Starting phenix.real_space_refine on Fri Aug 7 06:35:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tpj_56106/08_2026/9tpj_56106_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tpj_56106/08_2026/9tpj_56106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tpj_56106/08_2026/9tpj_56106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tpj_56106/08_2026/9tpj_56106.map" model { file = "/net/cci-nas-00/data/ceres_data/9tpj_56106/08_2026/9tpj_56106_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tpj_56106/08_2026/9tpj_56106_neut.cif" } resolution = 3.02 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 114 5.16 5 C 12293 2.51 5 N 3281 2.21 5 O 3641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19337 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7384 Classifications: {'peptide': 914} Link IDs: {'PTRANS': 32, 'TRANS': 881} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'M3L:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 7155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 7155 Classifications: {'peptide': 881} Link IDs: {'PTRANS': 31, 'TRANS': 849} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'M3L:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1248 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "D" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1256 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "E" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1108 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain breaks: 2 Chain: "F" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1120 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.76, per 1000 atoms: 0.19 Number of scatterers: 19337 At special positions: 0 Unit cell: (93.968, 163.269, 180.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 114 16.00 P 6 15.00 Mg 2 11.99 O 3641 8.00 N 3281 7.00 C 12293 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: 1.67 Conformation dependent library (CDL) restraints added in 689.0 milliseconds 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4498 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 16 sheets defined 58.7% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 removed outlier: 3.543A 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 29 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.653A pdb=" N SER A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 183 through 201 Processing helix chain 'A' and resid 215 through 231 removed outlier: 4.397A pdb=" N ASN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.760A pdb=" N ALA A 229 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 4.221A pdb=" N ILE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.208A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.755A pdb=" N ASP A 309 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.906A 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 340 removed outlier: 3.918A pdb=" N MET A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 Processing helix chain 'A' and resid 380 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 475 through 495 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.602A pdb=" N ILE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.955A pdb=" N MET A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.743A pdb=" N HIS A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.556A pdb=" N PHE A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 removed outlier: 3.733A pdb=" N SER A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 639 through 644' Processing helix chain 'A' and resid 646 through 664 removed outlier: 3.611A 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 715 through 722 Processing helix chain 'A' and resid 723 through 726 Processing helix chain 'A' and resid 731 through 736 removed outlier: 4.168A pdb=" N ILE A 736 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 749 removed outlier: 3.793A pdb=" N LYS A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 745 " --> pdb=" O GLY A 741 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 781 Processing helix chain 'A' and resid 781 through 823 Processing helix chain 'A' and resid 826 through 837 removed outlier: 4.074A pdb=" N MET A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 843 removed outlier: 4.310A pdb=" N LYS A 841 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 842 " --> pdb=" O LEU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 926 Processing helix chain 'B' and resid 4 through 10 Processing helix chain 'B' and resid 11 through 16 Proline residue: B 14 - end of helix No H-bonds generated for 'chain 'B' and resid 11 through 16' Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 97 through 111 removed outlier: 3.595A pdb=" N SER B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 153 through 169 removed outlier: 3.646A pdb=" N ILE B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.615A pdb=" N ILE B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Proline residue: B 225 - end of helix removed outlier: 4.055A pdb=" N PHE B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.554A pdb=" N VAL B 273 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 290 removed outlier: 4.148A pdb=" N TYR B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 removed outlier: 4.191A pdb=" N LEU B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.915A pdb=" N TYR B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.825A pdb=" N GLU B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 361 removed outlier: 3.569A pdb=" N ASN B 361 " --> pdb=" O MET B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 removed outlier: 3.953A pdb=" N ASP B 382 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.650A pdb=" N LEU B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 448 Processing helix chain 'B' and resid 472 through 494 Processing helix chain 'B' and resid 497 through 504 removed outlier: 3.879A pdb=" N TYR B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 526 Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 544 through 555 removed outlier: 4.091A pdb=" N ASP B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 599 removed outlier: 4.247A pdb=" N LYS B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 611 Processing helix chain 'B' and resid 614 through 621 removed outlier: 3.630A pdb=" N SER B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 664 removed outlier: 3.589A pdb=" N SER B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 697 through 707 removed outlier: 3.719A pdb=" N ARG B 703 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS B 705 " --> pdb=" O GLY B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 723 Processing helix chain 'B' and resid 738 through 748 removed outlier: 3.904A pdb=" N ALA B 742 " --> pdb=" O SER B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 827 removed outlier: 4.064A pdb=" N GLU B 800 " --> pdb=" O LEU B 796 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 825 " --> pdb=" O PHE B 821 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP B 827 " --> pdb=" O GLY B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 837 removed outlier: 3.635A pdb=" N LYS B 831 " --> pdb=" O TRP B 827 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 837 " --> pdb=" O TYR B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 925 removed outlier: 3.711A pdb=" N LYS B 847 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 925 " --> pdb=" O GLU B 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 60 removed outlier: 3.567A pdb=" N ILE C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 114 through 125 removed outlier: 4.526A pdb=" N LYS C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 138 removed outlier: 3.637A pdb=" N ARG C 138 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.681A pdb=" N VAL C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET C 173 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'D' and resid 47 through 57 removed outlier: 3.683A pdb=" N ILE D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 68 removed outlier: 3.603A pdb=" N GLU D 68 " --> pdb=" O PRO D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 88 through 95 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.839A pdb=" N MET D 117 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS D 125 " --> pdb=" O ILE D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.853A pdb=" N VAL D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 160 Processing helix chain 'D' and resid 165 through 173 removed outlier: 4.088A pdb=" N LYS D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET D 173 " --> pdb=" O VAL D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 195 Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.567A pdb=" N GLU E 31 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 3.842A pdb=" N ASP E 51 " --> pdb=" O ASN E 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 47 through 52' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 64 through 69 removed outlier: 3.725A pdb=" N GLU E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 64 through 69' Processing helix chain 'E' and resid 79 through 86 removed outlier: 4.432A pdb=" N LEU E 83 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 91 removed outlier: 4.216A pdb=" N LEU E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 107 removed outlier: 3.883A pdb=" N VAL E 105 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 123 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 131 through 142 removed outlier: 3.699A pdb=" N VAL E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 160 removed outlier: 4.031A pdb=" N LEU E 155 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR E 160 " --> pdb=" O VAL E 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 37 removed outlier: 3.975A pdb=" N ILE F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 65 through 73 Processing helix chain 'F' and resid 78 through 90 removed outlier: 3.531A pdb=" N THR F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS F 89 " --> pdb=" O MET F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 removed outlier: 4.146A pdb=" N ILE F 99 " --> pdb=" O PRO F 95 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP F 107 " --> pdb=" O PHE F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 removed outlier: 4.313A pdb=" N GLU F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N MET F 122 " --> pdb=" O TYR F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 161 removed outlier: 3.998A pdb=" N HIS F 157 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.440A pdb=" N ARG A 249 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 261 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 6.652A 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 363 through 366 removed outlier: 7.131A pdb=" N LYS A 363 " --> pdb=" O ASP A 376 " (cutoff:3.500A) 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 removed outlier: 3.605A pdb=" N PHE A 577 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 712 through 714 Processing sheet with id=AA8, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.385A pdb=" N LYS B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG B 54 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR B 60 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.564A 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 117 removed outlier: 6.559A pdb=" N CYS B 122 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE B 673 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR B 124 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 173 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN B 172 " --> pdb=" O GLY B 458 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU B 460 " --> pdb=" O GLN B 172 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 174 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR B 455 " --> pdb=" O PHE B 252 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS B 251 " --> pdb=" O ALA B 259 " (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 365 Processing sheet with id=AB3, first strand: chain 'B' and resid 577 through 581 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 714 removed outlier: 4.201A pdb=" N ASN B 711 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 70 through 71 Processing sheet with id=AB6, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AB7, first strand: chain 'D' and resid 147 through 149 975 hydrogen bonds defined for protein. 2829 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: 3.73 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5948 1.34 - 1.46: 2816 1.46 - 1.57: 10726 1.57 - 1.69: 6 1.69 - 1.81: 204 Bond restraints: 19700 Sorted by residual: bond pdb=" O3 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.569 1.503 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O2 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.567 1.502 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O4 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.568 1.504 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O3 PO4 B2002 " pdb=" P PO4 B2002 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" O2 PO4 B2002 " pdb=" P PO4 B2002 " ideal model delta sigma weight residual 1.567 1.505 0.062 2.00e-02 2.50e+03 9.59e+00 ... (remaining 19695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 26025 2.25 - 4.50: 402 4.50 - 6.75: 61 6.75 - 8.99: 15 8.99 - 11.24: 2 Bond angle restraints: 26505 Sorted by residual: angle pdb=" CG ARG B 869 " pdb=" CD ARG B 869 " pdb=" NE ARG B 869 " ideal model delta sigma weight residual 112.00 101.21 10.79 2.20e+00 2.07e-01 2.40e+01 angle pdb=" C GLU A 883 " pdb=" N LYS A 884 " pdb=" CA LYS A 884 " ideal model delta sigma weight residual 121.58 113.02 8.56 1.95e+00 2.63e-01 1.93e+01 angle pdb=" CA THR A 660 " pdb=" CB THR A 660 " pdb=" OG1 THR A 660 " ideal model delta sigma weight residual 109.60 103.52 6.08 1.50e+00 4.44e-01 1.64e+01 angle pdb=" N GLU A 864 " pdb=" CA GLU A 864 " pdb=" CB GLU A 864 " ideal model delta sigma weight residual 110.30 116.52 -6.22 1.54e+00 4.22e-01 1.63e+01 angle pdb=" N GLU A 883 " pdb=" CA GLU A 883 " pdb=" CB GLU A 883 " ideal model delta sigma weight residual 110.16 115.83 -5.67 1.48e+00 4.57e-01 1.47e+01 ... (remaining 26500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 10786 17.81 - 35.63: 982 35.63 - 53.44: 175 53.44 - 71.25: 52 71.25 - 89.06: 31 Dihedral angle restraints: 12026 sinusoidal: 5080 harmonic: 6946 Sorted by residual: dihedral pdb=" CA LYS B 83 " pdb=" C LYS B 83 " pdb=" N PHE B 84 " pdb=" CA PHE B 84 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA GLU A 474 " pdb=" C GLU A 474 " pdb=" N GLN A 475 " pdb=" CA GLN A 475 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA LEU A 277 " pdb=" C LEU A 277 " pdb=" N LYS A 278 " pdb=" CA LYS A 278 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 12023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2245 0.051 - 0.103: 528 0.103 - 0.154: 87 0.154 - 0.205: 4 0.205 - 0.256: 2 Chirality restraints: 2866 Sorted by residual: chirality pdb=" CB ILE B 585 " pdb=" CA ILE B 585 " pdb=" CG1 ILE B 585 " pdb=" CG2 ILE B 585 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE B 674 " pdb=" CA ILE B 674 " pdb=" CG1 ILE B 674 " pdb=" CG2 ILE B 674 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA LYS A 912 " pdb=" N LYS A 912 " pdb=" C LYS A 912 " pdb=" CB LYS A 912 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 2863 not shown) Planarity restraints: 3430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 834 " -0.016 2.00e-02 2.50e+03 1.77e-02 5.47e+00 pdb=" CG PHE B 834 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 834 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 834 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 834 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 834 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 834 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 856 " -0.015 2.00e-02 2.50e+03 1.73e-02 5.26e+00 pdb=" CG PHE B 856 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 856 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 856 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 856 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 856 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 856 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 816 " -0.021 2.00e-02 2.50e+03 1.42e-02 5.04e+00 pdb=" CG TRP B 816 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 816 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 816 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 816 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 816 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 816 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 816 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 816 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 816 " -0.001 2.00e-02 2.50e+03 ... (remaining 3427 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 165 2.51 - 3.11: 14645 3.11 - 3.70: 31630 3.70 - 4.30: 44223 4.30 - 4.90: 71730 Nonbonded interactions: 162393 Sorted by model distance: nonbonded pdb=" O1 PO4 B2002 " pdb="MG MG B2003 " model vdw 1.910 2.170 nonbonded pdb=" O1 PO4 A2002 " pdb="MG MG A2003 " model vdw 1.947 2.170 nonbonded pdb=" O2B ADP B2001 " pdb="MG MG B2003 " model vdw 1.952 2.170 nonbonded pdb=" O GLU A 269 " pdb=" OH TYR A 283 " model vdw 2.037 3.040 nonbonded pdb=" OH TYR A 109 " pdb=" O ASN A 126 " model vdw 2.154 3.040 ... (remaining 162388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 198 or resid 215 through 367 or resid 371 throug \ h 406 or resid 410 through 624 or resid 645 through 925 or resid 2001 through 20 \ 03)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 39 through 195) } ncs_group { reference = (chain 'E' and (resid 20 through 143 or resid 149 through 162)) selection = (chain 'F' and (resid 20 through 55 or resid 60 through 143 or resid 149 through \ 162)) } 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.170 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.004 0.066 19700 Z= 0.173 Angle : 0.694 11.244 26505 Z= 0.359 Chirality : 0.044 0.256 2866 Planarity : 0.004 0.056 3430 Dihedral : 14.911 89.063 7528 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.05 % Allowed : 0.29 % Favored : 99.66 % 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: -0.49 (0.17), residues: 2346 helix: 0.15 (0.15), residues: 1267 sheet: -1.36 (0.38), residues: 164 loop : -0.62 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 869 TYR 0.017 0.001 TYR A 266 PHE 0.041 0.002 PHE B 834 TRP 0.038 0.002 TRP B 816 HIS 0.009 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (19700) covalent geometry : angle 0.69364 / 0.36 (26505) hydrogen bonds : bond 0.13138 / 8.16 ( 975) hydrogen bonds : angle 6.27147 / 4.39 ( 2829) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 387 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 ASN cc_start: 0.8653 (t0) cc_final: 0.8336 (t0) REVERT: B 359 PHE cc_start: 0.7047 (m-80) cc_final: 0.6739 (m-80) REVERT: B 378 THR cc_start: 0.7202 (p) cc_final: 0.6996 (p) REVERT: B 397 LYS cc_start: 0.8289 (pptt) cc_final: 0.7959 (mmmt) REVERT: B 416 ASN cc_start: 0.7864 (t0) cc_final: 0.7648 (t0) REVERT: B 439 MET cc_start: 0.7425 (mtp) cc_final: 0.7133 (mtm) REVERT: B 524 ILE cc_start: 0.7258 (mm) cc_final: 0.6975 (mm) REVERT: B 695 CYS cc_start: 0.6875 (p) cc_final: 0.6541 (p) REVERT: B 871 LYS cc_start: 0.7587 (pptt) cc_final: 0.7280 (pttt) REVERT: C 47 THR cc_start: 0.5990 (p) cc_final: 0.5759 (t) REVERT: C 130 TYR cc_start: 0.6553 (t80) cc_final: 0.6097 (t80) REVERT: D 62 ASP cc_start: 0.6241 (t0) cc_final: 0.5910 (t0) REVERT: D 75 GLN cc_start: 0.6189 (mp10) cc_final: 0.5810 (mp10) REVERT: D 104 LEU cc_start: 0.7837 (tp) cc_final: 0.7622 (tt) REVERT: D 123 LYS cc_start: 0.7652 (pptt) cc_final: 0.7130 (pttm) REVERT: E 83 LEU cc_start: 0.6875 (mm) cc_final: 0.6583 (mp) REVERT: E 151 ASP cc_start: 0.6110 (m-30) cc_final: 0.5693 (p0) REVERT: F 69 MET cc_start: 0.1228 (ptt) cc_final: 0.0826 (ttt) REVERT: F 122 MET cc_start: 0.7076 (ptt) cc_final: 0.5517 (tpp) outliers start: 1 outliers final: 0 residues processed: 388 average time/residue: 0.1384 time to fit residues: 80.9468 Evaluate side-chains 276 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.0670 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 347 ASN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A 760 HIS ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 610 GLN B 666 HIS B 720 GLN B 890 GLN D 120 HIS D 191 HIS ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.215502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.172361 restraints weight = 28943.462| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 1.96 r_work: 0.3932 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19700 Z= 0.220 Angle : 0.712 11.015 26505 Z= 0.359 Chirality : 0.046 0.209 2866 Planarity : 0.005 0.066 3430 Dihedral : 5.518 52.820 2600 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.11 % Allowed : 10.10 % Favored : 88.79 % 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: -0.63 (0.17), residues: 2346 helix: 0.12 (0.14), residues: 1271 sheet: -1.47 (0.41), residues: 143 loop : -0.86 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 190 TYR 0.022 0.002 TYR A 266 PHE 0.029 0.002 PHE B 121 TRP 0.020 0.002 TRP B 816 HIS 0.008 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (19700) covalent geometry : angle 0.71208 / 0.36 (26505) hydrogen bonds : bond 0.04942 / 3.28 ( 975) hydrogen bonds : angle 5.27020 / 3.68 ( 2829) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 326 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.6524 (tmm) cc_final: 0.5918 (ttm) REVERT: A 904 ARG cc_start: 0.8121 (ppt170) cc_final: 0.7477 (ppt170) REVERT: A 905 CYS cc_start: 0.7923 (m) cc_final: 0.7575 (m) REVERT: B 306 ASN cc_start: 0.8754 (t0) cc_final: 0.8446 (t0) REVERT: B 397 LYS cc_start: 0.8254 (pptt) cc_final: 0.7889 (mmtm) REVERT: B 524 ILE cc_start: 0.7530 (mm) cc_final: 0.7181 (mm) REVERT: B 748 SER cc_start: 0.8486 (p) cc_final: 0.8271 (p) REVERT: B 818 ILE cc_start: 0.8949 (mp) cc_final: 0.8643 (tp) REVERT: B 871 LYS cc_start: 0.7723 (pptt) cc_final: 0.7458 (pttt) REVERT: C 47 THR cc_start: 0.5955 (p) cc_final: 0.5745 (t) REVERT: C 130 TYR cc_start: 0.6313 (t80) cc_final: 0.6059 (t80) REVERT: D 51 ILE cc_start: 0.7130 (mm) cc_final: 0.6790 (pt) REVERT: D 62 ASP cc_start: 0.6331 (t0) cc_final: 0.6121 (t0) REVERT: D 73 TYR cc_start: 0.5896 (m-80) cc_final: 0.5595 (m-80) REVERT: D 109 MET cc_start: 0.6196 (tmm) cc_final: 0.5486 (tpp) REVERT: D 123 LYS cc_start: 0.7762 (pptt) cc_final: 0.7100 (pttm) REVERT: D 178 ASP cc_start: 0.5489 (p0) cc_final: 0.5276 (p0) REVERT: D 193 MET cc_start: 0.5472 (ttm) cc_final: 0.5230 (ttm) REVERT: E 107 ASP cc_start: 0.2012 (p0) cc_final: 0.1784 (p0) REVERT: E 151 ASP cc_start: 0.6175 (m-30) cc_final: 0.5847 (p0) REVERT: F 27 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: F 69 MET cc_start: 0.0950 (ptt) cc_final: 0.0410 (ttt) REVERT: F 122 MET cc_start: 0.7233 (ptt) cc_final: 0.5596 (tpp) outliers start: 23 outliers final: 13 residues processed: 338 average time/residue: 0.1409 time to fit residues: 72.5633 Evaluate side-chains 295 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 281 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 778 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 157 HIS Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 65 optimal weight: 1.9990 chunk 194 optimal weight: 0.0000 chunk 140 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 179 optimal weight: 0.0970 chunk 146 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN A 415 GLN A 555 ASN A 676 ASN A 815 GLN B 193 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS B 720 GLN B 817 ASN D 191 HIS ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.217948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.161032 restraints weight = 29121.315| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.79 r_work: 0.3903 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19700 Z= 0.134 Angle : 0.631 10.868 26505 Z= 0.316 Chirality : 0.043 0.161 2866 Planarity : 0.004 0.059 3430 Dihedral : 5.301 49.936 2600 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.15 % Allowed : 12.99 % Favored : 85.86 % 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: -0.46 (0.17), residues: 2346 helix: 0.29 (0.15), residues: 1278 sheet: -1.48 (0.43), residues: 135 loop : -0.82 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 869 TYR 0.019 0.001 TYR D 185 PHE 0.036 0.001 PHE B 834 TRP 0.015 0.001 TRP B 593 HIS 0.009 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (19700) covalent geometry : angle 0.63115 / 0.32 (26505) hydrogen bonds : bond 0.04326 / 2.89 ( 975) hydrogen bonds : angle 4.96237 / 3.47 ( 2829) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 319 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.6392 (tmm) cc_final: 0.5510 (ttp) REVERT: A 169 ARG cc_start: 0.7896 (pmt170) cc_final: 0.7689 (ptt-90) REVERT: A 382 ASP cc_start: 0.7215 (p0) cc_final: 0.6917 (p0) REVERT: A 454 GLN cc_start: 0.8297 (tp40) cc_final: 0.8049 (tp40) REVERT: A 555 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.7144 (m-40) REVERT: A 906 ASP cc_start: 0.7660 (m-30) cc_final: 0.7340 (m-30) REVERT: B 306 ASN cc_start: 0.8755 (t0) cc_final: 0.8288 (t0) REVERT: B 330 MET cc_start: 0.7757 (tmm) cc_final: 0.7523 (ppp) REVERT: B 397 LYS cc_start: 0.8303 (pptt) cc_final: 0.7901 (mmtm) REVERT: B 503 LYS cc_start: 0.8190 (mptt) cc_final: 0.7650 (mptt) REVERT: B 524 ILE cc_start: 0.7569 (mm) cc_final: 0.7026 (mm) REVERT: B 659 MET cc_start: 0.7794 (mpp) cc_final: 0.7548 (mmm) REVERT: B 871 LYS cc_start: 0.7844 (pptt) cc_final: 0.7494 (pttt) REVERT: D 51 ILE cc_start: 0.7326 (mm) cc_final: 0.6882 (pt) REVERT: D 73 TYR cc_start: 0.5859 (m-80) cc_final: 0.5561 (m-80) REVERT: D 75 GLN cc_start: 0.6166 (mp10) cc_final: 0.5815 (mp10) REVERT: D 108 MET cc_start: 0.6847 (tpt) cc_final: 0.5959 (tpt) REVERT: D 109 MET cc_start: 0.5966 (tmm) cc_final: 0.5430 (tpp) REVERT: D 123 LYS cc_start: 0.7834 (pptt) cc_final: 0.7264 (pttm) REVERT: D 190 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7749 (mmtt) REVERT: D 193 MET cc_start: 0.5336 (ttm) cc_final: 0.5122 (ttm) REVERT: E 107 ASP cc_start: 0.1933 (p0) cc_final: 0.1669 (p0) REVERT: E 122 MET cc_start: 0.6509 (ppp) cc_final: 0.6000 (ppp) REVERT: E 151 ASP cc_start: 0.6709 (m-30) cc_final: 0.6134 (p0) REVERT: F 27 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: F 69 MET cc_start: 0.1067 (ptt) cc_final: 0.0473 (ttt) REVERT: F 122 MET cc_start: 0.7503 (ptt) cc_final: 0.5840 (tpp) outliers start: 24 outliers final: 8 residues processed: 334 average time/residue: 0.1444 time to fit residues: 74.1344 Evaluate side-chains 288 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 278 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 157 HIS Chi-restraints excluded: chain F residue 27 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 35 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A 753 HIS ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS B 720 GLN B 890 GLN C 50 GLN C 120 HIS D 191 HIS ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.215707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.164777 restraints weight = 28967.420| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.28 r_work: 0.3805 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 19700 Z= 0.279 Angle : 0.739 15.817 26505 Z= 0.373 Chirality : 0.048 0.195 2866 Planarity : 0.005 0.085 3430 Dihedral : 5.680 59.536 2600 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.12 % Allowed : 15.01 % Favored : 82.88 % 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: -0.81 (0.17), residues: 2346 helix: -0.01 (0.14), residues: 1291 sheet: -1.46 (0.41), residues: 155 loop : -0.99 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 904 TYR 0.027 0.002 TYR A 266 PHE 0.020 0.002 PHE A 577 TRP 0.011 0.002 TRP A 130 HIS 0.008 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.28 (19700) covalent geometry : angle 0.73914 / 0.37 (26505) hydrogen bonds : bond 0.04944 / 3.28 ( 975) hydrogen bonds : angle 5.20049 / 3.63 ( 2829) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 294 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ARG cc_start: 0.8148 (pmt170) cc_final: 0.7849 (ptt-90) REVERT: A 470 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6935 (p90) REVERT: A 620 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8522 (mp) REVERT: A 898 LEU cc_start: 0.8649 (mp) cc_final: 0.8359 (mp) REVERT: A 903 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6536 (tp30) REVERT: A 904 ARG cc_start: 0.8236 (ppt170) cc_final: 0.7658 (ppt170) REVERT: A 905 CYS cc_start: 0.8281 (m) cc_final: 0.7989 (m) REVERT: A 906 ASP cc_start: 0.7614 (m-30) cc_final: 0.7382 (m-30) REVERT: A 922 MET cc_start: 0.7317 (mtt) cc_final: 0.6565 (mtt) REVERT: B 90 MET cc_start: 0.6252 (mmp) cc_final: 0.4310 (mmt) REVERT: B 306 ASN cc_start: 0.8800 (t0) cc_final: 0.8336 (t0) REVERT: B 330 MET cc_start: 0.7788 (tmm) cc_final: 0.7545 (ppp) REVERT: B 397 LYS cc_start: 0.8206 (pptt) cc_final: 0.7859 (mmtm) REVERT: B 493 MET cc_start: 0.6547 (mtt) cc_final: 0.6156 (mtt) REVERT: B 524 ILE cc_start: 0.7518 (mm) cc_final: 0.7176 (mm) REVERT: B 659 MET cc_start: 0.7761 (mpp) cc_final: 0.7418 (mmm) REVERT: B 871 LYS cc_start: 0.7870 (pptt) cc_final: 0.7512 (pttt) REVERT: C 73 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5805 (m-80) REVERT: D 51 ILE cc_start: 0.7199 (mm) cc_final: 0.6824 (pt) REVERT: D 73 TYR cc_start: 0.5873 (m-80) cc_final: 0.5542 (m-80) REVERT: D 109 MET cc_start: 0.5665 (tmm) cc_final: 0.4599 (tmm) REVERT: D 123 LYS cc_start: 0.7835 (pptt) cc_final: 0.7312 (pttm) REVERT: E 97 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7439 (tm-30) REVERT: E 122 MET cc_start: 0.6075 (ppp) cc_final: 0.5194 (ppp) REVERT: F 27 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7411 (mp10) REVERT: F 69 MET cc_start: 0.0712 (ptt) cc_final: 0.0488 (ttt) REVERT: F 91 LYS cc_start: 0.4047 (pptt) cc_final: 0.3692 (ptmm) REVERT: F 122 MET cc_start: 0.7536 (ptt) cc_final: 0.5843 (tpp) outliers start: 44 outliers final: 27 residues processed: 320 average time/residue: 0.1381 time to fit residues: 67.0570 Evaluate side-chains 299 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 778 ASP Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 157 HIS Chi-restraints excluded: chain F residue 27 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 134 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 202 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN A 676 ASN A 753 HIS ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS D 191 HIS ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.216491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.166943 restraints weight = 28826.205| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.34 r_work: 0.3822 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19700 Z= 0.196 Angle : 0.681 13.667 26505 Z= 0.342 Chirality : 0.044 0.175 2866 Planarity : 0.005 0.073 3430 Dihedral : 5.614 59.051 2600 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.16 % Allowed : 16.98 % Favored : 80.86 % 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: -0.73 (0.17), residues: 2346 helix: 0.07 (0.14), residues: 1293 sheet: -1.43 (0.41), residues: 155 loop : -0.96 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 904 TYR 0.021 0.002 TYR A 266 PHE 0.018 0.002 PHE B 275 TRP 0.013 0.002 TRP A 130 HIS 0.009 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (19700) covalent geometry : angle 0.68140 / 0.34 (26505) hydrogen bonds : bond 0.04556 / 3.04 ( 975) hydrogen bonds : angle 5.08888 / 3.55 ( 2829) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7626 (mtp) REVERT: A 169 ARG cc_start: 0.8196 (pmt170) cc_final: 0.7884 (ptt-90) REVERT: A 470 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.6836 (p90) REVERT: A 898 LEU cc_start: 0.8656 (mp) cc_final: 0.8371 (mp) REVERT: A 903 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: A 905 CYS cc_start: 0.8205 (m) cc_final: 0.7560 (m) REVERT: B 90 MET cc_start: 0.6266 (mmp) cc_final: 0.4273 (mmt) REVERT: B 306 ASN cc_start: 0.8757 (t0) cc_final: 0.8312 (t0) REVERT: B 330 MET cc_start: 0.7781 (tmm) cc_final: 0.7578 (ppp) REVERT: B 333 ASP cc_start: 0.7808 (m-30) cc_final: 0.7151 (m-30) REVERT: B 397 LYS cc_start: 0.8239 (pptt) cc_final: 0.7885 (mmtm) REVERT: B 524 ILE cc_start: 0.7618 (mm) cc_final: 0.7312 (mm) REVERT: B 659 MET cc_start: 0.7780 (mpp) cc_final: 0.7461 (mmm) REVERT: B 690 MET cc_start: 0.7488 (tpt) cc_final: 0.7085 (tpp) REVERT: B 834 PHE cc_start: 0.5129 (t80) cc_final: 0.4828 (t80) REVERT: B 871 LYS cc_start: 0.7935 (pptt) cc_final: 0.7585 (pttt) REVERT: D 51 ILE cc_start: 0.7214 (mm) cc_final: 0.6843 (pt) REVERT: D 73 TYR cc_start: 0.5713 (m-80) cc_final: 0.5474 (m-80) REVERT: D 123 LYS cc_start: 0.7903 (pptt) cc_final: 0.7431 (pttm) REVERT: E 107 ASP cc_start: 0.2099 (p0) cc_final: 0.1799 (p0) REVERT: E 122 MET cc_start: 0.5823 (ppp) cc_final: 0.5239 (ppp) REVERT: F 27 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: F 69 MET cc_start: 0.1143 (ptt) cc_final: 0.0755 (ttt) REVERT: F 122 MET cc_start: 0.7580 (ptt) cc_final: 0.5895 (tpp) outliers start: 45 outliers final: 25 residues processed: 322 average time/residue: 0.1453 time to fit residues: 70.6090 Evaluate side-chains 295 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 266 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 778 ASP Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 157 HIS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 56 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 234 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 206 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS D 191 HIS ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.217336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.170973 restraints weight = 28706.883| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.21 r_work: 0.3883 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19700 Z= 0.159 Angle : 0.667 11.210 26505 Z= 0.334 Chirality : 0.044 0.175 2866 Planarity : 0.004 0.068 3430 Dihedral : 5.506 57.167 2600 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.07 % Allowed : 17.75 % Favored : 80.18 % 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: -0.57 (0.17), residues: 2346 helix: 0.21 (0.14), residues: 1291 sheet: -1.49 (0.40), residues: 168 loop : -0.87 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 904 TYR 0.020 0.001 TYR D 185 PHE 0.020 0.001 PHE B 275 TRP 0.013 0.001 TRP A 130 HIS 0.009 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (19700) covalent geometry : angle 0.66730 / 0.33 (26505) hydrogen bonds : bond 0.04318 / 2.88 ( 975) hydrogen bonds : angle 4.98299 / 3.48 ( 2829) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7507 (mtp) REVERT: A 169 ARG cc_start: 0.8120 (pmt170) cc_final: 0.7792 (ptt-90) REVERT: A 382 ASP cc_start: 0.7217 (p0) cc_final: 0.6896 (p0) REVERT: A 470 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.6829 (p90) REVERT: A 898 LEU cc_start: 0.8614 (mp) cc_final: 0.8310 (mp) REVERT: A 903 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6289 (mm-30) REVERT: B 90 MET cc_start: 0.6274 (mmp) cc_final: 0.4220 (mmt) REVERT: B 306 ASN cc_start: 0.8648 (t0) cc_final: 0.8218 (t0) REVERT: B 333 ASP cc_start: 0.7745 (m-30) cc_final: 0.7125 (m-30) REVERT: B 397 LYS cc_start: 0.8210 (pptt) cc_final: 0.7911 (mmtm) REVERT: B 524 ILE cc_start: 0.7540 (mm) cc_final: 0.7290 (mm) REVERT: B 659 MET cc_start: 0.7898 (mpp) cc_final: 0.7572 (mmm) REVERT: B 690 MET cc_start: 0.7355 (tpt) cc_final: 0.7086 (tpp) REVERT: B 871 LYS cc_start: 0.7851 (pptt) cc_final: 0.7520 (pttt) REVERT: D 51 ILE cc_start: 0.7066 (mm) cc_final: 0.6701 (pt) REVERT: D 123 LYS cc_start: 0.7815 (pptt) cc_final: 0.7379 (pttm) REVERT: F 27 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: F 69 MET cc_start: 0.1357 (ptt) cc_final: 0.1029 (ttt) REVERT: F 118 TYR cc_start: 0.5126 (p90) cc_final: 0.4739 (p90) REVERT: F 122 MET cc_start: 0.7449 (ptt) cc_final: 0.5785 (tpp) outliers start: 43 outliers final: 23 residues processed: 313 average time/residue: 0.1316 time to fit residues: 63.6737 Evaluate side-chains 291 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 778 ASP Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 157 HIS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 187 optimal weight: 10.0000 chunk 214 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 666 HIS B 720 GLN D 191 HIS ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.218560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.168132 restraints weight = 28968.918| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.16 r_work: 0.3893 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19700 Z= 0.147 Angle : 0.677 14.310 26505 Z= 0.336 Chirality : 0.043 0.176 2866 Planarity : 0.004 0.069 3430 Dihedral : 5.409 53.246 2600 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.83 % Allowed : 18.33 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.17), residues: 2346 helix: 0.29 (0.14), residues: 1300 sheet: -1.52 (0.41), residues: 156 loop : -0.88 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 904 TYR 0.041 0.001 TYR D 73 PHE 0.047 0.001 PHE B 834 TRP 0.012 0.001 TRP A 130 HIS 0.009 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (19700) covalent geometry : angle 0.67669 / 0.34 (26505) hydrogen bonds : bond 0.04154 / 2.78 ( 975) hydrogen bonds : angle 4.88786 / 3.42 ( 2829) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 288 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7052 (mm-40) REVERT: A 90 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7559 (mtp) REVERT: A 169 ARG cc_start: 0.7994 (pmt170) cc_final: 0.7668 (ptt-90) REVERT: A 470 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6825 (p90) REVERT: A 653 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8160 (tm-30) REVERT: A 903 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6405 (mm-30) REVERT: B 90 MET cc_start: 0.6101 (mmp) cc_final: 0.4202 (mmt) REVERT: B 306 ASN cc_start: 0.8690 (t0) cc_final: 0.8240 (t0) REVERT: B 312 PHE cc_start: 0.5201 (OUTLIER) cc_final: 0.3692 (m-10) REVERT: B 333 ASP cc_start: 0.7966 (m-30) cc_final: 0.7313 (m-30) REVERT: B 397 LYS cc_start: 0.8215 (pptt) cc_final: 0.7922 (mmtm) REVERT: B 524 ILE cc_start: 0.7524 (mm) cc_final: 0.7285 (mm) REVERT: B 690 MET cc_start: 0.7319 (tpt) cc_final: 0.7089 (tpp) REVERT: B 834 PHE cc_start: 0.5663 (t80) cc_final: 0.5403 (t80) REVERT: B 871 LYS cc_start: 0.7859 (pptt) cc_final: 0.7523 (pttt) REVERT: C 170 GLU cc_start: 0.7751 (pp20) cc_final: 0.7506 (pp20) REVERT: D 51 ILE cc_start: 0.7071 (mm) cc_final: 0.6672 (pt) REVERT: D 75 GLN cc_start: 0.6542 (mp10) cc_final: 0.6261 (mp10) REVERT: D 108 MET cc_start: 0.6686 (tpt) cc_final: 0.6191 (tpt) REVERT: D 123 LYS cc_start: 0.8016 (pptt) cc_final: 0.7583 (pttm) REVERT: E 107 ASP cc_start: 0.2054 (p0) cc_final: 0.1721 (p0) REVERT: E 122 MET cc_start: 0.6560 (ppp) cc_final: 0.5766 (ppp) REVERT: F 27 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7513 (mp10) REVERT: F 69 MET cc_start: 0.1572 (ptt) cc_final: 0.1249 (ttm) REVERT: F 91 LYS cc_start: 0.3979 (pptt) cc_final: 0.3602 (ptmm) outliers start: 38 outliers final: 25 residues processed: 311 average time/residue: 0.1304 time to fit residues: 61.8521 Evaluate side-chains 296 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 778 ASP Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 157 HIS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 215 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 99 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 HIS ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.219165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.165511 restraints weight = 28892.642| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 3.69 r_work: 0.3875 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19700 Z= 0.137 Angle : 0.672 12.392 26505 Z= 0.333 Chirality : 0.043 0.182 2866 Planarity : 0.004 0.066 3430 Dihedral : 5.333 50.932 2600 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.97 % Allowed : 18.47 % Favored : 79.56 % 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: -0.40 (0.17), residues: 2346 helix: 0.38 (0.15), residues: 1294 sheet: -1.44 (0.41), residues: 155 loop : -0.88 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 798 TYR 0.018 0.001 TYR D 185 PHE 0.036 0.001 PHE B 834 TRP 0.011 0.001 TRP A 130 HIS 0.010 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (19700) covalent geometry : angle 0.67203 / 0.33 (26505) hydrogen bonds : bond 0.04044 / 2.72 ( 975) hydrogen bonds : angle 4.84244 / 3.39 ( 2829) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.7040 (mm-40) REVERT: A 90 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7503 (mtp) REVERT: A 169 ARG cc_start: 0.8050 (pmt170) cc_final: 0.7760 (ptt-90) REVERT: A 470 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.6809 (p90) REVERT: A 502 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7274 (mppt) REVERT: A 653 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8235 (tm-30) REVERT: A 903 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6539 (tp30) REVERT: B 90 MET cc_start: 0.6296 (mmp) cc_final: 0.4332 (mmt) REVERT: B 277 LEU cc_start: 0.7147 (mm) cc_final: 0.6754 (mt) REVERT: B 306 ASN cc_start: 0.8708 (t0) cc_final: 0.8229 (t0) REVERT: B 312 PHE cc_start: 0.5192 (OUTLIER) cc_final: 0.3587 (m-10) REVERT: B 333 ASP cc_start: 0.7967 (m-30) cc_final: 0.7323 (m-30) REVERT: B 359 PHE cc_start: 0.6770 (m-80) cc_final: 0.6369 (m-80) REVERT: B 397 LYS cc_start: 0.8160 (pptt) cc_final: 0.7799 (mmtm) REVERT: B 503 LYS cc_start: 0.8219 (mptt) cc_final: 0.7840 (mptt) REVERT: B 524 ILE cc_start: 0.7523 (mm) cc_final: 0.7266 (mm) REVERT: B 834 PHE cc_start: 0.5827 (t80) cc_final: 0.5461 (t80) REVERT: B 871 LYS cc_start: 0.8024 (pptt) cc_final: 0.7730 (pttt) REVERT: B 920 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7775 (pttm) REVERT: C 170 GLU cc_start: 0.7734 (pp20) cc_final: 0.7515 (pp20) REVERT: D 108 MET cc_start: 0.6580 (tpt) cc_final: 0.6249 (tpt) REVERT: D 123 LYS cc_start: 0.8048 (pptt) cc_final: 0.7615 (pttm) REVERT: E 122 MET cc_start: 0.6543 (ppp) cc_final: 0.5817 (ppp) REVERT: F 27 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7532 (mp10) outliers start: 41 outliers final: 20 residues processed: 316 average time/residue: 0.1327 time to fit residues: 63.3415 Evaluate side-chains 297 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain E residue 157 HIS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 172 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 97 optimal weight: 30.0000 chunk 67 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 200 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS D 191 HIS ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.217913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.170806 restraints weight = 28760.678| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 2.20 r_work: 0.3916 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19700 Z= 0.157 Angle : 0.689 11.760 26505 Z= 0.342 Chirality : 0.044 0.185 2866 Planarity : 0.004 0.064 3430 Dihedral : 5.351 50.866 2600 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.68 % Allowed : 19.10 % Favored : 79.22 % 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: -0.38 (0.17), residues: 2346 helix: 0.42 (0.15), residues: 1292 sheet: -1.49 (0.41), residues: 155 loop : -0.87 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 904 TYR 0.018 0.001 TYR D 185 PHE 0.030 0.002 PHE B 834 TRP 0.021 0.002 TRP B 827 HIS 0.010 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (19700) covalent geometry : angle 0.68948 / 0.34 (26505) hydrogen bonds : bond 0.04146 / 2.79 ( 975) hydrogen bonds : angle 4.86291 / 3.40 ( 2829) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 279 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.8053 (mmm) cc_final: 0.6900 (mmt) REVERT: A 44 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6941 (mm-40) REVERT: A 90 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7611 (mtp) REVERT: A 169 ARG cc_start: 0.7949 (pmt170) cc_final: 0.7612 (ptt-90) REVERT: A 470 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6886 (p90) REVERT: A 653 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8185 (tm-30) REVERT: B 90 MET cc_start: 0.6173 (mmp) cc_final: 0.4259 (mmt) REVERT: B 277 LEU cc_start: 0.7155 (mm) cc_final: 0.6769 (mt) REVERT: B 306 ASN cc_start: 0.8552 (t0) cc_final: 0.8121 (t0) REVERT: B 312 PHE cc_start: 0.5237 (OUTLIER) cc_final: 0.3636 (m-10) REVERT: B 333 ASP cc_start: 0.7667 (m-30) cc_final: 0.7091 (m-30) REVERT: B 359 PHE cc_start: 0.6635 (m-80) cc_final: 0.6290 (m-80) REVERT: B 397 LYS cc_start: 0.8066 (pptt) cc_final: 0.7812 (mmtm) REVERT: B 503 LYS cc_start: 0.8187 (mptt) cc_final: 0.7805 (mptt) REVERT: B 659 MET cc_start: 0.7404 (mmm) cc_final: 0.7200 (mmm) REVERT: B 804 LEU cc_start: 0.8184 (tp) cc_final: 0.7960 (tp) REVERT: B 834 PHE cc_start: 0.5494 (t80) cc_final: 0.5205 (t80) REVERT: B 871 LYS cc_start: 0.7910 (pptt) cc_final: 0.7651 (pttt) REVERT: D 123 LYS cc_start: 0.7965 (pptt) cc_final: 0.7580 (pttm) REVERT: E 107 ASP cc_start: 0.2124 (p0) cc_final: 0.1799 (p0) REVERT: E 122 MET cc_start: 0.6261 (ppp) cc_final: 0.5225 (ppp) REVERT: F 27 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: F 69 MET cc_start: 0.1704 (ttp) cc_final: 0.1385 (ttt) REVERT: F 91 LYS cc_start: 0.3866 (pptt) cc_final: 0.3585 (ptmm) REVERT: F 138 MET cc_start: 0.5925 (pmm) cc_final: 0.5488 (pmm) outliers start: 35 outliers final: 24 residues processed: 301 average time/residue: 0.1225 time to fit residues: 55.9471 Evaluate side-chains 303 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 274 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 157 HIS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 132 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 43 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 686 ASN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN D 191 HIS ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.219445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.172424 restraints weight = 28977.431| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.16 r_work: 0.3897 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19700 Z= 0.130 Angle : 0.673 11.591 26505 Z= 0.334 Chirality : 0.043 0.166 2866 Planarity : 0.004 0.059 3430 Dihedral : 5.242 53.053 2600 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.49 % Allowed : 19.24 % Favored : 79.27 % 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: -0.30 (0.17), residues: 2346 helix: 0.49 (0.15), residues: 1291 sheet: -1.45 (0.41), residues: 156 loop : -0.85 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 904 TYR 0.018 0.001 TYR D 185 PHE 0.027 0.001 PHE B 834 TRP 0.024 0.002 TRP B 827 HIS 0.011 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (19700) covalent geometry : angle 0.67306 / 0.33 (26505) hydrogen bonds : bond 0.03963 / 2.68 ( 975) hydrogen bonds : angle 4.76173 / 3.33 ( 2829) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 291 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6962 (mm-40) REVERT: A 169 ARG cc_start: 0.7991 (pmt170) cc_final: 0.7656 (ptt-90) REVERT: A 386 TYR cc_start: 0.7215 (t80) cc_final: 0.6843 (t80) REVERT: A 470 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6812 (p90) REVERT: A 653 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8302 (tm-30) REVERT: A 780 ARG cc_start: 0.7047 (tpp80) cc_final: 0.6845 (tpp80) REVERT: B 90 MET cc_start: 0.6227 (mmp) cc_final: 0.4341 (mmt) REVERT: B 107 ASP cc_start: 0.7736 (m-30) cc_final: 0.7484 (m-30) REVERT: B 174 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7562 (mt) REVERT: B 277 LEU cc_start: 0.7141 (mm) cc_final: 0.6741 (mt) REVERT: B 306 ASN cc_start: 0.8643 (t0) cc_final: 0.8191 (t0) REVERT: B 312 PHE cc_start: 0.5074 (OUTLIER) cc_final: 0.3598 (m-10) REVERT: B 333 ASP cc_start: 0.7720 (m-30) cc_final: 0.7135 (m-30) REVERT: B 397 LYS cc_start: 0.8104 (pptt) cc_final: 0.7784 (mmtm) REVERT: B 493 MET cc_start: 0.6346 (mtt) cc_final: 0.5587 (mtt) REVERT: B 503 LYS cc_start: 0.8181 (mptt) cc_final: 0.7892 (mptt) REVERT: B 869 ARG cc_start: 0.7027 (ptm-80) cc_final: 0.6534 (ttp80) REVERT: B 871 LYS cc_start: 0.7934 (pptt) cc_final: 0.7657 (pttt) REVERT: B 904 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7397 (mtt90) REVERT: B 920 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7677 (pttt) REVERT: C 108 MET cc_start: 0.5718 (tpp) cc_final: 0.5346 (tpp) REVERT: D 123 LYS cc_start: 0.8030 (pptt) cc_final: 0.7633 (pttm) REVERT: E 122 MET cc_start: 0.6204 (ppp) cc_final: 0.5218 (ppp) REVERT: F 27 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: F 69 MET cc_start: 0.1221 (ttp) cc_final: 0.1011 (ttt) REVERT: F 91 LYS cc_start: 0.4063 (pptt) cc_final: 0.3742 (ptmm) outliers start: 31 outliers final: 23 residues processed: 311 average time/residue: 0.1367 time to fit residues: 63.6504 Evaluate side-chains 301 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 902 GLU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 157 HIS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 72 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 156 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS D 191 HIS ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.218323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.171826 restraints weight = 28818.078| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 2.10 r_work: 0.3912 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19700 Z= 0.154 Angle : 0.699 11.258 26505 Z= 0.349 Chirality : 0.044 0.289 2866 Planarity : 0.004 0.058 3430 Dihedral : 5.281 52.590 2600 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.59 % Allowed : 19.62 % Favored : 78.79 % 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: -0.34 (0.17), residues: 2346 helix: 0.45 (0.15), residues: 1284 sheet: -1.52 (0.40), residues: 161 loop : -0.83 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 904 TYR 0.018 0.001 TYR D 185 PHE 0.025 0.001 PHE B 275 TRP 0.024 0.002 TRP B 827 HIS 0.011 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (19700) covalent geometry : angle 0.69872 / 0.35 (26505) hydrogen bonds : bond 0.04088 / 2.75 ( 975) hydrogen bonds : angle 4.83585 / 3.37 ( 2829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6282.87 seconds wall clock time: 107 minutes 49.49 seconds (6469.49 seconds total)