Starting phenix.real_space_refine on Sat Jul 4 10:58:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nue_0519/07_2026/6nue_0519.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nue_0519/07_2026/6nue_0519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nue_0519/07_2026/6nue_0519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nue_0519/07_2026/6nue_0519.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nue_0519/07_2026/6nue_0519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nue_0519/07_2026/6nue_0519.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nue_0519/07_2026/6nue_0519.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nue_0519/07_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-dev-6108/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: {'RNA': 40} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 14, 'rna3p_pur': 8, 'rna3p_pyr': 11} Link IDs: {'rna2p': 21, 'rna3p': 18} Chain: "I" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2352 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 283} Chain: "M" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "N" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "O" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "P" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.21, per 1000 atoms: 0.21 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: 1.82 Conformation dependent library (CDL) restraints added in 860.6 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: 2.18 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: 3.05 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5945 1.33 - 1.45: 3242 1.45 - 1.57: 11268 1.57 - 1.69: 83 1.69 - 1.81: 66 Bond restraints: 20604 Sorted by residual: bond pdb=" C4 ATP J 801 " pdb=" C5 ATP J 801 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.81e+01 bond pdb=" C5 ATP J 801 " pdb=" C6 ATP J 801 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.38e+01 bond pdb=" C8 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.31e+01 bond pdb=" C5 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.387 1.346 0.041 1.00e-02 1.00e+04 1.70e+01 bond pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 1.374 1.335 0.039 1.00e-02 1.00e+04 1.49e+01 ... (remaining 20599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 27878 4.05 - 8.11: 25 8.11 - 12.16: 2 12.16 - 16.22: 0 16.22 - 20.27: 2 Bond angle restraints: 27907 Sorted by residual: angle pdb=" PB ATP J 801 " pdb=" O3B ATP J 801 " pdb=" PG ATP J 801 " ideal model delta sigma weight residual 139.87 119.60 20.27 1.00e+00 1.00e+00 4.11e+02 angle pdb=" PA ATP J 801 " pdb=" O3A ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 136.83 120.19 16.64 1.00e+00 1.00e+00 2.77e+02 angle pdb=" C5 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N3 ATP J 801 " ideal model delta sigma weight residual 126.80 118.69 8.11 1.00e+00 1.00e+00 6.58e+01 angle pdb=" N3 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 127.04 134.99 -7.95 1.15e+00 7.59e-01 4.80e+01 angle pdb=" C SER J 353 " pdb=" CA SER J 353 " pdb=" CB SER J 353 " ideal model delta sigma weight residual 117.23 110.41 6.82 1.36e+00 5.41e-01 2.52e+01 ... (remaining 27902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 12248 35.22 - 70.43: 120 70.43 - 105.65: 10 105.65 - 140.87: 0 140.87 - 176.08: 9 Dihedral angle restraints: 12387 sinusoidal: 5355 harmonic: 7032 Sorted by residual: dihedral pdb=" O4' C H 17 " pdb=" C1' C H 17 " pdb=" N1 C H 17 " pdb=" C2 C H 17 " ideal model delta sinusoidal sigma weight residual 200.00 51.91 148.09 1 1.50e+01 4.44e-03 7.89e+01 dihedral pdb=" O4' C H 40 " pdb=" C1' C H 40 " pdb=" N1 C H 40 " pdb=" C2 C H 40 " ideal model delta sinusoidal sigma weight residual 200.00 54.87 145.13 1 1.50e+01 4.44e-03 7.77e+01 dihedral pdb=" O4' C H 34 " pdb=" C1' C H 34 " pdb=" N1 C H 34 " pdb=" C2 C H 34 " ideal model delta sinusoidal sigma weight residual 200.00 55.25 144.75 1 1.50e+01 4.44e-03 7.75e+01 ... (remaining 12384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1880 0.027 - 0.053: 883 0.053 - 0.080: 198 0.080 - 0.106: 107 0.106 - 0.133: 46 Chirality restraints: 3114 Sorted by residual: chirality pdb=" C1' C H 40 " pdb=" O4' C H 40 " pdb=" C2' C H 40 " pdb=" N1 C H 40 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" C1' C H 34 " pdb=" O4' C H 34 " pdb=" C2' C H 34 " pdb=" N1 C H 34 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" C1' U H 22 " pdb=" O4' U H 22 " pdb=" C2' U H 22 " pdb=" N1 U H 22 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 3111 not shown) Planarity restraints: 3457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 196 " -0.016 5.00e-02 4.00e+02 2.42e-02 9.37e-01 pdb=" N PRO I 197 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO I 197 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO I 197 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 142 " -0.014 5.00e-02 4.00e+02 2.09e-02 7.00e-01 pdb=" N PRO J 143 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO J 143 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO J 143 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 71 " -0.014 5.00e-02 4.00e+02 2.08e-02 6.95e-01 pdb=" N PRO O 72 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO O 72 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO O 72 " -0.012 5.00e-02 4.00e+02 ... (remaining 3454 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2269 2.75 - 3.29: 18847 3.29 - 3.83: 30286 3.83 - 4.36: 35721 4.36 - 4.90: 61458 Nonbonded interactions: 148581 Sorted by model distance: nonbonded pdb=" OG SER I 28 " pdb=" OD1 ASP I 30 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR I 59 " pdb=" OH TYR I 289 " model vdw 2.263 3.040 nonbonded pdb=" O LEU I 60 " pdb=" OH TYR I 289 " model vdw 2.286 3.040 nonbonded pdb=" OG SER J 500 " pdb=" O ILE J 508 " model vdw 2.298 3.040 nonbonded pdb=" O2' C H 12 " pdb=" OP1 G H 13 " model vdw 2.299 3.040 ... (remaining 148576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.090 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- 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= 0.136 Angle : 0.469 20.272 27907 Z= 0.323 Chirality : 0.036 0.133 3114 Planarity : 0.002 0.024 3457 Dihedral : 11.147 176.083 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 0.00175 / 0.14 (20604) covalent geometry : angle 0.46925 / 0.32 (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 : 0.755 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: 0.1735 time to fit residues: 154.7268 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 : 0.781 ------------------------------------------------------------------------------- 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 169 GLN J 189 ASN J 223 ASN ** J 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 334 GLN J 356 ASN J 389 ASN J 403 HIS J 432 HIS J 440 ASN J 482 HIS J 489 GLN J 502 ASN J 560 GLN J 602 ASN J 737 ASN A 27 ASN B 27 ASN C 11 GLN C 85 ASN C 105 ASN C 134 ASN C 213 ASN E 85 ASN E 134 ASN E 206 ASN E 213 ASN I 83 GLN I 207 ASN I 233 HIS I 255 GLN I 284 HIS M 27 ASN M 71 GLN N 11 GLN N 85 ASN ** N 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.213793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.190756 restraints weight = 31013.109| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 2.44 r_work: 0.4273 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20604 Z= 0.167 Angle : 0.628 9.295 27907 Z= 0.324 Chirality : 0.043 0.165 3114 Planarity : 0.004 0.055 3457 Dihedral : 10.182 177.944 3117 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.42 % Favored : 88.28 % Rotamer: Outliers : 2.45 % Allowed : 12.75 % Favored : 84.79 % 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: -4.55 (0.13), residues: 2390 helix: -2.84 (0.14), residues: 705 sheet: -2.24 (0.27), residues: 286 loop : -3.44 (0.13), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 171 TYR 0.022 0.002 TYR J 706 PHE 0.027 0.002 PHE J 672 TRP 0.011 0.001 TRP J 733 HIS 0.006 0.001 HIS J 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (20604) covalent geometry : angle 0.62753 / 0.32 (27907) hydrogen bonds : bond 0.05844 / 4.01 ( 408) hydrogen bonds : angle 5.79327 / 4.38 ( 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 421 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 370 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 178 GLU cc_start: 0.8418 (pp20) cc_final: 0.7681 (tp30) REVERT: J 266 GLN cc_start: 0.8491 (pp30) cc_final: 0.8093 (pt0) REVERT: J 423 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7917 (mt) REVERT: J 470 LYS cc_start: 0.5529 (tmtt) cc_final: 0.4093 (tmtt) REVERT: J 602 ASN cc_start: 0.7797 (t0) cc_final: 0.7359 (t0) REVERT: J 648 ASP cc_start: 0.6514 (p0) cc_final: 0.6228 (p0) REVERT: J 671 PHE cc_start: 0.6044 (m-10) cc_final: 0.5766 (m-10) REVERT: J 706 TYR cc_start: 0.8174 (t80) cc_final: 0.7898 (t80) REVERT: J 742 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7989 (ttpt) REVERT: A 60 ASP cc_start: 0.8040 (t0) cc_final: 0.7710 (m-30) REVERT: B 88 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6325 (mm) REVERT: B 92 LYS cc_start: 0.7417 (mtmm) cc_final: 0.7089 (mtmm) REVERT: B 97 ARG cc_start: 0.7581 (tmm-80) cc_final: 0.7139 (ttp-170) REVERT: C 13 ARG cc_start: 0.7472 (ttt90) cc_final: 0.7242 (ttm-80) REVERT: C 87 LYS cc_start: 0.5908 (mmtt) cc_final: 0.5268 (ttpt) REVERT: C 139 GLU cc_start: 0.7331 (tt0) cc_final: 0.6886 (tm-30) REVERT: C 147 PHE cc_start: 0.6271 (m-80) cc_final: 0.6038 (m-80) REVERT: E 171 ARG cc_start: 0.6432 (ttm170) cc_final: 0.6230 (ttm170) REVERT: I 92 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8205 (tm-30) REVERT: O 60 LEU cc_start: 0.8412 (tt) cc_final: 0.8202 (tp) REVERT: O 70 GLU cc_start: 0.5924 (pm20) cc_final: 0.5666 (mm-30) REVERT: O 150 GLU cc_start: 0.6937 (pm20) cc_final: 0.6680 (pt0) REVERT: P 204 PHE cc_start: 0.3946 (OUTLIER) cc_final: 0.3673 (m-80) outliers start: 51 outliers final: 24 residues processed: 402 average time/residue: 0.1671 time to fit residues: 100.0309 Evaluate side-chains 303 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 276 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 418 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 560 GLN Chi-restraints excluded: chain 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 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 I residue 255 GLN Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 204 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 178 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 222 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 169 GLN J 201 HIS J 266 GLN ** J 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 334 GLN J 412 HIS J 440 ASN J 536 GLN C 19 HIS C 206 ASN I 14 HIS I 135 GLN ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.185765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.157893 restraints weight = 30817.097| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.73 r_work: 0.3910 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20604 Z= 0.208 Angle : 0.719 12.872 27907 Z= 0.367 Chirality : 0.046 0.266 3114 Planarity : 0.005 0.084 3457 Dihedral : 10.901 178.357 3117 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.16 % Favored : 90.63 % Rotamer: Outliers : 3.42 % Allowed : 14.77 % Favored : 81.81 % 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: -3.98 (0.14), residues: 2390 helix: -2.24 (0.16), residues: 748 sheet: -2.00 (0.26), residues: 340 loop : -3.17 (0.14), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 97 TYR 0.021 0.002 TYR J 661 PHE 0.030 0.002 PHE O 26 TRP 0.013 0.002 TRP J 600 HIS 0.007 0.002 HIS J 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (20604) covalent geometry : angle 0.71924 / 0.37 (27907) hydrogen bonds : bond 0.03723 / 2.55 ( 408) hydrogen bonds : angle 4.95933 / 3.65 ( 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 428 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 357 time to evaluate : 0.748 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: J 178 GLU cc_start: 0.8464 (pp20) cc_final: 0.7803 (tp30) REVERT: J 520 ASP cc_start: 0.6282 (t0) cc_final: 0.5875 (t0) REVERT: J 648 ASP cc_start: 0.7216 (p0) cc_final: 0.6922 (p0) REVERT: J 661 TYR cc_start: 0.6066 (OUTLIER) cc_final: 0.5798 (m-80) REVERT: J 706 TYR cc_start: 0.8142 (t80) cc_final: 0.7759 (t80) REVERT: J 714 LEU cc_start: 0.8872 (tt) cc_final: 0.8626 (tp) REVERT: J 742 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7901 (ttmm) REVERT: A 60 ASP cc_start: 0.7985 (t0) cc_final: 0.7720 (m-30) REVERT: A 63 TYR cc_start: 0.8275 (t80) cc_final: 0.8036 (t80) REVERT: E 166 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: E 175 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7950 (pptt) REVERT: E 204 PHE cc_start: 0.5172 (OUTLIER) cc_final: 0.4296 (m-80) REVERT: I 28 SER cc_start: 0.8400 (p) cc_final: 0.8011 (p) REVERT: I 45 LYS cc_start: 0.8160 (ptpt) cc_final: 0.7692 (pttp) REVERT: I 57 LYS cc_start: 0.8622 (tttt) cc_final: 0.8331 (ttpt) REVERT: I 92 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8068 (tp30) REVERT: O 117 TYR cc_start: 0.8502 (m-80) cc_final: 0.8204 (m-80) REVERT: P 15 GLU cc_start: 0.7229 (pt0) cc_final: 0.6395 (mm-30) REVERT: P 204 PHE cc_start: 0.6338 (OUTLIER) cc_final: 0.5106 (m-80) outliers start: 71 outliers final: 30 residues processed: 404 average time/residue: 0.1561 time to fit residues: 94.9682 Evaluate side-chains 280 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 440 ASN Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 661 TYR Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 68 VAL 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 204 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 163 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 234 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 161 optimal weight: 0.5980 chunk 110 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 266 GLN J 295 ASN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 667 GLN A 101 GLN C 11 GLN C 159 ASN E 19 HIS I 152 ASN ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 GLN N 137 GLN N 162 GLN O 105 ASN O 134 ASN O 159 ASN P 144 ASN P 206 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.185533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.157143 restraints weight = 30748.082| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.01 r_work: 0.3914 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20604 Z= 0.110 Angle : 0.556 13.580 27907 Z= 0.282 Chirality : 0.040 0.175 3114 Planarity : 0.004 0.071 3457 Dihedral : 10.656 179.864 3117 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.82 % Favored : 92.05 % Rotamer: Outliers : 2.55 % Allowed : 16.99 % Favored : 80.46 % 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: -3.48 (0.15), residues: 2390 helix: -1.60 (0.17), residues: 745 sheet: -1.65 (0.28), residues: 326 loop : -3.02 (0.15), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 115 TYR 0.019 0.001 TYR M 63 PHE 0.025 0.001 PHE J 672 TRP 0.006 0.001 TRP J 600 HIS 0.006 0.001 HIS J 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (20604) covalent geometry : angle 0.55575 / 0.28 (27907) hydrogen bonds : bond 0.02754 / 1.86 ( 408) hydrogen bonds : angle 4.48590 / 3.38 ( 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 325 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 178 GLU cc_start: 0.8410 (pp20) cc_final: 0.7724 (tp30) REVERT: J 648 ASP cc_start: 0.7250 (p0) cc_final: 0.6965 (p0) REVERT: J 661 TYR cc_start: 0.6631 (OUTLIER) cc_final: 0.5626 (m-80) REVERT: J 706 TYR cc_start: 0.8063 (t80) cc_final: 0.7667 (t80) REVERT: J 714 LEU cc_start: 0.8864 (tt) cc_final: 0.8570 (tp) REVERT: J 742 LYS cc_start: 0.8287 (ttpt) cc_final: 0.7914 (ttmm) REVERT: A 60 ASP cc_start: 0.7978 (t0) cc_final: 0.7725 (m-30) REVERT: C 13 ARG cc_start: 0.7751 (ttt90) cc_final: 0.7507 (ttm-80) REVERT: E 159 ASN cc_start: 0.7696 (m-40) cc_final: 0.7386 (m110) REVERT: E 166 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: E 175 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7970 (pptt) REVERT: E 204 PHE cc_start: 0.5129 (OUTLIER) cc_final: 0.4319 (m-80) REVERT: I 28 SER cc_start: 0.8335 (p) cc_final: 0.8033 (p) REVERT: I 45 LYS cc_start: 0.8104 (ptpt) cc_final: 0.7868 (ptpt) REVERT: I 92 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8046 (tp30) REVERT: N 134 ASN cc_start: 0.6415 (t0) cc_final: 0.6121 (t0) REVERT: O 117 TYR cc_start: 0.8533 (m-80) cc_final: 0.8319 (m-80) REVERT: P 15 GLU cc_start: 0.6945 (pt0) cc_final: 0.5962 (mm-30) REVERT: P 204 PHE cc_start: 0.5935 (OUTLIER) cc_final: 0.5198 (m-80) outliers start: 53 outliers final: 32 residues processed: 310 average time/residue: 0.1509 time to fit residues: 71.6484 Evaluate side-chains 282 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 216 LEU Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 351 ILE Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 517 ASP Chi-restraints excluded: chain J residue 569 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 A residue 38 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 204 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 186 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 163 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 194 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 113 optimal weight: 0.0060 chunk 105 optimal weight: 4.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 560 GLN M 71 GLN O 105 ASN O 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.183834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.156177 restraints weight = 30547.500| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.57 r_work: 0.3890 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20604 Z= 0.103 Angle : 0.521 9.226 27907 Z= 0.264 Chirality : 0.040 0.178 3114 Planarity : 0.004 0.075 3457 Dihedral : 10.612 179.554 3117 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.57 % Favored : 92.30 % Rotamer: Outliers : 3.03 % Allowed : 16.60 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.16), residues: 2390 helix: -1.11 (0.19), residues: 738 sheet: -1.56 (0.27), residues: 330 loop : -2.72 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 95 TYR 0.020 0.001 TYR P 64 PHE 0.020 0.001 PHE J 726 TRP 0.013 0.001 TRP J 38 HIS 0.004 0.001 HIS J 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (20604) covalent geometry : angle 0.52055 / 0.26 (27907) hydrogen bonds : bond 0.02489 / 1.68 ( 408) hydrogen bonds : angle 4.18107 / 3.19 ( 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 329 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 266 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 LYS cc_start: 0.7907 (mtpp) cc_final: 0.7567 (tptt) REVERT: J 178 GLU cc_start: 0.8422 (pp20) cc_final: 0.7772 (tp30) REVERT: J 519 ASP cc_start: 0.5731 (OUTLIER) cc_final: 0.5244 (p0) REVERT: J 661 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.5236 (m-80) REVERT: J 742 LYS cc_start: 0.8245 (ttpt) cc_final: 0.7867 (ttmm) REVERT: A 60 ASP cc_start: 0.7972 (t0) cc_final: 0.7737 (m-30) REVERT: C 171 ARG cc_start: 0.6789 (mmm160) cc_final: 0.6478 (mmm160) REVERT: C 198 LEU cc_start: 0.5724 (OUTLIER) cc_final: 0.5453 (tt) REVERT: E 117 TYR cc_start: 0.7177 (m-80) cc_final: 0.6942 (m-80) REVERT: E 159 ASN cc_start: 0.7706 (m-40) cc_final: 0.7477 (m110) REVERT: E 164 GLU cc_start: 0.8151 (pm20) cc_final: 0.7475 (mm-30) REVERT: E 166 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8123 (m-30) REVERT: E 175 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7913 (pptt) REVERT: E 204 PHE cc_start: 0.5248 (OUTLIER) cc_final: 0.4578 (m-80) REVERT: I 28 SER cc_start: 0.8366 (p) cc_final: 0.7953 (p) REVERT: N 129 ILE cc_start: 0.5782 (pt) cc_final: 0.5578 (pt) REVERT: N 134 ASN cc_start: 0.6490 (t0) cc_final: 0.6162 (t0) REVERT: O 117 TYR cc_start: 0.8535 (m-80) cc_final: 0.8311 (m-80) outliers start: 63 outliers final: 31 residues processed: 307 average time/residue: 0.1443 time to fit residues: 67.9950 Evaluate side-chains 279 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 519 ASP Chi-restraints excluded: chain J residue 644 LEU 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 B residue 61 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 204 PHE Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 130 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 173 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 110 optimal weight: 0.0050 chunk 223 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 295 ASN E 137 GLN O 105 ASN O 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.182024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.153884 restraints weight = 30383.226| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.63 r_work: 0.3868 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.7265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20604 Z= 0.103 Angle : 0.517 8.376 27907 Z= 0.263 Chirality : 0.040 0.182 3114 Planarity : 0.004 0.061 3457 Dihedral : 10.648 179.888 3117 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.20 % Favored : 92.68 % Rotamer: Outliers : 2.31 % Allowed : 17.71 % Favored : 79.98 % 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: -2.82 (0.16), residues: 2390 helix: -0.85 (0.19), residues: 736 sheet: -1.64 (0.26), residues: 344 loop : -2.63 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 36 TYR 0.022 0.001 TYR J 298 PHE 0.018 0.001 PHE J 726 TRP 0.008 0.001 TRP J 38 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (20604) covalent geometry : angle 0.51723 / 0.26 (27907) hydrogen bonds : bond 0.02426 / 1.63 ( 408) hydrogen bonds : angle 4.05298 / 3.12 ( 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 310 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7614 (tptt) REVERT: J 178 GLU cc_start: 0.8401 (pp20) cc_final: 0.7779 (tp30) REVERT: J 519 ASP cc_start: 0.5619 (OUTLIER) cc_final: 0.5194 (p0) REVERT: J 661 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.5037 (m-80) REVERT: J 706 TYR cc_start: 0.7917 (t80) cc_final: 0.7467 (t80) REVERT: J 742 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7792 (ttmm) REVERT: A 60 ASP cc_start: 0.7802 (t0) cc_final: 0.7569 (m-30) REVERT: A 101 GLN cc_start: 0.7765 (mt0) cc_final: 0.7557 (mt0) REVERT: C 198 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5487 (tt) REVERT: E 93 MET cc_start: 0.8109 (mmm) cc_final: 0.7840 (mmm) REVERT: E 119 GLU cc_start: 0.7583 (pm20) cc_final: 0.6581 (pm20) REVERT: E 159 ASN cc_start: 0.7801 (m-40) cc_final: 0.7593 (m110) REVERT: E 164 GLU cc_start: 0.8213 (pm20) cc_final: 0.7544 (mm-30) REVERT: E 166 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8144 (m-30) REVERT: I 92 GLU cc_start: 0.8644 (tm-30) cc_final: 0.7914 (tp30) REVERT: I 123 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7462 (pt0) REVERT: N 129 ILE cc_start: 0.5644 (pt) cc_final: 0.5425 (pt) REVERT: N 134 ASN cc_start: 0.6644 (t0) cc_final: 0.6291 (t0) REVERT: O 117 TYR cc_start: 0.8542 (m-80) cc_final: 0.8308 (m-80) outliers start: 48 outliers final: 34 residues processed: 294 average time/residue: 0.1430 time to fit residues: 65.1676 Evaluate side-chains 286 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 519 ASP Chi-restraints excluded: chain J residue 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 39 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 47 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 64 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 chunk 210 optimal weight: 0.6980 chunk 223 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 131 optimal weight: 0.4980 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 203 optimal weight: 0.0000 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 700 ASN O 134 ASN P 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.181937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.153724 restraints weight = 30605.304| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.68 r_work: 0.3870 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.7399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20604 Z= 0.094 Angle : 0.509 8.418 27907 Z= 0.258 Chirality : 0.039 0.176 3114 Planarity : 0.003 0.055 3457 Dihedral : 10.624 179.136 3117 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.95 % Favored : 92.93 % Rotamer: Outliers : 2.60 % Allowed : 18.67 % Favored : 78.73 % 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: -2.60 (0.16), residues: 2390 helix: -0.57 (0.20), residues: 731 sheet: -1.57 (0.26), residues: 344 loop : -2.55 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 36 TYR 0.022 0.001 TYR J 670 PHE 0.018 0.001 PHE J 726 TRP 0.010 0.001 TRP J 38 HIS 0.003 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (20604) covalent geometry : angle 0.50941 / 0.26 (27907) hydrogen bonds : bond 0.02254 / 1.51 ( 408) hydrogen bonds : angle 3.95245 / 3.05 ( 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 323 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 133 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7635 (tptt) REVERT: J 178 GLU cc_start: 0.8425 (pp20) cc_final: 0.7644 (tp30) REVERT: J 519 ASP cc_start: 0.5818 (OUTLIER) cc_final: 0.5385 (p0) REVERT: J 661 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.4910 (m-80) REVERT: J 706 TYR cc_start: 0.8000 (t80) cc_final: 0.7612 (t80) REVERT: J 742 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7799 (ttmm) REVERT: A 60 ASP cc_start: 0.7783 (t0) cc_final: 0.7568 (m-30) REVERT: A 101 GLN cc_start: 0.7793 (mt0) cc_final: 0.7585 (mt0) REVERT: C 198 LEU cc_start: 0.5772 (OUTLIER) cc_final: 0.5560 (tt) REVERT: E 93 MET cc_start: 0.8255 (mmm) cc_final: 0.8045 (mmm) REVERT: E 164 GLU cc_start: 0.8186 (pm20) cc_final: 0.7531 (mm-30) REVERT: E 166 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8165 (m-30) REVERT: I 123 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7569 (pt0) REVERT: N 129 ILE cc_start: 0.5763 (pt) cc_final: 0.5534 (pt) REVERT: N 134 ASN cc_start: 0.6564 (t0) cc_final: 0.6220 (t0) REVERT: O 117 TYR cc_start: 0.8536 (m-80) cc_final: 0.8300 (m-80) outliers start: 54 outliers final: 40 residues processed: 306 average time/residue: 0.1454 time to fit residues: 68.8312 Evaluate side-chains 290 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 216 LEU Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 289 LEU Chi-restraints excluded: chain J residue 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 519 ASP Chi-restraints excluded: chain J residue 521 LEU Chi-restraints excluded: chain J residue 577 VAL 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 78 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 47 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 114 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 222 HIS J 440 ASN J 489 GLN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 GLN O 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.166720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.138117 restraints weight = 30841.175| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.66 r_work: 0.3678 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.8589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20604 Z= 0.196 Angle : 0.689 13.098 27907 Z= 0.349 Chirality : 0.045 0.253 3114 Planarity : 0.004 0.063 3457 Dihedral : 11.146 169.707 3117 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.41 % Favored : 91.46 % Rotamer: Outliers : 2.84 % Allowed : 18.67 % Favored : 78.49 % 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: -2.71 (0.16), residues: 2390 helix: -0.91 (0.19), residues: 752 sheet: -1.48 (0.26), residues: 347 loop : -2.51 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 140 TYR 0.041 0.002 TYR J 298 PHE 0.024 0.002 PHE I 294 TRP 0.009 0.002 TRP J 38 HIS 0.006 0.001 HIS J 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (20604) covalent geometry : angle 0.68922 / 0.35 (27907) hydrogen bonds : bond 0.03241 / 2.17 ( 408) hydrogen bonds : angle 4.38441 / 3.24 ( 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 335 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 276 time to evaluate : 0.659 Fit side-chains REVERT: J 29 LYS cc_start: 0.8087 (mttt) cc_final: 0.7765 (mtpp) REVERT: J 133 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8002 (mmmt) REVERT: J 178 GLU cc_start: 0.8528 (pp20) cc_final: 0.7889 (tp30) REVERT: J 519 ASP cc_start: 0.5488 (OUTLIER) cc_final: 0.4992 (p0) REVERT: J 661 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.4954 (m-80) REVERT: J 742 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7802 (ttmm) REVERT: A 22 LYS cc_start: 0.6599 (ptpt) cc_final: 0.6389 (ptpp) REVERT: A 60 ASP cc_start: 0.7880 (t0) cc_final: 0.7664 (m-30) REVERT: E 164 GLU cc_start: 0.8332 (pm20) cc_final: 0.7759 (mm-30) REVERT: E 166 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: I 92 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8195 (tp30) REVERT: I 192 ASP cc_start: 0.7985 (m-30) cc_final: 0.7744 (m-30) REVERT: N 158 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6452 (mp0) REVERT: N 198 LEU cc_start: 0.8817 (tm) cc_final: 0.8574 (tp) outliers start: 59 outliers final: 39 residues processed: 317 average time/residue: 0.1562 time to fit residues: 75.1034 Evaluate side-chains 275 residues out of total 2078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 216 LEU 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 330 LEU Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 351 ILE Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 440 ASN Chi-restraints excluded: chain J residue 448 ASN Chi-restraints excluded: chain J residue 467 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 519 ASP Chi-restraints excluded: chain J residue 558 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 A residue 38 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 287 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain N residue 158 GLU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 47 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.7662 > 50: distance: 93 - 94: 3.126 distance: 93 - 96: 5.142 distance: 94 - 95: 4.842 distance: 94 - 103: 9.533 distance: 96 - 97: 6.685 distance: 97 - 98: 15.656 distance: 98 - 100: 7.173 distance: 99 - 101: 10.688 distance: 100 - 102: 4.489 distance: 101 - 102: 8.310 distance: 103 - 104: 5.152 distance: 104 - 105: 5.987 distance: 104 - 107: 9.654 distance: 105 - 106: 11.406 distance: 105 - 109: 7.918 distance: 107 - 108: 6.758 distance: 109 - 110: 5.291 distance: 110 - 111: 11.057 distance: 111 - 112: 8.499 distance: 111 - 120: 15.707 distance: 113 - 114: 15.024 distance: 114 - 115: 6.957 distance: 116 - 117: 9.505 distance: 117 - 118: 9.385 distance: 117 - 119: 4.445 distance: 120 - 121: 14.539 distance: 121 - 122: 16.612 distance: 121 - 124: 15.553 distance: 122 - 123: 17.541 distance: 122 - 127: 13.745 distance: 124 - 125: 13.329 distance: 124 - 126: 13.125 distance: 127 - 128: 13.083 distance: 128 - 129: 5.659 distance: 128 - 131: 12.211 distance: 129 - 130: 12.117 distance: 129 - 139: 7.217 distance: 131 - 132: 8.632 distance: 132 - 133: 10.002 distance: 132 - 134: 18.793 distance: 133 - 135: 14.397 distance: 134 - 136: 8.421 distance: 135 - 137: 15.697 distance: 136 - 137: 9.871 distance: 137 - 138: 6.709 distance: 140 - 141: 10.065 distance: 140 - 143: 9.667 distance: 141 - 142: 5.958 distance: 141 - 146: 7.390 distance: 143 - 144: 11.757 distance: 143 - 145: 3.861 distance: 146 - 147: 6.104 distance: 147 - 148: 5.544 distance: 147 - 150: 8.895 distance: 148 - 149: 6.155 distance: 148 - 155: 11.132 distance: 150 - 151: 16.157 distance: 151 - 152: 19.173 distance: 152 - 153: 14.185 distance: 153 - 154: 15.759 distance: 155 - 156: 9.640 distance: 156 - 157: 13.396 distance: 156 - 159: 10.691 distance: 157 - 158: 13.338 distance: 157 - 163: 16.802 distance: 159 - 160: 3.838 distance: 160 - 161: 16.376 distance: 160 - 162: 10.098 distance: 163 - 164: 7.012 distance: 164 - 165: 37.912 distance: 164 - 167: 24.722 distance: 165 - 166: 26.659 distance: 165 - 171: 14.101 distance: 168 - 169: 6.231 distance: 168 - 170: 5.062 distance: 171 - 172: 3.655 distance: 172 - 173: 13.696 distance: 172 - 175: 10.440 distance: 173 - 174: 3.491 distance: 173 - 183: 19.880 distance: 175 - 176: 7.016 distance: 176 - 177: 7.318 distance: 176 - 178: 12.475 distance: 177 - 179: 8.657 distance: 178 - 180: 5.128 distance: 179 - 181: 11.796 distance: 180 - 181: 18.579 distance: 181 - 182: 19.128