Starting phenix.real_space_refine on Thu Mar 5 07:27:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nue_0519/03_2026/6nue_0519.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nue_0519/03_2026/6nue_0519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nue_0519/03_2026/6nue_0519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nue_0519/03_2026/6nue_0519.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nue_0519/03_2026/6nue_0519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nue_0519/03_2026/6nue_0519.map" } resolution = 3.3 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= 0.135 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 42 5.49 5 S 39 5.16 5 C 12690 2.51 5 N 3403 2.21 5 O 4001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20175 Number of models: 1 Model: "" Number of chains: 12 Chain: "J" Number of atoms: 5928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5928 Classifications: {'peptide': 733} Link IDs: {'PTRANS': 8, 'TRANS': 724} Chain breaks: 1 Chain: "A" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "B" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "C" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "E" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "H" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 832 Classifications: {'RNA': 40} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 14, 'rna3p_pur': 8, 'rna3p_pyr': 11} Link IDs: {'rna2p': 21, 'rna3p': 18} Chain: "I" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2352 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 283} Chain: "M" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "N" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "O" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "P" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.54, per 1000 atoms: 0.23 Number of scatterers: 20175 At special positions: 0 Unit cell: (94.34, 120.84, 208.82, 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 39 16.00 P 42 15.00 O 4001 8.00 N 3403 7.00 C 12690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 961.8 milliseconds 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 22 sheets defined 36.4% alpha, 9.6% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'J' and resid 5 through 14 removed outlier: 4.182A pdb=" N PHE J 9 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR J 10 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU J 13 " --> pdb=" O PHE J 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU J 14 " --> pdb=" O TYR J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 25 removed outlier: 4.256A pdb=" N ILE J 21 " --> pdb=" O ILE J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 43 removed outlier: 3.522A pdb=" N GLY J 35 " --> pdb=" O HIS J 31 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE J 42 " --> pdb=" O TRP J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 54 removed outlier: 3.638A pdb=" N GLN J 51 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE J 52 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.517A pdb=" N ALA J 76 " --> pdb=" O ILE J 72 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN J 78 " --> pdb=" O TYR J 74 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 114 removed outlier: 3.620A pdb=" N VAL J 113 " --> pdb=" O ILE J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 159 removed outlier: 3.616A pdb=" N ILE J 156 " --> pdb=" O ILE J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 178 removed outlier: 3.526A pdb=" N GLU J 178 " --> pdb=" O LEU J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 184 removed outlier: 4.357A pdb=" N PHE J 183 " --> pdb=" O ILE J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 219 removed outlier: 3.721A pdb=" N ARG J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA J 207 " --> pdb=" O ARG J 203 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE J 208 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA J 209 " --> pdb=" O THR J 205 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS J 219 " --> pdb=" O TYR J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 265 removed outlier: 4.150A pdb=" N ALA J 263 " --> pdb=" O THR J 260 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA J 264 " --> pdb=" O SER J 261 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS J 265 " --> pdb=" O GLY J 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 260 through 265' Processing helix chain 'J' and resid 266 through 290 removed outlier: 3.711A pdb=" N LEU J 274 " --> pdb=" O ARG J 270 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET J 277 " --> pdb=" O TYR J 273 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU J 279 " --> pdb=" O ASP J 275 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA J 282 " --> pdb=" O SER J 278 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU J 286 " --> pdb=" O ALA J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 326 removed outlier: 3.672A pdb=" N VAL J 315 " --> pdb=" O THR J 311 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU J 316 " --> pdb=" O GLU J 312 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR J 317 " --> pdb=" O LYS J 313 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU J 318 " --> pdb=" O THR J 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN J 320 " --> pdb=" O GLU J 316 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN J 326 " --> pdb=" O GLU J 322 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 332 removed outlier: 4.167A pdb=" N ALA J 331 " --> pdb=" O GLN J 327 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN J 332 " --> pdb=" O PHE J 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 327 through 332' Processing helix chain 'J' and resid 347 through 351 removed outlier: 3.784A pdb=" N ASP J 350 " --> pdb=" O ALA J 347 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE J 351 " --> pdb=" O ALA J 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 347 through 351' Processing helix chain 'J' and resid 357 through 376 removed outlier: 3.903A pdb=" N TYR J 361 " --> pdb=" O SER J 357 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE J 364 " --> pdb=" O SER J 360 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR J 365 " --> pdb=" O TYR J 361 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA J 368 " --> pdb=" O ILE J 364 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG J 370 " --> pdb=" O GLN J 366 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N MET J 371 " --> pdb=" O LYS J 367 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE J 372 " --> pdb=" O ALA J 368 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER J 373 " --> pdb=" O SER J 369 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU J 374 " --> pdb=" O ARG J 370 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 389 removed outlier: 4.130A pdb=" N LEU J 388 " --> pdb=" O THR J 384 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN J 389 " --> pdb=" O LEU J 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 384 through 389' Processing helix chain 'J' and resid 421 through 428 removed outlier: 4.114A pdb=" N GLN J 425 " --> pdb=" O ARG J 421 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS J 428 " --> pdb=" O TYR J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 500 removed outlier: 4.092A pdb=" N LEU J 499 " --> pdb=" O LYS J 495 " (cutoff:3.500A) Processing helix chain 'J' and resid 539 through 555 removed outlier: 4.254A pdb=" N PHE J 546 " --> pdb=" O ARG J 542 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER J 547 " --> pdb=" O SER J 543 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG J 548 " --> pdb=" O ALA J 544 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU J 552 " --> pdb=" O ARG J 548 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE J 553 " --> pdb=" O SER J 549 " (cutoff:3.500A) Processing helix chain 'J' and resid 556 through 562 removed outlier: 3.993A pdb=" N GLN J 560 " --> pdb=" O VAL J 556 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 602 removed outlier: 3.564A pdb=" N ILE J 586 " --> pdb=" O SER J 582 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE J 587 " --> pdb=" O TRP J 583 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA J 588 " --> pdb=" O GLN J 584 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL J 591 " --> pdb=" O ILE J 587 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU J 592 " --> pdb=" O ALA J 588 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG J 594 " --> pdb=" O THR J 590 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN J 595 " --> pdb=" O VAL J 591 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN J 596 " --> pdb=" O GLU J 592 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS J 599 " --> pdb=" O GLN J 595 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 634 removed outlier: 4.050A pdb=" N THR J 627 " --> pdb=" O MET J 623 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY J 628 " --> pdb=" O ALA J 624 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU J 630 " --> pdb=" O GLN J 626 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU J 632 " --> pdb=" O GLY J 628 " (cutoff:3.500A) Processing helix chain 'J' and resid 653 through 658 removed outlier: 3.869A pdb=" N ILE J 657 " --> pdb=" O PHE J 653 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR J 658 " --> pdb=" O ASP J 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 653 through 658' Processing helix chain 'J' and resid 659 through 664 removed outlier: 3.551A pdb=" N LYS J 664 " --> pdb=" O VAL J 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 664 through 672 removed outlier: 3.691A pdb=" N ILE J 668 " --> pdb=" O LYS J 664 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG J 669 " --> pdb=" O LEU J 665 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR J 670 " --> pdb=" O GLU J 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 682 through 692 removed outlier: 4.148A pdb=" N GLU J 688 " --> pdb=" O TYR J 684 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG J 691 " --> pdb=" O ILE J 687 " (cutoff:3.500A) Processing helix chain 'J' and resid 697 through 714 removed outlier: 3.522A pdb=" N VAL J 701 " --> pdb=" O GLU J 697 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA J 702 " --> pdb=" O LYS J 698 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA J 705 " --> pdb=" O VAL J 701 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR J 706 " --> pdb=" O ALA J 702 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR J 707 " --> pdb=" O ARG J 703 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU J 708 " --> pdb=" O LEU J 704 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR J 709 " --> pdb=" O ALA J 705 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU J 711 " --> pdb=" O TYR J 707 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU J 712 " --> pdb=" O LEU J 708 " (cutoff:3.500A) Processing helix chain 'J' and resid 717 through 722 removed outlier: 3.740A pdb=" N ASP J 721 " --> pdb=" O ASP J 718 " (cutoff:3.500A) Processing helix chain 'J' and resid 725 through 733 Processing helix chain 'J' and resid 737 through 755 removed outlier: 3.879A pdb=" N LYS J 742 " --> pdb=" O GLU J 738 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU J 743 " --> pdb=" O SER J 739 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA J 744 " --> pdb=" O ASP J 740 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU J 745 " --> pdb=" O ARG J 741 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU J 746 " --> pdb=" O LYS J 742 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL J 752 " --> pdb=" O LEU J 748 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE J 755 " --> pdb=" O TYR J 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 4.008A pdb=" N CYS A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 removed outlier: 3.517A pdb=" N TYR A 46 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 50 " --> pdb=" O TYR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 72 removed outlier: 3.664A pdb=" N VAL A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 removed outlier: 4.074A pdb=" N LYS A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.927A pdb=" N LYS A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 118 removed outlier: 3.596A pdb=" N ARG A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 108 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 110 " --> pdb=" O TYR A 106 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 117 " --> pdb=" O TYR A 113 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 50 removed outlier: 3.609A pdb=" N CYS B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS B 50 " --> pdb=" O TYR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 71 removed outlier: 3.761A pdb=" N VAL B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 75 through 86 removed outlier: 4.127A pdb=" N LYS B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 4.023A pdb=" N LYS B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 113 removed outlier: 3.568A pdb=" N ARG B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 108 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 110 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 111 " --> pdb=" O MET B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 4.117A pdb=" N TYR B 117 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 118' Processing helix chain 'C' and resid 49 through 61 removed outlier: 3.563A pdb=" N LYS C 53 " --> pdb=" O GLY C 49 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.866A pdb=" N PHE C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 107 removed outlier: 4.268A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 107' Processing helix chain 'C' and resid 108 through 113 removed outlier: 4.020A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 162 through 178 removed outlier: 3.758A pdb=" N LYS C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 removed outlier: 4.077A pdb=" N THR E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 removed outlier: 4.250A pdb=" N ARG E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LEU E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE E 83 " --> pdb=" O LEU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 113 removed outlier: 4.424A pdb=" N ASP E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N SER E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 178 removed outlier: 3.724A pdb=" N LYS E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS E 175 " --> pdb=" O ARG E 171 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 removed outlier: 4.122A pdb=" N ARG E 188 " --> pdb=" O SER E 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.763A pdb=" N PHE I 33 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL I 37 " --> pdb=" O PHE I 33 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 54 removed outlier: 3.515A pdb=" N PHE I 49 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU I 50 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU I 52 " --> pdb=" O ALA I 48 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 102 removed outlier: 4.069A pdb=" N LYS I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU I 99 " --> pdb=" O ARG I 95 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER I 100 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 118 removed outlier: 4.233A pdb=" N GLU I 118 " --> pdb=" O TYR I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 170 Processing helix chain 'I' and resid 172 through 176 Processing helix chain 'I' and resid 225 through 230 Processing helix chain 'M' and resid 37 through 42 removed outlier: 3.832A pdb=" N CYS M 42 " --> pdb=" O LEU M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 50 removed outlier: 3.670A pdb=" N ASP M 47 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG M 48 " --> pdb=" O SER M 44 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS M 50 " --> pdb=" O TYR M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 72 removed outlier: 3.633A pdb=" N VAL M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER M 62 " --> pdb=" O ILE M 58 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL M 66 " --> pdb=" O SER M 62 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN M 67 " --> pdb=" O TYR M 63 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL M 69 " --> pdb=" O ARG M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 86 removed outlier: 4.072A pdb=" N LYS M 79 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP M 80 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU M 81 " --> pdb=" O ALA M 77 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS M 84 " --> pdb=" O ASP M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 94 removed outlier: 3.968A pdb=" N LYS M 92 " --> pdb=" O LEU M 88 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU M 93 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 113 removed outlier: 3.601A pdb=" N ARG M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE M 103 " --> pdb=" O THR M 99 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS M 104 " --> pdb=" O LEU M 100 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU M 108 " --> pdb=" O CYS M 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU M 110 " --> pdb=" O TYR M 106 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL M 111 " --> pdb=" O MET M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 118 removed outlier: 4.073A pdb=" N TYR M 117 " --> pdb=" O TYR M 113 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY M 118 " --> pdb=" O PHE M 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 113 through 118' Processing helix chain 'N' and resid 49 through 61 removed outlier: 3.681A pdb=" N LYS N 53 " --> pdb=" O GLY N 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS N 55 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR N 58 " --> pdb=" O GLY N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 81 removed outlier: 4.231A pdb=" N ARG N 81 " --> pdb=" O ASP N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 110 removed outlier: 4.411A pdb=" N ASP N 110 " --> pdb=" O ALA N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 179 removed outlier: 3.877A pdb=" N LYS N 168 " --> pdb=" O GLU N 164 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL N 169 " --> pdb=" O GLU N 165 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS N 175 " --> pdb=" O ARG N 171 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU N 178 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU N 179 " --> pdb=" O LYS N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 189 removed outlier: 3.957A pdb=" N ARG N 188 " --> pdb=" O SER N 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 57 removed outlier: 3.696A pdb=" N LYS O 53 " --> pdb=" O GLY O 49 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY O 54 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 84 removed outlier: 4.357A pdb=" N ARG O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU O 82 " --> pdb=" O ILE O 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 113 removed outlier: 4.225A pdb=" N ASP O 110 " --> pdb=" O ALA O 106 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N SER O 111 " --> pdb=" O ASP O 107 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU O 112 " --> pdb=" O GLU O 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY O 113 " --> pdb=" O LEU O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 162 through 178 removed outlier: 3.743A pdb=" N LYS O 168 " --> pdb=" O GLU O 164 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL O 169 " --> pdb=" O GLU O 165 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS O 175 " --> pdb=" O ARG O 171 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU O 178 " --> pdb=" O LEU O 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 61 removed outlier: 3.503A pdb=" N LYS P 53 " --> pdb=" O GLY P 49 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR P 58 " --> pdb=" O GLY P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 84 removed outlier: 4.294A pdb=" N ARG P 81 " --> pdb=" O ASP P 77 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 108 removed outlier: 4.269A pdb=" N ASP P 107 " --> pdb=" O SER P 104 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU P 108 " --> pdb=" O ASN P 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 104 through 108' Processing helix chain 'P' and resid 109 through 113 Processing helix chain 'P' and resid 162 through 178 removed outlier: 3.745A pdb=" N LYS P 168 " --> pdb=" O GLU P 164 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL P 169 " --> pdb=" O GLU P 165 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS P 175 " --> pdb=" O ARG P 171 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU P 178 " --> pdb=" O LEU P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 189 removed outlier: 4.373A pdb=" N ARG P 188 " --> pdb=" O SER P 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 306 through 308 removed outlier: 4.151A pdb=" N PHE J 241 " --> pdb=" O PHE J 346 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE J 346 " --> pdb=" O PHE J 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 409 through 410 Processing sheet with id=AA3, first strand: chain 'J' and resid 567 through 570 removed outlier: 3.545A pdb=" N ILE J 580 " --> pdb=" O SER J 568 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY J 581 " --> pdb=" O ALA J 512 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU J 511 " --> pdb=" O PHE J 614 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 517 through 518 removed outlier: 3.511A pdb=" N ASP J 517 " --> pdb=" O SER J 608 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER J 608 " --> pdb=" O ASP J 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'J' and resid 642 through 643 removed outlier: 3.502A pdb=" N ILE J 642 " --> pdb=" O PHE J 651 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 97 removed outlier: 7.610A pdb=" N LYS C 5 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR C 202 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS C 7 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA C 200 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N SER C 9 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU C 198 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 118 through 122 Processing sheet with id=AA8, first strand: chain 'E' and resid 96 through 97 Processing sheet with id=AA9, first strand: chain 'E' and resid 96 through 97 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.739A pdb=" N GLU E 119 " --> pdb=" O ARG E 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 64 through 66 removed outlier: 3.650A pdb=" N PHE I 64 " --> pdb=" O TYR I 157 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS I 4 " --> pdb=" O ALA I 160 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR I 9 " --> pdb=" O GLU I 190 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU I 190 " --> pdb=" O THR I 9 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 71 through 73 Processing sheet with id=AB4, first strand: chain 'I' and resid 126 through 134 removed outlier: 4.208A pdb=" N VAL I 127 " --> pdb=" O ARG I 149 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG I 149 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP I 129 " --> pdb=" O THR I 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 148 through 154 removed outlier: 7.529A pdb=" N LYS N 5 " --> pdb=" O THR N 202 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR N 202 " --> pdb=" O LYS N 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS N 7 " --> pdb=" O ALA N 200 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA N 200 " --> pdb=" O LYS N 7 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N SER N 9 " --> pdb=" O LEU N 198 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU N 198 " --> pdb=" O SER N 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 121 through 125 removed outlier: 3.584A pdb=" N GLU N 123 " --> pdb=" O ARG N 136 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR N 125 " --> pdb=" O ASN N 134 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN N 134 " --> pdb=" O THR N 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 96 through 97 Processing sheet with id=AB8, first strand: chain 'O' and resid 96 through 97 Processing sheet with id=AB9, first strand: chain 'O' and resid 118 through 119 removed outlier: 3.800A pdb=" N GLU O 119 " --> pdb=" O ARG O 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 96 through 97 Processing sheet with id=AC2, first strand: chain 'P' and resid 96 through 97 Processing sheet with id=AC3, first strand: chain 'P' and resid 118 through 122 removed outlier: 3.814A pdb=" N GLU P 119 " --> pdb=" O ARG P 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 125 through 126 removed outlier: 3.790A pdb=" N THR P 125 " --> pdb=" O ALA P 133 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5945 1.33 - 1.45: 3242 1.45 - 1.57: 11268 1.57 - 1.69: 83 1.69 - 1.81: 66 Bond restraints: 20604 Sorted by residual: bond pdb=" C4 ATP J 801 " pdb=" C5 ATP J 801 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.81e+01 bond pdb=" C5 ATP J 801 " pdb=" C6 ATP J 801 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.38e+01 bond pdb=" C8 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.31e+01 bond pdb=" C5 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.387 1.346 0.041 1.00e-02 1.00e+04 1.70e+01 bond pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 1.374 1.335 0.039 1.00e-02 1.00e+04 1.49e+01 ... (remaining 20599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 27878 4.05 - 8.11: 25 8.11 - 12.16: 2 12.16 - 16.22: 0 16.22 - 20.27: 2 Bond angle restraints: 27907 Sorted by residual: angle pdb=" PB ATP J 801 " pdb=" O3B ATP J 801 " pdb=" PG ATP J 801 " ideal model delta sigma weight residual 139.87 119.60 20.27 1.00e+00 1.00e+00 4.11e+02 angle pdb=" PA ATP J 801 " pdb=" O3A ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 136.83 120.19 16.64 1.00e+00 1.00e+00 2.77e+02 angle pdb=" C5 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N3 ATP J 801 " ideal model delta sigma weight residual 126.80 118.69 8.11 1.00e+00 1.00e+00 6.58e+01 angle pdb=" N3 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 127.04 134.99 -7.95 1.15e+00 7.59e-01 4.80e+01 angle pdb=" C SER J 353 " pdb=" CA SER J 353 " pdb=" CB SER J 353 " ideal model delta sigma weight residual 117.23 110.41 6.82 1.36e+00 5.41e-01 2.52e+01 ... (remaining 27902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 12361 35.22 - 70.43: 160 70.43 - 105.65: 18 105.65 - 140.87: 0 140.87 - 176.08: 9 Dihedral angle restraints: 12548 sinusoidal: 5516 harmonic: 7032 Sorted by residual: dihedral pdb=" O4' C H 17 " pdb=" C1' C H 17 " pdb=" N1 C H 17 " pdb=" C2 C H 17 " ideal model delta sinusoidal sigma weight residual 200.00 51.91 148.09 1 1.50e+01 4.44e-03 7.89e+01 dihedral pdb=" O4' C H 40 " pdb=" C1' C H 40 " pdb=" N1 C H 40 " pdb=" C2 C H 40 " ideal model delta sinusoidal sigma weight residual 200.00 54.87 145.13 1 1.50e+01 4.44e-03 7.77e+01 dihedral pdb=" O4' C H 34 " pdb=" C1' C H 34 " pdb=" N1 C H 34 " pdb=" C2 C H 34 " ideal model delta sinusoidal sigma weight residual 200.00 55.25 144.75 1 1.50e+01 4.44e-03 7.75e+01 ... (remaining 12545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1880 0.027 - 0.053: 883 0.053 - 0.080: 198 0.080 - 0.106: 107 0.106 - 0.133: 46 Chirality restraints: 3114 Sorted by residual: chirality pdb=" C1' C H 40 " pdb=" O4' C H 40 " pdb=" C2' C H 40 " pdb=" N1 C H 40 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" C1' C H 34 " pdb=" O4' C H 34 " pdb=" C2' C H 34 " pdb=" N1 C H 34 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" C1' U H 22 " pdb=" O4' U H 22 " pdb=" C2' U H 22 " pdb=" N1 U H 22 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 3111 not shown) Planarity restraints: 3457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 196 " -0.016 5.00e-02 4.00e+02 2.42e-02 9.37e-01 pdb=" N PRO I 197 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO I 197 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO I 197 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 142 " -0.014 5.00e-02 4.00e+02 2.09e-02 7.00e-01 pdb=" N PRO J 143 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO J 143 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO J 143 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 71 " -0.014 5.00e-02 4.00e+02 2.08e-02 6.95e-01 pdb=" N PRO O 72 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO O 72 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO O 72 " -0.012 5.00e-02 4.00e+02 ... (remaining 3454 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2269 2.75 - 3.29: 18847 3.29 - 3.83: 30286 3.83 - 4.36: 35721 4.36 - 4.90: 61458 Nonbonded interactions: 148581 Sorted by model distance: nonbonded pdb=" OG SER I 28 " pdb=" OD1 ASP I 30 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR I 59 " pdb=" OH TYR I 289 " model vdw 2.263 3.040 nonbonded pdb=" O LEU I 60 " pdb=" OH TYR I 289 " model vdw 2.286 3.040 nonbonded pdb=" OG SER J 500 " pdb=" O ILE J 508 " model vdw 2.298 3.040 nonbonded pdb=" O2' C H 12 " pdb=" OP1 G H 13 " model vdw 2.299 3.040 ... (remaining 148576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.980 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 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 : 0.002 0.083 20604 Z= 0.136 Angle : 0.469 20.272 27907 Z= 0.323 Chirality : 0.036 0.133 3114 Planarity : 0.002 0.024 3457 Dihedral : 12.108 176.083 8020 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 2.38 % Allowed : 15.31 % Favored : 82.30 % Rotamer: Outliers : 0.34 % Allowed : 5.82 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -5.57 (0.12), residues: 2390 helix: -4.37 (0.08), residues: 690 sheet: -3.08 (0.28), residues: 225 loop : -3.64 (0.13), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 188 TYR 0.005 0.000 TYR J 670 PHE 0.006 0.000 PHE J 229 TRP 0.002 0.000 TRP J 583 HIS 0.002 0.000 HIS J 68 Details of bonding type rmsd covalent geometry : bond 0.00175 (20604) covalent geometry : angle 0.46925 (27907) hydrogen bonds : bond 0.35117 ( 408) hydrogen bonds : angle 9.92173 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 603 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7882 (t0) cc_final: 0.7457 (m-30) REVERT: B 87 ILE cc_start: 0.7705 (mm) cc_final: 0.7412 (mt) REVERT: C 95 ARG cc_start: 0.4280 (mtm110) cc_final: 0.4007 (mtm110) REVERT: C 99 ARG cc_start: 0.6722 (ttt-90) cc_final: 0.6509 (mmt-90) REVERT: I 161 ASN cc_start: 0.5748 (t0) cc_final: 0.5519 (t0) REVERT: I 234 TYR cc_start: 0.6949 (p90) cc_final: 0.6706 (p90) REVERT: O 44 ILE cc_start: 0.8222 (mm) cc_final: 0.7766 (mm) REVERT: O 68 VAL cc_start: 0.5740 (t) cc_final: 0.5483 (m) outliers start: 7 outliers final: 0 residues processed: 608 average time/residue: 0.1591 time to fit residues: 141.5040 Evaluate side-chains 289 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.3980 chunk 235 optimal weight: 3.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 51 GLN J 68 HIS J 106 ASN J 189 ASN J 223 ASN ** J 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 334 GLN J 356 ASN J 389 ASN J 403 HIS J 432 HIS J 440 ASN J 482 HIS J 489 GLN J 502 ASN J 560 GLN J 602 ASN J 737 ASN A 27 ASN B 27 ASN C 11 GLN C 85 ASN C 105 ASN C 134 ASN C 213 ASN E 85 ASN E 134 ASN E 206 ASN E 213 ASN I 83 GLN I 207 ASN I 233 HIS I 284 HIS M 27 ASN M 71 GLN N 11 GLN N 85 ASN N 105 ASN ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 ASN N 213 ASN O 11 GLN O 213 ASN P 11 GLN P 85 ASN P 105 ASN P 134 ASN P 213 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.213606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.189716 restraints weight = 31037.157| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 2.50 r_work: 0.4262 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20604 Z= 0.152 Angle : 0.627 9.556 27907 Z= 0.322 Chirality : 0.043 0.176 3114 Planarity : 0.004 0.044 3457 Dihedral : 12.653 178.009 3278 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.92 % Favored : 88.79 % Rotamer: Outliers : 2.69 % Allowed : 12.42 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -4.58 (0.13), residues: 2390 helix: -2.94 (0.14), residues: 706 sheet: -2.22 (0.27), residues: 286 loop : -3.43 (0.13), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 140 TYR 0.024 0.002 TYR J 706 PHE 0.027 0.002 PHE J 672 TRP 0.011 0.001 TRP J 733 HIS 0.006 0.001 HIS J 412 Details of bonding type rmsd covalent geometry : bond 0.00332 (20604) covalent geometry : angle 0.62732 (27907) hydrogen bonds : bond 0.05615 ( 408) hydrogen bonds : angle 5.77923 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 368 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 178 GLU cc_start: 0.8432 (pp20) cc_final: 0.7682 (tp30) REVERT: J 266 GLN cc_start: 0.8489 (pp30) cc_final: 0.8117 (pt0) REVERT: J 423 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7981 (mt) REVERT: J 602 ASN cc_start: 0.7873 (t0) cc_final: 0.7452 (t0) REVERT: J 648 ASP cc_start: 0.6577 (p0) cc_final: 0.6255 (p0) REVERT: J 671 PHE cc_start: 0.5905 (m-10) cc_final: 0.5633 (m-10) REVERT: J 706 TYR cc_start: 0.8160 (t80) cc_final: 0.7921 (t80) REVERT: J 742 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7942 (ttpt) REVERT: A 60 ASP cc_start: 0.8034 (t0) cc_final: 0.7716 (m-30) REVERT: B 88 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6505 (mm) REVERT: B 92 LYS cc_start: 0.7470 (mtmm) cc_final: 0.7219 (mtmm) REVERT: B 97 ARG cc_start: 0.7535 (tmm-80) cc_final: 0.7084 (ttp-170) REVERT: C 13 ARG cc_start: 0.7477 (ttt90) cc_final: 0.7211 (ttm-80) REVERT: C 87 LYS cc_start: 0.6003 (mmtt) cc_final: 0.5365 (ttpt) REVERT: C 139 GLU cc_start: 0.7348 (tt0) cc_final: 0.6850 (tm-30) REVERT: C 147 PHE cc_start: 0.6260 (m-80) cc_final: 0.6021 (m-80) REVERT: E 190 TYR cc_start: 0.5535 (m-10) cc_final: 0.5332 (m-80) REVERT: N 175 LYS cc_start: 0.7155 (ptpp) cc_final: 0.6950 (mttp) REVERT: O 60 LEU cc_start: 0.8380 (tt) cc_final: 0.8170 (tp) REVERT: O 70 GLU cc_start: 0.6039 (pm20) cc_final: 0.5796 (mm-30) REVERT: O 150 GLU cc_start: 0.7014 (pm20) cc_final: 0.6774 (pt0) REVERT: P 204 PHE cc_start: 0.4010 (OUTLIER) cc_final: 0.3731 (m-80) outliers start: 56 outliers final: 24 residues processed: 401 average time/residue: 0.1521 time to fit residues: 89.8683 Evaluate side-chains 306 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 278 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 418 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 560 GLN Chi-restraints excluded: chain J residue 742 LYS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 127 ASP Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 204 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 178 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 0.0040 chunk 222 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 201 HIS J 266 GLN ** J 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 412 HIS J 440 ASN ** J 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 GLN C 19 HIS C 206 ASN I 14 HIS I 135 GLN I 161 ASN ** I 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN P 206 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.177873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.148919 restraints weight = 30832.537| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.90 r_work: 0.3800 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.6842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 20604 Z= 0.251 Angle : 0.779 11.892 27907 Z= 0.399 Chirality : 0.048 0.256 3114 Planarity : 0.005 0.074 3457 Dihedral : 13.420 173.479 3278 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.87 % Favored : 89.92 % Rotamer: Outliers : 3.66 % Allowed : 14.82 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -4.11 (0.14), residues: 2390 helix: -2.43 (0.15), residues: 753 sheet: -1.92 (0.26), residues: 341 loop : -3.24 (0.14), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG P 99 TYR 0.029 0.003 TYR M 113 PHE 0.030 0.003 PHE P 167 TRP 0.015 0.002 TRP J 600 HIS 0.009 0.002 HIS J 403 Details of bonding type rmsd covalent geometry : bond 0.00578 (20604) covalent geometry : angle 0.77921 (27907) hydrogen bonds : bond 0.04158 ( 408) hydrogen bonds : angle 5.14298 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 344 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 LYS cc_start: 0.8120 (mtpp) cc_final: 0.7706 (tptt) REVERT: J 178 GLU cc_start: 0.8569 (pp20) cc_final: 0.7831 (tp30) REVERT: J 352 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.5428 (ptp) REVERT: J 560 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8099 (pt0) REVERT: J 706 TYR cc_start: 0.8140 (t80) cc_final: 0.7891 (t80) REVERT: J 714 LEU cc_start: 0.8957 (tt) cc_final: 0.8676 (tp) REVERT: A 19 LEU cc_start: 0.6466 (tt) cc_final: 0.6249 (mm) REVERT: A 60 ASP cc_start: 0.8033 (t0) cc_final: 0.7752 (m-30) REVERT: C 13 ARG cc_start: 0.7761 (ttt90) cc_final: 0.7502 (ttm-80) REVERT: E 164 GLU cc_start: 0.7326 (tp30) cc_final: 0.7031 (pm20) REVERT: E 166 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: E 175 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8034 (pptt) REVERT: E 204 PHE cc_start: 0.5543 (OUTLIER) cc_final: 0.4771 (m-80) REVERT: I 28 SER cc_start: 0.8427 (p) cc_final: 0.8067 (p) REVERT: I 92 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8028 (tp30) REVERT: N 134 ASN cc_start: 0.7005 (t0) cc_final: 0.6584 (t0) REVERT: N 140 ARG cc_start: 0.8605 (ttp80) cc_final: 0.8136 (mmm-85) REVERT: N 175 LYS cc_start: 0.7936 (ptpp) cc_final: 0.7580 (mttp) REVERT: O 168 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8261 (ttmt) REVERT: P 15 GLU cc_start: 0.7418 (pt0) cc_final: 0.6490 (mm-30) REVERT: P 137 GLN cc_start: 0.8166 (pt0) cc_final: 0.7567 (pt0) REVERT: P 204 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.5149 (m-80) outliers start: 76 outliers final: 33 residues processed: 401 average time/residue: 0.1462 time to fit residues: 87.6927 Evaluate side-chains 280 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 240 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 352 MET Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 440 ASN Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 560 GLN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 193 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 204 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 163 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 234 optimal weight: 3.9990 chunk 134 optimal weight: 0.1980 chunk 87 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 110 optimal weight: 0.0000 chunk 42 optimal weight: 4.9990 overall best weight: 1.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 51 GLN J 266 GLN J 532 GLN J 536 GLN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN C 11 GLN N 137 GLN N 162 GLN O 105 ASN P 144 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.176520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.147905 restraints weight = 30756.720| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.67 r_work: 0.3801 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.7399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20604 Z= 0.142 Angle : 0.598 13.704 27907 Z= 0.305 Chirality : 0.042 0.185 3114 Planarity : 0.004 0.072 3457 Dihedral : 13.170 173.970 3278 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.91 % Favored : 91.97 % Rotamer: Outliers : 2.79 % Allowed : 17.52 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -3.49 (0.15), residues: 2390 helix: -1.74 (0.17), residues: 751 sheet: -1.56 (0.27), residues: 336 loop : -2.97 (0.15), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 140 TYR 0.034 0.002 TYR J 468 PHE 0.025 0.002 PHE J 672 TRP 0.005 0.001 TRP J 38 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00320 (20604) covalent geometry : angle 0.59775 (27907) hydrogen bonds : bond 0.03017 ( 408) hydrogen bonds : angle 4.58323 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 274 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 40 ASP cc_start: 0.6988 (p0) cc_final: 0.6652 (m-30) REVERT: J 126 THR cc_start: 0.7087 (p) cc_final: 0.6855 (t) REVERT: J 133 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7623 (tptt) REVERT: J 178 GLU cc_start: 0.8503 (pp20) cc_final: 0.7761 (tp30) REVERT: J 352 MET cc_start: 0.5538 (OUTLIER) cc_final: 0.5060 (ptp) REVERT: J 706 TYR cc_start: 0.8109 (t80) cc_final: 0.7760 (t80) REVERT: J 742 LYS cc_start: 0.8216 (ttpt) cc_final: 0.7807 (ttmm) REVERT: A 60 ASP cc_start: 0.7859 (t0) cc_final: 0.7595 (m-30) REVERT: C 13 ARG cc_start: 0.7737 (ttt90) cc_final: 0.7480 (ttm-80) REVERT: E 117 TYR cc_start: 0.7511 (m-80) cc_final: 0.7100 (m-80) REVERT: E 166 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8128 (m-30) REVERT: E 175 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7976 (pptt) REVERT: E 204 PHE cc_start: 0.5628 (OUTLIER) cc_final: 0.4862 (m-80) REVERT: I 3 TYR cc_start: 0.6755 (t80) cc_final: 0.5365 (m-10) REVERT: I 92 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8107 (tp30) REVERT: N 134 ASN cc_start: 0.6926 (t0) cc_final: 0.6502 (t0) REVERT: N 140 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7813 (mtm110) REVERT: P 109 LEU cc_start: 0.5752 (OUTLIER) cc_final: 0.5323 (mp) REVERT: P 137 GLN cc_start: 0.7902 (pt0) cc_final: 0.7365 (pt0) REVERT: P 204 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.5098 (m-80) outliers start: 58 outliers final: 35 residues processed: 312 average time/residue: 0.1460 time to fit residues: 69.8014 Evaluate side-chains 275 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 351 ILE Chi-restraints excluded: chain J residue 352 MET Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 559 ASN Chi-restraints excluded: chain J residue 587 ILE Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 204 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 186 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 74 optimal weight: 0.0970 chunk 194 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 231 optimal weight: 0.0670 chunk 157 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 532 GLN J 560 GLN E 137 GLN M 71 GLN O 105 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.178874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.150563 restraints weight = 30611.043| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.69 r_work: 0.3832 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.7502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20604 Z= 0.098 Angle : 0.534 9.289 27907 Z= 0.270 Chirality : 0.040 0.173 3114 Planarity : 0.003 0.057 3457 Dihedral : 13.083 177.545 3278 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.38 % Rotamer: Outliers : 2.55 % Allowed : 17.71 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -3.00 (0.16), residues: 2390 helix: -1.23 (0.18), residues: 742 sheet: -1.35 (0.28), residues: 317 loop : -2.71 (0.15), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 36 TYR 0.016 0.001 TYR I 175 PHE 0.020 0.001 PHE J 726 TRP 0.013 0.002 TRP J 38 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00211 (20604) covalent geometry : angle 0.53398 (27907) hydrogen bonds : bond 0.02619 ( 408) hydrogen bonds : angle 4.30908 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 40 ASP cc_start: 0.6907 (p0) cc_final: 0.6666 (m-30) REVERT: J 126 THR cc_start: 0.6969 (p) cc_final: 0.6732 (t) REVERT: J 133 LYS cc_start: 0.7936 (mtpp) cc_final: 0.7637 (tptt) REVERT: J 178 GLU cc_start: 0.8429 (pp20) cc_final: 0.7741 (tp30) REVERT: J 352 MET cc_start: 0.5504 (OUTLIER) cc_final: 0.5028 (ptp) REVERT: J 706 TYR cc_start: 0.8007 (t80) cc_final: 0.7604 (t80) REVERT: J 742 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7851 (ttmm) REVERT: A 60 ASP cc_start: 0.7811 (t0) cc_final: 0.7571 (m-30) REVERT: C 171 ARG cc_start: 0.6741 (mmm160) cc_final: 0.6403 (mmm160) REVERT: E 93 MET cc_start: 0.8176 (mmm) cc_final: 0.7911 (mmm) REVERT: E 117 TYR cc_start: 0.7413 (m-80) cc_final: 0.7119 (m-80) REVERT: E 119 GLU cc_start: 0.7458 (pm20) cc_final: 0.6486 (pm20) REVERT: E 166 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: I 92 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8113 (tp30) REVERT: N 134 ASN cc_start: 0.6758 (t0) cc_final: 0.6362 (t0) REVERT: P 137 GLN cc_start: 0.7887 (pt0) cc_final: 0.7375 (pt0) outliers start: 53 outliers final: 35 residues processed: 296 average time/residue: 0.1507 time to fit residues: 69.2091 Evaluate side-chains 269 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 352 MET Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 412 HIS Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 587 ILE Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 130 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 173 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 93 optimal weight: 8.9990 chunk 120 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 440 ASN J 489 GLN J 560 GLN A 101 GLN ** I 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.177634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.149335 restraints weight = 30409.611| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.60 r_work: 0.3824 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.7717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20604 Z= 0.102 Angle : 0.532 8.571 27907 Z= 0.268 Chirality : 0.040 0.169 3114 Planarity : 0.003 0.054 3457 Dihedral : 13.057 178.570 3278 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.53 % Favored : 92.34 % Rotamer: Outliers : 2.69 % Allowed : 18.24 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.77 (0.16), residues: 2390 helix: -0.87 (0.19), residues: 743 sheet: -1.41 (0.27), residues: 332 loop : -2.63 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 36 TYR 0.021 0.001 TYR J 298 PHE 0.015 0.001 PHE J 645 TRP 0.007 0.001 TRP J 38 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00225 (20604) covalent geometry : angle 0.53154 (27907) hydrogen bonds : bond 0.02400 ( 408) hydrogen bonds : angle 4.09062 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 29 LYS cc_start: 0.7877 (mttt) cc_final: 0.7610 (mtpp) REVERT: J 126 THR cc_start: 0.7195 (p) cc_final: 0.6934 (t) REVERT: J 133 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7730 (tptt) REVERT: J 178 GLU cc_start: 0.8353 (pp20) cc_final: 0.7723 (tp30) REVERT: J 352 MET cc_start: 0.5621 (OUTLIER) cc_final: 0.5151 (ptp) REVERT: J 470 LYS cc_start: 0.6243 (tmtt) cc_final: 0.5478 (tmtt) REVERT: J 706 TYR cc_start: 0.8036 (t80) cc_final: 0.7606 (t80) REVERT: J 732 LYS cc_start: 0.7862 (pttm) cc_final: 0.7519 (tptp) REVERT: J 742 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7802 (ttmm) REVERT: A 22 LYS cc_start: 0.6493 (ptpt) cc_final: 0.6259 (ptpp) REVERT: A 60 ASP cc_start: 0.7786 (t0) cc_final: 0.7544 (m-30) REVERT: E 93 MET cc_start: 0.8344 (mmm) cc_final: 0.8130 (mmm) REVERT: E 117 TYR cc_start: 0.7463 (m-80) cc_final: 0.7225 (m-80) REVERT: E 166 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8145 (m-30) REVERT: I 92 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8113 (tp30) REVERT: N 134 ASN cc_start: 0.6756 (t0) cc_final: 0.6378 (t0) REVERT: P 137 GLN cc_start: 0.7878 (pt0) cc_final: 0.7359 (pt0) outliers start: 56 outliers final: 39 residues processed: 298 average time/residue: 0.1448 time to fit residues: 66.8539 Evaluate side-chains 275 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 351 ILE Chi-restraints excluded: chain J residue 352 MET Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 412 HIS Chi-restraints excluded: chain J residue 440 ASN Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 521 LEU Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 130 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 64 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 chunk 75 optimal weight: 0.0970 chunk 131 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 121 optimal weight: 0.0770 chunk 203 optimal weight: 3.9990 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 152 ASN ** O 159 ASN ** 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 = 0.4269 r_free = 0.4269 target = 0.177735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.149210 restraints weight = 30721.536| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.73 r_work: 0.3813 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.7797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20604 Z= 0.095 Angle : 0.518 8.625 27907 Z= 0.261 Chirality : 0.039 0.163 3114 Planarity : 0.003 0.051 3457 Dihedral : 13.040 179.667 3278 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.15 % Favored : 92.72 % Rotamer: Outliers : 2.65 % Allowed : 19.15 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.57 (0.16), residues: 2390 helix: -0.70 (0.19), residues: 744 sheet: -1.29 (0.27), residues: 332 loop : -2.51 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 36 TYR 0.019 0.001 TYR J 298 PHE 0.021 0.001 PHE I 266 TRP 0.009 0.001 TRP J 38 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00210 (20604) covalent geometry : angle 0.51759 (27907) hydrogen bonds : bond 0.02310 ( 408) hydrogen bonds : angle 3.99818 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7729 (tptt) REVERT: J 178 GLU cc_start: 0.8401 (pp20) cc_final: 0.7739 (tp30) REVERT: J 470 LYS cc_start: 0.6309 (tmtt) cc_final: 0.5565 (tptt) REVERT: J 706 TYR cc_start: 0.8060 (t80) cc_final: 0.7587 (t80) REVERT: J 742 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7791 (ttmm) REVERT: A 22 LYS cc_start: 0.6427 (ptpt) cc_final: 0.6195 (ptpp) REVERT: A 60 ASP cc_start: 0.7762 (t0) cc_final: 0.7518 (m-30) REVERT: C 198 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5510 (tt) REVERT: E 117 TYR cc_start: 0.7404 (m-80) cc_final: 0.7177 (m-80) REVERT: E 166 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: I 6 TYR cc_start: 0.8541 (m-80) cc_final: 0.8293 (m-80) REVERT: I 92 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8100 (tp30) REVERT: N 134 ASN cc_start: 0.6709 (t0) cc_final: 0.6328 (t0) REVERT: O 91 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.5844 (p90) REVERT: P 137 GLN cc_start: 0.7950 (pt0) cc_final: 0.7376 (pt0) REVERT: P 140 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.7905 (mtp-110) outliers start: 55 outliers final: 40 residues processed: 286 average time/residue: 0.1475 time to fit residues: 65.2604 Evaluate side-chains 267 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 351 ILE Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 412 HIS Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 521 LEU Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 130 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 114 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 169 optimal weight: 0.0030 chunk 53 optimal weight: 0.0970 chunk 177 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 700 ASN I 67 GLN ** I 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.172175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.143230 restraints weight = 30744.795| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.80 r_work: 0.3749 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.8246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20604 Z= 0.133 Angle : 0.556 9.027 27907 Z= 0.283 Chirality : 0.041 0.223 3114 Planarity : 0.003 0.056 3457 Dihedral : 13.155 176.791 3278 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.82 % Favored : 92.09 % Rotamer: Outliers : 2.74 % Allowed : 19.10 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.49 (0.16), residues: 2390 helix: -0.56 (0.19), residues: 766 sheet: -1.36 (0.27), residues: 347 loop : -2.51 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 57 TYR 0.023 0.001 TYR J 670 PHE 0.036 0.001 PHE I 266 TRP 0.007 0.001 TRP J 38 HIS 0.003 0.001 HIS J 303 Details of bonding type rmsd covalent geometry : bond 0.00303 (20604) covalent geometry : angle 0.55649 (27907) hydrogen bonds : bond 0.02557 ( 408) hydrogen bonds : angle 4.04438 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 245 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 29 LYS cc_start: 0.7945 (mttt) cc_final: 0.7707 (mtpp) REVERT: J 133 LYS cc_start: 0.8241 (mtpp) cc_final: 0.7832 (tptt) REVERT: J 178 GLU cc_start: 0.8507 (pp20) cc_final: 0.7798 (tp30) REVERT: J 359 GLU cc_start: 0.8264 (pm20) cc_final: 0.8059 (pm20) REVERT: J 382 TYR cc_start: 0.7195 (t80) cc_final: 0.6976 (t80) REVERT: J 519 ASP cc_start: 0.5817 (OUTLIER) cc_final: 0.5403 (p0) REVERT: J 706 TYR cc_start: 0.8105 (t80) cc_final: 0.7696 (t80) REVERT: J 732 LYS cc_start: 0.7909 (pttm) cc_final: 0.7545 (tptp) REVERT: J 742 LYS cc_start: 0.8119 (ttpt) cc_final: 0.7760 (ttmm) REVERT: A 22 LYS cc_start: 0.6538 (ptpt) cc_final: 0.6304 (ptpp) REVERT: A 60 ASP cc_start: 0.7732 (t0) cc_final: 0.7476 (m-30) REVERT: C 198 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.5528 (tt) REVERT: E 117 TYR cc_start: 0.7678 (m-80) cc_final: 0.7189 (m-80) REVERT: E 166 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8216 (m-30) REVERT: I 92 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8102 (tp30) REVERT: N 91 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7837 (p90) REVERT: N 134 ASN cc_start: 0.7087 (t0) cc_final: 0.6593 (t0) REVERT: N 158 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6148 (mp0) REVERT: N 198 LEU cc_start: 0.8755 (tm) cc_final: 0.8475 (tp) REVERT: O 91 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.5970 (p90) REVERT: P 137 GLN cc_start: 0.7879 (pt0) cc_final: 0.7346 (pt0) REVERT: P 150 GLU cc_start: 0.7040 (pm20) cc_final: 0.6784 (pm20) outliers start: 57 outliers final: 40 residues processed: 288 average time/residue: 0.1436 time to fit residues: 64.2250 Evaluate side-chains 272 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 351 ILE Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 412 HIS Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 519 ASP Chi-restraints excluded: chain J residue 521 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain N residue 158 GLU Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 130 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 211 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 16 optimal weight: 0.0030 chunk 63 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 230 optimal weight: 5.9990 chunk 78 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 440 ASN I 161 ASN ** O 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 ASN ** O 159 ASN ** 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 = 0.4237 r_free = 0.4237 target = 0.174869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.146143 restraints weight = 30467.617| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.70 r_work: 0.3786 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.8305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20604 Z= 0.093 Angle : 0.520 9.134 27907 Z= 0.264 Chirality : 0.040 0.167 3114 Planarity : 0.003 0.055 3457 Dihedral : 13.097 179.406 3278 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.11 % Favored : 92.80 % Rotamer: Outliers : 2.55 % Allowed : 19.83 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.32 (0.17), residues: 2390 helix: -0.36 (0.20), residues: 761 sheet: -1.36 (0.26), residues: 344 loop : -2.41 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 36 TYR 0.018 0.001 TYR J 298 PHE 0.026 0.001 PHE I 266 TRP 0.010 0.001 TRP J 38 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00202 (20604) covalent geometry : angle 0.51996 (27907) hydrogen bonds : bond 0.02230 ( 408) hydrogen bonds : angle 3.91347 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 LYS cc_start: 0.8242 (mtpp) cc_final: 0.7831 (tptt) REVERT: J 178 GLU cc_start: 0.8423 (pp20) cc_final: 0.7740 (tp30) REVERT: J 470 LYS cc_start: 0.6554 (tmtt) cc_final: 0.5644 (tppt) REVERT: J 519 ASP cc_start: 0.5735 (OUTLIER) cc_final: 0.5346 (p0) REVERT: J 703 ARG cc_start: 0.8769 (ttp-170) cc_final: 0.8518 (ttm170) REVERT: J 742 LYS cc_start: 0.8086 (ttpt) cc_final: 0.7744 (ttmm) REVERT: A 22 LYS cc_start: 0.6475 (ptpt) cc_final: 0.6242 (ptpp) REVERT: C 198 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5540 (tt) REVERT: E 117 TYR cc_start: 0.7605 (m-80) cc_final: 0.7206 (m-80) REVERT: E 166 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: I 92 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8099 (tp30) REVERT: N 134 ASN cc_start: 0.6868 (t0) cc_final: 0.6419 (t0) REVERT: N 158 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: N 198 LEU cc_start: 0.8670 (tm) cc_final: 0.8380 (tp) REVERT: O 91 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.5933 (p90) REVERT: P 137 GLN cc_start: 0.7860 (pt0) cc_final: 0.7311 (pt0) REVERT: P 150 GLU cc_start: 0.7026 (pm20) cc_final: 0.6767 (pm20) outliers start: 53 outliers final: 40 residues processed: 277 average time/residue: 0.1418 time to fit residues: 60.9150 Evaluate side-chains 266 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 412 HIS Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain J residue 440 ASN Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 519 ASP Chi-restraints excluded: chain J residue 521 LEU Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain N residue 158 GLU Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 84 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 10 optimal weight: 0.0470 chunk 28 optimal weight: 0.7980 chunk 189 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.9478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 440 ASN ** O 159 ASN ** 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 = 0.4199 r_free = 0.4199 target = 0.171142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.142058 restraints weight = 30921.572| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.78 r_work: 0.3737 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.8530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20604 Z= 0.128 Angle : 0.561 10.435 27907 Z= 0.285 Chirality : 0.041 0.202 3114 Planarity : 0.003 0.053 3457 Dihedral : 13.165 177.733 3278 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.99 % Favored : 91.92 % Rotamer: Outliers : 2.17 % Allowed : 20.40 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.22 (0.17), residues: 2390 helix: -0.28 (0.20), residues: 766 sheet: -0.90 (0.28), residues: 325 loop : -2.47 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 48 TYR 0.027 0.001 TYR J 706 PHE 0.030 0.001 PHE I 266 TRP 0.008 0.001 TRP J 38 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00292 (20604) covalent geometry : angle 0.56117 (27907) hydrogen bonds : bond 0.02458 ( 408) hydrogen bonds : angle 3.95553 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 LYS cc_start: 0.8369 (mtpp) cc_final: 0.7959 (mmmt) REVERT: J 178 GLU cc_start: 0.8513 (pp20) cc_final: 0.7794 (tp30) REVERT: J 519 ASP cc_start: 0.5770 (OUTLIER) cc_final: 0.5347 (p0) REVERT: J 706 TYR cc_start: 0.7952 (t80) cc_final: 0.7658 (t80) REVERT: J 732 LYS cc_start: 0.7907 (pttm) cc_final: 0.7433 (tptp) REVERT: J 742 LYS cc_start: 0.8093 (ttpt) cc_final: 0.7726 (ttmm) REVERT: A 22 LYS cc_start: 0.6595 (ptpt) cc_final: 0.6339 (ptpp) REVERT: C 198 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5598 (tt) REVERT: E 117 TYR cc_start: 0.7685 (m-80) cc_final: 0.7274 (m-80) REVERT: E 166 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: I 92 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8090 (tp30) REVERT: N 134 ASN cc_start: 0.7056 (t0) cc_final: 0.6567 (t0) REVERT: N 198 LEU cc_start: 0.8757 (tm) cc_final: 0.8468 (tp) REVERT: O 91 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.6652 (p90) REVERT: P 137 GLN cc_start: 0.7875 (pt0) cc_final: 0.7314 (pt0) outliers start: 45 outliers final: 39 residues processed: 263 average time/residue: 0.1499 time to fit residues: 60.8774 Evaluate side-chains 262 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 412 HIS Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 519 ASP Chi-restraints excluded: chain J residue 521 LEU Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain N residue 201 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 91 PHE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 215 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 89 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 206 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.170371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.141203 restraints weight = 30850.914| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.83 r_work: 0.3729 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.8758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20604 Z= 0.121 Angle : 0.553 9.862 27907 Z= 0.281 Chirality : 0.041 0.183 3114 Planarity : 0.003 0.049 3457 Dihedral : 13.205 177.154 3278 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.20 % Favored : 92.72 % Rotamer: Outliers : 2.41 % Allowed : 20.50 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.13 (0.17), residues: 2390 helix: -0.16 (0.20), residues: 755 sheet: -1.14 (0.28), residues: 347 loop : -2.34 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 140 TYR 0.021 0.001 TYR J 298 PHE 0.028 0.001 PHE I 266 TRP 0.010 0.001 TRP J 38 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00273 (20604) covalent geometry : angle 0.55292 (27907) hydrogen bonds : bond 0.02413 ( 408) hydrogen bonds : angle 3.93436 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4148.03 seconds wall clock time: 71 minutes 57.43 seconds (4317.43 seconds total)