Starting phenix.real_space_refine on Sun Sep 13 03:03:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nue_0519/09_2026/6nue_0519.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nue_0519/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6nue_0519/09_2026/6nue_0519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nue_0519/09_2026/6nue_0519.map" model { file = "/net/cci-nas-00/data/ceres_data/6nue_0519/09_2026/6nue_0519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nue_0519/09_2026/6nue_0519.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6nue_0519/09_2026/6nue_0519.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nue_0519/09_2026/6nue_0519.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 40} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 14, 'rna3p_pur': 8, 'rna3p_pyr': 11} Link IDs: {'rna2p': 21, 'rna3p': 18} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 4.45, per 1000 atoms: 0.22 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: 1.71 Conformation dependent library (CDL) restraints added in 866.7 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: 2.55 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: 3.01 Time building geometry restraints manager: 2.31 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: 27835 4.05 - 8.11: 68 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 - 34.31: 12148 34.31 - 68.61: 202 68.61 - 102.92: 36 102.92 - 137.23: 0 137.23 - 171.53: 1 Dihedral angle restraints: 12387 sinusoidal: 5355 harmonic: 7032 Sorted by residual: dihedral pdb=" C4' U H 9 " pdb=" C3' U H 9 " pdb=" C2' U H 9 " pdb=" C1' U H 9 " ideal model delta sinusoidal sigma weight residual 36.35 -35.90 72.25 1 3.10e+00 1.04e-01 6.94e+02 dihedral pdb=" C4' G H 13 " pdb=" C3' G H 13 " pdb=" C2' G H 13 " pdb=" C1' G H 13 " ideal model delta sinusoidal sigma weight residual 36.34 -35.81 72.16 1 3.10e+00 1.04e-01 6.93e+02 dihedral pdb=" C4' C H 27 " pdb=" C3' C H 27 " pdb=" C2' C H 27 " pdb=" C1' C H 27 " ideal model delta sinusoidal sigma weight residual 36.35 -35.71 72.06 1 3.10e+00 1.04e-01 6.91e+02 ... (remaining 12384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2830 0.065 - 0.131: 203 0.131 - 0.196: 0 0.196 - 0.261: 59 0.261 - 0.327: 22 Chirality restraints: 3114 Sorted by residual: chirality pdb=" P G H 13 " pdb=" OP1 G H 13 " pdb=" OP2 G H 13 " pdb=" O5' G H 13 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C2' U H 39 " pdb=" C3' U H 39 " pdb=" O2' U H 39 " pdb=" C1' U H 39 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C2' U H 25 " pdb=" C3' U H 25 " pdb=" O2' U H 25 " pdb=" C1' U H 25 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (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: 6.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.320 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 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= 0.140 Angle : 0.548 20.272 27907 Z= 0.340 Chirality : 0.054 0.327 3114 Planarity : 0.002 0.024 3457 Dihedral : 12.050 171.533 7859 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/Z covalent geometry : bond 0.00189 / 0.14 (20604) covalent geometry : angle 0.54773 / 0.34 (27907) hydrogen bonds : bond 0.35117 / 22.72 ( 408) hydrogen bonds : angle 9.92173 / 7.20 ( 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 : 0.768 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: 0.1805 time to fit residues: 160.9525 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 : 0.813 ------------------------------------------------------------------------------- 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... J 51 GLN J 68 HIS J 106 ASN J 189 ASN J 223 ASN J 266 GLN ** 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 482 HIS J 489 GLN J 502 ASN J 560 GLN J 602 ASN J 737 ASN A 27 ASN B 27 ASN 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 85 ASN N 134 ASN N 213 ASN O 11 GLN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.214871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.189541 restraints weight = 30966.002| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 2.96 r_work: 0.4272 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20604 Z= 0.177 Angle : 0.945 23.204 27907 Z= 0.412 Chirality : 0.081 1.021 3114 Planarity : 0.004 0.037 3457 Dihedral : 9.345 177.615 3117 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.25 % Favored : 89.46 % Rotamer: Outliers : 2.60 % Allowed : 12.37 % Favored : 85.03 % 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: -4.47 (0.13), residues: 2390 helix: -2.71 (0.15), residues: 710 sheet: -2.22 (0.27), residues: 286 loop : -3.42 (0.13), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 140 TYR 0.026 0.002 TYR J 706 PHE 0.027 0.002 PHE J 672 TRP 0.010 0.001 TRP J 733 HIS 0.007 0.001 HIS J 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (20604) covalent geometry : angle 0.94525 / 0.41 (27907) hydrogen bonds : bond 0.05083 / 3.54 ( 408) hydrogen bonds : angle 5.71567 / 4.35 ( 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 432 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 378 time to evaluate : 0.602 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: 0.8501 (pp20) cc_final: 0.7698 (tp30) REVERT: J 266 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: J 423 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7963 (mt) REVERT: J 470 LYS cc_start: 0.5479 (tmtt) cc_final: 0.4009 (tmtt) REVERT: J 602 ASN cc_start: 0.7859 (t0) cc_final: 0.7411 (t0) REVERT: J 648 ASP cc_start: 0.6567 (p0) cc_final: 0.6274 (p0) REVERT: J 671 PHE cc_start: 0.6002 (m-10) cc_final: 0.5771 (m-10) REVERT: J 706 TYR cc_start: 0.8177 (t80) cc_final: 0.7972 (t80) REVERT: J 742 LYS cc_start: 0.8231 (ttpt) cc_final: 0.7996 (ttpt) REVERT: A 60 ASP cc_start: 0.8007 (t0) cc_final: 0.7665 (m-30) REVERT: B 88 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6302 (mm) REVERT: B 92 LYS cc_start: 0.7510 (mtmm) cc_final: 0.7250 (mtmm) REVERT: B 97 ARG cc_start: 0.7431 (tmm-80) cc_final: 0.7048 (ttp-170) REVERT: C 13 ARG cc_start: 0.7454 (ttt90) cc_final: 0.7169 (ttm-80) REVERT: C 87 LYS cc_start: 0.5982 (mmtt) cc_final: 0.5360 (ttpt) REVERT: C 139 GLU cc_start: 0.7357 (tt0) cc_final: 0.6870 (tm-30) REVERT: C 147 PHE cc_start: 0.6288 (m-80) cc_final: 0.6050 (m-80) REVERT: N 175 LYS cc_start: 0.7174 (ptpp) cc_final: 0.6936 (mttp) REVERT: O 60 LEU cc_start: 0.8447 (tt) cc_final: 0.8214 (tp) REVERT: O 68 VAL cc_start: 0.7592 (t) cc_final: 0.7323 (m) REVERT: O 70 GLU cc_start: 0.6058 (pm20) cc_final: 0.5733 (mm-30) REVERT: O 150 GLU cc_start: 0.6800 (pm20) cc_final: 0.6553 (pt0) REVERT: P 207 TYR cc_start: 0.6281 (t80) cc_final: 0.5920 (t80) outliers start: 54 outliers final: 21 residues processed: 408 average time/residue: 0.1599 time to fit residues: 96.7249 Evaluate side-chains 305 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 266 GLN Chi-restraints excluded: chain J residue 418 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 560 GLN 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 30 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 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: 4.9990 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 51 GLN J 201 HIS J 266 GLN J 412 HIS J 440 ASN ** J 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 HIS C 206 ASN I 14 HIS ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 ASN ** N 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.170247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.141177 restraints weight = 31085.396| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.82 r_work: 0.3715 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 0.009 0.149 20604 Z= 0.393 Angle : 1.137 18.659 27907 Z= 0.541 Chirality : 0.081 1.119 3114 Planarity : 0.007 0.090 3457 Dihedral : 11.695 173.628 3117 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.71 % Favored : 89.08 % Rotamer: Outliers : 4.04 % Allowed : 14.68 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.14), residues: 2390 helix: -2.59 (0.15), residues: 748 sheet: -1.70 (0.27), residues: 324 loop : -3.33 (0.14), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 756 TYR 0.027 0.004 TYR I 252 PHE 0.041 0.003 PHE I 294 TRP 0.016 0.003 TRP J 600 HIS 0.010 0.003 HIS J 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00881 / 0.39 (20604) covalent geometry : angle 1.13685 / 0.54 (27907) hydrogen bonds : bond 0.04711 / 3.18 ( 408) hydrogen bonds : angle 5.56143 / 4.04 ( 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 439 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 355 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 133 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7945 (tptt) REVERT: J 178 GLU cc_start: 0.8609 (pp20) cc_final: 0.7915 (tp30) REVERT: J 266 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7963 (pt0) REVERT: J 661 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: C 13 ARG cc_start: 0.7796 (ttt90) cc_final: 0.7411 (ttm-80) REVERT: E 89 LYS cc_start: 0.7754 (mmpt) cc_final: 0.7398 (tmmt) REVERT: E 166 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: I 3 TYR cc_start: 0.7050 (t80) cc_final: 0.5856 (m-10) REVERT: I 57 LYS cc_start: 0.8738 (tttt) cc_final: 0.8404 (ttpt) REVERT: I 92 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8129 (tp30) REVERT: I 198 LEU cc_start: 0.8038 (mt) cc_final: 0.7831 (mt) REVERT: N 171 ARG cc_start: 0.6273 (ttt-90) cc_final: 0.6064 (mmt180) REVERT: N 172 ASP cc_start: 0.8346 (t70) cc_final: 0.8117 (t0) REVERT: N 175 LYS cc_start: 0.8134 (ptpp) cc_final: 0.7741 (mttp) REVERT: N 179 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8303 (mt) REVERT: N 198 LEU cc_start: 0.8634 (tm) cc_final: 0.8430 (tp) REVERT: O 168 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8436 (ttmt) REVERT: P 15 GLU cc_start: 0.7640 (pt0) cc_final: 0.6946 (mm-30) REVERT: P 109 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5859 (mp) REVERT: P 137 GLN cc_start: 0.8023 (pt0) cc_final: 0.7533 (pt0) outliers start: 84 outliers final: 36 residues processed: 415 average time/residue: 0.1616 time to fit residues: 99.8467 Evaluate side-chains 285 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 218 ASP Chi-restraints excluded: chain J residue 266 GLN 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 343 TRP Chi-restraints excluded: chain J residue 400 GLU 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 J residue 569 ILE Chi-restraints excluded: chain J residue 661 TYR Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 94 ILE 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 E residue 63 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 201 THR 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 29 ILE Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 206 ASN 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 79 LEU Chi-restraints excluded: chain P residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 163 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.0370 chunk 234 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 161 optimal weight: 0.5980 chunk 110 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 51 GLN J 532 GLN J 536 GLN J 560 GLN A 71 GLN I 161 ASN N 11 GLN N 137 GLN N 162 GLN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 144 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.175199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.146948 restraints weight = 30812.726| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.60 r_work: 0.3782 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.7997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20604 Z= 0.128 Angle : 0.741 13.630 27907 Z= 0.347 Chirality : 0.062 0.846 3114 Planarity : 0.004 0.064 3457 Dihedral : 11.283 175.466 3117 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.66 % Favored : 92.22 % Rotamer: Outliers : 2.89 % Allowed : 17.42 % 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: -3.60 (0.15), residues: 2390 helix: -1.89 (0.17), residues: 762 sheet: -1.58 (0.27), residues: 334 loop : -3.02 (0.15), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 95 TYR 0.033 0.002 TYR J 468 PHE 0.021 0.002 PHE O 26 TRP 0.010 0.001 TRP J 733 HIS 0.005 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (20604) covalent geometry : angle 0.74126 / 0.35 (27907) hydrogen bonds : bond 0.03081 / 2.08 ( 408) hydrogen bonds : angle 4.71709 / 3.51 ( 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 356 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 296 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 40 ASP cc_start: 0.6983 (p0) cc_final: 0.6773 (m-30) REVERT: J 133 LYS cc_start: 0.8246 (mtpp) cc_final: 0.7901 (tptt) REVERT: J 178 GLU cc_start: 0.8502 (pp20) cc_final: 0.7805 (tp30) REVERT: J 298 TYR cc_start: 0.8505 (t80) cc_final: 0.8244 (t80) REVERT: J 352 MET cc_start: 0.5636 (OUTLIER) cc_final: 0.5348 (ptp) REVERT: J 661 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.5617 (m-80) REVERT: J 742 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7813 (ttmm) REVERT: A 60 ASP cc_start: 0.7609 (t0) cc_final: 0.7249 (m-30) REVERT: C 13 ARG cc_start: 0.7733 (ttt90) cc_final: 0.7449 (ttm-80) REVERT: E 166 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8215 (m-30) REVERT: I 57 LYS cc_start: 0.8730 (tttt) cc_final: 0.8327 (ttpt) REVERT: I 92 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8160 (tp30) REVERT: M 79 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7919 (mmmm) REVERT: N 129 ILE cc_start: 0.5839 (pt) cc_final: 0.5618 (pt) REVERT: N 175 LYS cc_start: 0.7924 (ptpp) cc_final: 0.7542 (mttp) REVERT: P 109 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.5444 (mp) REVERT: P 137 GLN cc_start: 0.7907 (pt0) cc_final: 0.7339 (pt0) outliers start: 60 outliers final: 29 residues processed: 341 average time/residue: 0.1393 time to fit residues: 72.2608 Evaluate side-chains 269 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 448 ASN Chi-restraints excluded: chain J residue 451 LEU 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 644 LEU Chi-restraints excluded: chain J residue 661 TYR 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 61 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 130 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 186 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 113 optimal weight: 0.0060 chunk 105 optimal weight: 3.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 532 GLN J 560 GLN A 101 GLN N 134 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.171462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142612 restraints weight = 30763.044| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.71 r_work: 0.3737 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.8358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20604 Z= 0.141 Angle : 0.715 12.811 27907 Z= 0.333 Chirality : 0.060 0.732 3114 Planarity : 0.004 0.062 3457 Dihedral : 11.507 177.478 3117 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.33 % Favored : 91.55 % Rotamer: Outliers : 2.89 % Allowed : 18.29 % Favored : 78.83 % 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: -3.06 (0.16), residues: 2390 helix: -1.32 (0.18), residues: 752 sheet: -1.30 (0.28), residues: 317 loop : -2.74 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 90 TYR 0.026 0.001 TYR J 706 PHE 0.018 0.002 PHE I 294 TRP 0.007 0.001 TRP J 733 HIS 0.004 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (20604) covalent geometry : angle 0.71459 / 0.33 (27907) hydrogen bonds : bond 0.02866 / 1.93 ( 408) hydrogen bonds : angle 4.38014 / 3.25 ( 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 322 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 262 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: J 133 LYS cc_start: 0.8421 (mtpp) cc_final: 0.7909 (tptt) REVERT: J 178 GLU cc_start: 0.8488 (pp20) cc_final: 0.7780 (tp30) REVERT: J 352 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5272 (ptp) REVERT: J 661 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.4787 (m-80) REVERT: J 732 LYS cc_start: 0.7825 (pttm) cc_final: 0.7604 (tptp) REVERT: J 742 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7872 (ttmm) REVERT: A 60 ASP cc_start: 0.7535 (t0) cc_final: 0.7222 (m-30) REVERT: C 67 LYS cc_start: 0.5295 (tmtt) cc_final: 0.4935 (tptp) REVERT: C 151 LEU cc_start: 0.6667 (tp) cc_final: 0.6405 (tt) REVERT: E 93 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8148 (mmm) REVERT: E 166 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8205 (m-30) REVERT: I 57 LYS cc_start: 0.8706 (tttt) cc_final: 0.8262 (ttpt) REVERT: I 92 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8136 (tp30) REVERT: M 79 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7972 (mmmm) REVERT: N 129 ILE cc_start: 0.5882 (pt) cc_final: 0.5663 (pt) REVERT: N 175 LYS cc_start: 0.7721 (ptpp) cc_final: 0.7517 (mttp) REVERT: N 198 LEU cc_start: 0.8857 (tm) cc_final: 0.8536 (tp) REVERT: O 91 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.5866 (p90) REVERT: P 109 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5769 (mp) REVERT: P 137 GLN cc_start: 0.7798 (pt0) cc_final: 0.7333 (pt0) REVERT: P 150 GLU cc_start: 0.6990 (pm20) cc_final: 0.6695 (pm20) outliers start: 60 outliers final: 39 residues processed: 306 average time/residue: 0.1428 time to fit residues: 66.9623 Evaluate side-chains 275 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 229 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 289 LEU Chi-restraints excluded: chain J residue 314 THR 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 448 ASN Chi-restraints excluded: chain J residue 451 LEU 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 586 ILE Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 661 TYR 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 88 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain M residue 79 LYS 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 O residue 193 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 173 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 GLN B 34 GLN ** I 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN O 105 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.166828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.138456 restraints weight = 30611.807| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.62 r_work: 0.3703 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.8877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20604 Z= 0.167 Angle : 0.721 10.608 27907 Z= 0.339 Chirality : 0.060 0.622 3114 Planarity : 0.004 0.075 3457 Dihedral : 11.433 179.768 3117 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.24 % Favored : 91.63 % Rotamer: Outliers : 3.42 % Allowed : 18.53 % Favored : 78.06 % 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: -2.88 (0.16), residues: 2390 helix: -1.07 (0.18), residues: 761 sheet: -1.38 (0.27), residues: 347 loop : -2.67 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 13 TYR 0.022 0.002 TYR I 3 PHE 0.018 0.002 PHE I 294 TRP 0.006 0.001 TRP J 600 HIS 0.004 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (20604) covalent geometry : angle 0.72062 / 0.34 (27907) hydrogen bonds : bond 0.02911 / 1.95 ( 408) hydrogen bonds : angle 4.36453 / 3.23 ( 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 329 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 258 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 133 LYS cc_start: 0.8487 (mtpp) cc_final: 0.8071 (mmmt) REVERT: J 178 GLU cc_start: 0.8511 (pp20) cc_final: 0.7977 (tt0) REVERT: J 352 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5344 (ptp) REVERT: J 661 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.4995 (m-80) REVERT: J 742 LYS cc_start: 0.8264 (ttpt) cc_final: 0.7865 (ttmm) REVERT: A 60 ASP cc_start: 0.7495 (t0) cc_final: 0.7249 (m-30) REVERT: B 34 GLN cc_start: 0.5927 (OUTLIER) cc_final: 0.5636 (pt0) REVERT: C 151 LEU cc_start: 0.6750 (tp) cc_final: 0.6483 (tt) REVERT: C 198 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5657 (tt) REVERT: E 93 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8404 (mmm) REVERT: E 117 TYR cc_start: 0.7706 (m-80) cc_final: 0.7430 (m-80) REVERT: E 166 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8144 (m-30) REVERT: I 57 LYS cc_start: 0.8678 (tttt) cc_final: 0.8272 (ttpt) REVERT: I 92 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8063 (tp30) REVERT: I 196 ILE cc_start: 0.6794 (mp) cc_final: 0.6431 (tp) REVERT: N 158 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: N 163 VAL cc_start: 0.8459 (t) cc_final: 0.8230 (p) REVERT: N 198 LEU cc_start: 0.8816 (tm) cc_final: 0.8522 (tp) REVERT: O 91 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7414 (p90) REVERT: P 93 MET cc_start: 0.8413 (mmt) cc_final: 0.8131 (mmt) REVERT: P 109 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5839 (mp) REVERT: P 137 GLN cc_start: 0.7729 (pt0) cc_final: 0.7355 (pt0) outliers start: 71 outliers final: 43 residues processed: 309 average time/residue: 0.1459 time to fit residues: 69.0144 Evaluate side-chains 277 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 221 ARG Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 289 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 448 ASN Chi-restraints excluded: chain J residue 451 LEU 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 586 ILE Chi-restraints excluded: chain J residue 644 LEU Chi-restraints excluded: chain J residue 661 TYR 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 17 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 34 GLN 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 198 LEU Chi-restraints excluded: chain E residue 93 MET 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 41 LEU Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 59 THR 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 M residue 69 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain N residue 158 GLU Chi-restraints excluded: chain N residue 202 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 46 ILE 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 O residue 179 LEU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 223 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 0.0870 chunk 121 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 667 GLN C 159 ASN ** I 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 ASN ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.169000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.140263 restraints weight = 30842.392| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.88 r_work: 0.3717 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.8963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20604 Z= 0.119 Angle : 0.659 10.287 27907 Z= 0.311 Chirality : 0.056 0.541 3114 Planarity : 0.003 0.055 3457 Dihedral : 11.292 178.854 3117 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.70 % Favored : 92.18 % Rotamer: Outliers : 3.03 % Allowed : 19.73 % Favored : 77.24 % 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: -2.67 (0.16), residues: 2390 helix: -0.85 (0.19), residues: 781 sheet: -1.31 (0.27), residues: 345 loop : -2.58 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 90 TYR 0.027 0.001 TYR J 706 PHE 0.014 0.001 PHE O 26 TRP 0.006 0.001 TRP J 38 HIS 0.004 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (20604) covalent geometry : angle 0.65914 / 0.31 (27907) hydrogen bonds : bond 0.02577 / 1.73 ( 408) hydrogen bonds : angle 4.18356 / 3.11 ( 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 316 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 253 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: J 54 TYR cc_start: 0.8009 (m-80) cc_final: 0.7806 (m-80) REVERT: J 133 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8010 (tptt) REVERT: J 177 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: J 178 GLU cc_start: 0.8533 (pp20) cc_final: 0.7848 (tp30) REVERT: J 352 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.5344 (ptp) REVERT: J 519 ASP cc_start: 0.5539 (OUTLIER) cc_final: 0.5130 (p0) REVERT: J 661 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.4970 (m-80) REVERT: J 732 LYS cc_start: 0.7940 (pttm) cc_final: 0.7471 (tptp) REVERT: J 742 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7801 (ttmm) REVERT: C 13 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.7240 (ttt90) REVERT: E 117 TYR cc_start: 0.7648 (m-80) cc_final: 0.7430 (m-80) REVERT: E 166 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8252 (m-30) REVERT: I 57 LYS cc_start: 0.8731 (tttt) cc_final: 0.8289 (ttpt) REVERT: I 92 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8044 (tp30) REVERT: I 196 ILE cc_start: 0.6791 (mp) cc_final: 0.6423 (tp) REVERT: M 22 LYS cc_start: 0.8095 (mptt) cc_final: 0.7859 (mmtp) REVERT: N 158 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: N 198 LEU cc_start: 0.8891 (tm) cc_final: 0.8599 (tp) REVERT: O 91 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7340 (p90) REVERT: P 93 MET cc_start: 0.8379 (mmt) cc_final: 0.8105 (mmt) REVERT: P 137 GLN cc_start: 0.7782 (pt0) cc_final: 0.7282 (pt0) REVERT: P 176 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8676 (tt) outliers start: 63 outliers final: 48 residues processed: 296 average time/residue: 0.1425 time to fit residues: 64.3595 Evaluate side-chains 287 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 231 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 177 PHE 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 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 484 PHE Chi-restraints excluded: chain J residue 493 ILE 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 586 ILE Chi-restraints excluded: chain J residue 661 TYR 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 17 ILE 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 E residue 46 ILE Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain N residue 158 GLU Chi-restraints excluded: chain N residue 202 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain O residue 46 ILE 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 O residue 179 LEU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 176 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 114 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 150 optimal weight: 0.0570 chunk 200 optimal weight: 0.7980 chunk 181 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 489 GLN ** J 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.169300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140306 restraints weight = 30844.473| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.84 r_work: 0.3720 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.9056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20604 Z= 0.116 Angle : 0.644 10.146 27907 Z= 0.305 Chirality : 0.055 0.500 3114 Planarity : 0.003 0.056 3457 Dihedral : 11.196 178.709 3117 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.82 % Favored : 92.05 % Rotamer: Outliers : 3.27 % Allowed : 19.73 % Favored : 77.00 % 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: -2.42 (0.17), residues: 2390 helix: -0.48 (0.19), residues: 755 sheet: -1.24 (0.27), residues: 345 loop : -2.48 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 171 TYR 0.021 0.001 TYR J 670 PHE 0.017 0.001 PHE M 54 TRP 0.005 0.001 TRP J 38 HIS 0.004 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (20604) covalent geometry : angle 0.64426 / 0.31 (27907) hydrogen bonds : bond 0.02469 / 1.66 ( 408) hydrogen bonds : angle 4.06068 / 3.04 ( 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 321 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 253 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8019 (tptt) REVERT: J 177 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: J 178 GLU cc_start: 0.8510 (pp20) cc_final: 0.7962 (tt0) REVERT: J 352 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.5349 (ptp) REVERT: J 519 ASP cc_start: 0.5340 (OUTLIER) cc_final: 0.4994 (p0) REVERT: J 661 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.4984 (m-80) REVERT: J 732 LYS cc_start: 0.7986 (pttm) cc_final: 0.7478 (tptp) REVERT: A 53 LYS cc_start: 0.8462 (mttp) cc_final: 0.7978 (ptmt) REVERT: C 40 PRO cc_start: 0.6984 (Cg_endo) cc_final: 0.6567 (Cg_exo) REVERT: C 71 LYS cc_start: 0.6561 (pttm) cc_final: 0.6037 (pttm) REVERT: C 198 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5596 (tt) REVERT: E 166 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: I 57 LYS cc_start: 0.8708 (tttt) cc_final: 0.8322 (ttpt) REVERT: I 92 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8072 (tp30) REVERT: I 196 ILE cc_start: 0.6750 (mp) cc_final: 0.6422 (tp) REVERT: N 129 ILE cc_start: 0.6136 (pt) cc_final: 0.5814 (pt) REVERT: N 158 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: N 172 ASP cc_start: 0.8094 (t0) cc_final: 0.7893 (m-30) REVERT: N 198 LEU cc_start: 0.8860 (tm) cc_final: 0.8569 (tp) REVERT: O 91 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7520 (p90) REVERT: P 93 MET cc_start: 0.8297 (mmt) cc_final: 0.8086 (mmt) REVERT: P 137 GLN cc_start: 0.7759 (pt0) cc_final: 0.7285 (pt0) REVERT: P 176 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8722 (tt) outliers start: 68 outliers final: 50 residues processed: 300 average time/residue: 0.1382 time to fit residues: 63.9323 Evaluate side-chains 297 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 238 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 177 PHE Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 221 ARG 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 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 419 ILE Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 519 ASP Chi-restraints excluded: chain J residue 558 ILE Chi-restraints excluded: chain J residue 580 ILE Chi-restraints excluded: chain J residue 586 ILE Chi-restraints excluded: chain J residue 661 TYR 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 17 ILE 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 198 LEU Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 158 GLU Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain O residue 46 ILE 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 O residue 179 LEU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 176 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 211 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 214 optimal weight: 0.6980 chunk 16 optimal weight: 0.0970 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4182 r_free = 0.4182 target = 0.169655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140812 restraints weight = 30691.889| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.89 r_work: 0.3741 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.9139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20604 Z= 0.109 Angle : 0.631 9.987 27907 Z= 0.299 Chirality : 0.053 0.465 3114 Planarity : 0.003 0.052 3457 Dihedral : 11.131 179.011 3117 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.70 % Favored : 92.22 % Rotamer: Outliers : 2.98 % Allowed : 20.26 % Favored : 76.76 % 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: -2.26 (0.17), residues: 2390 helix: -0.33 (0.19), residues: 760 sheet: -1.19 (0.27), residues: 345 loop : -2.39 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 182 TYR 0.027 0.001 TYR J 706 PHE 0.014 0.001 PHE I 294 TRP 0.005 0.001 TRP J 38 HIS 0.004 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (20604) covalent geometry : angle 0.63085 / 0.30 (27907) hydrogen bonds : bond 0.02355 / 1.58 ( 408) hydrogen bonds : angle 3.97549 / 3.00 ( 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 300 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 238 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8023 (tptt) REVERT: J 178 GLU cc_start: 0.8535 (pp20) cc_final: 0.7960 (tt0) REVERT: J 352 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5315 (ptp) REVERT: J 519 ASP cc_start: 0.5316 (OUTLIER) cc_final: 0.4988 (p0) REVERT: J 661 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.4909 (m-80) REVERT: C 13 ARG cc_start: 0.7598 (ttm-80) cc_final: 0.7367 (ttt90) REVERT: C 71 LYS cc_start: 0.6665 (pttm) cc_final: 0.6130 (pttm) REVERT: C 165 GLU cc_start: 0.5905 (tm-30) cc_final: 0.5681 (tm-30) REVERT: C 198 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5562 (tt) REVERT: E 166 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: I 6 TYR cc_start: 0.8593 (m-80) cc_final: 0.8198 (m-80) REVERT: I 57 LYS cc_start: 0.8796 (tttt) cc_final: 0.8410 (ttpt) REVERT: I 92 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8027 (tp30) REVERT: I 153 ASP cc_start: 0.6532 (p0) cc_final: 0.6237 (p0) REVERT: I 196 ILE cc_start: 0.6809 (mp) cc_final: 0.6455 (tp) REVERT: N 158 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: N 172 ASP cc_start: 0.8149 (t0) cc_final: 0.7919 (m-30) REVERT: O 68 VAL cc_start: 0.8514 (t) cc_final: 0.8253 (p) REVERT: O 91 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7650 (p90) REVERT: P 89 LYS cc_start: 0.7335 (mmmt) cc_final: 0.6963 (mmmt) REVERT: P 204 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.5046 (m-80) outliers start: 62 outliers final: 49 residues processed: 281 average time/residue: 0.1388 time to fit residues: 60.3211 Evaluate side-chains 285 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 221 ARG 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 328 PHE 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 419 ILE Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 519 ASP Chi-restraints excluded: chain J residue 558 ILE Chi-restraints excluded: chain J residue 586 ILE Chi-restraints excluded: chain J residue 661 TYR 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 88 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 158 GLU Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 46 ILE 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 O residue 179 LEU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 204 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 84 optimal weight: 8.9990 chunk 121 optimal weight: 0.0570 chunk 76 optimal weight: 8.9990 chunk 10 optimal weight: 0.0020 chunk 28 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 152 optimal weight: 0.0670 chunk 106 optimal weight: 10.0000 overall best weight: 0.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 GLN ** 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 = 0.4184 r_free = 0.4184 target = 0.169667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.141016 restraints weight = 31004.133| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.86 r_work: 0.3732 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.9209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20604 Z= 0.111 Angle : 0.630 10.007 27907 Z= 0.300 Chirality : 0.053 0.452 3114 Planarity : 0.003 0.048 3457 Dihedral : 11.098 179.355 3117 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.49 % Favored : 92.43 % Rotamer: Outliers : 2.98 % Allowed : 20.69 % Favored : 76.32 % 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: -0.18 (0.20), residues: 767 sheet: -1.15 (0.28), residues: 345 loop : -2.34 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 140 TYR 0.025 0.001 TYR J 670 PHE 0.018 0.001 PHE J 645 TRP 0.006 0.001 TRP J 38 HIS 0.004 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (20604) covalent geometry : angle 0.63047 / 0.30 (27907) hydrogen bonds : bond 0.02365 / 1.60 ( 408) hydrogen bonds : angle 3.96940 / 2.99 ( 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 292 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 230 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 LYS cc_start: 0.8507 (mtpp) cc_final: 0.8058 (mmmt) REVERT: J 178 GLU cc_start: 0.8542 (pp20) cc_final: 0.7964 (tt0) REVERT: J 266 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7631 (pt0) REVERT: J 352 MET cc_start: 0.5774 (OUTLIER) cc_final: 0.5295 (ptp) REVERT: J 519 ASP cc_start: 0.5419 (OUTLIER) cc_final: 0.5090 (p0) REVERT: J 661 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.4982 (m-80) REVERT: J 732 LYS cc_start: 0.8102 (pttm) cc_final: 0.7481 (tptp) REVERT: C 13 ARG cc_start: 0.7572 (ttm-80) cc_final: 0.7327 (ttt90) REVERT: C 198 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5522 (tt) REVERT: E 166 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8265 (m-30) REVERT: I 57 LYS cc_start: 0.8755 (tttt) cc_final: 0.8343 (ttpt) REVERT: I 92 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8026 (tp30) REVERT: I 196 ILE cc_start: 0.6933 (mp) cc_final: 0.6559 (tp) REVERT: N 108 GLU cc_start: 0.7807 (pp20) cc_final: 0.7327 (pt0) REVERT: N 158 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: O 68 VAL cc_start: 0.8587 (t) cc_final: 0.8345 (p) REVERT: O 91 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7820 (p90) REVERT: P 93 MET cc_start: 0.8431 (mmt) cc_final: 0.7902 (mmp) REVERT: P 204 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.5112 (m-80) outliers start: 62 outliers final: 51 residues processed: 274 average time/residue: 0.1363 time to fit residues: 58.0786 Evaluate side-chains 284 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 266 GLN Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 328 PHE 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 419 ILE Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 519 ASP Chi-restraints excluded: chain J residue 558 ILE Chi-restraints excluded: chain J residue 586 ILE Chi-restraints excluded: chain J residue 661 TYR 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 88 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 158 GLU Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 46 ILE 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 O residue 179 LEU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 204 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 215 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 0.0470 chunk 7 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 85 ASN ** 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 = 0.4173 r_free = 0.4173 target = 0.168641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141214 restraints weight = 30892.856| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.48 r_work: 0.3728 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.9329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20604 Z= 0.117 Angle : 0.635 11.526 27907 Z= 0.301 Chirality : 0.053 0.463 3114 Planarity : 0.003 0.047 3457 Dihedral : 11.096 179.641 3117 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.62 % Favored : 92.30 % Rotamer: Outliers : 3.08 % Allowed : 20.79 % Favored : 76.13 % 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: -2.10 (0.17), residues: 2390 helix: -0.08 (0.20), residues: 767 sheet: -1.26 (0.27), residues: 355 loop : -2.34 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 140 TYR 0.029 0.001 TYR J 706 PHE 0.028 0.001 PHE J 645 TRP 0.005 0.001 TRP J 38 HIS 0.004 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (20604) covalent geometry : angle 0.63497 / 0.30 (27907) hydrogen bonds : bond 0.02346 / 1.58 ( 408) hydrogen bonds : angle 3.94447 / 2.97 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4051.18 seconds wall clock time: 70 minutes 35.29 seconds (4235.29 seconds total)