Starting phenix.real_space_refine on Sat Aug 8 07:56:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfx_37499/08_2026/8wfx_37499.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfx_37499/08_2026/8wfx_37499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wfx_37499/08_2026/8wfx_37499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfx_37499/08_2026/8wfx_37499.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wfx_37499/08_2026/8wfx_37499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfx_37499/08_2026/8wfx_37499.map" } resolution = 3.73 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 50 5.49 5 S 66 5.16 5 C 16987 2.51 5 N 4781 2.21 5 O 5292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 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: 27176 Number of models: 1 Model: "" Number of chains: 15 Chain: "M" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2231 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 16, 'TRANS': 279} Chain: "O" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1061 Classifications: {'RNA': 50} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 15, 'rna3p_pur': 14, 'rna3p_pyr': 10} Link IDs: {'rna2p': 25, 'rna3p': 24} Chain: "A" Number of atoms: 6382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6382 Classifications: {'peptide': 801} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 775} Chain: "N" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2092 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 246} Chain breaks: 9 Chain: "E" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 966 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1006 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 976 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 968 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "F" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 976 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "I" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain: "J" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1747 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 Chain: "K" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1761 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "L" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1787 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain breaks: 2 Chain: "H" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1719 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 210} Chain breaks: 2 Time building chain proxies: 5.81, per 1000 atoms: 0.21 Number of scatterers: 27176 At special positions: 0 Unit cell: (99.84, 114.4, 253.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 50 15.00 O 5292 8.00 N 4781 7.00 C 16987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6136 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 38 sheets defined 37.7% alpha, 9.5% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'M' and resid 31 through 37 Processing helix chain 'M' and resid 47 through 52 Processing helix chain 'M' and resid 86 through 94 removed outlier: 3.705A pdb=" N ALA M 92 " --> pdb=" O GLN M 88 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS M 93 " --> pdb=" O LYS M 89 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS M 94 " --> pdb=" O LYS M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 107 Processing helix chain 'M' and resid 119 through 123 Processing helix chain 'M' and resid 164 through 170 Processing helix chain 'M' and resid 170 through 176 Processing helix chain 'M' and resid 223 through 227 Processing helix chain 'A' and resid 9 through 13 removed outlier: 4.194A pdb=" N LEU A 13 " --> pdb=" O ILE A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 43 removed outlier: 3.789A pdb=" N ALA A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS A 41 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.909A pdb=" N LEU A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 88 removed outlier: 3.539A pdb=" N ASN A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 removed outlier: 4.379A pdb=" N VAL A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 138 removed outlier: 4.024A pdb=" N ARG A 138 " --> pdb=" O VAL A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.867A pdb=" N VAL A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 removed outlier: 3.682A pdb=" N LEU A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLU A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.924A pdb=" N LEU A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.853A pdb=" N ILE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN A 242 " --> pdb=" O TRP A 238 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA A 243 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.913A pdb=" N ASP A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.548A pdb=" N ILE A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 313 removed outlier: 3.610A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 305 " --> pdb=" O MET A 301 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.562A pdb=" N GLU A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN A 357 " --> pdb=" O TRP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.571A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.133A pdb=" N ARG A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.313A pdb=" N GLN A 429 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.648A pdb=" N TYR A 543 " --> pdb=" O PHE A 540 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 544 " --> pdb=" O GLY A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.529A pdb=" N ALA A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 587 through 596 removed outlier: 4.420A pdb=" N SER A 593 " --> pdb=" O SER A 589 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 606 Processing helix chain 'A' and resid 639 through 649 removed outlier: 3.745A pdb=" N GLU A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 647 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 653 Processing helix chain 'A' and resid 675 through 679 removed outlier: 3.797A pdb=" N VAL A 678 " --> pdb=" O PRO A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 690 removed outlier: 3.547A pdb=" N LEU A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 714 removed outlier: 3.849A pdb=" N LEU A 714 " --> pdb=" O TRP A 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 710 through 714' Processing helix chain 'A' and resid 721 through 729 removed outlier: 3.734A pdb=" N ALA A 726 " --> pdb=" O TYR A 722 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASP A 727 " --> pdb=" O ARG A 723 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR A 728 " --> pdb=" O HIS A 724 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE A 729 " --> pdb=" O ILE A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 747 removed outlier: 3.645A pdb=" N ILE A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 743 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU A 745 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.804A pdb=" N LEU A 783 " --> pdb=" O PHE A 779 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A 788 " --> pdb=" O HIS A 784 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP A 789 " --> pdb=" O GLN A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 807 removed outlier: 3.773A pdb=" N GLN A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 803 " --> pdb=" O ALA A 799 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 48 removed outlier: 4.245A pdb=" N TYR N 47 " --> pdb=" O GLU N 44 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA N 48 " --> pdb=" O ARG N 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 44 through 48' Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.571A pdb=" N GLU N 81 " --> pdb=" O TRP N 78 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN N 82 " --> pdb=" O ILE N 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 82' Processing helix chain 'N' and resid 138 through 147 removed outlier: 3.987A pdb=" N LEU N 146 " --> pdb=" O VAL N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 removed outlier: 4.396A pdb=" N LEU N 154 " --> pdb=" O TYR N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 169 through 174 removed outlier: 4.335A pdb=" N ARG N 174 " --> pdb=" O THR N 170 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 178 Processing helix chain 'N' and resid 215 through 219 removed outlier: 4.083A pdb=" N ASP N 218 " --> pdb=" O ARG N 215 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU N 219 " --> pdb=" O THR N 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 215 through 219' Processing helix chain 'N' and resid 269 through 273 removed outlier: 4.162A pdb=" N LEU N 272 " --> pdb=" O GLU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 339 removed outlier: 4.035A pdb=" N HIS N 338 " --> pdb=" O LYS N 335 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL N 339 " --> pdb=" O ILE N 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 335 through 339' Processing helix chain 'E' and resid 9 through 16 removed outlier: 4.000A pdb=" N GLU E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 16 " --> pdb=" O ALA E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 48 removed outlier: 3.699A pdb=" N LEU E 39 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN E 42 " --> pdb=" O SER E 38 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU E 46 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.686A pdb=" N ARG E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP E 61 " --> pdb=" O PRO E 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 56 through 61' Processing helix chain 'E' and resid 61 through 75 removed outlier: 3.882A pdb=" N VAL E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 88 removed outlier: 3.760A pdb=" N ARG E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL E 82 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU E 85 " --> pdb=" O ARG E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 94 removed outlier: 3.940A pdb=" N GLU E 92 " --> pdb=" O GLY E 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA E 94 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 100 through 115 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 9 through 14 removed outlier: 4.693A pdb=" N ALA C 12 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 13 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 40 through 48 removed outlier: 4.191A pdb=" N GLU C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.526A pdb=" N ASP C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 77 removed outlier: 3.502A pdb=" N ALA C 74 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 75 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 77 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 85 removed outlier: 3.663A pdb=" N VAL C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 85' Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.873A pdb=" N GLU C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 120 removed outlier: 3.633A pdb=" N MET C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 14 removed outlier: 3.968A pdb=" N VAL B 9 " --> pdb=" O ASP B 6 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN B 11 " --> pdb=" O TYR B 8 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA B 12 " --> pdb=" O VAL B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 32 Processing helix chain 'B' and resid 33 through 50 removed outlier: 3.948A pdb=" N LEU B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 48 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 50 " --> pdb=" O GLU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.695A pdb=" N ASP B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 77 removed outlier: 3.626A pdb=" N TYR B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 75 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 removed outlier: 3.654A pdb=" N PHE B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 removed outlier: 3.648A pdb=" N ALA B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 120 removed outlier: 3.754A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 19 removed outlier: 3.734A pdb=" N VAL D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 removed outlier: 3.524A pdb=" N LEU D 33 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG D 34 " --> pdb=" O THR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 48 removed outlier: 3.792A pdb=" N GLU D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 76 removed outlier: 3.546A pdb=" N ARG D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG D 69 " --> pdb=" O TYR D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 88 removed outlier: 3.534A pdb=" N VAL D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 95 Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.593A pdb=" N HIS D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 111 " --> pdb=" O CYS D 107 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 16 removed outlier: 3.820A pdb=" N GLN F 11 " --> pdb=" O ASP F 7 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 34 removed outlier: 3.539A pdb=" N GLN F 32 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG F 34 " --> pdb=" O THR F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 48 removed outlier: 4.034A pdb=" N LEU F 43 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU F 46 " --> pdb=" O GLN F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.625A pdb=" N ASP F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 77 removed outlier: 4.328A pdb=" N LEU F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 removed outlier: 3.597A pdb=" N GLU F 85 " --> pdb=" O ARG F 81 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA F 87 " --> pdb=" O PHE F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 94 through 98 removed outlier: 4.016A pdb=" N GLY F 97 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 120 removed outlier: 3.836A pdb=" N LEU F 103 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 112 " --> pdb=" O HIS F 108 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL F 114 " --> pdb=" O MET F 110 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS F 117 " --> pdb=" O LEU F 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 67 removed outlier: 4.044A pdb=" N LYS I 57 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU I 61 " --> pdb=" O LYS I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 removed outlier: 4.238A pdb=" N LEU I 87 " --> pdb=" O GLN I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 115 Processing helix chain 'I' and resid 175 through 193 removed outlier: 4.654A pdb=" N ILE I 184 " --> pdb=" O ASP I 180 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA I 185 " --> pdb=" O PHE I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 234 removed outlier: 4.359A pdb=" N MET I 228 " --> pdb=" O SER I 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 59 removed outlier: 3.576A pdb=" N LEU J 54 " --> pdb=" O PRO J 50 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 67 removed outlier: 4.345A pdb=" N GLN J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 89 removed outlier: 5.360A pdb=" N LEU J 87 " --> pdb=" O GLN J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 115 removed outlier: 3.798A pdb=" N LEU J 112 " --> pdb=" O ASN J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 193 removed outlier: 3.877A pdb=" N ASP J 180 " --> pdb=" O GLU J 176 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU J 190 " --> pdb=" O ARG J 186 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU J 191 " --> pdb=" O GLY J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 228 removed outlier: 4.105A pdb=" N GLU J 227 " --> pdb=" O ARG J 223 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET J 228 " --> pdb=" O SER J 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 223 through 228' Processing helix chain 'J' and resid 228 through 236 removed outlier: 4.096A pdb=" N GLU J 232 " --> pdb=" O MET J 228 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU J 233 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA J 234 " --> pdb=" O ASN J 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 61 Processing helix chain 'K' and resid 81 through 86 Processing helix chain 'K' and resid 108 through 115 removed outlier: 3.516A pdb=" N LEU K 112 " --> pdb=" O ASN K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 194 removed outlier: 3.509A pdb=" N GLU K 179 " --> pdb=" O ASP K 175 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP K 180 " --> pdb=" O GLU K 176 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE K 181 " --> pdb=" O ILE K 177 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN K 182 " --> pdb=" O ILE K 178 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU K 190 " --> pdb=" O ARG K 186 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU K 191 " --> pdb=" O GLY K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 234 removed outlier: 4.066A pdb=" N LEU K 226 " --> pdb=" O ASP K 222 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU K 227 " --> pdb=" O ARG K 223 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET K 228 " --> pdb=" O SER K 224 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU K 232 " --> pdb=" O MET K 228 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU K 233 " --> pdb=" O LEU K 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 62 removed outlier: 3.737A pdb=" N VAL L 58 " --> pdb=" O LEU L 54 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR L 60 " --> pdb=" O GLY L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 80 removed outlier: 3.590A pdb=" N ASP L 80 " --> pdb=" O PRO L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 88 Processing helix chain 'L' and resid 108 through 113 removed outlier: 4.042A pdb=" N GLU L 113 " --> pdb=" O LYS L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 190 removed outlier: 4.628A pdb=" N LEU L 190 " --> pdb=" O ARG L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 193 No H-bonds generated for 'chain 'L' and resid 191 through 193' Processing helix chain 'L' and resid 224 through 235 removed outlier: 3.549A pdb=" N ASN L 230 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS L 231 " --> pdb=" O GLU L 227 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU L 232 " --> pdb=" O MET L 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 63 removed outlier: 4.685A pdb=" N LYS G 57 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 86 Processing helix chain 'G' and resid 109 through 115 Processing helix chain 'G' and resid 176 through 193 removed outlier: 3.965A pdb=" N ASP G 180 " --> pdb=" O GLU G 176 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 190 " --> pdb=" O ARG G 186 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU G 191 " --> pdb=" O GLY G 187 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU G 192 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 193 " --> pdb=" O LYS G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 235 removed outlier: 3.635A pdb=" N LEU G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS G 231 " --> pdb=" O GLU G 227 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU G 232 " --> pdb=" O MET G 228 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU G 233 " --> pdb=" O LEU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 66 removed outlier: 3.840A pdb=" N LEU H 54 " --> pdb=" O PRO H 50 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS H 55 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER H 63 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG H 64 " --> pdb=" O THR H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 89 removed outlier: 4.425A pdb=" N LEU H 87 " --> pdb=" O GLN H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 114 Processing helix chain 'H' and resid 173 through 193 removed outlier: 3.696A pdb=" N ILE H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA H 185 " --> pdb=" O PHE H 181 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU H 190 " --> pdb=" O ARG H 186 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU H 192 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 235 removed outlier: 4.226A pdb=" N GLU H 227 " --> pdb=" O ARG H 223 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU H 232 " --> pdb=" O MET H 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.581A pdb=" N LEU M 5 " --> pdb=" O SER M 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'M' and resid 70 through 71 removed outlier: 3.935A pdb=" N ASP M 70 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU M 64 " --> pdb=" O TRP M 158 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY M 156 " --> pdb=" O TYR M 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 73 through 74 Processing sheet with id=AA5, first strand: chain 'M' and resid 128 through 132 removed outlier: 3.742A pdb=" N VAL M 146 " --> pdb=" O SER M 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 213 through 214 removed outlier: 4.580A pdb=" N MET M 213 " --> pdb=" O LEU M 295 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 242 through 243 Processing sheet with id=AA8, first strand: chain 'M' and resid 276 through 277 Processing sheet with id=AA9, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.509A pdb=" N LEU A 132 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 331 through 333 Processing sheet with id=AB2, first strand: chain 'A' and resid 272 through 273 removed outlier: 3.689A pdb=" N ASP A 272 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 365 " --> pdb=" O ASP A 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 485 through 487 removed outlier: 3.714A pdb=" N ALA A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 474 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 624 through 629 removed outlier: 6.913A pdb=" N PHE A 634 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER A 628 " --> pdb=" O ASP A 632 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ASP A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP A 559 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 664 " --> pdb=" O ASP A 559 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 698 through 699 Processing sheet with id=AB6, first strand: chain 'N' and resid 247 through 256 removed outlier: 3.596A pdb=" N THR N 247 " --> pdb=" O CYS N 14 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS N 14 " --> pdb=" O THR N 247 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU N 251 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU N 10 " --> pdb=" O LEU N 251 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU N 9 " --> pdb=" O ARG N 372 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG N 372 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 99 through 100 removed outlier: 3.582A pdb=" N VAL I 155 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE I 152 " --> pdb=" O GLY I 12 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL I 218 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU I 9 " --> pdb=" O ALA I 216 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA I 216 " --> pdb=" O GLU I 9 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR I 11 " --> pdb=" O ALA I 214 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA I 214 " --> pdb=" O THR I 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 15 through 16 Processing sheet with id=AB9, first strand: chain 'I' and resid 121 through 123 Processing sheet with id=AC1, first strand: chain 'J' and resid 6 through 10 removed outlier: 3.729A pdb=" N LYS J 7 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL J 218 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU J 9 " --> pdb=" O ALA J 216 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA J 216 " --> pdb=" O GLU J 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'J' and resid 149 through 151 Processing sheet with id=AC3, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AC4, first strand: chain 'J' and resid 121 through 122 Processing sheet with id=AC5, first strand: chain 'J' and resid 125 through 129 removed outlier: 3.643A pdb=" N GLU J 126 " --> pdb=" O ARG J 139 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG J 139 " --> pdb=" O GLU J 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 100 through 101 removed outlier: 3.798A pdb=" N VAL K 100 " --> pdb=" O VAL K 155 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 100 through 101 removed outlier: 3.798A pdb=" N VAL K 100 " --> pdb=" O VAL K 155 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU K 9 " --> pdb=" O ALA K 214 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ALA K 214 " --> pdb=" O GLU K 9 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR K 11 " --> pdb=" O LEU K 212 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU K 212 " --> pdb=" O THR K 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 40 through 41 removed outlier: 3.845A pdb=" N TRP K 46 " --> pdb=" O ASP K 41 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 124 through 129 removed outlier: 3.547A pdb=" N LYS K 124 " --> pdb=" O MET K 141 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 99 through 100 removed outlier: 3.507A pdb=" N VAL L 100 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE L 152 " --> pdb=" O GLY L 12 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR L 15 " --> pdb=" O LYS L 208 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 99 through 100 removed outlier: 3.507A pdb=" N VAL L 100 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE L 152 " --> pdb=" O GLY L 12 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS L 7 " --> pdb=" O ALA L 217 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 121 through 123 Processing sheet with id=AD4, first strand: chain 'L' and resid 126 through 128 Processing sheet with id=AD5, first strand: chain 'G' and resid 100 through 101 Processing sheet with id=AD6, first strand: chain 'G' and resid 48 through 49 Processing sheet with id=AD7, first strand: chain 'G' and resid 123 through 126 Processing sheet with id=AD8, first strand: chain 'H' and resid 149 through 155 removed outlier: 3.803A pdb=" N PHE H 152 " --> pdb=" O GLY H 12 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY H 12 " --> pdb=" O PHE H 152 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 149 through 155 removed outlier: 3.803A pdb=" N PHE H 152 " --> pdb=" O GLY H 12 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY H 12 " --> pdb=" O PHE H 152 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 48 through 49 removed outlier: 3.597A pdb=" N THR H 104 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 125 through 126 removed outlier: 3.855A pdb=" N ARG H 139 " --> pdb=" O GLU H 126 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7121 1.33 - 1.45: 5320 1.45 - 1.57: 15107 1.57 - 1.69: 100 1.69 - 1.81: 112 Bond restraints: 27760 Sorted by residual: bond pdb=" C SER N 258 " pdb=" N PRO N 259 " ideal model delta sigma weight residual 1.331 1.380 -0.048 7.90e-03 1.60e+04 3.73e+01 bond pdb=" N1 C O 25 " pdb=" C6 C O 25 " ideal model delta sigma weight residual 1.367 1.343 0.024 6.00e-03 2.78e+04 1.54e+01 bond pdb=" N9 A O 7 " pdb=" C4 A O 7 " ideal model delta sigma weight residual 1.374 1.353 0.021 6.00e-03 2.78e+04 1.17e+01 bond pdb=" CB TYR G 195 " pdb=" CG TYR G 195 " ideal model delta sigma weight residual 1.512 1.442 0.070 2.20e-02 2.07e+03 1.01e+01 bond pdb=" N9 A O 11 " pdb=" C4 A O 11 " ideal model delta sigma weight residual 1.374 1.356 0.018 6.00e-03 2.78e+04 9.19e+00 ... (remaining 27755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 37214 3.62 - 7.23: 436 7.23 - 10.85: 42 10.85 - 14.47: 9 14.47 - 18.09: 1 Bond angle restraints: 37702 Sorted by residual: angle pdb=" N1 C O 16 " pdb=" C2 C O 16 " pdb=" O2 C O 16 " ideal model delta sigma weight residual 118.90 123.16 -4.26 6.00e-01 2.78e+00 5.05e+01 angle pdb=" N GLN M 47 " pdb=" CA GLN M 47 " pdb=" C GLN M 47 " ideal model delta sigma weight residual 114.04 106.63 7.41 1.24e+00 6.50e-01 3.57e+01 angle pdb=" N GLY F 24 " pdb=" CA GLY F 24 " pdb=" C GLY F 24 " ideal model delta sigma weight residual 113.79 106.94 6.85 1.17e+00 7.31e-01 3.43e+01 angle pdb=" C5 G O 4 " pdb=" C4 G O 4 " pdb=" N3 G O 4 " ideal model delta sigma weight residual 128.60 125.79 2.81 5.00e-01 4.00e+00 3.17e+01 angle pdb=" N GLY L 205 " pdb=" CA GLY L 205 " pdb=" C GLY L 205 " ideal model delta sigma weight residual 113.48 121.54 -8.06 1.46e+00 4.69e-01 3.05e+01 ... (remaining 37697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 16336 35.81 - 71.62: 513 71.62 - 107.43: 42 107.43 - 143.24: 1 143.24 - 179.06: 3 Dihedral angle restraints: 16895 sinusoidal: 7355 harmonic: 9540 Sorted by residual: dihedral pdb=" O4' U O 39 " pdb=" C1' U O 39 " pdb=" N1 U O 39 " pdb=" C2 U O 39 " ideal model delta sinusoidal sigma weight residual 232.00 52.94 179.06 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C O 2 " pdb=" C1' C O 2 " pdb=" N1 C O 2 " pdb=" C2 C O 2 " ideal model delta sinusoidal sigma weight residual 232.00 53.45 178.55 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C O 49 " pdb=" C1' C O 49 " pdb=" N1 C O 49 " pdb=" C2 C O 49 " ideal model delta sinusoidal sigma weight residual -128.00 49.26 -177.26 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2933 0.056 - 0.112: 1057 0.112 - 0.168: 217 0.168 - 0.224: 39 0.224 - 0.280: 11 Chirality restraints: 4257 Sorted by residual: chirality pdb=" CB ILE N 304 " pdb=" CA ILE N 304 " pdb=" CG1 ILE N 304 " pdb=" CG2 ILE N 304 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB VAL A 9 " pdb=" CA VAL A 9 " pdb=" CG1 VAL A 9 " pdb=" CG2 VAL A 9 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL A 531 " pdb=" CA VAL A 531 " pdb=" CG1 VAL A 531 " pdb=" CG2 VAL A 531 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 4254 not shown) Planarity restraints: 4717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 121 " 0.066 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO C 122 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO C 122 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 122 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 204 " 0.019 2.00e-02 2.50e+03 2.68e-02 1.43e+01 pdb=" CG TYR H 204 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR H 204 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR H 204 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR H 204 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR H 204 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR H 204 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 204 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 145 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO H 146 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO H 146 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO H 146 " -0.047 5.00e-02 4.00e+02 ... (remaining 4714 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4750 2.76 - 3.29: 25906 3.29 - 3.83: 46412 3.83 - 4.36: 54843 4.36 - 4.90: 89792 Nonbonded interactions: 221703 Sorted by model distance: nonbonded pdb=" OD1 ASP M 17 " pdb=" OG SER M 22 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR G 104 " pdb=" O ALA G 151 " model vdw 2.225 3.040 nonbonded pdb=" O2' C O 25 " pdb=" O ASN I 127 " model vdw 2.236 3.040 nonbonded pdb=" OG SER I 173 " pdb=" OD1 ASP I 175 " model vdw 2.242 3.040 nonbonded pdb=" OE2 GLU G 126 " pdb=" OH TYR G 204 " model vdw 2.243 3.040 ... (remaining 221698 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 'B' and resid 8 through 125) selection = (chain 'C' and resid 8 through 125) selection = (chain 'D' and resid 8 through 125) selection = (chain 'E' and resid 8 through 125) selection = (chain 'F' and resid 8 through 125) } ncs_group { reference = (chain 'G' and (resid 6 through 161 or resid 170 through 236)) selection = (chain 'H' and (resid 6 through 25 or resid 34 through 161 or resid 170 through \ 216 or resid 222 through 236)) selection = (chain 'I' and (resid 6 through 25 or resid 34 through 161 or resid 170 through \ 216 or resid 222 through 236)) selection = (chain 'J' and (resid 6 through 25 or resid 34 through 216 or resid 222 through \ 236)) selection = (chain 'K' and (resid 6 through 25 or resid 34 through 161 or resid 170 through \ 216 or resid 222 through 236)) selection = (chain 'L' and (resid 6 through 25 or resid 34 through 161 or resid 170 through \ 216 or resid 222 through 236)) } 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 group one per residue 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: 5.730 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.690 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 0.007 0.087 27760 Z= 0.376 Angle : 1.085 18.087 37702 Z= 0.638 Chirality : 0.060 0.280 4257 Planarity : 0.008 0.100 4717 Dihedral : 17.476 179.056 10759 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.30 % Favored : 89.60 % Rotamer: Outliers : 0.79 % Allowed : 12.62 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -5.44 (0.11), residues: 3261 helix: -4.32 (0.08), residues: 1007 sheet: -3.24 (0.22), residues: 368 loop : -3.39 (0.12), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG J 139 TYR 0.062 0.003 TYR H 204 PHE 0.038 0.003 PHE H 181 TRP 0.021 0.002 TRP A 238 HIS 0.008 0.002 HIS J 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.38 (27760) covalent geometry : angle 1.08549 / 0.64 (37702) hydrogen bonds : bond 0.30803 / 20.64 ( 677) hydrogen bonds : angle 11.29828 / 7.65 ( 1917) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 349 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 148 TYR cc_start: 0.7882 (m-80) cc_final: 0.7595 (m-80) REVERT: M 189 PHE cc_start: 0.8292 (m-80) cc_final: 0.8055 (m-10) REVERT: A 159 MET cc_start: 0.5989 (ptm) cc_final: 0.5434 (ptp) REVERT: A 703 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8106 (t0) REVERT: N 37 MET cc_start: -0.2883 (mtt) cc_final: -0.3516 (mtm) REVERT: N 164 ARG cc_start: 0.6094 (mtm-85) cc_final: 0.5414 (tpt170) REVERT: N 375 GLU cc_start: 0.5481 (tt0) cc_final: 0.5078 (mp0) REVERT: C 8 TYR cc_start: 0.6021 (OUTLIER) cc_final: 0.5485 (m-10) REVERT: C 53 GLN cc_start: 0.8160 (tt0) cc_final: 0.7658 (tm-30) REVERT: D 113 LEU cc_start: 0.7914 (mt) cc_final: 0.7666 (mt) REVERT: F 67 ARG cc_start: 0.8832 (ttt180) cc_final: 0.8261 (ttm170) REVERT: F 76 ARG cc_start: 0.7284 (tpt90) cc_final: 0.6454 (mmm160) REVERT: F 100 ARG cc_start: 0.8053 (ptm160) cc_final: 0.7645 (ptm160) REVERT: K 73 PHE cc_start: 0.6372 (t80) cc_final: 0.5715 (t80) REVERT: L 226 LEU cc_start: 0.8518 (pt) cc_final: 0.8295 (pp) REVERT: L 227 GLU cc_start: 0.8684 (pt0) cc_final: 0.8299 (pm20) REVERT: G 231 HIS cc_start: 0.8420 (m90) cc_final: 0.7779 (m-70) outliers start: 22 outliers final: 5 residues processed: 371 average time/residue: 0.2102 time to fit residues: 117.2527 Evaluate side-chains 265 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 258 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain C residue 8 TYR Chi-restraints excluded: chain H residue 143 ARG Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 120 GLN M 272 GLN ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN A 239 HIS A 262 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN A 381 ASN A 562 ASN A 580 ASN A 654 HIS A 801 HIS A 807 ASN N 3 GLN N 82 ASN N 90 ASN N 125 HIS E 64 GLN C 5 GLN C 53 GLN B 32 GLN B 64 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 231 HIS K 83 GLN K 167 GLN K 230 ASN L 206 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.130278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.106680 restraints weight = 94782.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.106994 restraints weight = 67837.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.107687 restraints weight = 40238.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.108040 restraints weight = 34941.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.108015 restraints weight = 31511.049| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27760 Z= 0.201 Angle : 0.744 12.244 37702 Z= 0.396 Chirality : 0.046 0.318 4257 Planarity : 0.007 0.076 4717 Dihedral : 14.328 179.209 4434 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.24 % Favored : 89.73 % Rotamer: Outliers : 2.45 % Allowed : 17.91 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.86 (0.12), residues: 3261 helix: -3.50 (0.11), residues: 1085 sheet: -3.08 (0.25), residues: 335 loop : -3.16 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 131 TYR 0.025 0.002 TYR H 204 PHE 0.021 0.002 PHE A 729 TRP 0.014 0.001 TRP A 238 HIS 0.006 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (27760) covalent geometry : angle 0.74386 / 0.40 (37702) hydrogen bonds : bond 0.06352 / 4.17 ( 677) hydrogen bonds : angle 7.56216 / 5.10 ( 1917) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 284 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.7376 (ptt) cc_final: 0.7053 (ptt) REVERT: M 189 PHE cc_start: 0.8204 (m-80) cc_final: 0.7896 (m-80) REVERT: M 272 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6681 (pp30) REVERT: N 37 MET cc_start: -0.3394 (mtt) cc_final: -0.3823 (mtm) REVERT: N 136 TYR cc_start: 0.8256 (p90) cc_final: 0.7672 (p90) REVERT: N 164 ARG cc_start: 0.6084 (mtm-85) cc_final: 0.5436 (tpt170) REVERT: N 375 GLU cc_start: 0.5075 (tt0) cc_final: 0.4728 (mp0) REVERT: E 10 LYS cc_start: 0.8886 (tppt) cc_final: 0.8649 (tppt) REVERT: E 60 ARG cc_start: 0.7252 (ttm110) cc_final: 0.6725 (mtt-85) REVERT: E 62 LYS cc_start: 0.9042 (tttm) cc_final: 0.8830 (mtpp) REVERT: E 124 GLU cc_start: 0.7413 (tp30) cc_final: 0.7212 (tp30) REVERT: C 8 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.5204 (m-10) REVERT: C 53 GLN cc_start: 0.7705 (tt0) cc_final: 0.7412 (tm-30) REVERT: D 113 LEU cc_start: 0.7892 (mt) cc_final: 0.7614 (mt) REVERT: F 76 ARG cc_start: 0.6954 (tpt90) cc_final: 0.6125 (mmm160) REVERT: K 73 PHE cc_start: 0.6369 (t80) cc_final: 0.5746 (t80) REVERT: L 149 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7553 (mm-30) REVERT: G 231 HIS cc_start: 0.8492 (m90) cc_final: 0.8262 (m-70) outliers start: 68 outliers final: 43 residues processed: 328 average time/residue: 0.1849 time to fit residues: 94.7694 Evaluate side-chains 304 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 272 GLN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain C residue 8 TYR Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 12 optimal weight: 7.9990 chunk 258 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 283 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 194 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN A 507 GLN ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN F 108 HIS I 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.127118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.104593 restraints weight = 96468.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.104663 restraints weight = 55238.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.105378 restraints weight = 41605.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.105343 restraints weight = 33255.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.105929 restraints weight = 31138.024| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 27760 Z= 0.323 Angle : 0.839 12.990 37702 Z= 0.438 Chirality : 0.050 0.325 4257 Planarity : 0.007 0.081 4717 Dihedral : 14.384 178.818 4425 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.37 % Favored : 86.60 % Rotamer: Outliers : 4.17 % Allowed : 21.54 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.61 (0.12), residues: 3261 helix: -3.08 (0.12), residues: 1089 sheet: -3.18 (0.24), residues: 358 loop : -3.09 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 143 TYR 0.028 0.002 TYR H 204 PHE 0.028 0.003 PHE B 44 TRP 0.026 0.002 TRP N 78 HIS 0.007 0.001 HIS M 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.32 (27760) covalent geometry : angle 0.83881 / 0.44 (37702) hydrogen bonds : bond 0.05518 / 3.65 ( 677) hydrogen bonds : angle 7.14964 / 4.83 ( 1917) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 261 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 71 TYR cc_start: 0.5725 (t80) cc_final: 0.5517 (t80) REVERT: M 189 PHE cc_start: 0.8332 (m-80) cc_final: 0.7743 (m-80) REVERT: N 37 MET cc_start: -0.2813 (mtt) cc_final: -0.3355 (mtm) REVERT: N 60 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: N 136 TYR cc_start: 0.8201 (p90) cc_final: 0.7575 (p90) REVERT: N 164 ARG cc_start: 0.6102 (mtm-85) cc_final: 0.5398 (tpt170) REVERT: N 375 GLU cc_start: 0.5177 (tt0) cc_final: 0.4867 (mp0) REVERT: E 60 ARG cc_start: 0.7391 (ttm110) cc_final: 0.7004 (mtp85) REVERT: E 100 ARG cc_start: 0.8482 (mtp-110) cc_final: 0.8153 (mtm110) REVERT: C 8 TYR cc_start: 0.6224 (OUTLIER) cc_final: 0.5184 (m-10) REVERT: C 53 GLN cc_start: 0.7853 (tt0) cc_final: 0.7539 (tm-30) REVERT: B 42 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 90 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7312 (mm) REVERT: D 54 ASN cc_start: 0.8359 (p0) cc_final: 0.8023 (p0) REVERT: D 113 LEU cc_start: 0.8075 (mt) cc_final: 0.7811 (mt) REVERT: F 48 GLN cc_start: 0.7258 (mt0) cc_final: 0.7042 (mt0) REVERT: F 76 ARG cc_start: 0.6742 (tpt90) cc_final: 0.5955 (mmm160) REVERT: I 71 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: J 66 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: K 73 PHE cc_start: 0.6373 (t80) cc_final: 0.5762 (t80) REVERT: L 149 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7600 (mm-30) REVERT: G 75 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7430 (ttp80) REVERT: G 141 MET cc_start: 0.7405 (mpp) cc_final: 0.7135 (mpp) REVERT: G 231 HIS cc_start: 0.8474 (m90) cc_final: 0.8135 (m-70) outliers start: 116 outliers final: 81 residues processed: 357 average time/residue: 0.1722 time to fit residues: 97.7825 Evaluate side-chains 329 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 242 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 287 TYR Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain N residue 364 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain C residue 8 TYR Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 137 ASN Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 66 TYR Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 237 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 131 optimal weight: 30.0000 chunk 325 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 304 optimal weight: 0.1980 chunk 35 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN N 204 GLN B 42 GLN I 230 ASN ** J 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.132222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.109959 restraints weight = 94639.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.109776 restraints weight = 62336.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.110636 restraints weight = 40597.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.110735 restraints weight = 35774.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.110929 restraints weight = 30153.443| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27760 Z= 0.127 Angle : 0.653 9.493 37702 Z= 0.342 Chirality : 0.043 0.287 4257 Planarity : 0.005 0.066 4717 Dihedral : 13.937 178.944 4425 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.51 % Favored : 92.46 % Rotamer: Outliers : 3.42 % Allowed : 23.77 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.13), residues: 3261 helix: -2.70 (0.13), residues: 1093 sheet: -3.04 (0.25), residues: 333 loop : -2.80 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 98 TYR 0.044 0.002 TYR H 204 PHE 0.021 0.002 PHE D 83 TRP 0.013 0.001 TRP A 238 HIS 0.003 0.001 HIS N 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (27760) covalent geometry : angle 0.65329 / 0.34 (37702) hydrogen bonds : bond 0.04012 / 2.64 ( 677) hydrogen bonds : angle 6.50925 / 4.41 ( 1917) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 291 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.6798 (ptt) cc_final: 0.6283 (ppp) REVERT: M 71 TYR cc_start: 0.5507 (t80) cc_final: 0.5255 (t80) REVERT: M 295 LEU cc_start: 0.8721 (tp) cc_final: 0.8452 (tp) REVERT: A 301 MET cc_start: 0.7695 (mmm) cc_final: 0.7420 (mmm) REVERT: A 703 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8009 (t70) REVERT: A 759 TRP cc_start: 0.8233 (t-100) cc_final: 0.8013 (t-100) REVERT: N 37 MET cc_start: -0.2919 (mtt) cc_final: -0.3460 (mtm) REVERT: N 60 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: N 136 TYR cc_start: 0.8135 (p90) cc_final: 0.7515 (p90) REVERT: N 164 ARG cc_start: 0.6154 (mtm-85) cc_final: 0.5444 (tpt170) REVERT: N 375 GLU cc_start: 0.5282 (tt0) cc_final: 0.4924 (mp0) REVERT: E 60 ARG cc_start: 0.7281 (ttm110) cc_final: 0.6771 (mtt-85) REVERT: E 95 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7231 (tm-30) REVERT: E 100 ARG cc_start: 0.8401 (mtp-110) cc_final: 0.8091 (mtm110) REVERT: C 8 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.5174 (m-10) REVERT: C 53 GLN cc_start: 0.7825 (tt0) cc_final: 0.7477 (tm-30) REVERT: D 54 ASN cc_start: 0.8455 (p0) cc_final: 0.8138 (p0) REVERT: D 113 LEU cc_start: 0.8085 (mt) cc_final: 0.7867 (mt) REVERT: F 48 GLN cc_start: 0.7055 (mt0) cc_final: 0.6821 (mt0) REVERT: F 76 ARG cc_start: 0.6811 (tpt90) cc_final: 0.6497 (tpt-90) REVERT: F 100 ARG cc_start: 0.7165 (ptm160) cc_final: 0.6780 (ptm160) REVERT: I 71 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: J 122 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7323 (pp20) REVERT: K 73 PHE cc_start: 0.6337 (t80) cc_final: 0.5750 (t80) REVERT: K 108 ASN cc_start: 0.7746 (p0) cc_final: 0.7535 (p0) REVERT: L 149 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7489 (mm-30) REVERT: G 96 THR cc_start: 0.4366 (OUTLIER) cc_final: 0.4089 (p) REVERT: G 231 HIS cc_start: 0.8449 (m90) cc_final: 0.8121 (m-70) REVERT: H 64 ARG cc_start: 0.7384 (mtm180) cc_final: 0.6974 (mtm180) REVERT: H 99 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7385 (mm) outliers start: 95 outliers final: 45 residues processed: 369 average time/residue: 0.1806 time to fit residues: 105.5031 Evaluate side-chains 311 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 364 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain C residue 8 TYR Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 143 ARG Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 11 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 201 optimal weight: 0.6980 chunk 258 optimal weight: 7.9990 chunk 256 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 300 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 HIS A 784 HIS N 125 HIS ** J 65 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 = 0.4366 r_free = 0.4366 target = 0.131950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.108942 restraints weight = 94425.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.109954 restraints weight = 62740.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.110107 restraints weight = 38865.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.110453 restraints weight = 36052.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.111035 restraints weight = 29704.621| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27760 Z= 0.130 Angle : 0.629 8.731 37702 Z= 0.328 Chirality : 0.043 0.281 4257 Planarity : 0.005 0.062 4717 Dihedral : 13.766 179.613 4425 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.59 % Favored : 91.38 % Rotamer: Outliers : 3.96 % Allowed : 24.09 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.13), residues: 3261 helix: -2.46 (0.13), residues: 1105 sheet: -2.95 (0.25), residues: 333 loop : -2.64 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 13 TYR 0.027 0.001 TYR H 204 PHE 0.027 0.001 PHE F 106 TRP 0.009 0.001 TRP A 639 HIS 0.006 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (27760) covalent geometry : angle 0.62902 / 0.33 (37702) hydrogen bonds : bond 0.03771 / 2.48 ( 677) hydrogen bonds : angle 6.20264 / 4.19 ( 1917) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 264 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 MET cc_start: 0.6830 (ptt) cc_final: 0.6284 (ppp) REVERT: A 133 TYR cc_start: 0.7514 (m-80) cc_final: 0.6718 (m-80) REVERT: A 270 THR cc_start: 0.6749 (OUTLIER) cc_final: 0.6401 (p) REVERT: A 301 MET cc_start: 0.7713 (mmm) cc_final: 0.7348 (mmm) REVERT: A 703 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7997 (t70) REVERT: N 37 MET cc_start: -0.2752 (mtt) cc_final: -0.3364 (mtm) REVERT: N 60 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: N 136 TYR cc_start: 0.8103 (p90) cc_final: 0.7517 (p90) REVERT: N 164 ARG cc_start: 0.6179 (mtm-85) cc_final: 0.5447 (tpt170) REVERT: N 375 GLU cc_start: 0.5305 (tt0) cc_final: 0.4844 (mp0) REVERT: E 34 ARG cc_start: 0.8912 (mmm160) cc_final: 0.8688 (mmm160) REVERT: E 60 ARG cc_start: 0.7214 (ttm110) cc_final: 0.6571 (mtt-85) REVERT: E 100 ARG cc_start: 0.8438 (mtp-110) cc_final: 0.8224 (mtm110) REVERT: C 8 TYR cc_start: 0.5990 (OUTLIER) cc_final: 0.5076 (m-10) REVERT: C 53 GLN cc_start: 0.7834 (tt0) cc_final: 0.7495 (tm-30) REVERT: D 13 GLU cc_start: 0.7981 (tp30) cc_final: 0.7258 (mm-30) REVERT: D 54 ASN cc_start: 0.8442 (p0) cc_final: 0.8175 (p0) REVERT: D 55 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6604 (mm) REVERT: D 113 LEU cc_start: 0.8077 (mt) cc_final: 0.7865 (mt) REVERT: F 48 GLN cc_start: 0.7123 (mt0) cc_final: 0.6904 (mt0) REVERT: F 100 ARG cc_start: 0.7125 (ptm160) cc_final: 0.6585 (ptm160) REVERT: I 71 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: K 73 PHE cc_start: 0.6247 (t80) cc_final: 0.5658 (t80) REVERT: K 141 MET cc_start: 0.7609 (mmm) cc_final: 0.7312 (mmm) REVERT: K 164 ASP cc_start: 0.5138 (OUTLIER) cc_final: 0.4226 (p0) REVERT: L 149 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7599 (mm-30) REVERT: G 96 THR cc_start: 0.4544 (OUTLIER) cc_final: 0.4292 (p) REVERT: G 99 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8230 (mt) REVERT: G 231 HIS cc_start: 0.8470 (m90) cc_final: 0.8122 (m-70) REVERT: H 22 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6513 (mt) REVERT: H 64 ARG cc_start: 0.7415 (mtm180) cc_final: 0.7056 (mtm180) outliers start: 110 outliers final: 69 residues processed: 350 average time/residue: 0.1714 time to fit residues: 96.1383 Evaluate side-chains 331 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 252 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 MET Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 64 MET Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 247 THR Chi-restraints excluded: chain N residue 364 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain C residue 8 TYR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 123 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN I 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.126673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.103894 restraints weight = 97423.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.103978 restraints weight = 68103.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.104231 restraints weight = 46757.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.104489 restraints weight = 39714.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.105056 restraints weight = 35283.844| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 27760 Z= 0.373 Angle : 0.869 13.498 37702 Z= 0.448 Chirality : 0.052 0.322 4257 Planarity : 0.007 0.085 4717 Dihedral : 14.188 177.463 4425 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.55 % Favored : 86.42 % Rotamer: Outliers : 5.21 % Allowed : 24.74 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.13), residues: 3261 helix: -2.58 (0.13), residues: 1087 sheet: -3.20 (0.24), residues: 350 loop : -2.84 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 139 TYR 0.029 0.003 TYR J 195 PHE 0.039 0.003 PHE M 189 TRP 0.014 0.002 TRP A 530 HIS 0.011 0.002 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00823 / 0.37 (27760) covalent geometry : angle 0.86878 / 0.45 (37702) hydrogen bonds : bond 0.04823 / 3.20 ( 677) hydrogen bonds : angle 6.66847 / 4.52 ( 1917) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 248 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 71 TYR cc_start: 0.5694 (t80) cc_final: 0.5452 (t80) REVERT: A 57 GLU cc_start: 0.3820 (OUTLIER) cc_final: 0.3530 (tt0) REVERT: A 270 THR cc_start: 0.6663 (OUTLIER) cc_final: 0.6321 (p) REVERT: A 301 MET cc_start: 0.7739 (mmm) cc_final: 0.7480 (mmm) REVERT: N 60 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: N 136 TYR cc_start: 0.8190 (p90) cc_final: 0.7533 (p90) REVERT: N 164 ARG cc_start: 0.6129 (mtm-85) cc_final: 0.5508 (tpt170) REVERT: N 375 GLU cc_start: 0.5242 (tt0) cc_final: 0.4883 (mp0) REVERT: E 34 ARG cc_start: 0.8857 (mmm160) cc_final: 0.8614 (mmm160) REVERT: E 60 ARG cc_start: 0.7390 (ttm110) cc_final: 0.6812 (mtt-85) REVERT: C 8 TYR cc_start: 0.6206 (OUTLIER) cc_final: 0.4996 (m-10) REVERT: C 53 GLN cc_start: 0.7842 (tt0) cc_final: 0.7499 (tm-30) REVERT: B 85 GLU cc_start: 0.7763 (pm20) cc_final: 0.7507 (pm20) REVERT: B 90 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7150 (mm) REVERT: D 13 GLU cc_start: 0.7975 (tp30) cc_final: 0.7516 (tp30) REVERT: D 54 ASN cc_start: 0.8424 (p0) cc_final: 0.8130 (p0) REVERT: D 55 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6598 (mm) REVERT: D 113 LEU cc_start: 0.8201 (mt) cc_final: 0.7963 (mt) REVERT: I 71 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: J 99 LEU cc_start: 0.9050 (tp) cc_final: 0.8655 (tp) REVERT: J 122 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7367 (pp20) REVERT: K 73 PHE cc_start: 0.6376 (t80) cc_final: 0.5841 (t80) REVERT: K 164 ASP cc_start: 0.5299 (OUTLIER) cc_final: 0.4275 (p0) REVERT: L 149 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7585 (mm-30) REVERT: G 96 THR cc_start: 0.4702 (OUTLIER) cc_final: 0.4440 (p) REVERT: H 22 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7591 (mt) REVERT: H 112 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7548 (mp) outliers start: 145 outliers final: 101 residues processed: 370 average time/residue: 0.1564 time to fit residues: 93.3470 Evaluate side-chains 353 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 240 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 247 THR Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain N residue 364 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain C residue 8 TYR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 174 SER Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 131 ARG Chi-restraints excluded: chain L residue 182 ASN Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 93 optimal weight: 8.9990 chunk 220 optimal weight: 0.7980 chunk 318 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 303 optimal weight: 4.9990 chunk 267 optimal weight: 0.3980 chunk 162 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 212 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 ASN ** J 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.131384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.108499 restraints weight = 94402.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.109102 restraints weight = 74416.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.109749 restraints weight = 40777.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.109876 restraints weight = 35630.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.111113 restraints weight = 30035.172| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27760 Z= 0.128 Angle : 0.655 11.272 37702 Z= 0.338 Chirality : 0.043 0.287 4257 Planarity : 0.005 0.086 4717 Dihedral : 13.830 178.211 4425 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.07 % Favored : 91.90 % Rotamer: Outliers : 3.16 % Allowed : 27.26 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.13), residues: 3261 helix: -2.25 (0.13), residues: 1102 sheet: -2.96 (0.25), residues: 327 loop : -2.66 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 75 TYR 0.045 0.002 TYR H 204 PHE 0.041 0.002 PHE M 189 TRP 0.012 0.001 TRP A 639 HIS 0.012 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (27760) covalent geometry : angle 0.65520 / 0.34 (37702) hydrogen bonds : bond 0.03726 / 2.47 ( 677) hydrogen bonds : angle 6.19508 / 4.19 ( 1917) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 269 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 71 TYR cc_start: 0.5379 (t80) cc_final: 0.5149 (t80) REVERT: A 133 TYR cc_start: 0.7492 (m-80) cc_final: 0.6684 (m-80) REVERT: A 301 MET cc_start: 0.7674 (mmm) cc_final: 0.7462 (mmm) REVERT: A 703 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7975 (t70) REVERT: N 60 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: N 136 TYR cc_start: 0.8164 (p90) cc_final: 0.7528 (p90) REVERT: N 164 ARG cc_start: 0.6122 (mtm-85) cc_final: 0.5492 (tpt170) REVERT: N 375 GLU cc_start: 0.5496 (tt0) cc_final: 0.4996 (mp0) REVERT: E 34 ARG cc_start: 0.8788 (mmm160) cc_final: 0.8587 (mmm160) REVERT: E 60 ARG cc_start: 0.7367 (ttm110) cc_final: 0.6887 (mtt-85) REVERT: E 100 ARG cc_start: 0.8528 (mtp-110) cc_final: 0.8186 (mtm110) REVERT: C 8 TYR cc_start: 0.6070 (OUTLIER) cc_final: 0.5018 (m-10) REVERT: C 53 GLN cc_start: 0.7883 (tt0) cc_final: 0.7496 (tm-30) REVERT: B 90 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7175 (mm) REVERT: D 13 GLU cc_start: 0.7954 (tp30) cc_final: 0.7577 (tp30) REVERT: D 54 ASN cc_start: 0.8519 (p0) cc_final: 0.8216 (p0) REVERT: D 113 LEU cc_start: 0.8127 (mt) cc_final: 0.7894 (mt) REVERT: F 25 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6987 (p0) REVERT: F 100 ARG cc_start: 0.7180 (ptm160) cc_final: 0.6794 (ptm160) REVERT: I 71 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: J 122 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7485 (pp20) REVERT: K 73 PHE cc_start: 0.6272 (t80) cc_final: 0.5744 (t80) REVERT: K 141 MET cc_start: 0.7678 (mmm) cc_final: 0.7382 (mmm) REVERT: K 164 ASP cc_start: 0.5084 (OUTLIER) cc_final: 0.4243 (p0) REVERT: L 149 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7591 (mm-30) REVERT: G 96 THR cc_start: 0.4522 (OUTLIER) cc_final: 0.4247 (p) REVERT: H 22 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6794 (mt) REVERT: H 64 ARG cc_start: 0.7486 (mtm180) cc_final: 0.7120 (mtm180) REVERT: H 112 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7455 (mp) outliers start: 88 outliers final: 61 residues processed: 344 average time/residue: 0.1644 time to fit residues: 91.0031 Evaluate side-chains 322 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 250 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 MET Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain C residue 8 TYR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 299 optimal weight: 1.9990 chunk 128 optimal weight: 50.0000 chunk 70 optimal weight: 0.4980 chunk 194 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 312 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN I 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.130285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.107242 restraints weight = 95498.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.108381 restraints weight = 64051.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.108475 restraints weight = 39128.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.108914 restraints weight = 36642.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.109125 restraints weight = 30020.486| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27760 Z= 0.166 Angle : 0.661 10.806 37702 Z= 0.340 Chirality : 0.044 0.287 4257 Planarity : 0.005 0.065 4717 Dihedral : 13.773 178.487 4425 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.54 % Favored : 90.43 % Rotamer: Outliers : 3.78 % Allowed : 26.65 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.14), residues: 3261 helix: -2.15 (0.14), residues: 1108 sheet: -2.90 (0.26), residues: 332 loop : -2.61 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 75 TYR 0.041 0.002 TYR H 204 PHE 0.022 0.002 PHE D 83 TRP 0.009 0.001 TRP A 238 HIS 0.005 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (27760) covalent geometry : angle 0.66107 / 0.34 (37702) hydrogen bonds : bond 0.03768 / 2.48 ( 677) hydrogen bonds : angle 6.08914 / 4.12 ( 1917) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 257 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 71 TYR cc_start: 0.5456 (t80) cc_final: 0.5152 (t80) REVERT: M 148 TYR cc_start: 0.7973 (m-80) cc_final: 0.7554 (m-80) REVERT: M 250 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5457 (mp0) REVERT: A 57 GLU cc_start: 0.3781 (OUTLIER) cc_final: 0.3560 (tt0) REVERT: A 133 TYR cc_start: 0.7469 (m-80) cc_final: 0.6676 (m-80) REVERT: A 270 THR cc_start: 0.6773 (OUTLIER) cc_final: 0.6432 (p) REVERT: A 703 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7965 (t70) REVERT: N 60 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: N 136 TYR cc_start: 0.8037 (p90) cc_final: 0.7445 (p90) REVERT: N 164 ARG cc_start: 0.6185 (mtm-85) cc_final: 0.5542 (tpt170) REVERT: N 375 GLU cc_start: 0.5498 (tt0) cc_final: 0.5012 (mp0) REVERT: E 60 ARG cc_start: 0.7340 (ttm110) cc_final: 0.6863 (mtt-85) REVERT: E 100 ARG cc_start: 0.8501 (mtp-110) cc_final: 0.8008 (mtm110) REVERT: C 8 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.5109 (m-10) REVERT: C 53 GLN cc_start: 0.7965 (tt0) cc_final: 0.7546 (tm-30) REVERT: B 90 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7141 (mm) REVERT: D 13 GLU cc_start: 0.7915 (tp30) cc_final: 0.7575 (tp30) REVERT: D 54 ASN cc_start: 0.8474 (p0) cc_final: 0.8165 (p0) REVERT: F 100 ARG cc_start: 0.7013 (ptm160) cc_final: 0.6633 (ptm160) REVERT: I 71 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: J 122 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7520 (pp20) REVERT: K 73 PHE cc_start: 0.6307 (t80) cc_final: 0.5743 (t80) REVERT: K 141 MET cc_start: 0.7809 (mmm) cc_final: 0.7516 (mmm) REVERT: K 164 ASP cc_start: 0.5156 (OUTLIER) cc_final: 0.4284 (p0) REVERT: L 149 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7544 (mm-30) REVERT: G 96 THR cc_start: 0.4698 (OUTLIER) cc_final: 0.4420 (p) REVERT: G 228 MET cc_start: 0.8771 (pmm) cc_final: 0.8440 (pmm) REVERT: H 22 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6815 (mt) REVERT: H 53 SER cc_start: 0.7305 (t) cc_final: 0.7092 (p) REVERT: H 64 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7229 (mtm180) REVERT: H 112 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7381 (mp) outliers start: 105 outliers final: 81 residues processed: 341 average time/residue: 0.1672 time to fit residues: 92.5147 Evaluate side-chains 342 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 248 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 43 MET Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 250 GLU Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain C residue 8 TYR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 140 GLN Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 217 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 206 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 329 optimal weight: 0.2980 chunk 325 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 170 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN J 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.132789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.111403 restraints weight = 94206.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.111225 restraints weight = 57390.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.111892 restraints weight = 40548.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.112100 restraints weight = 33725.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.112427 restraints weight = 28160.666| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 27760 Z= 0.118 Angle : 0.633 11.341 37702 Z= 0.323 Chirality : 0.042 0.263 4257 Planarity : 0.005 0.065 4717 Dihedral : 13.555 179.754 4425 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.82 % Favored : 92.15 % Rotamer: Outliers : 3.20 % Allowed : 27.29 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.14), residues: 3261 helix: -1.96 (0.14), residues: 1120 sheet: -2.66 (0.27), residues: 327 loop : -2.48 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 34 TYR 0.034 0.001 TYR H 204 PHE 0.026 0.001 PHE M 189 TRP 0.018 0.001 TRP N 78 HIS 0.005 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (27760) covalent geometry : angle 0.63271 / 0.32 (37702) hydrogen bonds : bond 0.03448 / 2.27 ( 677) hydrogen bonds : angle 5.85601 / 3.96 ( 1917) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 266 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 250 GLU cc_start: 0.5528 (OUTLIER) cc_final: 0.5210 (mp0) REVERT: M 295 LEU cc_start: 0.8546 (tp) cc_final: 0.8331 (tp) REVERT: A 133 TYR cc_start: 0.7382 (m-80) cc_final: 0.6605 (m-80) REVERT: A 377 MET cc_start: 0.3856 (mmt) cc_final: 0.3562 (mmt) REVERT: A 703 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7838 (t70) REVERT: N 60 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: N 136 TYR cc_start: 0.7877 (p90) cc_final: 0.7395 (p90) REVERT: N 164 ARG cc_start: 0.6178 (mtm-85) cc_final: 0.5519 (tpt170) REVERT: N 375 GLU cc_start: 0.5601 (tt0) cc_final: 0.5000 (mp0) REVERT: E 60 ARG cc_start: 0.7222 (ttm110) cc_final: 0.6769 (mtt-85) REVERT: E 100 ARG cc_start: 0.8461 (mtp-110) cc_final: 0.7928 (mtm110) REVERT: C 8 TYR cc_start: 0.5800 (OUTLIER) cc_final: 0.4988 (m-10) REVERT: C 53 GLN cc_start: 0.7965 (tt0) cc_final: 0.7561 (tm-30) REVERT: B 90 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7170 (mm) REVERT: D 13 GLU cc_start: 0.7862 (tp30) cc_final: 0.7591 (tp30) REVERT: F 67 ARG cc_start: 0.8679 (ttm-80) cc_final: 0.8073 (ttt180) REVERT: F 100 ARG cc_start: 0.6948 (ptm160) cc_final: 0.6629 (ptm160) REVERT: I 71 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: J 122 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7506 (pp20) REVERT: J 141 MET cc_start: 0.7444 (ppp) cc_final: 0.6795 (ppp) REVERT: K 73 PHE cc_start: 0.6186 (t80) cc_final: 0.5669 (t80) REVERT: K 141 MET cc_start: 0.7583 (mmm) cc_final: 0.7297 (mmm) REVERT: K 164 ASP cc_start: 0.5059 (OUTLIER) cc_final: 0.4277 (p0) REVERT: L 149 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7603 (mm-30) REVERT: L 227 GLU cc_start: 0.7941 (pt0) cc_final: 0.7547 (pt0) REVERT: G 96 THR cc_start: 0.4527 (OUTLIER) cc_final: 0.4212 (p) REVERT: H 112 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7326 (mp) outliers start: 89 outliers final: 67 residues processed: 336 average time/residue: 0.1680 time to fit residues: 89.9449 Evaluate side-chains 335 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 258 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 MET Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 250 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 64 MET Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain C residue 8 TYR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 263 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 329 optimal weight: 6.9990 chunk 312 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 chunk 234 optimal weight: 8.9990 chunk 206 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.132072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.109314 restraints weight = 95032.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.110227 restraints weight = 61705.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.110369 restraints weight = 39163.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.110642 restraints weight = 35123.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.110901 restraints weight = 29288.397| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27760 Z= 0.136 Angle : 0.634 11.496 37702 Z= 0.324 Chirality : 0.043 0.459 4257 Planarity : 0.005 0.067 4717 Dihedral : 13.485 179.446 4423 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.34 % Favored : 91.63 % Rotamer: Outliers : 2.98 % Allowed : 27.69 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.14), residues: 3261 helix: -1.90 (0.14), residues: 1130 sheet: -2.60 (0.27), residues: 331 loop : -2.44 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 37 TYR 0.034 0.002 TYR H 204 PHE 0.021 0.001 PHE D 83 TRP 0.012 0.001 TRP A 238 HIS 0.007 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (27760) covalent geometry : angle 0.63398 / 0.32 (37702) hydrogen bonds : bond 0.03443 / 2.26 ( 677) hydrogen bonds : angle 5.77250 / 3.91 ( 1917) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 262 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 250 GLU cc_start: 0.5749 (OUTLIER) cc_final: 0.5467 (mp0) REVERT: M 295 LEU cc_start: 0.8603 (tp) cc_final: 0.8392 (tp) REVERT: A 133 TYR cc_start: 0.7424 (m-80) cc_final: 0.6655 (m-80) REVERT: A 703 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7899 (t70) REVERT: N 60 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: N 136 TYR cc_start: 0.7974 (p90) cc_final: 0.7434 (p90) REVERT: N 164 ARG cc_start: 0.6200 (mtm-85) cc_final: 0.5533 (tpt170) REVERT: N 375 GLU cc_start: 0.5484 (tt0) cc_final: 0.4932 (mp0) REVERT: E 100 ARG cc_start: 0.8511 (mtp-110) cc_final: 0.7998 (mtm110) REVERT: C 8 TYR cc_start: 0.5827 (OUTLIER) cc_final: 0.5120 (m-10) REVERT: C 53 GLN cc_start: 0.8003 (tt0) cc_final: 0.7577 (tm-30) REVERT: B 85 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8390 (pm20) REVERT: B 90 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7209 (mm) REVERT: D 13 GLU cc_start: 0.7986 (tp30) cc_final: 0.7677 (tp30) REVERT: D 55 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6842 (mm) REVERT: F 100 ARG cc_start: 0.6902 (ptm160) cc_final: 0.6577 (ptm160) REVERT: I 71 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: J 122 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7523 (pp20) REVERT: J 141 MET cc_start: 0.7448 (ppp) cc_final: 0.6785 (ppp) REVERT: K 73 PHE cc_start: 0.6181 (t80) cc_final: 0.5652 (t80) REVERT: K 141 MET cc_start: 0.7682 (mmm) cc_final: 0.7381 (mmm) REVERT: K 164 ASP cc_start: 0.5115 (OUTLIER) cc_final: 0.4308 (p0) REVERT: L 149 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7626 (mm-30) REVERT: L 227 GLU cc_start: 0.7898 (pt0) cc_final: 0.7496 (pt0) REVERT: G 96 THR cc_start: 0.4556 (OUTLIER) cc_final: 0.4251 (p) REVERT: H 22 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6428 (mt) REVERT: H 112 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7328 (mp) outliers start: 83 outliers final: 67 residues processed: 328 average time/residue: 0.1588 time to fit residues: 83.7886 Evaluate side-chains 338 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 259 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 MET Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 250 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain C residue 8 TYR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 140 GLN Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 266 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 219 optimal weight: 0.0060 chunk 56 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 290 optimal weight: 0.3980 chunk 235 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 overall best weight: 3.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.130582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.107668 restraints weight = 95265.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.108362 restraints weight = 63169.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.108672 restraints weight = 39701.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.108977 restraints weight = 35747.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.109099 restraints weight = 29964.037| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27760 Z= 0.186 Angle : 0.672 11.242 37702 Z= 0.343 Chirality : 0.045 0.386 4257 Planarity : 0.005 0.067 4717 Dihedral : 13.568 179.215 4423 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.63 % Favored : 90.34 % Rotamer: Outliers : 3.45 % Allowed : 27.44 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.14), residues: 3261 helix: -1.91 (0.14), residues: 1135 sheet: -2.61 (0.26), residues: 349 loop : -2.44 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 156 TYR 0.036 0.002 TYR H 204 PHE 0.023 0.002 PHE M 189 TRP 0.011 0.001 TRP A 238 HIS 0.006 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (27760) covalent geometry : angle 0.67158 / 0.34 (37702) hydrogen bonds : bond 0.03572 / 2.35 ( 677) hydrogen bonds : angle 5.82288 / 3.94 ( 1917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4570.13 seconds wall clock time: 79 minutes 55.89 seconds (4795.89 seconds total)