C 23460 6.00 B 6 5.00 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.8 seconds 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8732 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 44 sheets defined 46.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'F' and resid 30 through 38 Processing helix chain 'F' and resid 117 through 139 removed outlier: 3.755A pdb=" N VAL F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 149 removed outlier: 3.676A pdb=" N GLN F 148 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 155 removed outlier: 4.040A pdb=" N GLY F 154 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR F 155 " --> pdb=" O VAL F 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 151 through 155' Processing helix chain 'F' and resid 157 through 167 Processing helix chain 'F' and resid 172 through 182 removed outlier: 3.717A pdb=" N LYS F 176 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 239 removed outlier: 3.891A pdb=" N LEU F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY F 239 " --> pdb=" O LYS F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 254 removed outlier: 3.817A pdb=" N LYS F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 271 removed outlier: 4.107A pdb=" N LYS F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU F 269 " --> pdb=" O LYS F 265 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP F 271 " --> pdb=" O LEU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 294 removed outlier: 3.956A pdb=" N ARG F 287 " --> pdb=" O ALA F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 319 Processing helix chain 'F' and resid 322 through 339 removed outlier: 3.740A pdb=" N TYR F 332 " --> pdb=" O ARG F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 370 Processing helix chain 'F' and resid 403 through 411 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 447 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 506 through 513 Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.729A pdb=" N ILE F 527 " --> pdb=" O THR F 523 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 561 Processing helix chain 'F' and resid 573 through 578 removed outlier: 3.940A pdb=" N TYR F 577 " --> pdb=" O ASP F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 646 Processing helix chain 'F' and resid 679 through 693 removed outlier: 3.591A pdb=" N ALA F 686 " --> pdb=" O THR F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 717 through 728 removed outlier: 3.729A pdb=" N LYS F 721 " --> pdb=" O GLY F 717 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA F 728 " --> pdb=" O ALA F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 746 removed outlier: 4.417A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU F 744 " --> pdb=" O ALA F 741 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 Processing helix chain 'F' and resid 762 through 770 removed outlier: 3.626A pdb=" N LEU F 770 " --> pdb=" O LEU F 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 removed outlier: 3.782A pdb=" N GLY B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 137 removed outlier: 4.430A pdb=" N VAL B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 166 Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 172 through 181 removed outlier: 3.944A pdb=" N LYS B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 236 removed outlier: 3.514A pdb=" N ARG B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.755A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.574A pdb=" N THR B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 339 removed outlier: 3.599A pdb=" N LYS B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.765A pdb=" N GLU B 389 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 423 through 427 removed outlier: 4.162A pdb=" N MET B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.938A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLU B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 removed outlier: 4.278A pdb=" N THR B 476 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 473 through 477' Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.800A pdb=" N ASP B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 505 through 513 removed outlier: 3.688A pdb=" N LYS B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 540 through 561 removed outlier: 3.576A pdb=" N GLU B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.820A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.658A pdb=" N ALA B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 660 removed outlier: 3.698A pdb=" N LYS B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 656 through 660' Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.530A pdb=" N ALA B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 746 removed outlier: 4.479A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 742 " --> pdb=" O ASN B 739 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU B 744 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 745 " --> pdb=" O GLN B 742 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 746 " --> pdb=" O LEU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.745A pdb=" N GLU B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 770 removed outlier: 3.798A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 770 " --> pdb=" O LEU B 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 38 removed outlier: 4.038A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 138 removed outlier: 3.563A pdb=" N LYS D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 4.344A pdb=" N LEU D 142 " --> pdb=" O HIS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 168 removed outlier: 3.918A pdb=" N HIS D 168 " --> pdb=" O THR D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.983A pdb=" N LYS D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 237 removed outlier: 3.617A pdb=" N ARG D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 254 removed outlier: 3.737A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 275 removed outlier: 3.548A pdb=" N ARG D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 294 removed outlier: 4.018A pdb=" N THR D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.709A pdb=" N THR D 311 " --> pdb=" O ASP D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 339 removed outlier: 3.610A pdb=" N LYS D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 372 removed outlier: 4.064A pdb=" N ARG D 366 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.901A pdb=" N GLU D 389 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 412 Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.882A pdb=" N MET D 427 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 442 removed outlier: 3.650A pdb=" N GLU D 441 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 513 removed outlier: 3.783A pdb=" N LYS D 509 " --> pdb=" O TYR D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.839A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 561 removed outlier: 3.557A pdb=" N ARG D 545 " --> pdb=" O ARG D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.550A pdb=" N TYR D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 647 removed outlier: 3.508A pdb=" N LYS D 634 " --> pdb=" O GLY D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 692 removed outlier: 3.506A pdb=" N SER D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 728 removed outlier: 3.589A pdb=" N ALA D 728 " --> pdb=" O ALA D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 745 removed outlier: 4.856A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 743 " --> pdb=" O GLU D 740 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU D 745 " --> pdb=" O GLN D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.838A pdb=" N VAL D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 770 " --> pdb=" O LEU D 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 removed outlier: 3.926A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 137 Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.975A pdb=" N LYS C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 237 Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.602A pdb=" N VAL C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 317 removed outlier: 3.851A pdb=" N GLN C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 339 Processing helix chain 'C' and resid 360 through 372 removed outlier: 3.594A pdb=" N LEU C 364 " --> pdb=" O GLY C 360 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 403 through 413 Processing helix chain 'C' and resid 423 through 427 removed outlier: 3.896A pdb=" N MET C 427 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 4.129A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 494 through 505 removed outlier: 3.682A pdb=" N ALA C 500 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 514 removed outlier: 3.723A pdb=" N LYS C 509 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.639A pdb=" N ILE C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 removed outlier: 3.641A pdb=" N GLU C 560 " --> pdb=" O LYS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.730A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 647 Processing helix chain 'C' and resid 647 through 652 removed outlier: 4.441A pdb=" N TYR C 651 " --> pdb=" O HIS C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 727 Processing helix chain 'C' and resid 738 through 746 removed outlier: 4.526A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 745 " --> pdb=" O GLN C 742 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 746 " --> pdb=" O LEU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.731A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 39 Processing helix chain 'E' and resid 117 through 139 removed outlier: 3.646A pdb=" N VAL E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 157 through 169 removed outlier: 4.005A pdb=" N LEU E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 181 Processing helix chain 'E' and resid 184 through 237 Processing helix chain 'E' and resid 244 through 255 removed outlier: 3.609A pdb=" N GLU E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 276 removed outlier: 3.524A pdb=" N ARG E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET E 276 " --> pdb=" O ARG E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 292 removed outlier: 4.407A pdb=" N THR E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TRP E 292 " --> pdb=" O THR E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 319 removed outlier: 3.625A pdb=" N GLU E 317 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 339 removed outlier: 3.576A pdb=" N THR E 339 " --> pdb=" O VAL E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 403 through 412 removed outlier: 4.296A pdb=" N HIS E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 439 removed outlier: 3.994A pdb=" N MET E 439 " --> pdb=" O ALA E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 483 removed outlier: 3.561A 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 513 removed outlier: 3.772A pdb=" N LYS E 509 " --> pdb=" O TYR E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.842A pdb=" N THR E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 560 removed outlier: 3.519A pdb=" N GLU E 544 " --> pdb=" O VAL E 540 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG E 545 " --> pdb=" O ARG E 541 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU E 546 " --> pdb=" O GLY E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 579 Processing helix chain 'E' and resid 630 through 647 removed outlier: 3.600A pdb=" N GLN E 638 " --> pdb=" O LYS E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 693 Processing helix chain 'E' and resid 717 through 727 removed outlier: 3.798A pdb=" N LYS E 721 " --> pdb=" O GLY E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 746 removed outlier: 4.433A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN E 742 " --> pdb=" O ASN E 739 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU E 744 " --> pdb=" O ALA E 741 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 746 " --> pdb=" O LEU E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 754 Processing helix chain 'E' and resid 761 through 770 removed outlier: 3.972A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 118 through 142 removed outlier: 4.029A pdb=" N ALA A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 removed outlier: 3.869A pdb=" N HIS A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.638A pdb=" N LYS A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 239 removed outlier: 4.100A pdb=" N GLY A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.996A pdb=" N GLU A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.762A pdb=" N THR A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.914A pdb=" N ARG A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 3.922A pdb=" N SER A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 434 through 440 removed outlier: 3.720A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 450 removed outlier: 3.586A pdb=" N THR A 450 " --> pdb=" O GLN A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 450' Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.769A pdb=" N ASP A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.840A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 561 removed outlier: 3.707A pdb=" N GLU A 546 " --> pdb=" O GLY A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.883A pdb=" N TYR A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 647 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.715A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 746 removed outlier: 4.497A pdb=" N ALA A 741 " --> pdb=" O ASP A 738 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 744 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 746 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.874A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 7 through 10 removed outlier: 4.342A pdb=" N VAL F 47 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 10 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE F 44 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL F 71 " --> pdb=" O GLU F 87 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU F 87 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN F 73 " --> pdb=" O MET F 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 379 through 380 removed outlier: 6.019A pdb=" N ILE F 419 " --> pdb=" O ILE F 468 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR F 470 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU F 421 " --> pdb=" O THR F 470 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU F 351 " --> pdb=" O THR F 469 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA F 471 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU F 353 " --> pdb=" O ALA F 471 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 451 through 452 removed outlier: 4.176A pdb=" N PHE F 451 " --> pdb=" O TYR F 460 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.775A 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 622 through 626 removed outlier: 3.934A pdb=" N LYS F 622 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY F 606 " --> pdb=" O THR F 603 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N MET F 702 " --> pdb=" O THR F 596 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN F 598 " --> pdb=" O MET F 702 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA F 701 " --> pdb=" O VAL F 734 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 705 through 706 Processing sheet with id=AA7, first strand: chain 'B' and resid 7 through 9 removed outlier: 3.662A pdb=" N VAL B 47 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY B 66 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG B 91 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLN B 68 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 89 " --> pdb=" O GLN B 68 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 86 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 21 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 380 removed outlier: 6.302A pdb=" N LEU B 351 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA B 471 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU B 353 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE B 350 " --> pdb=" O GLU B 486 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE B 488 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 352 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AB1, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.849A pdb=" N GLU B 521 " --> pdb=" O ILE B 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 623 through 626 removed outlier: 6.309A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR B 596 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N MET B 702 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN B 598 " --> pdb=" O MET B 702 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 705 through 706 Processing sheet with id=AB4, first strand: chain 'D' and resid 23 through 24 removed outlier: 3.922A pdb=" N VAL D 23 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET D 75 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN D 73 " --> pdb=" O MET D 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 43 through 45 Processing sheet with id=AB6, first strand: chain 'D' and resid 376 through 380 Processing sheet with id=AB7, first strand: chain 'D' and resid 397 through 398 Processing sheet with id=AB8, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.962A pdb=" N GLU D 521 " --> pdb=" O ILE D 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 596 through 603 removed outlier: 5.950A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 701 through 702 removed outlier: 6.600A pdb=" N ALA D 701 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 705 through 706 Processing sheet with id=AC3, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.959A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AC5, first strand: chain 'C' and resid 94 through 96 removed outlier: 6.435A pdb=" N ARG C 106 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 376 through 380 removed outlier: 6.763A pdb=" N ILE C 350 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE C 488 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AC8, first strand: chain 'C' and resid 521 through 522 removed outlier: 6.886A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 596 through 602 removed outlier: 5.852A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.907A pdb=" N ALA C 701 " --> pdb=" O VAL C 734 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 705 through 706 Processing sheet with id=AD3, first strand: chain 'E' and resid 20 through 21 removed outlier: 3.706A pdb=" N VAL E 86 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA E 90 " --> pdb=" O GLN E 68 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.842A pdb=" N GLN E 83 " --> pdb=" O MET E 75 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 377 through 380 removed outlier: 6.969A pdb=" N HIS E 377 " --> pdb=" O LEU E 420 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ASP E 422 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE E 379 " --> pdb=" O ASP E 422 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE E 419 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR E 470 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU E 421 " --> pdb=" O THR E 470 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU E 351 " --> pdb=" O PHE E 467 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.943A pdb=" N GLU E 521 " --> pdb=" O ILE E 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 596 through 602 removed outlier: 5.932A pdb=" N LYS E 622 " --> pdb=" O LEU E 663 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL E 665 " --> pdb=" O LYS E 622 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER E 624 " --> pdb=" O VAL E 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 701 through 702 removed outlier: 6.986A pdb=" N ALA E 701 " --> pdb=" O VAL E 734 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 705 through 706 Processing sheet with id=AE1, first strand: chain 'A' and resid 7 through 8 removed outlier: 3.634A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 67 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 21 through 22 removed outlier: 4.070A pdb=" N THR A 21 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 86 " --> pdb=" O THR A 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'A' and resid 376 through 380 removed outlier: 6.932A pdb=" N HIS A 377 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASP A 422 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 379 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 470 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU A 351 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ALA A 471 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU A 353 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 352 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 451 through 452 Processing sheet with id=AE5, first strand: chain 'A' and resid 520 through 522 removed outlier: 7.035A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'A' and resid 596 through 603 removed outlier: 3.544A pdb=" N GLY A 606 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LYS A 622 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL A 665 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AE8, first strand: chain 'A' and resid 705 through 706 1551 hydrogen bonds defined for protein. 4509 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: 8.76 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.32: 7826 1.32 - 1.48: 14193 1.48 - 1.64: 15582 1.64 - 1.80: 211 1.80 - 1.95: 56 Bond restraints: 37868 Sorted by residual: bond pdb=" C ALA D 679 " pdb=" N GLY D 680 " ideal model delta sigma weight residual 1.331 1.228 0.102 1.46e-02 4.69e+03 4.90e+01 bond pdb=" N PRO A 677 " pdb=" CA PRO A 677 " ideal model delta sigma weight residual 1.474 1.428 0.046 7.40e-03 1.83e+04 3.80e+01 bond pdb=" C ALA B 679 " pdb=" N GLY B 680 " ideal model delta sigma weight residual 1.331 1.244 0.086 1.46e-02 4.69e+03 3.49e+01 bond pdb=" C PRO A 677 " pdb=" O PRO A 677 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.33e-02 5.65e+03 2.90e+01 bond pdb=" C PRO F 673 " pdb=" O PRO F 673 " ideal model delta sigma weight residual 1.233 1.175 0.057 1.16e-02 7.43e+03 2.45e+01 ... (remaining 37863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 49821 3.12 - 6.25: 1367 6.25 - 9.37: 135 9.37 - 12.50: 30 12.50 - 15.62: 13 Bond angle restraints: 51366 Sorted by residual: angle pdb=" O ALA A 679 " pdb=" C ALA A 679 " pdb=" N GLY A 680 " ideal model delta sigma weight residual 122.06 106.66 15.40 1.34e+00 5.57e-01 1.32e+02 angle pdb=" O ALA B 679 " pdb=" C ALA B 679 " pdb=" N GLY B 680 " ideal model delta sigma weight residual 121.97 106.53 15.44 1.35e+00 5.49e-01 1.31e+02 angle pdb=" N LYS F 404 " pdb=" CA LYS F 404 " pdb=" C LYS F 404 " ideal model delta sigma weight residual 111.28 100.15 11.13 1.09e+00 8.42e-01 1.04e+02 angle pdb=" CA ALA B 679 " pdb=" C ALA B 679 " pdb=" N GLY B 680 " ideal model delta sigma weight residual 116.73 131.58 -14.85 1.64e+00 3.72e-01 8.20e+01 angle pdb=" N HIS F 407 " pdb=" CA HIS F 407 " pdb=" C HIS F 407 " ideal model delta sigma weight residual 111.07 103.04 8.03 1.07e+00 8.73e-01 5.63e+01 ... (remaining 51361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 23109 35.17 - 70.33: 217 70.33 - 105.50: 42 105.50 - 140.67: 4 140.67 - 175.83: 3 Dihedral angle restraints: 23375 sinusoidal: 9816 harmonic: 13559 Sorted by residual: dihedral pdb=" CA ASP A 51 " pdb=" C ASP A 51 " pdb=" N PRO A 52 " pdb=" CA PRO A 52 " ideal model delta harmonic sigma weight residual 180.00 -107.06 -72.94 0 5.00e+00 4.00e-02 2.13e+02 dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta harmonic sigma weight residual -180.00 -108.60 -71.40 0 5.00e+00 4.00e-02 2.04e+02 dihedral pdb=" CA ASP C 51 " pdb=" C ASP C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta harmonic sigma weight residual 180.00 -111.37 -68.63 0 5.00e+00 4.00e-02 1.88e+02 ... (remaining 23372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4951 0.099 - 0.198: 824 0.198 - 0.297: 54 0.297 - 0.396: 11 0.396 - 0.495: 2 Chirality restraints: 5842 Sorted by residual: chirality pdb=" CG LEU A 547 " pdb=" CB LEU A 547 " pdb=" CD1 LEU A 547 " pdb=" CD2 LEU A 547 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CB VAL B 540 " pdb=" CA VAL B 540 " pdb=" CG1 VAL B 540 " pdb=" CG2 VAL B 540 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA HIS F 407 " pdb=" N HIS F 407 " pdb=" C HIS F 407 " pdb=" CB HIS F 407 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 5839 not shown) Planarity restraints: 6658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 4KZ C 802 " -0.206 2.00e-02 2.50e+03 2.22e-01 6.17e+02 pdb=" C18 4KZ C 802 " 0.138 2.00e-02 2.50e+03 pdb=" C21 4KZ C 802 " -0.263 2.00e-02 2.50e+03 pdb=" N20 4KZ C 802 " 0.341 2.00e-02 2.50e+03 pdb=" O19 4KZ C 802 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 4KZ A 802 " 0.200 2.00e-02 2.50e+03 2.15e-01 5.78e+02 pdb=" C18 4KZ A 802 " -0.126 2.00e-02 2.50e+03 pdb=" C21 4KZ A 802 " 0.257 2.00e-02 2.50e+03 pdb=" N20 4KZ A 802 " -0.330 2.00e-02 2.50e+03 pdb=" O19 4KZ A 802 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 4KZ F 802 " -0.155 2.00e-02 2.50e+03 1.66e-01 3.43e+02 pdb=" C18 4KZ F 802 " 0.102 2.00e-02 2.50e+03 pdb=" C21 4KZ F 802 " -0.196 2.00e-02 2.50e+03 pdb=" N20 4KZ F 802 " 0.254 2.00e-02 2.50e+03 pdb=" O19 4KZ F 802 " -0.004 2.00e-02 2.50e+03 ... (remaining 6655 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4679 2.74 - 3.28: 33773 3.28 - 3.82: 58453 3.82 - 4.36: 69718 4.36 - 4.90: 119893 Nonbonded interactions: 286516 Sorted by model distance: nonbonded pdb=" O VAL C 359 " pdb=" O2B AGS C 801 " model vdw 2.203 3.040 nonbonded pdb=" O VAL A 359 " pdb=" O2B AGS A 801 " model vdw 2.210 3.040 nonbonded pdb=" O ASN A 138 " pdb=" OG SER A 141 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR E 95 " pdb=" O GLY E 107 " model vdw 2.270 3.040 nonbonded pdb=" O ASP E 291 " pdb=" OG1 THR E 294 " model vdw 2.271 3.040 ... (remaining 286511 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 780 or resid 802)) selection = (chain 'B' and (resid 2 through 780 or resid 802)) selection = (chain 'C' and (resid 2 through 780 or resid 802)) selection = (chain 'D' and (resid 2 through 780 or resid 802)) selection = (chain 'E' and (resid 2 through 780 or resid 802)) selection = (chain 'F' and (resid 2 through 780 or resid 802)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 37.890 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.070 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:8.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 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 : 0.014 0.127 37874 Z= 0.609 Angle : 1.233 15.621 51366 Z= 0.671 Chirality : 0.072 0.495 5842 Planarity : 0.010 0.222 6658 Dihedral : 11.850 175.834 14643 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 0.51 % Allowed : 3.31 % Favored : 96.18 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 2.54 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.10), residues: 4662 helix: -2.39 (0.09), residues: 2001 sheet: -1.27 (0.20), residues: 632 loop : -2.95 (0.11), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG B 552 TYR 0.041 0.004 TYR B 505 PHE 0.039 0.004 PHE A 110 TRP 0.047 0.004 TRP A 171 HIS 0.017 0.003 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.01435 / 0.61 (37868) covalent geometry : angle 1.23314 / 0.67 (51366) hydrogen bonds : bond 0.18360 / 11.97 ( 1551) hydrogen bonds : angle 7.05702 / 4.96 ( 4509) Misc. bond : bond 0.01394 / 0.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 321 time to evaluate : 1.449 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 258 MET cc_start: 0.5884 (ptp) cc_final: 0.5180 (ppp) REVERT: F 419 ILE cc_start: 0.8413 (mt) cc_final: 0.8147 (mt) REVERT: F 454 HIS cc_start: 0.6944 (m-70) cc_final: 0.6648 (m-70) REVERT: F 544 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7817 (mt-10) REVERT: B 385 ARG cc_start: 0.7866 (ppt-90) cc_final: 0.7523 (ptp-170) REVERT: B 713 MET cc_start: 0.8911 (mtp) cc_final: 0.8601 (mtp) REVERT: B 748 LYS cc_start: 0.8736 (mmtm) cc_final: 0.8516 (mmtm) REVERT: D 276 MET cc_start: 0.8718 (ptp) cc_final: 0.8490 (ptm) REVERT: D 304 GLU cc_start: 0.7584 (tt0) cc_final: 0.7286 (tp30) REVERT: D 373 ASN cc_start: 0.9005 (m110) cc_final: 0.8755 (t0) REVERT: D 401 MET cc_start: 0.8365 (ptt) cc_final: 0.7974 (ptp) REVERT: D 432 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6494 (mtt-85) REVERT: D 479 ARG cc_start: 0.8151 (mmt-90) cc_final: 0.7688 (mmp80) REVERT: D 713 MET cc_start: 0.8876 (mtt) cc_final: 0.8629 (mtp) REVERT: C 385 ARG cc_start: 0.8065 (ptt-90) cc_final: 0.7648 (ptm160) REVERT: C 649 GLN cc_start: 0.8685 (pm20) cc_final: 0.8338 (pm20) REVERT: C 713 MET cc_start: 0.8755 (mtt) cc_final: 0.8437 (mtp) REVERT: E 407 HIS cc_start: 0.7386 (m-70) cc_final: 0.7084 (m90) REVERT: E 430 ASP cc_start: 0.2089 (m-30) cc_final: 0.1592 (t0) REVERT: E 479 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.6975 (ttt90) REVERT: A 347 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7601 (ptpt) REVERT: A 432 ARG cc_start: 0.8031 (ppp80) cc_final: 0.7812 (ptt-90) REVERT: A 660 LYS cc_start: 0.8670 (mtpp) cc_final: 0.8294 (mtpt) REVERT: A 713 MET cc_start: 0.8796 (mtp) cc_final: 0.8585 (mtp) outliers start: 20 outliers final: 5 residues processed: 339 average time/residue: 1.0000 time to fit residues: 390.1914 Evaluate side-chains 210 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 204 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 432 ARG Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain A residue 67 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.0770 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 40.0000 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 138 ASN F 211 GLN F 319 HIS F 407 HIS F 472 ASN F 495 ASN F 666 HIS F 739 ASN B 83 GLN B 277 GLN B 319 HIS B 664 HIS B 739 ASN D 18 HIS D 83 GLN D 407 HIS D 475 GLN D 664 HIS D 739 ASN D 742 GLN C 234 GLN C 309 ASN C 666 HIS E 12 ASN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN E 407 HIS E 510 GLN E 598 GLN E 666 HIS E 739 ASN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 177 GLN A 216 GLN A 319 HIS A 346 ASN ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 647 HIS A 664 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.180622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109099 restraints weight = 66926.326| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.98 r_work: 0.3102 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37874 Z= 0.151 Angle : 0.669 9.105 51366 Z= 0.340 Chirality : 0.045 0.209 5842 Planarity : 0.006 0.079 6658 Dihedral : 10.258 178.518 5377 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 1.78 % Allowed : 6.77 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 2.17 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.11), residues: 4662 helix: -0.53 (0.11), residues: 2034 sheet: -0.60 (0.21), residues: 615 loop : -2.43 (0.12), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 479 TYR 0.035 0.002 TYR B 224 PHE 0.015 0.001 PHE E 466 TRP 0.019 0.002 TRP E 298 HIS 0.006 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (37868) covalent geometry : angle 0.66862 / 0.34 (51366) hydrogen bonds : bond 0.05277 / 3.52 ( 1551) hydrogen bonds : angle 4.98741 / 3.50 ( 4509) Misc. bond : bond 0.00176 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 238 time to evaluate : 1.522 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: F 258 MET cc_start: 0.5900 (ptp) cc_final: 0.5085 (ppp) REVERT: F 292 TRP cc_start: 0.6455 (t-100) cc_final: 0.5566 (t-100) REVERT: F 343 ASP cc_start: 0.6482 (m-30) cc_final: 0.6187 (p0) REVERT: F 409 MET cc_start: 0.7806 (tpt) cc_final: 0.7545 (tpt) REVERT: F 544 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8224 (mt-10) REVERT: F 594 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8840 (t) REVERT: F 769 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8625 (mp) REVERT: B 85 MET cc_start: 0.0689 (tpp) cc_final: 0.0210 (mpp) REVERT: B 385 ARG cc_start: 0.8520 (ppt-90) cc_final: 0.7576 (ptp-170) REVERT: B 537 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8143 (pt0) REVERT: B 713 MET cc_start: 0.9053 (mtp) cc_final: 0.8780 (mtp) REVERT: B 767 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8588 (mp0) REVERT: D 50 ARG cc_start: -0.0236 (OUTLIER) cc_final: -0.1250 (ptt90) REVERT: D 217 MET cc_start: 0.4665 (OUTLIER) cc_final: 0.4307 (mpp) REVERT: D 230 MET cc_start: 0.7413 (tpp) cc_final: 0.6973 (tmm) REVERT: D 243 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5794 (tp) REVERT: D 276 MET cc_start: 0.8489 (ptp) cc_final: 0.8182 (ptm) REVERT: D 304 GLU cc_start: 0.8145 (tt0) cc_final: 0.7357 (tp30) REVERT: D 401 MET cc_start: 0.8528 (ptt) cc_final: 0.8208 (ptp) REVERT: D 432 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6273 (mtt-85) REVERT: D 479 ARG cc_start: 0.8495 (mmt-90) cc_final: 0.8195 (mmp80) REVERT: D 713 MET cc_start: 0.9070 (mtt) cc_final: 0.8857 (mtp) REVERT: C 649 GLN cc_start: 0.9090 (pm20) cc_final: 0.8680 (pm20) REVERT: E 479 ARG cc_start: 0.7307 (mmm-85) cc_final: 0.6746 (ttt90) REVERT: E 713 MET cc_start: 0.8447 (mpp) cc_final: 0.8191 (mmm) REVERT: A 347 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7420 (ptpt) REVERT: A 373 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8360 (m-40) REVERT: A 432 ARG cc_start: 0.8021 (ppp80) cc_final: 0.7680 (ppp80) REVERT: A 591 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8138 (pt0) REVERT: A 660 LYS cc_start: 0.9027 (mtpp) cc_final: 0.8721 (mmmt) outliers start: 70 outliers final: 15 residues processed: 289 average time/residue: 0.8100 time to fit residues: 278.4726 Evaluate side-chains 225 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 432 ARG Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 547 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 245 optimal weight: 30.0000 chunk 265 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 235 optimal weight: 30.0000 chunk 259 optimal weight: 5.9990 chunk 19 optimal weight: 50.0000 chunk 283 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 18 HIS F 377 HIS ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN B 448 ASN D 373 ASN D 475 GLN C 309 ASN E 168 HIS ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** 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 = 0.4374 r_free = 0.4374 target = 0.178934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103529 restraints weight = 66261.450| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.35 r_work: 0.2991 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 37874 Z= 0.216 Angle : 0.664 8.524 51366 Z= 0.334 Chirality : 0.047 0.252 5842 Planarity : 0.005 0.072 6658 Dihedral : 9.796 179.027 5376 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.83 % Rotamer: Outliers : 1.91 % Allowed : 8.12 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 2.17 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.12), residues: 4662 helix: 0.20 (0.11), residues: 2045 sheet: -0.58 (0.21), residues: 651 loop : -2.18 (0.12), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 345 TYR 0.029 0.002 TYR B 224 PHE 0.020 0.001 PHE C 466 TRP 0.029 0.002 TRP E 298 HIS 0.009 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (37868) covalent geometry : angle 0.66406 / 0.33 (51366) hydrogen bonds : bond 0.05423 / 3.61 ( 1551) hydrogen bonds : angle 4.73786 / 3.33 ( 4509) Misc. bond : bond 0.00075 / 0.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 204 time to evaluate : 1.470 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 258 MET cc_start: 0.5948 (ptp) cc_final: 0.5135 (ppp) REVERT: F 343 ASP cc_start: 0.6640 (m-30) cc_final: 0.6171 (p0) REVERT: F 401 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5690 (pp-130) REVERT: F 409 MET cc_start: 0.7734 (tpt) cc_final: 0.7309 (tpt) REVERT: F 544 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8245 (mt-10) REVERT: F 769 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8612 (mp) REVERT: B 385 ARG cc_start: 0.8492 (ppt-90) cc_final: 0.7505 (ptp-170) REVERT: B 487 VAL cc_start: 0.9344 (OUTLIER) cc_final: 0.9039 (t) REVERT: B 713 MET cc_start: 0.9058 (mtp) cc_final: 0.8827 (mtp) REVERT: B 767 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8623 (mp0) REVERT: D 50 ARG cc_start: -0.0402 (OUTLIER) cc_final: -0.1128 (ptt90) REVERT: D 217 MET cc_start: 0.5021 (OUTLIER) cc_final: 0.4788 (mpt) REVERT: D 276 MET cc_start: 0.8457 (ptp) cc_final: 0.8152 (ptm) REVERT: D 304 GLU cc_start: 0.8180 (tt0) cc_final: 0.7319 (tp30) REVERT: D 401 MET cc_start: 0.8501 (ptt) cc_final: 0.8180 (ptp) REVERT: D 432 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.6210 (mtt-85) REVERT: D 479 ARG cc_start: 0.8510 (mmt-90) cc_final: 0.8188 (mmp80) REVERT: D 713 MET cc_start: 0.9064 (mtt) cc_final: 0.8828 (mtp) REVERT: C 38 MET cc_start: 0.4614 (OUTLIER) cc_final: 0.3743 (mmp) REVERT: C 649 GLN cc_start: 0.9106 (pm20) cc_final: 0.8689 (pm20) REVERT: E 75 MET cc_start: 0.2482 (ptt) cc_final: 0.2042 (ppp) REVERT: E 479 ARG cc_start: 0.7240 (mmm-85) cc_final: 0.6723 (ttt90) REVERT: A 75 MET cc_start: 0.2347 (pmt) cc_final: 0.1118 (ttt) REVERT: A 160 MET cc_start: 0.2708 (mmt) cc_final: 0.2502 (mmt) REVERT: A 268 LYS cc_start: 0.8951 (tppt) cc_final: 0.8640 (ttpp) REVERT: A 347 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7457 (ptpt) REVERT: A 373 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8345 (m-40) REVERT: A 432 ARG cc_start: 0.8064 (ppp80) cc_final: 0.7835 (ppp80) REVERT: A 591 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8128 (pt0) REVERT: A 660 LYS cc_start: 0.9051 (mtpp) cc_final: 0.8720 (mmmt) outliers start: 75 outliers final: 30 residues processed: 257 average time/residue: 0.7803 time to fit residues: 240.5353 Evaluate side-chains 233 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 683 MET Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 432 ARG Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 40 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 391 optimal weight: 40.0000 chunk 253 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 chunk 240 optimal weight: 40.0000 chunk 22 optimal weight: 9.9990 chunk 333 optimal weight: 8.9990 chunk 336 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 727 GLN B 472 ASN D 83 GLN C 309 ASN C 495 ASN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.177483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.102013 restraints weight = 66278.349| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.89 r_work: 0.2959 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 37874 Z= 0.334 Angle : 0.746 12.071 51366 Z= 0.375 Chirality : 0.052 0.318 5842 Planarity : 0.006 0.072 6658 Dihedral : 9.549 177.609 5375 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.53 % Favored : 94.40 % Rotamer: Outliers : 2.47 % Allowed : 9.06 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.12), residues: 4662 helix: 0.43 (0.11), residues: 2037 sheet: -0.44 (0.20), residues: 664 loop : -2.09 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 345 TYR 0.026 0.002 TYR B 224 PHE 0.025 0.002 PHE B 466 TRP 0.023 0.002 TRP E 298 HIS 0.017 0.002 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00825 / 0.33 (37868) covalent geometry : angle 0.74580 / 0.37 (51366) hydrogen bonds : bond 0.06148 / 4.09 ( 1551) hydrogen bonds : angle 4.71458 / 3.31 ( 4509) Misc. bond : bond 0.00087 / 0.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 200 time to evaluate : 1.494 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 343 ASP cc_start: 0.6795 (m-30) cc_final: 0.6278 (p0) REVERT: F 401 MET cc_start: 0.6106 (OUTLIER) cc_final: 0.5792 (pp-130) REVERT: F 409 MET cc_start: 0.7700 (tpt) cc_final: 0.7236 (tpt) REVERT: F 544 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8266 (mt-10) REVERT: F 769 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8602 (mp) REVERT: B 385 ARG cc_start: 0.8551 (ppt-90) cc_final: 0.7527 (ptp-170) REVERT: D 217 MET cc_start: 0.5096 (OUTLIER) cc_final: 0.4863 (mpt) REVERT: D 401 MET cc_start: 0.8519 (ptt) cc_final: 0.8147 (ptp) REVERT: D 432 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6231 (mtt-85) REVERT: D 479 ARG cc_start: 0.8534 (mmt-90) cc_final: 0.8096 (mmp80) REVERT: D 713 MET cc_start: 0.9074 (mtt) cc_final: 0.8850 (mtp) REVERT: C 38 MET cc_start: 0.4437 (mpp) cc_final: 0.3762 (mmp) REVERT: C 649 GLN cc_start: 0.9073 (pm20) cc_final: 0.8686 (pm20) REVERT: E 75 MET cc_start: 0.2902 (ptt) cc_final: 0.2359 (ppp) REVERT: E 217 MET cc_start: 0.7212 (tpp) cc_final: 0.6873 (tmm) REVERT: E 405 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6958 (tt) REVERT: E 479 ARG cc_start: 0.7257 (mmm-85) cc_final: 0.6673 (ttt180) REVERT: E 713 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8579 (mtm) REVERT: A 75 MET cc_start: 0.2330 (pmt) cc_final: 0.0946 (tmm) REVERT: A 160 MET cc_start: 0.3004 (mmt) cc_final: 0.2801 (mmt) REVERT: A 230 MET cc_start: 0.5720 (tmm) cc_final: 0.5492 (mmm) REVERT: A 240 GLU cc_start: 0.1868 (OUTLIER) cc_final: 0.1344 (pm20) REVERT: A 268 LYS cc_start: 0.8977 (tppt) cc_final: 0.8617 (ttpp) REVERT: A 347 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7520 (ptpt) REVERT: A 373 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8314 (m-40) REVERT: A 394 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7883 (mpt90) REVERT: A 660 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8715 (mmmt) outliers start: 97 outliers final: 48 residues processed: 269 average time/residue: 0.7704 time to fit residues: 248.8556 Evaluate side-chains 249 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 401 MET Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 683 MET Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain F residue 779 VAL Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 432 ARG Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain C residue 171 TRP Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 713 MET Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 352 optimal weight: 7.9990 chunk 265 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 429 optimal weight: 6.9990 chunk 84 optimal weight: 0.4980 chunk 391 optimal weight: 50.0000 chunk 232 optimal weight: 40.0000 chunk 245 optimal weight: 2.9990 chunk 430 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN C 309 ASN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.180125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106179 restraints weight = 66299.834| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.60 r_work: 0.3020 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37874 Z= 0.118 Angle : 0.571 8.669 51366 Z= 0.288 Chirality : 0.044 0.204 5842 Planarity : 0.005 0.066 6658 Dihedral : 9.165 178.777 5375 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.40 % Favored : 95.54 % Rotamer: Outliers : 1.60 % Allowed : 10.46 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.12), residues: 4662 helix: 1.00 (0.12), residues: 2034 sheet: -0.13 (0.21), residues: 656 loop : -1.92 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 479 TYR 0.026 0.001 TYR B 224 PHE 0.012 0.001 PHE E 657 TRP 0.033 0.001 TRP E 298 HIS 0.006 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (37868) covalent geometry : angle 0.57141 / 0.29 (51366) hydrogen bonds : bond 0.03979 / 2.67 ( 1551) hydrogen bonds : angle 4.24073 / 2.99 ( 4509) Misc. bond : bond 0.00025 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 201 time to evaluate : 1.511 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 258 MET cc_start: 0.5936 (ptp) cc_final: 0.5109 (ppp) REVERT: F 343 ASP cc_start: 0.6698 (m-30) cc_final: 0.6094 (p0) REVERT: F 409 MET cc_start: 0.7570 (tpt) cc_final: 0.7038 (tpt) REVERT: F 489 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7032 (mp0) REVERT: F 544 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7973 (mt-10) REVERT: F 769 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8468 (mp) REVERT: B 323 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7959 (mppt) REVERT: B 385 ARG cc_start: 0.8476 (ppt-90) cc_final: 0.7495 (ptp-170) REVERT: D 149 LEU cc_start: 0.1111 (OUTLIER) cc_final: 0.0702 (mp) REVERT: D 217 MET cc_start: 0.5092 (OUTLIER) cc_final: 0.4800 (mpt) REVERT: D 243 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5747 (tm) REVERT: D 300 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7455 (tmtt) REVERT: D 401 MET cc_start: 0.8361 (ptt) cc_final: 0.8047 (ptp) REVERT: D 432 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6227 (mpp80) REVERT: D 441 GLU cc_start: 0.8564 (pt0) cc_final: 0.8330 (pt0) REVERT: D 479 ARG cc_start: 0.8402 (mmt-90) cc_final: 0.8126 (mmp80) REVERT: D 693 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7768 (mmm160) REVERT: D 713 MET cc_start: 0.8892 (mtt) cc_final: 0.8634 (mtp) REVERT: C 38 MET cc_start: 0.4442 (OUTLIER) cc_final: 0.3738 (mmp) REVERT: C 649 GLN cc_start: 0.8960 (pm20) cc_final: 0.8589 (pm20) REVERT: E 75 MET cc_start: 0.2416 (ptt) cc_final: 0.2035 (ppp) REVERT: E 217 MET cc_start: 0.7288 (tpp) cc_final: 0.6873 (tmm) REVERT: E 479 ARG cc_start: 0.7186 (mmm-85) cc_final: 0.6553 (ttt90) REVERT: E 713 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8317 (mtm) REVERT: E 761 ASP cc_start: 0.8104 (t70) cc_final: 0.7844 (t70) REVERT: A 75 MET cc_start: 0.1873 (pmt) cc_final: 0.0441 (tmm) REVERT: A 160 MET cc_start: 0.3281 (mmt) cc_final: 0.3050 (mmt) REVERT: A 268 LYS cc_start: 0.8910 (tppt) cc_final: 0.8580 (ttpp) REVERT: A 347 LYS cc_start: 0.8004 (mmtm) cc_final: 0.7522 (ptpt) REVERT: A 479 ARG cc_start: 0.8470 (mmm160) cc_final: 0.8257 (tpm-80) REVERT: A 660 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8433 (mtpt) outliers start: 63 outliers final: 24 residues processed: 243 average time/residue: 0.7510 time to fit residues: 218.5382 Evaluate side-chains 227 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 432 ARG Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 713 MET Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 380 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 chunk 370 optimal weight: 7.9990 chunk 231 optimal weight: 40.0000 chunk 384 optimal weight: 6.9990 chunk 297 optimal weight: 2.9990 chunk 93 optimal weight: 50.0000 chunk 185 optimal weight: 10.0000 chunk 337 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN C 309 ASN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.177955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102552 restraints weight = 66046.885| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.47 r_work: 0.3001 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 37874 Z= 0.228 Angle : 0.647 11.440 51366 Z= 0.322 Chirality : 0.047 0.264 5842 Planarity : 0.005 0.067 6658 Dihedral : 9.069 178.910 5375 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 2.42 % Allowed : 10.33 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.12), residues: 4662 helix: 1.05 (0.12), residues: 2046 sheet: 0.01 (0.21), residues: 634 loop : -1.88 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 479 TYR 0.024 0.002 TYR B 224 PHE 0.018 0.001 PHE C 466 TRP 0.024 0.002 TRP E 298 HIS 0.011 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.23 (37868) covalent geometry : angle 0.64691 / 0.32 (51366) hydrogen bonds : bond 0.05155 / 3.45 ( 1551) hydrogen bonds : angle 4.31688 / 3.04 ( 4509) Misc. bond : bond 0.00060 / 0.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 197 time to evaluate : 1.514 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 343 ASP cc_start: 0.6886 (m-30) cc_final: 0.6329 (p0) REVERT: F 409 MET cc_start: 0.7563 (tpt) cc_final: 0.7092 (tpt) REVERT: F 428 SER cc_start: 0.4919 (OUTLIER) cc_final: 0.4578 (m) REVERT: F 489 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7016 (mp0) REVERT: F 544 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8174 (mt-10) REVERT: F 769 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8495 (mp) REVERT: B 224 TYR cc_start: 0.6392 (OUTLIER) cc_final: 0.6118 (p90) REVERT: B 323 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8120 (mppt) REVERT: B 385 ARG cc_start: 0.8550 (ppt-90) cc_final: 0.7496 (ptp-170) REVERT: B 713 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8698 (mtp) REVERT: B 752 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8319 (mp0) REVERT: D 300 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7400 (tmtt) REVERT: D 401 MET cc_start: 0.8458 (ptt) cc_final: 0.8137 (ptp) REVERT: D 432 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6219 (mtt-85) REVERT: D 479 ARG cc_start: 0.8532 (mmt-90) cc_final: 0.8221 (mmp80) REVERT: D 713 MET cc_start: 0.9018 (mtt) cc_final: 0.8791 (mtp) REVERT: C 38 MET cc_start: 0.4457 (OUTLIER) cc_final: 0.3829 (mmp) REVERT: C 649 GLN cc_start: 0.8994 (pm20) cc_final: 0.8638 (pm20) REVERT: E 75 MET cc_start: 0.2911 (ptt) cc_final: 0.2464 (ppp) REVERT: E 85 MET cc_start: 0.1831 (tpt) cc_final: 0.1538 (mmt) REVERT: E 217 MET cc_start: 0.7184 (tpp) cc_final: 0.6789 (tmm) REVERT: E 479 ARG cc_start: 0.7243 (mmm-85) cc_final: 0.6608 (ttt180) REVERT: E 713 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8534 (mtm) REVERT: A 75 MET cc_start: 0.2479 (pmt) cc_final: 0.1107 (tmm) REVERT: A 268 LYS cc_start: 0.8937 (tppt) cc_final: 0.8581 (ttpp) REVERT: A 347 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7530 (ptpt) REVERT: A 394 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7765 (mpt90) REVERT: A 479 ARG cc_start: 0.8497 (mmm160) cc_final: 0.8273 (tpm-80) REVERT: A 591 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8091 (pt0) REVERT: A 660 LYS cc_start: 0.9001 (mtpp) cc_final: 0.8518 (mtpt) outliers start: 95 outliers final: 49 residues processed: 265 average time/residue: 0.7704 time to fit residues: 246.4037 Evaluate side-chains 252 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 192 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 683 MET Chi-restraints excluded: chain F residue 713 MET Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain F residue 779 VAL Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 432 ARG Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 171 TRP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 713 MET Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 186 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 414 optimal weight: 0.9990 chunk 436 optimal weight: 0.8980 chunk 333 optimal weight: 7.9990 chunk 387 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 300 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 453 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.179864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105472 restraints weight = 66082.984| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.89 r_work: 0.3017 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37874 Z= 0.111 Angle : 0.563 10.075 51366 Z= 0.280 Chirality : 0.043 0.267 5842 Planarity : 0.004 0.066 6658 Dihedral : 8.818 179.478 5375 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.29 % Favored : 95.67 % Rotamer: Outliers : 1.68 % Allowed : 11.22 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.12), residues: 4662 helix: 1.34 (0.12), residues: 2053 sheet: 0.12 (0.21), residues: 640 loop : -1.77 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 479 TYR 0.025 0.001 TYR B 224 PHE 0.024 0.001 PHE D 132 TRP 0.029 0.001 TRP E 298 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (37868) covalent geometry : angle 0.56276 / 0.28 (51366) hydrogen bonds : bond 0.03752 / 2.53 ( 1551) hydrogen bonds : angle 4.02259 / 2.83 ( 4509) Misc. bond : bond 0.00025 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 200 time to evaluate : 1.503 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: symmetry clash REVERT: F 343 ASP cc_start: 0.6758 (m-30) cc_final: 0.6285 (p0) REVERT: F 409 MET cc_start: 0.7532 (tpt) cc_final: 0.7088 (tpt) REVERT: F 428 SER cc_start: 0.4531 (OUTLIER) cc_final: 0.4149 (m) REVERT: F 489 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7020 (mp0) REVERT: F 544 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8011 (mt-10) REVERT: F 769 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8411 (mp) REVERT: B 224 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.6113 (p90) REVERT: B 385 ARG cc_start: 0.8374 (ppt-90) cc_final: 0.7342 (ptp-170) REVERT: D 300 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7413 (tttp) REVERT: D 389 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8523 (pt0) REVERT: D 401 MET cc_start: 0.8390 (ptt) cc_final: 0.8100 (ptp) REVERT: D 479 ARG cc_start: 0.8423 (mmt-90) cc_final: 0.8163 (mmp80) REVERT: D 713 MET cc_start: 0.8873 (mtt) cc_final: 0.8621 (mtp) REVERT: C 38 MET cc_start: 0.4356 (OUTLIER) cc_final: 0.3697 (mmp) REVERT: C 472 ASN cc_start: 0.7853 (p0) cc_final: 0.7646 (p0) REVERT: C 649 GLN cc_start: 0.8905 (pm20) cc_final: 0.8595 (pm20) REVERT: E 75 MET cc_start: 0.2635 (ptt) cc_final: 0.2216 (ppp) REVERT: E 85 MET cc_start: 0.1976 (tpt) cc_final: 0.1610 (mmt) REVERT: E 217 MET cc_start: 0.7181 (tpp) cc_final: 0.6739 (tmm) REVERT: E 267 LEU cc_start: 0.4813 (OUTLIER) cc_final: 0.4436 (tm) REVERT: E 479 ARG cc_start: 0.7353 (mmm-85) cc_final: 0.6702 (ttt90) REVERT: E 713 MET cc_start: 0.8683 (mpp) cc_final: 0.8329 (mtm) REVERT: E 761 ASP cc_start: 0.8095 (t70) cc_final: 0.7745 (t0) REVERT: A 75 MET cc_start: 0.2286 (pmt) cc_final: 0.0637 (tmm) REVERT: A 160 MET cc_start: 0.2389 (mmt) cc_final: 0.0136 (ppp) REVERT: A 268 LYS cc_start: 0.8867 (tppt) cc_final: 0.8532 (ttpp) REVERT: A 347 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7507 (ptpt) REVERT: A 479 ARG cc_start: 0.8431 (mmm160) cc_final: 0.8150 (tpm-80) REVERT: A 660 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8460 (mtpt) REVERT: A 761 ASP cc_start: 0.8114 (t0) cc_final: 0.7885 (t0) outliers start: 66 outliers final: 34 residues processed: 250 average time/residue: 0.7857 time to fit residues: 235.5034 Evaluate side-chains 238 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 683 MET Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 432 ARG Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 290 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 15 optimal weight: 50.0000 chunk 432 optimal weight: 6.9990 chunk 458 optimal weight: 1.9990 chunk 273 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 454 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.178814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104661 restraints weight = 65743.157| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.62 r_work: 0.2992 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37874 Z= 0.164 Angle : 0.593 11.261 51366 Z= 0.294 Chirality : 0.045 0.232 5842 Planarity : 0.004 0.064 6658 Dihedral : 8.706 179.575 5375 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 1.78 % Allowed : 11.32 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.12), residues: 4662 helix: 1.42 (0.12), residues: 2046 sheet: 0.19 (0.21), residues: 634 loop : -1.69 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 385 TYR 0.024 0.001 TYR B 224 PHE 0.013 0.001 PHE C 466 TRP 0.027 0.001 TRP E 298 HIS 0.007 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (37868) covalent geometry : angle 0.59273 / 0.29 (51366) hydrogen bonds : bond 0.04332 / 2.91 ( 1551) hydrogen bonds : angle 4.04395 / 2.84 ( 4509) Misc. bond : bond 0.00041 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 199 time to evaluate : 1.463 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 343 ASP cc_start: 0.6922 (m-30) cc_final: 0.6348 (p0) REVERT: F 409 MET cc_start: 0.7526 (tpt) cc_final: 0.7045 (tpt) REVERT: F 428 SER cc_start: 0.4383 (OUTLIER) cc_final: 0.4033 (m) REVERT: F 489 GLU cc_start: 0.7596 (mt-10) cc_final: 0.6990 (mp0) REVERT: F 544 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8011 (mt-10) REVERT: F 769 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8299 (mp) REVERT: B 224 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.6092 (p90) REVERT: B 385 ARG cc_start: 0.8424 (ppt-90) cc_final: 0.7417 (ptp-170) REVERT: D 243 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5527 (tm) REVERT: D 300 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7352 (tmtt) REVERT: D 401 MET cc_start: 0.8391 (ptt) cc_final: 0.8080 (ptp) REVERT: D 430 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.5760 (p0) REVERT: D 432 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6258 (mpp80) REVERT: D 479 ARG cc_start: 0.8417 (mmt-90) cc_final: 0.8196 (mmm160) REVERT: D 713 MET cc_start: 0.8889 (mtt) cc_final: 0.8634 (mtp) REVERT: C 38 MET cc_start: 0.4408 (OUTLIER) cc_final: 0.3757 (mmp) REVERT: C 649 GLN cc_start: 0.8910 (pm20) cc_final: 0.8578 (pm20) REVERT: E 75 MET cc_start: 0.2602 (ptt) cc_final: 0.2175 (ppp) REVERT: E 85 MET cc_start: 0.2036 (tpt) cc_final: 0.1627 (mmt) REVERT: E 217 MET cc_start: 0.7215 (tpp) cc_final: 0.6777 (tmm) REVERT: E 267 LEU cc_start: 0.4805 (OUTLIER) cc_final: 0.4418 (tm) REVERT: E 479 ARG cc_start: 0.7302 (mmm-85) cc_final: 0.6653 (ttt90) REVERT: E 713 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8352 (mtm) REVERT: E 761 ASP cc_start: 0.8097 (t70) cc_final: 0.7729 (t0) REVERT: A 75 MET cc_start: 0.2335 (pmt) cc_final: 0.0720 (tmm) REVERT: A 240 GLU cc_start: 0.2271 (OUTLIER) cc_final: 0.1754 (pm20) REVERT: A 268 LYS cc_start: 0.8902 (tppt) cc_final: 0.8563 (ttpp) REVERT: A 347 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7529 (ptpt) REVERT: A 479 ARG cc_start: 0.8438 (mmm160) cc_final: 0.8137 (tpm-80) REVERT: A 660 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8421 (mtpt) outliers start: 70 outliers final: 43 residues processed: 254 average time/residue: 0.7008 time to fit residues: 213.3115 Evaluate side-chains 248 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 683 MET Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain F residue 779 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 432 ARG Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 713 MET Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 445 optimal weight: 0.7980 chunk 275 optimal weight: 0.9990 chunk 244 optimal weight: 30.0000 chunk 126 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 424 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 242 optimal weight: 0.3980 chunk 163 optimal weight: 6.9990 chunk 340 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.179943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.106132 restraints weight = 65875.942| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.68 r_work: 0.2974 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37874 Z= 0.117 Angle : 0.558 12.585 51366 Z= 0.275 Chirality : 0.043 0.199 5842 Planarity : 0.004 0.061 6658 Dihedral : 8.565 179.884 5375 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.20 % Favored : 95.75 % Rotamer: Outliers : 1.68 % Allowed : 11.50 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.13), residues: 4662 helix: 1.62 (0.12), residues: 2041 sheet: 0.27 (0.21), residues: 631 loop : -1.63 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 385 TYR 0.024 0.001 TYR B 224 PHE 0.024 0.001 PHE E 451 TRP 0.031 0.001 TRP E 298 HIS 0.005 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (37868) covalent geometry : angle 0.55816 / 0.28 (51366) hydrogen bonds : bond 0.03601 / 2.43 ( 1551) hydrogen bonds : angle 3.87545 / 2.73 ( 4509) Misc. bond : bond 0.00026 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 203 time to evaluate : 1.354 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 343 ASP cc_start: 0.6932 (m-30) cc_final: 0.6308 (p0) REVERT: F 409 MET cc_start: 0.7504 (tpt) cc_final: 0.7046 (tpt) REVERT: F 428 SER cc_start: 0.4341 (OUTLIER) cc_final: 0.4024 (m) REVERT: F 489 GLU cc_start: 0.7601 (mt-10) cc_final: 0.6984 (mp0) REVERT: F 544 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7986 (mt-10) REVERT: F 769 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 224 TYR cc_start: 0.6594 (OUTLIER) cc_final: 0.6288 (p90) REVERT: B 385 ARG cc_start: 0.8387 (ppt-90) cc_final: 0.7333 (ptp-170) REVERT: D 243 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5387 (tm) REVERT: D 287 ARG cc_start: 0.8161 (tpt90) cc_final: 0.7926 (tpt90) REVERT: D 300 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7310 (tmtt) REVERT: D 401 MET cc_start: 0.8315 (ptt) cc_final: 0.8029 (ptp) REVERT: D 430 ASP cc_start: 0.6794 (OUTLIER) cc_final: 0.5600 (p0) REVERT: D 432 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6249 (mpp80) REVERT: D 713 MET cc_start: 0.8781 (mtt) cc_final: 0.8503 (mtp) REVERT: C 38 MET cc_start: 0.4470 (OUTLIER) cc_final: 0.3919 (mmp) REVERT: C 385 ARG cc_start: 0.8454 (ptt-90) cc_final: 0.7895 (ptt90) REVERT: C 649 GLN cc_start: 0.8896 (pm20) cc_final: 0.8531 (pm20) REVERT: E 75 MET cc_start: 0.2878 (ptt) cc_final: 0.2427 (ppp) REVERT: E 85 MET cc_start: 0.1924 (tpt) cc_final: 0.1548 (mmt) REVERT: E 217 MET cc_start: 0.7107 (tpp) cc_final: 0.6702 (tmm) REVERT: E 267 LEU cc_start: 0.4896 (OUTLIER) cc_final: 0.4502 (tm) REVERT: E 479 ARG cc_start: 0.7259 (mmm-85) cc_final: 0.6586 (ttt90) REVERT: E 713 MET cc_start: 0.8661 (mpp) cc_final: 0.8253 (mtm) REVERT: E 761 ASP cc_start: 0.8010 (t70) cc_final: 0.7629 (t0) REVERT: A 75 MET cc_start: 0.2440 (pmt) cc_final: 0.1101 (tmm) REVERT: A 160 MET cc_start: 0.2469 (mmt) cc_final: 0.0431 (ppp) REVERT: A 240 GLU cc_start: 0.2407 (OUTLIER) cc_final: 0.1907 (pm20) REVERT: A 268 LYS cc_start: 0.8845 (tppt) cc_final: 0.8513 (ttpp) REVERT: A 347 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7515 (ptpt) REVERT: A 660 LYS cc_start: 0.8853 (mtpp) cc_final: 0.8357 (mtpt) outliers start: 66 outliers final: 41 residues processed: 256 average time/residue: 0.6936 time to fit residues: 214.2043 Evaluate side-chains 246 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 683 MET Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain F residue 779 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 432 ARG Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 140 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 147 optimal weight: 0.9980 chunk 372 optimal weight: 0.0470 chunk 277 optimal weight: 3.9990 chunk 455 optimal weight: 5.9990 chunk 219 optimal weight: 0.1980 chunk 391 optimal weight: 6.9990 chunk 436 optimal weight: 0.9990 chunk 281 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN C 309 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.180931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.107821 restraints weight = 65834.614| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.87 r_work: 0.3041 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 37874 Z= 0.099 Angle : 0.549 11.428 51366 Z= 0.269 Chirality : 0.042 0.183 5842 Planarity : 0.004 0.059 6658 Dihedral : 8.308 178.653 5375 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.42 % Favored : 95.54 % Rotamer: Outliers : 1.45 % Allowed : 11.88 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.13), residues: 4662 helix: 1.78 (0.12), residues: 2052 sheet: 0.47 (0.21), residues: 624 loop : -1.54 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 336 TYR 0.026 0.001 TYR F 332 PHE 0.012 0.001 PHE F 466 TRP 0.015 0.001 TRP C 431 HIS 0.003 0.000 HIS F 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (37868) covalent geometry : angle 0.54887 / 0.27 (51366) hydrogen bonds : bond 0.03213 / 2.18 ( 1551) hydrogen bonds : angle 3.72943 / 2.63 ( 4509) Misc. bond : bond 0.00034 / 0.02 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 1.774 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 343 ASP cc_start: 0.6815 (m-30) cc_final: 0.6308 (p0) REVERT: F 409 MET cc_start: 0.7471 (tpt) cc_final: 0.6995 (tpt) REVERT: F 479 ARG cc_start: 0.7872 (tpp80) cc_final: 0.7600 (tpp-160) REVERT: F 489 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6954 (mp0) REVERT: F 544 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8014 (mt-10) REVERT: B 224 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.6140 (p90) REVERT: B 385 ARG cc_start: 0.8449 (ppt-90) cc_final: 0.7408 (ptp-170) REVERT: B 449 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8245 (OUTLIER) REVERT: B 713 MET cc_start: 0.8757 (mtt) cc_final: 0.8541 (mtt) REVERT: D 217 MET cc_start: 0.2889 (tmm) cc_final: 0.2530 (mtm) REVERT: D 243 LEU cc_start: 0.5652 (OUTLIER) cc_final: 0.4849 (tm) REVERT: D 300 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7497 (tmtt) REVERT: D 389 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8580 (pt0) REVERT: D 401 MET cc_start: 0.8276 (ptt) cc_final: 0.8044 (ptp) REVERT: D 430 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.5846 (p0) REVERT: D 432 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6304 (mpp80) REVERT: D 713 MET cc_start: 0.8812 (mtt) cc_final: 0.8547 (mtp) REVERT: C 38 MET cc_start: 0.4258 (OUTLIER) cc_final: 0.3694 (mmp) REVERT: C 385 ARG cc_start: 0.8381 (ptt-90) cc_final: 0.7785 (ptt90) REVERT: C 649 GLN cc_start: 0.8863 (pm20) cc_final: 0.8523 (pm20) REVERT: E 75 MET cc_start: 0.2358 (ptt) cc_final: 0.1956 (ppp) REVERT: E 217 MET cc_start: 0.7218 (tpp) cc_final: 0.6794 (tmm) REVERT: E 267 LEU cc_start: 0.4952 (OUTLIER) cc_final: 0.4567 (tm) REVERT: E 479 ARG cc_start: 0.7372 (mmm-85) cc_final: 0.6707 (ttt90) REVERT: E 761 ASP cc_start: 0.8064 (t70) cc_final: 0.7737 (t0) REVERT: A 75 MET cc_start: 0.2179 (pmt) cc_final: 0.0414 (tmm) REVERT: A 160 MET cc_start: 0.2827 (mmt) cc_final: 0.0479 (ppp) REVERT: A 268 LYS cc_start: 0.8911 (tppt) cc_final: 0.8588 (ttpp) REVERT: A 347 LYS cc_start: 0.7988 (mmtm) cc_final: 0.7497 (ptpt) REVERT: A 660 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8433 (mtpt) outliers start: 57 outliers final: 36 residues processed: 247 average time/residue: 0.7624 time to fit residues: 226.1405 Evaluate side-chains 233 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 683 MET Chi-restraints excluded: chain F residue 779 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 432 ARG Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 400 optimal weight: 40.0000 chunk 70 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 265 optimal weight: 7.9990 chunk 322 optimal weight: 30.0000 chunk 216 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 398 optimal weight: 50.0000 chunk 247 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 409 optimal weight: 20.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 138 ASN ** F 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.178289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.103573 restraints weight = 65809.370| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.98 r_work: 0.3005 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 37874 Z= 0.223 Angle : 0.644 11.932 51366 Z= 0.318 Chirality : 0.047 0.264 5842 Planarity : 0.005 0.059 6658 Dihedral : 8.492 179.171 5375 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 1.53 % Allowed : 11.98 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.13), residues: 4662 helix: 1.60 (0.12), residues: 2050 sheet: 0.36 (0.21), residues: 629 loop : -1.58 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 336 TYR 0.024 0.001 TYR B 224 PHE 0.025 0.002 PHE E 451 TRP 0.017 0.002 TRP C 171 HIS 0.009 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.22 (37868) covalent geometry : angle 0.64409 / 0.32 (51366) hydrogen bonds : bond 0.04721 / 3.17 ( 1551) hydrogen bonds : angle 4.02224 / 2.83 ( 4509) Misc. bond : bond 0.00055 / 0.03 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24661.52 seconds wall clock time: 417 minutes 20.19 seconds (25040.19 seconds total)