Starting phenix.real_space_refine on Mon May 4 10:52:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yp9_73288/05_2026/9yp9_73288.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yp9_73288/05_2026/9yp9_73288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yp9_73288/05_2026/9yp9_73288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yp9_73288/05_2026/9yp9_73288.map" model { file = "/net/cci-nas-00/data/ceres_data/9yp9_73288/05_2026/9yp9_73288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yp9_73288/05_2026/9yp9_73288.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 112 5.16 5 C 12624 2.51 5 N 3390 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19908 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7587 Classifications: {'peptide': 940} Link IDs: {'PTRANS': 33, 'TRANS': 906} Chain: "B" Number of atoms: 7587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7587 Classifications: {'peptide': 940} Link IDs: {'PTRANS': 33, 'TRANS': 906} Chain: "C" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1188 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "D" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1188 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "E" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1127 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "F" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1127 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'ADP': 1, 'PO4': 1, 'XB2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'ADP': 1, 'PO4': 1, 'XB2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.67, per 1000 atoms: 0.23 Number of scatterers: 19908 At special positions: 0 Unit cell: (92.13, 161.85, 177.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 6 15.00 O 3776 8.00 N 3390 7.00 C 12624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 853.5 milliseconds 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4628 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 17 sheets defined 60.7% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 removed outlier: 3.592A pdb=" N ALA A 12 " --> pdb=" O PHE A 9 " (cutoff:3.500A) Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.501A pdb=" N VAL A 76 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A 77 " --> pdb=" O ASP A 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 77' Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.933A pdb=" N ASP A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 131 through 134 removed outlier: 4.200A pdb=" N TYR A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 135 through 141 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 183 through 202 removed outlier: 4.452A pdb=" N GLY A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.555A pdb=" N ILE A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.817A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 4.272A pdb=" N ILE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.125A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.616A pdb=" N LEU A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.589A pdb=" N ASP A 309 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 306 through 310' Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.594A pdb=" N MET A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 362 removed outlier: 3.557A pdb=" N GLY A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN A 361 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 448 Processing helix chain 'A' and resid 472 through 495 Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.677A pdb=" N LEU A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 614 through 621 Processing helix chain 'A' and resid 646 through 664 removed outlier: 3.528A pdb=" N SER A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 697 through 708 Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 723 through 726 Processing helix chain 'A' and resid 737 through 749 Processing helix chain 'A' and resid 768 through 822 removed outlier: 3.635A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 787 " --> pdb=" O ARG A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 837 Processing helix chain 'A' and resid 843 through 943 removed outlier: 3.920A pdb=" N LYS A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 872 " --> pdb=" O ALA A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.692A pdb=" N LEU B 93 " --> pdb=" O MET B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 111 Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.822A pdb=" N ALA B 150 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 183 through 200 Processing helix chain 'B' and resid 215 through 231 removed outlier: 4.253A pdb=" N ASN B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Proline residue: B 225 - end of helix removed outlier: 3.744A pdb=" N PHE B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 removed outlier: 4.303A pdb=" N ILE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 removed outlier: 4.096A pdb=" N TYR B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.700A pdb=" N LEU B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 314 removed outlier: 5.007A pdb=" N ALA B 311 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE B 312 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.603A pdb=" N GLU B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 362 removed outlier: 3.955A pdb=" N GLY B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN B 361 " --> pdb=" O MET B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 416 through 448 Processing helix chain 'B' and resid 472 through 494 Processing helix chain 'B' and resid 494 through 504 removed outlier: 3.536A pdb=" N GLN B 498 " --> pdb=" O PHE B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 525 Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 544 through 557 Processing helix chain 'B' and resid 592 through 599 Processing helix chain 'B' and resid 602 through 611 Processing helix chain 'B' and resid 614 through 621 removed outlier: 3.546A pdb=" N PHE B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 645 removed outlier: 4.107A pdb=" N GLN B 645 " --> pdb=" O SER B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 663 Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 697 through 708 Processing helix chain 'B' and resid 715 through 723 Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 737 through 747 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 768 through 826 removed outlier: 4.098A pdb=" N VAL B 813 " --> pdb=" O ASP B 809 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN B 826 " --> pdb=" O MET B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 833 Processing helix chain 'B' and resid 841 through 843 No H-bonds generated for 'chain 'B' and resid 841 through 843' Processing helix chain 'B' and resid 844 through 943 removed outlier: 3.705A pdb=" N GLU B 848 " --> pdb=" O GLU B 844 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 892 " --> pdb=" O GLN B 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 56 removed outlier: 4.456A pdb=" N ASP C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE C 49 " --> pdb=" O GLN C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.801A pdb=" N ALA C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 116 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 122 through 131 Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 143 through 153 Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'D' and resid 42 through 57 Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 68 through 77 removed outlier: 3.658A pdb=" N GLY D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.628A pdb=" N LEU D 89 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 103 through 118 Proline residue: D 109 - end of helix removed outlier: 4.317A pdb=" N LYS D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 158 through 166 Processing helix chain 'D' and resid 177 through 187 Processing helix chain 'E' and resid 23 through 38 Processing helix chain 'E' and resid 47 through 55 removed outlier: 3.628A pdb=" N ARG E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 92 removed outlier: 3.857A pdb=" N LYS E 90 " --> pdb=" O MET E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 132 through 140 removed outlier: 4.604A pdb=" N ILE E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 162 Processing helix chain 'F' and resid 28 through 38 removed outlier: 4.316A pdb=" N GLU F 32 " --> pdb=" O GLN F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 56 removed outlier: 3.839A pdb=" N LEU F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA F 55 " --> pdb=" O ARG F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 66 removed outlier: 3.771A pdb=" N GLU F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 74 Processing helix chain 'F' and resid 80 through 91 Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.537A pdb=" N ILE F 100 " --> pdb=" O PRO F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'F' and resid 135 through 143 removed outlier: 4.357A pdb=" N TRP F 140 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA F 141 " --> pdb=" O LYS F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 161 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 7.046A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ARG A 54 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.668A pdb=" N CYS A 122 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE A 673 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR A 124 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLN A 172 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LEU A 460 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 174 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE A 247 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE A 263 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG A 249 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA A 261 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N HIS A 251 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 366 Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 406 Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 564 Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.615A pdb=" N ASN A 711 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 68 through 72 removed outlier: 6.618A pdb=" N LYS B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG B 54 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR B 60 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET B 77 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.772A pdb=" N CYS B 122 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE B 673 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR B 124 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER B 173 " --> pdb=" O HIS B 668 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL B 670 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 175 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N CYS B 672 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR B 177 " --> pdb=" O CYS B 672 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 455 " --> pdb=" O PHE B 252 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 250 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 260 " --> pdb=" O HIS B 251 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=AB2, first strand: chain 'B' and resid 364 through 366 Processing sheet with id=AB3, first strand: chain 'B' and resid 563 through 564 removed outlier: 3.776A pdb=" N PHE B 577 " --> pdb=" O TYR B 588 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.667A pdb=" N ASN B 711 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB6, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB7, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AB8, first strand: chain 'E' and resid 114 through 116 1093 hydrogen bonds defined for protein. 3189 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: 3.84 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5121 1.33 - 1.46: 3838 1.46 - 1.58: 11111 1.58 - 1.70: 8 1.70 - 1.82: 198 Bond restraints: 20276 Sorted by residual: bond pdb=" C GLU F 48 " pdb=" N ASP F 49 " ideal model delta sigma weight residual 1.334 1.422 -0.087 1.27e-02 6.20e+03 4.71e+01 bond pdb=" C4 ADP B1403 " pdb=" C5 ADP B1403 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C09 XB2 A1402 " pdb=" N10 XB2 A1402 " ideal model delta sigma weight residual 1.344 1.453 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C09 XB2 B1402 " pdb=" N10 XB2 B1402 " ideal model delta sigma weight residual 1.344 1.453 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C GLU C 170 " pdb=" N ASP C 171 " ideal model delta sigma weight residual 1.332 1.264 0.068 1.40e-02 5.10e+03 2.38e+01 ... (remaining 20271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 26656 2.49 - 4.97: 527 4.97 - 7.46: 64 7.46 - 9.94: 17 9.94 - 12.43: 4 Bond angle restraints: 27268 Sorted by residual: angle pdb=" CA GLU F 48 " pdb=" C GLU F 48 " pdb=" N ASP F 49 " ideal model delta sigma weight residual 118.14 111.44 6.70 1.31e+00 5.83e-01 2.62e+01 angle pdb=" N GLN C 46 " pdb=" CA GLN C 46 " pdb=" C GLN C 46 " ideal model delta sigma weight residual 113.88 107.85 6.03 1.23e+00 6.61e-01 2.40e+01 angle pdb=" CA PHE B 456 " pdb=" CB PHE B 456 " pdb=" CG PHE B 456 " ideal model delta sigma weight residual 113.80 118.63 -4.83 1.00e+00 1.00e+00 2.33e+01 angle pdb=" O GLU F 48 " pdb=" C GLU F 48 " pdb=" N ASP F 49 " ideal model delta sigma weight residual 122.43 128.46 -6.03 1.34e+00 5.57e-01 2.03e+01 angle pdb=" CA PHE A 456 " pdb=" CB PHE A 456 " pdb=" CG PHE A 456 " ideal model delta sigma weight residual 113.80 118.20 -4.40 1.00e+00 1.00e+00 1.94e+01 ... (remaining 27263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.08: 11690 29.08 - 58.17: 612 58.17 - 87.25: 91 87.25 - 116.33: 6 116.33 - 145.42: 1 Dihedral angle restraints: 12400 sinusoidal: 5236 harmonic: 7164 Sorted by residual: dihedral pdb=" O2A ADP B1403 " pdb=" O3A ADP B1403 " pdb=" PA ADP B1403 " pdb=" PB ADP B1403 " ideal model delta sinusoidal sigma weight residual -60.00 85.42 -145.42 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" C5' ADP B1403 " pdb=" O5' ADP B1403 " pdb=" PA ADP B1403 " pdb=" O2A ADP B1403 " ideal model delta sinusoidal sigma weight residual -60.00 -172.40 112.41 1 2.00e+01 2.50e-03 3.31e+01 dihedral pdb=" O1B ADP B1403 " pdb=" O3A ADP B1403 " pdb=" PB ADP B1403 " pdb=" PA ADP B1403 " ideal model delta sinusoidal sigma weight residual -60.00 -156.96 96.95 1 2.00e+01 2.50e-03 2.69e+01 ... (remaining 12397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2437 0.063 - 0.126: 427 0.126 - 0.190: 55 0.190 - 0.253: 17 0.253 - 0.316: 2 Chirality restraints: 2938 Sorted by residual: chirality pdb=" CG LEU B 887 " pdb=" CB LEU B 887 " pdb=" CD1 LEU B 887 " pdb=" CD2 LEU B 887 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA ILE D 64 " pdb=" N ILE D 64 " pdb=" C ILE D 64 " pdb=" CB ILE D 64 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2935 not shown) Planarity restraints: 3544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 XB2 B1402 " 0.014 2.00e-02 2.50e+03 8.57e-02 2.02e+02 pdb=" C04 XB2 B1402 " 0.064 2.00e-02 2.50e+03 pdb=" C07 XB2 B1402 " -0.024 2.00e-02 2.50e+03 pdb=" C08 XB2 B1402 " -0.069 2.00e-02 2.50e+03 pdb=" C09 XB2 B1402 " -0.078 2.00e-02 2.50e+03 pdb=" C11 XB2 B1402 " 0.210 2.00e-02 2.50e+03 pdb=" N03 XB2 B1402 " 0.017 2.00e-02 2.50e+03 pdb=" N10 XB2 B1402 " -0.129 2.00e-02 2.50e+03 pdb=" N19 XB2 B1402 " -0.033 2.00e-02 2.50e+03 pdb=" O01 XB2 B1402 " 0.048 2.00e-02 2.50e+03 pdb=" O20 XB2 B1402 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 XB2 A1402 " -0.008 2.00e-02 2.50e+03 4.22e-02 4.90e+01 pdb=" C04 XB2 A1402 " -0.031 2.00e-02 2.50e+03 pdb=" C07 XB2 A1402 " 0.013 2.00e-02 2.50e+03 pdb=" C08 XB2 A1402 " 0.035 2.00e-02 2.50e+03 pdb=" C09 XB2 A1402 " 0.038 2.00e-02 2.50e+03 pdb=" C11 XB2 A1402 " -0.103 2.00e-02 2.50e+03 pdb=" N03 XB2 A1402 " -0.008 2.00e-02 2.50e+03 pdb=" N10 XB2 A1402 " 0.064 2.00e-02 2.50e+03 pdb=" N19 XB2 A1402 " 0.016 2.00e-02 2.50e+03 pdb=" O01 XB2 A1402 " -0.024 2.00e-02 2.50e+03 pdb=" O20 XB2 A1402 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 780 " -0.535 9.50e-02 1.11e+02 2.40e-01 3.52e+01 pdb=" NE ARG A 780 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 780 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 780 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 780 " -0.017 2.00e-02 2.50e+03 ... (remaining 3541 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3457 2.76 - 3.30: 20675 3.30 - 3.83: 34619 3.83 - 4.37: 41076 4.37 - 4.90: 69153 Nonbonded interactions: 168980 Sorted by model distance: nonbonded pdb=" O GLU B 269 " pdb=" OH TYR B 283 " model vdw 2.230 3.040 nonbonded pdb=" O GLU A 269 " pdb=" OH TYR A 283 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP B 239 " pdb=" OG SER B 322 " model vdw 2.249 3.040 nonbonded pdb=" OG SER D 42 " pdb=" OE2 GLU D 44 " model vdw 2.265 3.040 nonbonded pdb=" N GLU B 55 " pdb=" OE1 GLU B 55 " model vdw 2.268 3.120 ... (remaining 168975 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.810 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.020 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 20276 Z= 0.358 Angle : 0.802 12.428 27268 Z= 0.495 Chirality : 0.050 0.316 2938 Planarity : 0.009 0.240 3544 Dihedral : 16.990 145.416 7772 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 0.47 % Allowed : 21.04 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.17), residues: 2456 helix: 1.45 (0.14), residues: 1363 sheet: -0.78 (0.41), residues: 148 loop : -0.80 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 723 TYR 0.016 0.001 TYR B 386 PHE 0.018 0.001 PHE B 456 TRP 0.028 0.001 TRP B 829 HIS 0.007 0.001 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00569 (20276) covalent geometry : angle 0.80231 (27268) hydrogen bonds : bond 0.14083 ( 1093) hydrogen bonds : angle 5.82661 ( 3189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 301 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 827 TRP cc_start: 0.7331 (OUTLIER) cc_final: 0.6675 (t60) REVERT: B 904 ARG cc_start: 0.9106 (tpt170) cc_final: 0.8711 (tpm170) REVERT: C 68 GLN cc_start: 0.8761 (mt0) cc_final: 0.8349 (mt0) REVERT: E 30 PHE cc_start: 0.9491 (m-80) cc_final: 0.9174 (m-80) REVERT: E 54 PHE cc_start: 0.9092 (t80) cc_final: 0.8872 (t80) REVERT: E 100 ILE cc_start: 0.8569 (mm) cc_final: 0.8105 (mm) REVERT: E 104 PHE cc_start: 0.8189 (m-80) cc_final: 0.7796 (m-80) REVERT: F 39 GLN cc_start: 0.9189 (mm110) cc_final: 0.8858 (mm110) REVERT: F 62 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.7006 (p) REVERT: F 143 PHE cc_start: 0.6798 (t80) cc_final: 0.6585 (t80) outliers start: 10 outliers final: 5 residues processed: 307 average time/residue: 0.5592 time to fit residues: 196.9956 Evaluate side-chains 269 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 262 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 827 TRP Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 63 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 0.0030 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN A 817 ASN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN B 911 ASN C 46 GLN C 94 ASN C 169 GLN D 46 GLN D 68 GLN D 112 GLN E 28 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN F 61 ASN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.141083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.081338 restraints weight = 34081.235| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.46 r_work: 0.2954 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20276 Z= 0.137 Angle : 0.593 12.850 27268 Z= 0.294 Chirality : 0.041 0.255 2938 Planarity : 0.004 0.093 3544 Dihedral : 5.698 126.036 2702 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.95 % Allowed : 20.24 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2456 helix: 1.74 (0.14), residues: 1378 sheet: -0.71 (0.42), residues: 149 loop : -0.66 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 131 TYR 0.018 0.001 TYR C 178 PHE 0.017 0.001 PHE E 119 TRP 0.025 0.001 TRP B 829 HIS 0.005 0.001 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00305 (20276) covalent geometry : angle 0.59319 (27268) hydrogen bonds : bond 0.04262 ( 1093) hydrogen bonds : angle 4.70863 ( 3189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 282 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7938 (mpp) cc_final: 0.7714 (mtt) REVERT: A 378 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8289 (m) REVERT: B 528 MET cc_start: 0.8273 (tpp) cc_final: 0.8036 (tpp) REVERT: B 556 HIS cc_start: 0.7071 (OUTLIER) cc_final: 0.6690 (p-80) REVERT: B 877 MET cc_start: 0.8601 (tpp) cc_final: 0.8204 (mmm) REVERT: B 904 ARG cc_start: 0.8956 (tpt170) cc_final: 0.8479 (tpm170) REVERT: C 112 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8339 (mm-40) REVERT: D 46 GLN cc_start: 0.7853 (mt0) cc_final: 0.7622 (mt0) REVERT: D 112 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7788 (tp40) REVERT: E 26 GLN cc_start: 0.9237 (mm110) cc_final: 0.7914 (pp30) REVERT: E 30 PHE cc_start: 0.9437 (m-80) cc_final: 0.9078 (m-80) REVERT: E 104 PHE cc_start: 0.9172 (m-80) cc_final: 0.8181 (m-80) REVERT: F 39 GLN cc_start: 0.9245 (mm110) cc_final: 0.8877 (mm110) REVERT: F 62 VAL cc_start: 0.7133 (OUTLIER) cc_final: 0.6770 (p) REVERT: F 70 MET cc_start: 0.7886 (mmp) cc_final: 0.7261 (ppp) REVERT: F 143 PHE cc_start: 0.6911 (t80) cc_final: 0.6632 (t80) outliers start: 63 outliers final: 10 residues processed: 320 average time/residue: 0.4983 time to fit residues: 185.0250 Evaluate side-chains 269 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 255 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 827 TRP Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 63 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 17 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 166 optimal weight: 0.0670 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 GLN D 68 GLN D 112 GLN E 28 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.139132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.078723 restraints weight = 33919.645| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.41 r_work: 0.2936 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20276 Z= 0.161 Angle : 0.582 9.851 27268 Z= 0.289 Chirality : 0.041 0.190 2938 Planarity : 0.004 0.084 3544 Dihedral : 5.546 119.572 2700 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.81 % Allowed : 20.67 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2456 helix: 1.76 (0.14), residues: 1362 sheet: -0.66 (0.42), residues: 147 loop : -0.59 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 807 TYR 0.016 0.001 TYR C 178 PHE 0.027 0.001 PHE F 34 TRP 0.019 0.001 TRP B 829 HIS 0.004 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00372 (20276) covalent geometry : angle 0.58239 (27268) hydrogen bonds : bond 0.03981 ( 1093) hydrogen bonds : angle 4.51266 ( 3189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 275 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8081 (mpp) cc_final: 0.7777 (mtt) REVERT: A 378 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8257 (m) REVERT: A 877 MET cc_start: 0.8685 (tmm) cc_final: 0.8452 (tpt) REVERT: A 890 GLN cc_start: 0.7841 (mt0) cc_final: 0.7588 (mt0) REVERT: B 528 MET cc_start: 0.8335 (tpp) cc_final: 0.8118 (tpp) REVERT: B 556 HIS cc_start: 0.7098 (OUTLIER) cc_final: 0.6746 (p-80) REVERT: B 877 MET cc_start: 0.8528 (tpp) cc_final: 0.8227 (mmm) REVERT: B 904 ARG cc_start: 0.8996 (tpt170) cc_final: 0.8524 (tpm170) REVERT: C 68 GLN cc_start: 0.8798 (mt0) cc_final: 0.8124 (mp10) REVERT: C 112 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8291 (mm-40) REVERT: D 46 GLN cc_start: 0.7718 (mt0) cc_final: 0.7514 (mt0) REVERT: E 26 GLN cc_start: 0.9210 (mm110) cc_final: 0.7883 (pp30) REVERT: E 30 PHE cc_start: 0.9518 (m-80) cc_final: 0.9189 (m-80) REVERT: E 104 PHE cc_start: 0.9163 (m-80) cc_final: 0.8286 (m-80) REVERT: F 39 GLN cc_start: 0.9218 (mm110) cc_final: 0.8840 (mm110) REVERT: F 57 MET cc_start: 0.8319 (mmp) cc_final: 0.8023 (tmm) REVERT: F 70 MET cc_start: 0.7907 (mmp) cc_final: 0.7123 (ppp) REVERT: F 143 PHE cc_start: 0.6966 (t80) cc_final: 0.6701 (t80) REVERT: F 153 TYR cc_start: 0.7216 (p90) cc_final: 0.7005 (p90) outliers start: 60 outliers final: 14 residues processed: 313 average time/residue: 0.4942 time to fit residues: 179.8667 Evaluate side-chains 270 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 254 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 827 TRP Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 86 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 228 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 134 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 236 optimal weight: 0.0870 chunk 218 optimal weight: 8.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 911 ASN C 169 GLN D 68 GLN D 112 GLN E 28 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 HIS F 61 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.141527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.081971 restraints weight = 34010.657| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.46 r_work: 0.2967 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20276 Z= 0.121 Angle : 0.575 9.750 27268 Z= 0.282 Chirality : 0.040 0.257 2938 Planarity : 0.003 0.064 3544 Dihedral : 5.426 113.899 2698 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.72 % Allowed : 21.60 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2456 helix: 1.88 (0.14), residues: 1374 sheet: -0.74 (0.42), residues: 151 loop : -0.59 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 131 TYR 0.027 0.001 TYR E 153 PHE 0.024 0.001 PHE F 54 TRP 0.007 0.001 TRP A 130 HIS 0.005 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00268 (20276) covalent geometry : angle 0.57511 (27268) hydrogen bonds : bond 0.03696 ( 1093) hydrogen bonds : angle 4.39001 ( 3189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 271 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8234 (m) REVERT: A 890 GLN cc_start: 0.7786 (mt0) cc_final: 0.7514 (mt0) REVERT: B 556 HIS cc_start: 0.6879 (OUTLIER) cc_final: 0.6511 (p-80) REVERT: B 858 ARG cc_start: 0.9190 (ppp80) cc_final: 0.8938 (ptm-80) REVERT: B 877 MET cc_start: 0.8431 (tpp) cc_final: 0.8164 (mmm) REVERT: B 904 ARG cc_start: 0.8960 (tpt170) cc_final: 0.8533 (tpm170) REVERT: C 112 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8327 (mm-40) REVERT: D 46 GLN cc_start: 0.7673 (mt0) cc_final: 0.7459 (mt0) REVERT: D 169 GLN cc_start: 0.7692 (mp10) cc_final: 0.7452 (pm20) REVERT: E 26 GLN cc_start: 0.9177 (mm110) cc_final: 0.8914 (mm110) REVERT: E 30 PHE cc_start: 0.9545 (m-80) cc_final: 0.9330 (m-80) REVERT: E 104 PHE cc_start: 0.9148 (m-80) cc_final: 0.8297 (m-80) REVERT: E 153 TYR cc_start: 0.8231 (p90) cc_final: 0.7814 (p90) REVERT: F 39 GLN cc_start: 0.9201 (mm110) cc_final: 0.8807 (mm110) REVERT: F 54 PHE cc_start: 0.9044 (m-80) cc_final: 0.8376 (m-80) REVERT: F 70 MET cc_start: 0.7612 (mmp) cc_final: 0.7089 (tmt) REVERT: F 112 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6925 (pptt) REVERT: F 143 PHE cc_start: 0.6966 (t80) cc_final: 0.6743 (t80) outliers start: 58 outliers final: 12 residues processed: 305 average time/residue: 0.5329 time to fit residues: 187.4404 Evaluate side-chains 274 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 259 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 827 TRP Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 112 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 234 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 ASN D 68 GLN D 112 GLN E 28 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.136676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.075580 restraints weight = 33851.806| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.44 r_work: 0.2880 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 20276 Z= 0.296 Angle : 0.662 10.195 27268 Z= 0.329 Chirality : 0.045 0.291 2938 Planarity : 0.004 0.067 3544 Dihedral : 5.667 114.431 2698 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.66 % Allowed : 21.79 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.17), residues: 2456 helix: 1.63 (0.14), residues: 1385 sheet: -0.78 (0.41), residues: 149 loop : -0.73 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 807 TYR 0.017 0.002 TYR E 153 PHE 0.030 0.002 PHE F 34 TRP 0.009 0.001 TRP A 130 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00702 (20276) covalent geometry : angle 0.66191 (27268) hydrogen bonds : bond 0.04299 ( 1093) hydrogen bonds : angle 4.55442 ( 3189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 264 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 730 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8217 (pp) REVERT: A 890 GLN cc_start: 0.7962 (mt0) cc_final: 0.7680 (mt0) REVERT: B 17 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7959 (ttt180) REVERT: B 556 HIS cc_start: 0.7236 (OUTLIER) cc_final: 0.6845 (p-80) REVERT: B 799 MET cc_start: 0.8371 (mmp) cc_final: 0.8142 (mtp) REVERT: B 858 ARG cc_start: 0.9218 (ppp80) cc_final: 0.8984 (ptm-80) REVERT: B 904 ARG cc_start: 0.9025 (tpt170) cc_final: 0.8687 (tpm170) REVERT: C 68 GLN cc_start: 0.8874 (mt0) cc_final: 0.8576 (mt0) REVERT: C 112 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8383 (mm-40) REVERT: C 177 ASN cc_start: 0.8806 (t0) cc_final: 0.8473 (t0) REVERT: D 46 GLN cc_start: 0.7686 (mt0) cc_final: 0.7477 (mt0) REVERT: E 26 GLN cc_start: 0.9164 (mm110) cc_final: 0.8890 (mm110) REVERT: E 30 PHE cc_start: 0.9554 (m-80) cc_final: 0.9346 (m-80) REVERT: E 79 ASN cc_start: 0.7924 (m-40) cc_final: 0.7508 (p0) REVERT: E 104 PHE cc_start: 0.9148 (m-80) cc_final: 0.8329 (m-80) REVERT: E 153 TYR cc_start: 0.8286 (p90) cc_final: 0.7838 (p90) REVERT: F 39 GLN cc_start: 0.9179 (mm110) cc_final: 0.8798 (mm110) REVERT: F 54 PHE cc_start: 0.9064 (m-80) cc_final: 0.8459 (m-80) REVERT: F 67 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8579 (mm) REVERT: F 70 MET cc_start: 0.7690 (mmp) cc_final: 0.7112 (ppp) REVERT: F 112 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.7007 (pptt) REVERT: F 143 PHE cc_start: 0.7040 (t80) cc_final: 0.6788 (t80) outliers start: 78 outliers final: 25 residues processed: 315 average time/residue: 0.5225 time to fit residues: 190.3566 Evaluate side-chains 281 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 827 TRP Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 151 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 174 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 68 GLN D 112 GLN E 28 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.139050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.078446 restraints weight = 33508.685| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.46 r_work: 0.2933 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20276 Z= 0.141 Angle : 0.618 10.957 27268 Z= 0.301 Chirality : 0.041 0.337 2938 Planarity : 0.003 0.067 3544 Dihedral : 5.523 108.513 2698 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.34 % Allowed : 23.38 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.17), residues: 2456 helix: 1.75 (0.14), residues: 1375 sheet: -0.87 (0.41), residues: 151 loop : -0.69 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 807 TYR 0.015 0.001 TYR E 153 PHE 0.024 0.001 PHE C 107 TRP 0.009 0.001 TRP A 130 HIS 0.007 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00323 (20276) covalent geometry : angle 0.61799 (27268) hydrogen bonds : bond 0.03773 ( 1093) hydrogen bonds : angle 4.40440 ( 3189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 264 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.8995 (t70) cc_final: 0.8787 (t70) REVERT: A 362 MET cc_start: 0.9048 (mtp) cc_final: 0.8826 (mtp) REVERT: A 378 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8263 (m) REVERT: A 890 GLN cc_start: 0.7923 (mt0) cc_final: 0.7621 (mt0) REVERT: B 556 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.6628 (p-80) REVERT: B 799 MET cc_start: 0.8377 (mmp) cc_final: 0.8147 (mtp) REVERT: B 858 ARG cc_start: 0.9270 (ppp80) cc_final: 0.9056 (ptm-80) REVERT: B 904 ARG cc_start: 0.9024 (tpt170) cc_final: 0.8674 (tpm170) REVERT: C 68 GLN cc_start: 0.8832 (mt0) cc_final: 0.8475 (mt0) REVERT: C 112 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8349 (mm-40) REVERT: C 177 ASN cc_start: 0.8755 (t0) cc_final: 0.8392 (t0) REVERT: E 26 GLN cc_start: 0.9171 (mm110) cc_final: 0.8919 (mm110) REVERT: E 28 GLN cc_start: 0.9374 (tp40) cc_final: 0.8837 (mp10) REVERT: E 54 PHE cc_start: 0.8890 (t80) cc_final: 0.8648 (t80) REVERT: E 79 ASN cc_start: 0.7923 (m-40) cc_final: 0.7537 (p0) REVERT: E 153 TYR cc_start: 0.8285 (p90) cc_final: 0.7873 (p90) REVERT: F 39 GLN cc_start: 0.9166 (mm110) cc_final: 0.8794 (mm110) REVERT: F 54 PHE cc_start: 0.9058 (m-80) cc_final: 0.8154 (m-80) REVERT: F 63 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7875 (mttt) REVERT: F 67 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8626 (mm) REVERT: F 70 MET cc_start: 0.7728 (mmp) cc_final: 0.7218 (ppp) REVERT: F 112 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.7003 (pptt) REVERT: F 143 PHE cc_start: 0.6986 (t80) cc_final: 0.6749 (t80) outliers start: 50 outliers final: 18 residues processed: 298 average time/residue: 0.5012 time to fit residues: 173.1477 Evaluate side-chains 274 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 827 TRP Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 151 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 55 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 158 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 GLN D 45 GLN D 46 GLN D 68 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN F 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.138979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078721 restraints weight = 33846.927| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.46 r_work: 0.2935 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20276 Z= 0.147 Angle : 0.622 15.317 27268 Z= 0.303 Chirality : 0.041 0.324 2938 Planarity : 0.003 0.050 3544 Dihedral : 5.454 106.083 2698 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.62 % Allowed : 23.15 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2456 helix: 1.78 (0.14), residues: 1369 sheet: -0.89 (0.41), residues: 151 loop : -0.66 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 131 TYR 0.013 0.001 TYR E 153 PHE 0.036 0.001 PHE E 30 TRP 0.011 0.001 TRP B 829 HIS 0.008 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00341 (20276) covalent geometry : angle 0.62187 (27268) hydrogen bonds : bond 0.03714 ( 1093) hydrogen bonds : angle 4.36233 ( 3189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 266 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.9003 (t70) cc_final: 0.8763 (t70) REVERT: A 362 MET cc_start: 0.9026 (mtp) cc_final: 0.8822 (mtp) REVERT: A 378 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8223 (m) REVERT: B 556 HIS cc_start: 0.6901 (OUTLIER) cc_final: 0.6520 (p-80) REVERT: B 740 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8244 (mptp) REVERT: B 799 MET cc_start: 0.8382 (mmp) cc_final: 0.8142 (mtp) REVERT: B 827 TRP cc_start: 0.6952 (OUTLIER) cc_final: 0.6417 (t60) REVERT: B 845 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8539 (ppp80) REVERT: C 68 GLN cc_start: 0.8836 (mt0) cc_final: 0.8601 (mt0) REVERT: C 89 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8515 (tm) REVERT: C 112 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8359 (mm-40) REVERT: C 177 ASN cc_start: 0.8731 (t0) cc_final: 0.8360 (t0) REVERT: D 68 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: D 111 MET cc_start: 0.7699 (tpt) cc_final: 0.7397 (tpp) REVERT: E 26 GLN cc_start: 0.9125 (mm110) cc_final: 0.8762 (mm-40) REVERT: E 28 GLN cc_start: 0.9373 (tp40) cc_final: 0.8842 (mp10) REVERT: E 30 PHE cc_start: 0.9494 (m-80) cc_final: 0.9256 (m-80) REVERT: E 79 ASN cc_start: 0.7808 (m-40) cc_final: 0.7492 (p0) REVERT: E 153 TYR cc_start: 0.8299 (p90) cc_final: 0.7908 (p90) REVERT: F 37 ILE cc_start: 0.8625 (pp) cc_final: 0.7953 (tp) REVERT: F 39 GLN cc_start: 0.9169 (mm110) cc_final: 0.8784 (mm110) REVERT: F 54 PHE cc_start: 0.9053 (m-80) cc_final: 0.8264 (m-80) REVERT: F 63 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7910 (mttm) REVERT: F 67 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8635 (mm) REVERT: F 70 MET cc_start: 0.7686 (mmp) cc_final: 0.7250 (ppp) REVERT: F 112 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6998 (pptt) REVERT: F 143 PHE cc_start: 0.7009 (t80) cc_final: 0.6768 (t80) outliers start: 56 outliers final: 21 residues processed: 305 average time/residue: 0.5503 time to fit residues: 193.0328 Evaluate side-chains 286 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 827 TRP Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 827 TRP Chi-restraints excluded: chain B residue 845 ARG Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 151 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 101 optimal weight: 0.7980 chunk 237 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 210 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 890 GLN C 169 GLN D 46 GLN D 68 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.139340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.078793 restraints weight = 33774.781| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.48 r_work: 0.2941 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20276 Z= 0.146 Angle : 0.642 13.754 27268 Z= 0.311 Chirality : 0.042 0.365 2938 Planarity : 0.003 0.040 3544 Dihedral : 5.424 103.945 2698 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.30 % Allowed : 24.27 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2456 helix: 1.80 (0.14), residues: 1365 sheet: -0.90 (0.41), residues: 151 loop : -0.68 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 807 TYR 0.013 0.001 TYR A 310 PHE 0.027 0.001 PHE C 107 TRP 0.012 0.001 TRP B 829 HIS 0.010 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00337 (20276) covalent geometry : angle 0.64222 (27268) hydrogen bonds : bond 0.03675 ( 1093) hydrogen bonds : angle 4.34892 ( 3189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.8998 (t70) cc_final: 0.8723 (t70) REVERT: A 378 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8206 (m) REVERT: A 870 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8002 (ttp80) REVERT: B 556 HIS cc_start: 0.6851 (OUTLIER) cc_final: 0.6464 (p-80) REVERT: B 740 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8242 (mptp) REVERT: B 799 MET cc_start: 0.8368 (mmp) cc_final: 0.8126 (mtp) REVERT: B 827 TRP cc_start: 0.6987 (OUTLIER) cc_final: 0.6464 (t60) REVERT: B 845 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8547 (ppp80) REVERT: B 877 MET cc_start: 0.8709 (tpp) cc_final: 0.8394 (mmm) REVERT: B 904 ARG cc_start: 0.8819 (tpm170) cc_final: 0.8564 (tpm170) REVERT: C 68 GLN cc_start: 0.8796 (mt0) cc_final: 0.8537 (mt0) REVERT: C 89 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8523 (tm) REVERT: C 112 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8152 (mm-40) REVERT: C 177 ASN cc_start: 0.8717 (t0) cc_final: 0.8357 (t0) REVERT: D 111 MET cc_start: 0.7662 (tpt) cc_final: 0.7326 (tpp) REVERT: E 26 GLN cc_start: 0.9113 (mm110) cc_final: 0.8763 (mm-40) REVERT: E 28 GLN cc_start: 0.9363 (tp40) cc_final: 0.8806 (mp10) REVERT: E 30 PHE cc_start: 0.9488 (m-80) cc_final: 0.9240 (m-80) REVERT: E 79 ASN cc_start: 0.7860 (m-40) cc_final: 0.7534 (p0) REVERT: E 153 TYR cc_start: 0.8306 (p90) cc_final: 0.7941 (p90) REVERT: F 37 ILE cc_start: 0.8644 (pp) cc_final: 0.7975 (tp) REVERT: F 39 GLN cc_start: 0.9178 (mm110) cc_final: 0.8806 (mm110) REVERT: F 54 PHE cc_start: 0.9046 (m-80) cc_final: 0.8242 (m-80) REVERT: F 63 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7979 (mttm) REVERT: F 67 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8606 (mm) REVERT: F 70 MET cc_start: 0.7729 (mmp) cc_final: 0.7263 (ppp) REVERT: F 112 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7046 (pptt) REVERT: F 143 PHE cc_start: 0.7035 (t80) cc_final: 0.6765 (t80) outliers start: 49 outliers final: 24 residues processed: 298 average time/residue: 0.5432 time to fit residues: 187.0162 Evaluate side-chains 292 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 827 TRP Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 827 TRP Chi-restraints excluded: chain B residue 845 ARG Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 151 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 190 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 184 optimal weight: 9.9990 chunk 1 optimal weight: 0.4980 chunk 179 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 220 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.139983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.080027 restraints weight = 33577.566| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.44 r_work: 0.2964 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20276 Z= 0.128 Angle : 0.647 18.349 27268 Z= 0.314 Chirality : 0.041 0.311 2938 Planarity : 0.003 0.053 3544 Dihedral : 5.348 99.296 2698 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.16 % Allowed : 24.51 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2456 helix: 1.86 (0.14), residues: 1369 sheet: -0.87 (0.41), residues: 151 loop : -0.66 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 807 TYR 0.014 0.001 TYR F 153 PHE 0.033 0.001 PHE C 107 TRP 0.009 0.001 TRP B 829 HIS 0.010 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00290 (20276) covalent geometry : angle 0.64656 (27268) hydrogen bonds : bond 0.03562 ( 1093) hydrogen bonds : angle 4.29734 ( 3189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.9010 (t70) cc_final: 0.8725 (t70) REVERT: A 378 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8165 (m) REVERT: A 807 ARG cc_start: 0.7603 (ttp80) cc_final: 0.7252 (tmm160) REVERT: A 870 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7968 (ttp80) REVERT: B 556 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.6335 (p-80) REVERT: B 740 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8241 (mptp) REVERT: B 799 MET cc_start: 0.8385 (mmp) cc_final: 0.8149 (mtp) REVERT: B 827 TRP cc_start: 0.7015 (OUTLIER) cc_final: 0.6475 (t60) REVERT: B 845 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8573 (ppp80) REVERT: B 877 MET cc_start: 0.8722 (tpp) cc_final: 0.8401 (mmm) REVERT: B 904 ARG cc_start: 0.8813 (tpm170) cc_final: 0.8531 (tpm170) REVERT: C 68 GLN cc_start: 0.8854 (mt0) cc_final: 0.8618 (mt0) REVERT: C 112 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8333 (mm-40) REVERT: C 177 ASN cc_start: 0.8689 (t0) cc_final: 0.8336 (t0) REVERT: D 68 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: D 111 MET cc_start: 0.7658 (tpt) cc_final: 0.7359 (tpp) REVERT: D 117 ASN cc_start: 0.8469 (m-40) cc_final: 0.8125 (t0) REVERT: E 26 GLN cc_start: 0.9119 (mm110) cc_final: 0.8764 (mm-40) REVERT: E 28 GLN cc_start: 0.9361 (tp40) cc_final: 0.8791 (mp10) REVERT: E 30 PHE cc_start: 0.9496 (m-80) cc_final: 0.9249 (m-80) REVERT: E 54 PHE cc_start: 0.8906 (t80) cc_final: 0.8670 (t80) REVERT: E 79 ASN cc_start: 0.7746 (m-40) cc_final: 0.7490 (p0) REVERT: E 153 TYR cc_start: 0.8310 (p90) cc_final: 0.7858 (p90) REVERT: F 37 ILE cc_start: 0.8616 (pp) cc_final: 0.7947 (tp) REVERT: F 39 GLN cc_start: 0.9201 (mm110) cc_final: 0.8859 (mm110) REVERT: F 54 PHE cc_start: 0.9029 (m-80) cc_final: 0.8271 (m-80) REVERT: F 63 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8150 (mttm) REVERT: F 70 MET cc_start: 0.7730 (mmp) cc_final: 0.7323 (ppp) REVERT: F 112 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7126 (pptt) REVERT: F 143 PHE cc_start: 0.7022 (t80) cc_final: 0.6816 (t80) outliers start: 46 outliers final: 20 residues processed: 303 average time/residue: 0.5203 time to fit residues: 183.3488 Evaluate side-chains 291 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 827 TRP Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 827 TRP Chi-restraints excluded: chain B residue 845 ARG Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 112 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 245 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 199 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.142896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.085950 restraints weight = 34510.526| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.65 r_work: 0.2908 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20276 Z= 0.198 Angle : 0.687 20.589 27268 Z= 0.332 Chirality : 0.043 0.300 2938 Planarity : 0.004 0.046 3544 Dihedral : 5.427 100.594 2698 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.69 % Allowed : 25.07 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2456 helix: 1.76 (0.14), residues: 1381 sheet: -0.84 (0.41), residues: 149 loop : -0.71 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 807 TYR 0.013 0.001 TYR B 386 PHE 0.031 0.002 PHE C 107 TRP 0.014 0.001 TRP B 829 HIS 0.012 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00470 (20276) covalent geometry : angle 0.68663 (27268) hydrogen bonds : bond 0.03792 ( 1093) hydrogen bonds : angle 4.38056 ( 3189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 263 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.8923 (t70) cc_final: 0.8576 (t70) REVERT: A 378 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8187 (m) REVERT: A 870 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7988 (ttp80) REVERT: B 556 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6493 (p-80) REVERT: B 799 MET cc_start: 0.8328 (mmp) cc_final: 0.8089 (mtp) REVERT: B 827 TRP cc_start: 0.6945 (OUTLIER) cc_final: 0.6402 (t60) REVERT: B 845 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8583 (ppp80) REVERT: B 877 MET cc_start: 0.8732 (tpp) cc_final: 0.8417 (mmm) REVERT: B 904 ARG cc_start: 0.8796 (tpm170) cc_final: 0.8465 (tpm170) REVERT: B 922 MET cc_start: 0.4171 (pmm) cc_final: 0.3718 (pmt) REVERT: C 112 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8393 (mm-40) REVERT: C 177 ASN cc_start: 0.8705 (t0) cc_final: 0.8367 (t0) REVERT: D 111 MET cc_start: 0.7618 (tpt) cc_final: 0.7366 (tpp) REVERT: D 117 ASN cc_start: 0.8497 (m-40) cc_final: 0.8156 (t0) REVERT: E 26 GLN cc_start: 0.9103 (mm110) cc_final: 0.8735 (mm-40) REVERT: E 30 PHE cc_start: 0.9495 (m-80) cc_final: 0.9252 (m-80) REVERT: E 79 ASN cc_start: 0.7778 (m-40) cc_final: 0.7502 (p0) REVERT: E 153 TYR cc_start: 0.8283 (p90) cc_final: 0.7864 (p90) REVERT: F 37 ILE cc_start: 0.8653 (pp) cc_final: 0.7971 (tp) REVERT: F 39 GLN cc_start: 0.9183 (mm110) cc_final: 0.8828 (mm110) REVERT: F 54 PHE cc_start: 0.9032 (m-80) cc_final: 0.8280 (m-80) REVERT: F 63 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8194 (mttp) REVERT: F 70 MET cc_start: 0.7731 (mmp) cc_final: 0.7284 (tmm) REVERT: F 112 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7136 (pptt) REVERT: F 143 PHE cc_start: 0.7042 (t80) cc_final: 0.6804 (t80) outliers start: 36 outliers final: 22 residues processed: 291 average time/residue: 0.5114 time to fit residues: 172.3472 Evaluate side-chains 289 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 260 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 827 TRP Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 827 TRP Chi-restraints excluded: chain B residue 845 ARG Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 112 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 11 optimal weight: 0.0980 chunk 177 optimal weight: 0.0020 chunk 207 optimal weight: 4.9990 chunk 95 optimal weight: 0.0980 chunk 14 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 224 optimal weight: 20.0000 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 890 GLN B 555 ASN D 68 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.140102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.079993 restraints weight = 33918.428| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.47 r_work: 0.2963 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20276 Z= 0.126 Angle : 0.674 17.821 27268 Z= 0.328 Chirality : 0.042 0.296 2938 Planarity : 0.004 0.053 3544 Dihedral : 5.393 97.215 2698 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.55 % Allowed : 25.26 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2456 helix: 1.82 (0.14), residues: 1371 sheet: -0.91 (0.42), residues: 151 loop : -0.67 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 807 TYR 0.018 0.001 TYR F 153 PHE 0.033 0.002 PHE C 107 TRP 0.010 0.001 TRP B 829 HIS 0.011 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00278 (20276) covalent geometry : angle 0.67430 (27268) hydrogen bonds : bond 0.03628 ( 1093) hydrogen bonds : angle 4.34058 ( 3189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8851.24 seconds wall clock time: 151 minutes 25.41 seconds (9085.41 seconds total)