Starting phenix.real_space_refine on Tue Aug 26 13:55:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d00_7782/08_2025/6d00_7782.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d00_7782/08_2025/6d00_7782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6d00_7782/08_2025/6d00_7782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d00_7782/08_2025/6d00_7782.map" model { file = "/net/cci-nas-00/data/ceres_data/6d00_7782/08_2025/6d00_7782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d00_7782/08_2025/6d00_7782.cif" } resolution = 4.0 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= 0.001 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 24 5.49 5 S 150 5.16 5 C 23910 2.51 5 N 6960 2.21 5 O 7284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38328 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "2" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "3" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "4" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "5" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "6" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "1" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.42, per 1000 atoms: 0.19 Number of scatterers: 38328 At special positions: 0 Unit cell: (187.62, 179.14, 154.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 24 15.00 O 7284 8.00 N 6960 7.00 C 23910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9156 Finding SS restraints... Secondary structure from input PDB file: 261 helices and 34 sheets defined 61.1% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain '1' and resid 7 through 23 removed outlier: 3.506A pdb=" N THR 1 11 " --> pdb=" O THR 1 7 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA 1 17 " --> pdb=" O THR 1 13 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS 1 19 " --> pdb=" O ASN 1 15 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR 1 20 " --> pdb=" O ALA 1 16 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA 1 21 " --> pdb=" O ALA 1 17 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA 1 22 " --> pdb=" O ALA 1 18 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU 1 23 " --> pdb=" O LYS 1 19 " (cutoff:3.500A) Processing helix chain '1' and resid 31 through 39 removed outlier: 4.166A pdb=" N ALA 1 35 " --> pdb=" O PRO 1 31 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL 1 36 " --> pdb=" O SER 1 32 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 53 removed outlier: 3.573A pdb=" N ILE 1 49 " --> pdb=" O LEU 1 45 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU 1 50 " --> pdb=" O PHE 1 46 " (cutoff:3.500A) Processing helix chain '1' and resid 56 through 70 removed outlier: 3.633A pdb=" N ILE 1 60 " --> pdb=" O ASP 1 56 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS 1 65 " --> pdb=" O GLU 1 61 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS 1 66 " --> pdb=" O ARG 1 62 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE 1 67 " --> pdb=" O GLY 1 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET 1 68 " --> pdb=" O PHE 1 64 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG 1 70 " --> pdb=" O LYS 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 84 through 97 removed outlier: 4.112A pdb=" N LYS 1 89 " --> pdb=" O PRO 1 85 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA 1 94 " --> pdb=" O LEU 1 90 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU 1 96 " --> pdb=" O HIS 1 92 " (cutoff:3.500A) Processing helix chain '1' and resid 114 through 118 removed outlier: 3.621A pdb=" N ASP 1 117 " --> pdb=" O ALA 1 114 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU 1 118 " --> pdb=" O LEU 1 115 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 114 through 118' Processing helix chain '1' and resid 121 through 129 removed outlier: 4.334A pdb=" N LEU 1 125 " --> pdb=" O MET 1 121 " (cutoff:3.500A) Processing helix chain '1' and resid 131 through 142 removed outlier: 4.211A pdb=" N GLU 1 136 " --> pdb=" O LYS 1 132 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN 1 137 " --> pdb=" O LYS 1 133 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL 1 139 " --> pdb=" O LEU 1 135 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS 1 141 " --> pdb=" O ASN 1 137 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL 1 142 " --> pdb=" O ALA 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 158 through 163 Processing helix chain '1' and resid 167 through 173 removed outlier: 3.682A pdb=" N ALA 1 172 " --> pdb=" O THR 1 168 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER 1 173 " --> pdb=" O GLU 1 169 " (cutoff:3.500A) Processing helix chain '1' and resid 182 through 194 removed outlier: 3.693A pdb=" N ARG 1 191 " --> pdb=" O SER 1 187 " (cutoff:3.500A) Processing helix chain '1' and resid 211 through 225 removed outlier: 3.912A pdb=" N ALA 1 215 " --> pdb=" O LYS 1 211 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA 1 219 " --> pdb=" O ALA 1 215 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN 1 220 " --> pdb=" O GLU 1 216 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG 1 221 " --> pdb=" O GLY 1 217 " (cutoff:3.500A) Processing helix chain '1' and resid 239 through 244 removed outlier: 4.014A pdb=" N LEU 1 243 " --> pdb=" O ASP 1 239 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU 1 244 " --> pdb=" O ILE 1 240 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 239 through 244' Processing helix chain '1' and resid 252 through 266 removed outlier: 3.720A pdb=" N LYS 1 258 " --> pdb=" O GLU 1 254 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU 1 266 " --> pdb=" O LYS 1 262 " (cutoff:3.500A) Processing helix chain '1' and resid 275 through 280 removed outlier: 4.272A pdb=" N VAL 1 279 " --> pdb=" O GLU 1 275 " (cutoff:3.500A) Processing helix chain '1' and resid 294 through 301 removed outlier: 3.755A pdb=" N MET 1 298 " --> pdb=" O LEU 1 294 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG 1 301 " --> pdb=" O PRO 1 297 " (cutoff:3.500A) Processing helix chain '1' and resid 314 through 319 Processing helix chain '1' and resid 322 through 327 removed outlier: 3.699A pdb=" N GLU 1 326 " --> pdb=" O ASP 1 322 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG 1 327 " --> pdb=" O PRO 1 323 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 322 through 327' Processing helix chain '1' and resid 338 through 349 removed outlier: 3.562A pdb=" N SER 1 344 " --> pdb=" O THR 1 340 " (cutoff:3.500A) Processing helix chain '1' and resid 363 through 372 removed outlier: 4.278A pdb=" N VAL 1 367 " --> pdb=" O ASP 1 363 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA 1 370 " --> pdb=" O ILE 1 366 " (cutoff:3.500A) Processing helix chain '1' and resid 383 through 403 removed outlier: 4.192A pdb=" N ASP 1 388 " --> pdb=" O ASP 1 384 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU 1 389 " --> pdb=" O LYS 1 385 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE 1 390 " --> pdb=" O ALA 1 386 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA 1 393 " --> pdb=" O LEU 1 389 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN 1 396 " --> pdb=" O GLU 1 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR 1 397 " --> pdb=" O ALA 1 393 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG 1 398 " --> pdb=" O CYS 1 394 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL 1 399 " --> pdb=" O ALA 1 395 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN 1 400 " --> pdb=" O ASN 1 396 " (cutoff:3.500A) Processing helix chain '1' and resid 405 through 428 removed outlier: 3.685A pdb=" N LYS 1 410 " --> pdb=" O GLU 1 406 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU 1 411 " --> pdb=" O ALA 1 407 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG 1 414 " --> pdb=" O LYS 1 410 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS 1 415 " --> pdb=" O LEU 1 411 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL 1 420 " --> pdb=" O LEU 1 416 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU 1 421 " --> pdb=" O GLN 1 417 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR 1 423 " --> pdb=" O GLU 1 419 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA 1 424 " --> pdb=" O VAL 1 420 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU 1 428 " --> pdb=" O ALA 1 424 " (cutoff:3.500A) Processing helix chain '1' and resid 433 through 486 removed outlier: 3.605A pdb=" N GLN 1 438 " --> pdb=" O LYS 1 434 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU 1 439 " --> pdb=" O GLN 1 435 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG 1 446 " --> pdb=" O ALA 1 442 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU 1 450 " --> pdb=" O ARG 1 446 " (cutoff:3.500A) Proline residue: 1 453 - end of helix removed outlier: 4.375A pdb=" N LYS 1 457 " --> pdb=" O PRO 1 453 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR 1 458 " --> pdb=" O LEU 1 454 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER 1 460 " --> pdb=" O MET 1 456 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG 1 464 " --> pdb=" O SER 1 460 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP 1 466 " --> pdb=" O LYS 1 462 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG 1 469 " --> pdb=" O LEU 1 465 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG 1 474 " --> pdb=" O ASN 1 470 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU 1 483 " --> pdb=" O LYS 1 479 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP 1 484 " --> pdb=" O ALA 1 480 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA 1 485 " --> pdb=" O LYS 1 481 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU 1 486 " --> pdb=" O ALA 1 482 " (cutoff:3.500A) Processing helix chain '1' and resid 490 through 498 removed outlier: 3.799A pdb=" N ASP 1 496 " --> pdb=" O ALA 1 492 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE 1 497 " --> pdb=" O ARG 1 493 " (cutoff:3.500A) Processing helix chain '1' and resid 500 through 518 removed outlier: 3.655A pdb=" N ARG 1 508 " --> pdb=" O ASP 1 504 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU 1 509 " --> pdb=" O LEU 1 505 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN 1 518 " --> pdb=" O ALA 1 514 " (cutoff:3.500A) Processing helix chain '1' and resid 533 through 545 removed outlier: 4.250A pdb=" N GLU 1 539 " --> pdb=" O ASP 1 535 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL 1 540 " --> pdb=" O GLN 1 536 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL 1 541 " --> pdb=" O ILE 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 548 through 552 Processing helix chain '1' and resid 555 through 560 removed outlier: 3.868A pdb=" N LEU 1 560 " --> pdb=" O GLU 1 556 " (cutoff:3.500A) Processing helix chain '1' and resid 562 through 567 removed outlier: 3.586A pdb=" N MET 1 567 " --> pdb=" O MET 1 563 " (cutoff:3.500A) Processing helix chain '1' and resid 574 through 579 removed outlier: 4.166A pdb=" N LYS 1 579 " --> pdb=" O ASP 1 575 " (cutoff:3.500A) Processing helix chain '1' and resid 580 through 586 removed outlier: 4.113A pdb=" N ALA 1 584 " --> pdb=" O ALA 1 580 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE 1 585 " --> pdb=" O ILE 1 581 " (cutoff:3.500A) Processing helix chain '1' and resid 613 through 623 removed outlier: 3.738A pdb=" N ALA 1 620 " --> pdb=" O VAL 1 616 " (cutoff:3.500A) Processing helix chain '1' and resid 662 through 669 removed outlier: 3.756A pdb=" N ARG 1 669 " --> pdb=" O GLU 1 665 " (cutoff:3.500A) Processing helix chain '1' and resid 685 through 691 removed outlier: 3.593A pdb=" N ASN 1 689 " --> pdb=" O LYS 1 685 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU 1 690 " --> pdb=" O ASP 1 686 " (cutoff:3.500A) Processing helix chain '1' and resid 739 through 750 removed outlier: 3.664A pdb=" N LEU 1 743 " --> pdb=" O LYS 1 739 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA 1 744 " --> pdb=" O ASN 1 740 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR 1 745 " --> pdb=" O ALA 1 741 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA 1 746 " --> pdb=" O VAL 1 742 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG 1 747 " --> pdb=" O LEU 1 743 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG 1 748 " --> pdb=" O ALA 1 744 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS 1 749 " --> pdb=" O THR 1 745 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE 1 750 " --> pdb=" O ALA 1 746 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 739 through 750' Processing helix chain '1' and resid 751 through 756 removed outlier: 3.665A pdb=" N ILE 1 755 " --> pdb=" O ALA 1 751 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN 1 756 " --> pdb=" O ASN 1 752 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 751 through 756' Processing helix chain '1' and resid 768 through 786 removed outlier: 4.390A pdb=" N ARG 1 773 " --> pdb=" O PRO 1 769 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS 1 774 " --> pdb=" O SER 1 770 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE 1 775 " --> pdb=" O ASN 1 771 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP 1 777 " --> pdb=" O ARG 1 773 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL 1 778 " --> pdb=" O LYS 1 774 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU 1 780 " --> pdb=" O VAL 1 776 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS 1 781 " --> pdb=" O ASP 1 777 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU 1 782 " --> pdb=" O VAL 1 778 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL 1 783 " --> pdb=" O ARG 1 779 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG 1 786 " --> pdb=" O GLU 1 782 " (cutoff:3.500A) Processing helix chain '1' and resid 787 through 791 Processing helix chain '1' and resid 799 through 807 removed outlier: 3.754A pdb=" N LEU 1 803 " --> pdb=" O LYS 1 799 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA 1 805 " --> pdb=" O LYS 1 801 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN 1 807 " --> pdb=" O LEU 1 803 " (cutoff:3.500A) Processing helix chain '1' and resid 816 through 826 removed outlier: 3.808A pdb=" N ARG 1 820 " --> pdb=" O ARG 1 816 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS 1 824 " --> pdb=" O ARG 1 820 " (cutoff:3.500A) Processing helix chain '1' and resid 826 through 834 removed outlier: 3.790A pdb=" N LEU 1 830 " --> pdb=" O LEU 1 826 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU 1 834 " --> pdb=" O LEU 1 830 " (cutoff:3.500A) Processing helix chain '2' and resid 7 through 23 removed outlier: 3.915A pdb=" N LEU 2 14 " --> pdb=" O ALA 2 10 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN 2 15 " --> pdb=" O THR 2 11 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU 2 23 " --> pdb=" O LYS 2 19 " (cutoff:3.500A) Processing helix chain '2' and resid 31 through 39 removed outlier: 4.246A pdb=" N ALA 2 35 " --> pdb=" O PRO 2 31 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL 2 36 " --> pdb=" O SER 2 32 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 54 removed outlier: 4.440A pdb=" N SER 2 48 " --> pdb=" O SER 2 44 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU 2 50 " --> pdb=" O PHE 2 46 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS 2 52 " --> pdb=" O SER 2 48 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA 2 53 " --> pdb=" O ILE 2 49 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 70 removed outlier: 3.659A pdb=" N ILE 2 67 " --> pdb=" O GLY 2 63 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET 2 68 " --> pdb=" O PHE 2 64 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL 2 69 " --> pdb=" O LYS 2 65 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG 2 70 " --> pdb=" O LYS 2 66 " (cutoff:3.500A) Processing helix chain '2' and resid 84 through 97 removed outlier: 3.913A pdb=" N LYS 2 89 " --> pdb=" O PRO 2 85 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU 2 90 " --> pdb=" O GLU 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 98 through 100 No H-bonds generated for 'chain '2' and resid 98 through 100' Processing helix chain '2' and resid 110 through 117 removed outlier: 3.954A pdb=" N ALA 2 114 " --> pdb=" O HIS 2 110 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU 2 115 " --> pdb=" O LEU 2 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP 2 117 " --> pdb=" O LEU 2 113 " (cutoff:3.500A) Processing helix chain '2' and resid 118 through 129 removed outlier: 3.640A pdb=" N GLN 2 123 " --> pdb=" O PRO 2 119 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL 2 124 " --> pdb=" O SER 2 120 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 2 125 " --> pdb=" O MET 2 121 " (cutoff:3.500A) Processing helix chain '2' and resid 131 through 142 removed outlier: 3.745A pdb=" N LEU 2 135 " --> pdb=" O THR 2 131 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU 2 136 " --> pdb=" O LYS 2 132 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN 2 137 " --> pdb=" O LYS 2 133 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL 2 139 " --> pdb=" O LEU 2 135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR 2 140 " --> pdb=" O GLU 2 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS 2 141 " --> pdb=" O ASN 2 137 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL 2 142 " --> pdb=" O ALA 2 138 " (cutoff:3.500A) Processing helix chain '2' and resid 158 through 163 removed outlier: 3.953A pdb=" N LYS 2 162 " --> pdb=" O GLU 2 158 " (cutoff:3.500A) Processing helix chain '2' and resid 167 through 173 Processing helix chain '2' and resid 182 through 194 removed outlier: 3.786A pdb=" N SER 2 187 " --> pdb=" O ASP 2 183 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG 2 188 " --> pdb=" O GLU 2 184 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG 2 191 " --> pdb=" O SER 2 187 " (cutoff:3.500A) Processing helix chain '2' and resid 211 through 224 removed outlier: 4.130A pdb=" N ALA 2 215 " --> pdb=" O LYS 2 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU 2 216 " --> pdb=" O THR 2 212 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY 2 217 " --> pdb=" O ALA 2 213 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU 2 218 " --> pdb=" O ILE 2 214 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA 2 219 " --> pdb=" O ALA 2 215 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN 2 220 " --> pdb=" O GLU 2 216 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG 2 221 " --> pdb=" O GLY 2 217 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE 2 222 " --> pdb=" O LEU 2 218 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL 2 223 " --> pdb=" O ALA 2 219 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS 2 224 " --> pdb=" O ASN 2 220 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 211 through 224' Processing helix chain '2' and resid 239 through 244 removed outlier: 3.643A pdb=" N LEU 2 243 " --> pdb=" O ASP 2 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU 2 244 " --> pdb=" O ILE 2 240 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 239 through 244' Processing helix chain '2' and resid 252 through 268 removed outlier: 3.866A pdb=" N ARG 2 256 " --> pdb=" O GLU 2 252 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA 2 259 " --> pdb=" O GLU 2 255 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL 2 260 " --> pdb=" O ARG 2 256 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU 2 266 " --> pdb=" O LYS 2 262 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA 2 267 " --> pdb=" O GLU 2 263 " (cutoff:3.500A) Processing helix chain '2' and resid 275 through 280 removed outlier: 4.120A pdb=" N VAL 2 279 " --> pdb=" O GLU 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 291 through 294 removed outlier: 3.670A pdb=" N LEU 2 294 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 291 through 294' Processing helix chain '2' and resid 295 through 301 Processing helix chain '2' and resid 311 through 316 removed outlier: 3.783A pdb=" N ARG 2 316 " --> pdb=" O LEU 2 312 " (cutoff:3.500A) Processing helix chain '2' and resid 322 through 327 removed outlier: 3.540A pdb=" N GLU 2 326 " --> pdb=" O ASP 2 322 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG 2 327 " --> pdb=" O PRO 2 323 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 322 through 327' Processing helix chain '2' and resid 338 through 349 removed outlier: 3.915A pdb=" N ILE 2 343 " --> pdb=" O VAL 2 339 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER 2 344 " --> pdb=" O THR 2 340 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY 2 348 " --> pdb=" O SER 2 344 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU 2 349 " --> pdb=" O ILE 2 345 " (cutoff:3.500A) Processing helix chain '2' and resid 349 through 357 removed outlier: 3.524A pdb=" N TYR 2 353 " --> pdb=" O LEU 2 349 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS 2 356 " --> pdb=" O ARG 2 352 " (cutoff:3.500A) Processing helix chain '2' and resid 363 through 373 removed outlier: 4.052A pdb=" N VAL 2 367 " --> pdb=" O ASP 2 363 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA 2 368 " --> pdb=" O ALA 2 364 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA 2 370 " --> pdb=" O ILE 2 366 " (cutoff:3.500A) Processing helix chain '2' and resid 383 through 403 removed outlier: 4.051A pdb=" N ASP 2 388 " --> pdb=" O ASP 2 384 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU 2 389 " --> pdb=" O LYS 2 385 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE 2 390 " --> pdb=" O ALA 2 386 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR 2 397 " --> pdb=" O ALA 2 393 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG 2 398 " --> pdb=" O CYS 2 394 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL 2 399 " --> pdb=" O ALA 2 395 " (cutoff:3.500A) Processing helix chain '2' and resid 405 through 427 removed outlier: 4.394A pdb=" N LEU 2 411 " --> pdb=" O ALA 2 407 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU 2 418 " --> pdb=" O ARG 2 414 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU 2 421 " --> pdb=" O GLN 2 417 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA 2 424 " --> pdb=" O VAL 2 420 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU 2 425 " --> pdb=" O GLU 2 421 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS 2 427 " --> pdb=" O THR 2 423 " (cutoff:3.500A) Processing helix chain '2' and resid 430 through 488 removed outlier: 3.952A pdb=" N GLN 2 435 " --> pdb=" O ALA 2 431 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG 2 436 " --> pdb=" O ALA 2 432 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU 2 439 " --> pdb=" O GLN 2 435 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU 2 443 " --> pdb=" O GLU 2 439 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG 2 446 " --> pdb=" O ALA 2 442 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE 2 447 " --> pdb=" O GLU 2 443 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU 2 450 " --> pdb=" O ARG 2 446 " (cutoff:3.500A) Proline residue: 2 453 - end of helix removed outlier: 3.650A pdb=" N LYS 2 457 " --> pdb=" O PRO 2 453 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY 2 463 " --> pdb=" O GLU 2 459 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG 2 464 " --> pdb=" O SER 2 460 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG 2 469 " --> pdb=" O LEU 2 465 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG 2 474 " --> pdb=" O ASN 2 470 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU 2 475 " --> pdb=" O LEU 2 471 " (cutoff:3.500A) Processing helix chain '2' and resid 493 through 497 Processing helix chain '2' and resid 505 through 523 removed outlier: 3.811A pdb=" N ALA 2 521 " --> pdb=" O SER 2 517 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU 2 522 " --> pdb=" O GLN 2 518 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG 2 523 " --> pdb=" O ALA 2 519 " (cutoff:3.500A) Processing helix chain '2' and resid 533 through 544 removed outlier: 3.520A pdb=" N GLU 2 539 " --> pdb=" O ASP 2 535 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL 2 540 " --> pdb=" O GLN 2 536 " (cutoff:3.500A) Processing helix chain '2' and resid 548 through 552 Processing helix chain '2' and resid 555 through 562 removed outlier: 3.728A pdb=" N LEU 2 560 " --> pdb=" O GLU 2 556 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU 2 561 " --> pdb=" O LYS 2 557 " (cutoff:3.500A) Processing helix chain '2' and resid 563 through 568 removed outlier: 3.717A pdb=" N LYS 2 568 " --> pdb=" O GLU 2 564 " (cutoff:3.500A) Processing helix chain '2' and resid 574 through 590 removed outlier: 3.923A pdb=" N LYS 2 579 " --> pdb=" O ASP 2 575 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA 2 580 " --> pdb=" O GLU 2 576 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS 2 582 " --> pdb=" O ILE 2 578 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA 2 584 " --> pdb=" O ALA 2 580 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU 2 587 " --> pdb=" O ASP 2 583 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER 2 588 " --> pdb=" O ALA 2 584 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG 2 589 " --> pdb=" O ILE 2 585 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR 2 590 " --> pdb=" O ARG 2 586 " (cutoff:3.500A) Processing helix chain '2' and resid 613 through 621 removed outlier: 3.671A pdb=" N ALA 2 620 " --> pdb=" O VAL 2 616 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA 2 621 " --> pdb=" O LYS 2 617 " (cutoff:3.500A) Processing helix chain '2' and resid 640 through 644 Processing helix chain '2' and resid 662 through 670 removed outlier: 3.514A pdb=" N ARG 2 668 " --> pdb=" O THR 2 664 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG 2 669 " --> pdb=" O GLU 2 665 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG 2 670 " --> pdb=" O ALA 2 666 " (cutoff:3.500A) Processing helix chain '2' and resid 679 through 683 Processing helix chain '2' and resid 684 through 691 removed outlier: 4.088A pdb=" N SER 2 688 " --> pdb=" O HIS 2 684 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU 2 690 " --> pdb=" O ASP 2 686 " (cutoff:3.500A) Processing helix chain '2' and resid 691 through 698 removed outlier: 3.591A pdb=" N LEU 2 695 " --> pdb=" O LEU 2 691 " (cutoff:3.500A) Processing helix chain '2' and resid 739 through 750 removed outlier: 3.693A pdb=" N ALA 2 746 " --> pdb=" O VAL 2 742 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG 2 747 " --> pdb=" O LEU 2 743 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG 2 748 " --> pdb=" O ALA 2 744 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS 2 749 " --> pdb=" O THR 2 745 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE 2 750 " --> pdb=" O ALA 2 746 " (cutoff:3.500A) Processing helix chain '2' and resid 753 through 758 removed outlier: 3.734A pdb=" N ILE 2 758 " --> pdb=" O PHE 2 754 " (cutoff:3.500A) Processing helix chain '2' and resid 768 through 770 No H-bonds generated for 'chain '2' and resid 768 through 770' Processing helix chain '2' and resid 771 through 786 removed outlier: 3.559A pdb=" N VAL 2 776 " --> pdb=" O ILE 2 772 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP 2 777 " --> pdb=" O ARG 2 773 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU 2 780 " --> pdb=" O VAL 2 776 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS 2 781 " --> pdb=" O ASP 2 777 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU 2 782 " --> pdb=" O VAL 2 778 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL 2 783 " --> pdb=" O ARG 2 779 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN 2 784 " --> pdb=" O LEU 2 780 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 791 Processing helix chain '2' and resid 797 through 808 removed outlier: 3.596A pdb=" N LYS 2 801 " --> pdb=" O ASP 2 797 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP 2 802 " --> pdb=" O ASP 2 798 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU 2 803 " --> pdb=" O LYS 2 799 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU 2 804 " --> pdb=" O ALA 2 800 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA 2 805 " --> pdb=" O LYS 2 801 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN 2 806 " --> pdb=" O ASP 2 802 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN 2 807 " --> pdb=" O LEU 2 803 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY 2 808 " --> pdb=" O LEU 2 804 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 797 through 808' Processing helix chain '2' and resid 815 through 824 removed outlier: 4.193A pdb=" N ASN 2 819 " --> pdb=" O ALA 2 815 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG 2 820 " --> pdb=" O ARG 2 816 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE 2 822 " --> pdb=" O LEU 2 818 " (cutoff:3.500A) Processing helix chain '2' and resid 825 through 831 removed outlier: 3.508A pdb=" N GLN 2 829 " --> pdb=" O ALA 2 825 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER 2 831 " --> pdb=" O LEU 2 827 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 24 removed outlier: 3.505A pdb=" N THR 3 13 " --> pdb=" O LYS 3 9 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA 3 18 " --> pdb=" O LEU 3 14 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS 3 19 " --> pdb=" O ASN 3 15 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN 3 24 " --> pdb=" O TYR 3 20 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 40 removed outlier: 4.192A pdb=" N ALA 3 35 " --> pdb=" O PRO 3 31 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL 3 36 " --> pdb=" O SER 3 32 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL 3 37 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP 3 40 " --> pdb=" O VAL 3 36 " (cutoff:3.500A) Processing helix chain '3' and resid 46 through 53 removed outlier: 3.640A pdb=" N LEU 3 50 " --> pdb=" O PHE 3 46 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU 3 51 " --> pdb=" O ARG 3 47 " (cutoff:3.500A) Processing helix chain '3' and resid 56 through 61 removed outlier: 3.748A pdb=" N ILE 3 60 " --> pdb=" O ASP 3 56 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU 3 61 " --> pdb=" O VAL 3 57 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 56 through 61' Processing helix chain '3' and resid 64 through 71 removed outlier: 3.732A pdb=" N MET 3 68 " --> pdb=" O PHE 3 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL 3 69 " --> pdb=" O LYS 3 65 " (cutoff:3.500A) Processing helix chain '3' and resid 87 through 99 removed outlier: 3.696A pdb=" N LEU 3 91 " --> pdb=" O LEU 3 87 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU 3 96 " --> pdb=" O HIS 3 92 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS 3 97 " --> pdb=" O TYR 3 93 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS 3 99 " --> pdb=" O HIS 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 111 removed outlier: 3.698A pdb=" N HIS 3 110 " --> pdb=" O ALA 3 107 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU 3 111 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 107 through 111' Processing helix chain '3' and resid 112 through 117 removed outlier: 3.704A pdb=" N ALA 3 116 " --> pdb=" O LEU 3 113 " (cutoff:3.500A) Processing helix chain '3' and resid 121 through 129 removed outlier: 3.586A pdb=" N LEU 3 125 " --> pdb=" O MET 3 121 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY 3 128 " --> pdb=" O VAL 3 124 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 137 removed outlier: 3.874A pdb=" N GLU 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN 3 137 " --> pdb=" O LYS 3 133 " (cutoff:3.500A) Processing helix chain '3' and resid 137 through 142 removed outlier: 3.950A pdb=" N HIS 3 141 " --> pdb=" O ASN 3 137 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL 3 142 " --> pdb=" O ALA 3 138 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 137 through 142' Processing helix chain '3' and resid 158 through 163 removed outlier: 3.523A pdb=" N TYR 3 163 " --> pdb=" O ALA 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 167 through 173 Processing helix chain '3' and resid 182 through 194 removed outlier: 4.092A pdb=" N SER 3 187 " --> pdb=" O ASP 3 183 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG 3 188 " --> pdb=" O GLU 3 184 " (cutoff:3.500A) Processing helix chain '3' and resid 211 through 223 removed outlier: 3.857A pdb=" N ALA 3 215 " --> pdb=" O LYS 3 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY 3 217 " --> pdb=" O ALA 3 213 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU 3 218 " --> pdb=" O ILE 3 214 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA 3 219 " --> pdb=" O ALA 3 215 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN 3 220 " --> pdb=" O GLU 3 216 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG 3 221 " --> pdb=" O GLY 3 217 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL 3 223 " --> pdb=" O ALA 3 219 " (cutoff:3.500A) Processing helix chain '3' and resid 239 through 245 removed outlier: 4.034A pdb=" N LEU 3 243 " --> pdb=" O ASP 3 239 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU 3 244 " --> pdb=" O ILE 3 240 " (cutoff:3.500A) Processing helix chain '3' and resid 252 through 267 removed outlier: 3.537A pdb=" N LEU 3 257 " --> pdb=" O PHE 3 253 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA 3 259 " --> pdb=" O GLU 3 255 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL 3 260 " --> pdb=" O ARG 3 256 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS 3 265 " --> pdb=" O LEU 3 261 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU 3 266 " --> pdb=" O LYS 3 262 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA 3 267 " --> pdb=" O GLU 3 263 " (cutoff:3.500A) Processing helix chain '3' and resid 275 through 281 removed outlier: 3.836A pdb=" N VAL 3 279 " --> pdb=" O GLU 3 275 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY 3 281 " --> pdb=" O HIS 3 277 " (cutoff:3.500A) Processing helix chain '3' and resid 291 through 294 removed outlier: 3.715A pdb=" N LEU 3 294 " --> pdb=" O ALA 3 291 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 291 through 294' Processing helix chain '3' and resid 295 through 301 Processing helix chain '3' and resid 314 through 319 removed outlier: 3.678A pdb=" N TYR 3 318 " --> pdb=" O GLU 3 314 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL 3 319 " --> pdb=" O TYR 3 315 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 314 through 319' Processing helix chain '3' and resid 339 through 349 removed outlier: 3.614A pdb=" N ILE 3 343 " --> pdb=" O VAL 3 339 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER 3 344 " --> pdb=" O THR 3 340 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY 3 348 " --> pdb=" O SER 3 344 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU 3 349 " --> pdb=" O ILE 3 345 " (cutoff:3.500A) Processing helix chain '3' and resid 349 through 358 Processing helix chain '3' and resid 363 through 373 removed outlier: 3.770A pdb=" N VAL 3 367 " --> pdb=" O ASP 3 363 " (cutoff:3.500A) Processing helix chain '3' and resid 383 through 403 removed outlier: 3.909A pdb=" N ASP 3 388 " --> pdb=" O ASP 3 384 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU 3 389 " --> pdb=" O LYS 3 385 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE 3 390 " --> pdb=" O ALA 3 386 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA 3 393 " --> pdb=" O LEU 3 389 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR 3 397 " --> pdb=" O ALA 3 393 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG 3 398 " --> pdb=" O CYS 3 394 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL 3 399 " --> pdb=" O ALA 3 395 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN 3 400 " --> pdb=" O ASN 3 396 " (cutoff:3.500A) Processing helix chain '3' and resid 405 through 428 removed outlier: 4.294A pdb=" N LEU 3 411 " --> pdb=" O ALA 3 407 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN 3 417 " --> pdb=" O ARG 3 413 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL 3 420 " --> pdb=" O LEU 3 416 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS 3 427 " --> pdb=" O THR 3 423 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU 3 428 " --> pdb=" O ALA 3 424 " (cutoff:3.500A) Processing helix chain '3' and resid 430 through 488 removed outlier: 3.599A pdb=" N LYS 3 434 " --> pdb=" O ASP 3 430 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN 3 435 " --> pdb=" O ALA 3 431 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG 3 436 " --> pdb=" O ALA 3 432 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN 3 438 " --> pdb=" O LYS 3 434 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU 3 439 " --> pdb=" O GLN 3 435 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA 3 442 " --> pdb=" O GLN 3 438 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA 3 445 " --> pdb=" O ARG 3 441 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG 3 446 " --> pdb=" O ALA 3 442 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU 3 449 " --> pdb=" O ALA 3 445 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU 3 450 " --> pdb=" O ARG 3 446 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG 3 452 " --> pdb=" O GLN 3 448 " (cutoff:3.500A) Proline residue: 3 453 - end of helix removed outlier: 4.715A pdb=" N LYS 3 457 " --> pdb=" O PRO 3 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR 3 458 " --> pdb=" O LEU 3 454 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG 3 464 " --> pdb=" O SER 3 460 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU 3 467 " --> pdb=" O GLY 3 463 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG 3 469 " --> pdb=" O LEU 3 465 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU 3 477 " --> pdb=" O GLN 3 473 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA 3 480 " --> pdb=" O ASP 3 476 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU 3 483 " --> pdb=" O LYS 3 479 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP 3 484 " --> pdb=" O ALA 3 480 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA 3 485 " --> pdb=" O LYS 3 481 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU 3 486 " --> pdb=" O ALA 3 482 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG 3 487 " --> pdb=" O GLU 3 483 " (cutoff:3.500A) Processing helix chain '3' and resid 490 through 495 removed outlier: 3.773A pdb=" N ALA 3 494 " --> pdb=" O ASP 3 490 " (cutoff:3.500A) Processing helix chain '3' and resid 501 through 522 removed outlier: 3.988A pdb=" N LYS 3 507 " --> pdb=" O PRO 3 503 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG 3 508 " --> pdb=" O ASP 3 504 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU 3 509 " --> pdb=" O LEU 3 505 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA 3 510 " --> pdb=" O GLU 3 506 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA 3 514 " --> pdb=" O ALA 3 510 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU 3 515 " --> pdb=" O GLN 3 511 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER 3 517 " --> pdb=" O GLN 3 513 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN 3 518 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA 3 519 " --> pdb=" O GLU 3 515 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA 3 521 " --> pdb=" O SER 3 517 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU 3 522 " --> pdb=" O GLN 3 518 " (cutoff:3.500A) Processing helix chain '3' and resid 533 through 542 removed outlier: 3.522A pdb=" N ILE 3 537 " --> pdb=" O GLY 3 533 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU 3 539 " --> pdb=" O ASP 3 535 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL 3 540 " --> pdb=" O GLN 3 536 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 3 541 " --> pdb=" O ILE 3 537 " (cutoff:3.500A) Processing helix chain '3' and resid 555 through 562 removed outlier: 3.636A pdb=" N LYS 3 559 " --> pdb=" O SER 3 555 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU 3 561 " --> pdb=" O LYS 3 557 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS 3 562 " --> pdb=" O GLU 3 558 " (cutoff:3.500A) Processing helix chain '3' and resid 563 through 568 removed outlier: 3.972A pdb=" N LYS 3 568 " --> pdb=" O GLU 3 564 " (cutoff:3.500A) Processing helix chain '3' and resid 577 through 584 removed outlier: 3.528A pdb=" N ILE 3 581 " --> pdb=" O ALA 3 577 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS 3 582 " --> pdb=" O ILE 3 578 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP 3 583 " --> pdb=" O LYS 3 579 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA 3 584 " --> pdb=" O ALA 3 580 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 577 through 584' Processing helix chain '3' and resid 585 through 590 Processing helix chain '3' and resid 613 through 619 removed outlier: 3.731A pdb=" N LEU 3 619 " --> pdb=" O CYS 3 615 " (cutoff:3.500A) Processing helix chain '3' and resid 662 through 667 removed outlier: 3.623A pdb=" N VAL 3 667 " --> pdb=" O LEU 3 663 " (cutoff:3.500A) Processing helix chain '3' and resid 684 through 691 removed outlier: 3.596A pdb=" N SER 3 688 " --> pdb=" O HIS 3 684 " (cutoff:3.500A) Processing helix chain '3' and resid 691 through 697 removed outlier: 3.705A pdb=" N LEU 3 695 " --> pdb=" O LEU 3 691 " (cutoff:3.500A) Processing helix chain '3' and resid 742 through 750 removed outlier: 4.328A pdb=" N ALA 3 746 " --> pdb=" O VAL 3 742 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG 3 747 " --> pdb=" O LEU 3 743 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG 3 748 " --> pdb=" O ALA 3 744 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE 3 750 " --> pdb=" O ALA 3 746 " (cutoff:3.500A) Processing helix chain '3' and resid 768 through 771 Processing helix chain '3' and resid 772 through 785 removed outlier: 3.686A pdb=" N VAL 3 776 " --> pdb=" O ILE 3 772 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP 3 777 " --> pdb=" O ARG 3 773 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL 3 778 " --> pdb=" O LYS 3 774 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG 3 779 " --> pdb=" O ILE 3 775 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS 3 781 " --> pdb=" O ASP 3 777 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU 3 782 " --> pdb=" O VAL 3 778 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL 3 783 " --> pdb=" O ARG 3 779 " (cutoff:3.500A) Processing helix chain '3' and resid 799 through 808 removed outlier: 3.506A pdb=" N LEU 3 803 " --> pdb=" O LYS 3 799 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN 3 806 " --> pdb=" O ASP 3 802 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN 3 807 " --> pdb=" O LEU 3 803 " (cutoff:3.500A) Processing helix chain '3' and resid 815 through 822 removed outlier: 3.585A pdb=" N ARG 3 820 " --> pdb=" O ARG 3 816 " (cutoff:3.500A) Processing helix chain '3' and resid 825 through 834 removed outlier: 4.183A pdb=" N GLN 3 829 " --> pdb=" O ALA 3 825 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU 3 830 " --> pdb=" O LEU 3 826 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG 3 832 " --> pdb=" O THR 3 828 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU 3 833 " --> pdb=" O GLN 3 829 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU 3 834 " --> pdb=" O LEU 3 830 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 24 removed outlier: 3.582A pdb=" N LYS 4 19 " --> pdb=" O ASN 4 15 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN 4 24 " --> pdb=" O TYR 4 20 " (cutoff:3.500A) Processing helix chain '4' and resid 31 through 39 removed outlier: 4.391A pdb=" N ALA 4 35 " --> pdb=" O PRO 4 31 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL 4 36 " --> pdb=" O SER 4 32 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 4 39 " --> pdb=" O ALA 4 35 " (cutoff:3.500A) Processing helix chain '4' and resid 46 through 54 removed outlier: 3.846A pdb=" N LEU 4 50 " --> pdb=" O PHE 4 46 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU 4 51 " --> pdb=" O ARG 4 47 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS 4 52 " --> pdb=" O SER 4 48 " (cutoff:3.500A) Processing helix chain '4' and resid 56 through 62 Processing helix chain '4' and resid 63 through 71 removed outlier: 4.217A pdb=" N ILE 4 67 " --> pdb=" O GLY 4 63 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 99 removed outlier: 3.954A pdb=" N LYS 4 89 " --> pdb=" O PRO 4 85 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS 4 95 " --> pdb=" O LEU 4 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU 4 96 " --> pdb=" O HIS 4 92 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS 4 99 " --> pdb=" O HIS 4 95 " (cutoff:3.500A) Processing helix chain '4' and resid 107 through 113 removed outlier: 4.016A pdb=" N LEU 4 111 " --> pdb=" O ALA 4 107 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE 4 112 " --> pdb=" O GLN 4 108 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU 4 113 " --> pdb=" O ASP 4 109 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 107 through 113' Processing helix chain '4' and resid 121 through 129 removed outlier: 4.020A pdb=" N LEU 4 125 " --> pdb=" O MET 4 121 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY 4 128 " --> pdb=" O VAL 4 124 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY 4 129 " --> pdb=" O LEU 4 125 " (cutoff:3.500A) Processing helix chain '4' and resid 131 through 137 removed outlier: 3.542A pdb=" N ASN 4 137 " --> pdb=" O LYS 4 133 " (cutoff:3.500A) Processing helix chain '4' and resid 138 through 144 removed outlier: 3.800A pdb=" N VAL 4 142 " --> pdb=" O ALA 4 138 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG 4 143 " --> pdb=" O VAL 4 139 " (cutoff:3.500A) Processing helix chain '4' and resid 158 through 163 removed outlier: 3.650A pdb=" N TYR 4 163 " --> pdb=" O ALA 4 159 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 173 Processing helix chain '4' and resid 185 through 194 removed outlier: 3.861A pdb=" N ILE 4 190 " --> pdb=" O ILE 4 186 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG 4 191 " --> pdb=" O SER 4 187 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL 4 192 " --> pdb=" O ARG 4 188 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER 4 194 " --> pdb=" O ILE 4 190 " (cutoff:3.500A) Processing helix chain '4' and resid 211 through 225 removed outlier: 4.058A pdb=" N ALA 4 215 " --> pdb=" O LYS 4 211 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU 4 218 " --> pdb=" O ILE 4 214 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 4 219 " --> pdb=" O ALA 4 215 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN 4 220 " --> pdb=" O GLU 4 216 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG 4 221 " --> pdb=" O GLY 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 228 through 232 removed outlier: 4.080A pdb=" N GLN 4 232 " --> pdb=" O SER 4 229 " (cutoff:3.500A) Processing helix chain '4' and resid 252 through 267 removed outlier: 4.030A pdb=" N LYS 4 258 " --> pdb=" O GLU 4 254 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU 4 263 " --> pdb=" O ALA 4 259 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU 4 264 " --> pdb=" O VAL 4 260 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS 4 265 " --> pdb=" O LEU 4 261 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU 4 266 " --> pdb=" O LYS 4 262 " (cutoff:3.500A) Processing helix chain '4' and resid 275 through 280 removed outlier: 4.347A pdb=" N VAL 4 279 " --> pdb=" O GLU 4 275 " (cutoff:3.500A) Processing helix chain '4' and resid 291 through 301 removed outlier: 3.857A pdb=" N LEU 4 295 " --> pdb=" O ALA 4 291 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS 4 296 " --> pdb=" O ALA 4 292 " (cutoff:3.500A) Proline residue: 4 297 - end of helix Processing helix chain '4' and resid 312 through 319 removed outlier: 3.652A pdb=" N ARG 4 316 " --> pdb=" O LEU 4 312 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN 4 317 " --> pdb=" O THR 4 313 " (cutoff:3.500A) Processing helix chain '4' and resid 322 through 327 Processing helix chain '4' and resid 338 through 349 removed outlier: 3.635A pdb=" N ILE 4 343 " --> pdb=" O VAL 4 339 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER 4 344 " --> pdb=" O THR 4 340 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU 4 349 " --> pdb=" O ILE 4 345 " (cutoff:3.500A) Processing helix chain '4' and resid 349 through 357 removed outlier: 4.004A pdb=" N THR 4 355 " --> pdb=" O GLU 4 351 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS 4 356 " --> pdb=" O ARG 4 352 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS 4 357 " --> pdb=" O TYR 4 353 " (cutoff:3.500A) Processing helix chain '4' and resid 363 through 374 removed outlier: 4.423A pdb=" N VAL 4 367 " --> pdb=" O ASP 4 363 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA 4 368 " --> pdb=" O ALA 4 364 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA 4 369 " --> pdb=" O ALA 4 365 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA 4 370 " --> pdb=" O ILE 4 366 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN 4 371 " --> pdb=" O VAL 4 367 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA 4 374 " --> pdb=" O ALA 4 370 " (cutoff:3.500A) Processing helix chain '4' and resid 383 through 403 removed outlier: 3.611A pdb=" N ASP 4 388 " --> pdb=" O ASP 4 384 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU 4 389 " --> pdb=" O LYS 4 385 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE 4 390 " --> pdb=" O ALA 4 386 " (cutoff:3.500A) Processing helix chain '4' and resid 405 through 425 removed outlier: 3.618A pdb=" N LYS 4 410 " --> pdb=" O GLU 4 406 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU 4 411 " --> pdb=" O ALA 4 407 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG 4 414 " --> pdb=" O LYS 4 410 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN 4 417 " --> pdb=" O ARG 4 413 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL 4 420 " --> pdb=" O LEU 4 416 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU 4 421 " --> pdb=" O GLN 4 417 " (cutoff:3.500A) Processing helix chain '4' and resid 430 through 488 removed outlier: 4.150A pdb=" N GLN 4 435 " --> pdb=" O ALA 4 431 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG 4 436 " --> pdb=" O ALA 4 432 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN 4 438 " --> pdb=" O LYS 4 434 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU 4 439 " --> pdb=" O GLN 4 435 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 4 442 " --> pdb=" O GLN 4 438 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG 4 446 " --> pdb=" O ALA 4 442 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU 4 450 " --> pdb=" O ARG 4 446 " (cutoff:3.500A) Proline residue: 4 453 - end of helix removed outlier: 3.760A pdb=" N LYS 4 457 " --> pdb=" O PRO 4 453 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER 4 460 " --> pdb=" O MET 4 456 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG 4 464 " --> pdb=" O SER 4 460 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP 4 476 " --> pdb=" O SER 4 472 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU 4 477 " --> pdb=" O GLN 4 473 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA 4 480 " --> pdb=" O ASP 4 476 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU 4 483 " --> pdb=" O LYS 4 479 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP 4 484 " --> pdb=" O ALA 4 480 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA 4 485 " --> pdb=" O LYS 4 481 " (cutoff:3.500A) Processing helix chain '4' and resid 490 through 501 removed outlier: 4.313A pdb=" N ASP 4 496 " --> pdb=" O ALA 4 492 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 4 497 " --> pdb=" O ARG 4 493 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA 4 501 " --> pdb=" O ILE 4 497 " (cutoff:3.500A) Processing helix chain '4' and resid 501 through 522 removed outlier: 3.632A pdb=" N LYS 4 507 " --> pdb=" O PRO 4 503 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG 4 508 " --> pdb=" O ASP 4 504 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU 4 509 " --> pdb=" O LEU 4 505 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU 4 515 " --> pdb=" O GLN 4 511 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER 4 517 " --> pdb=" O GLN 4 513 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN 4 518 " --> pdb=" O ALA 4 514 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU 4 522 " --> pdb=" O GLN 4 518 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 545 removed outlier: 3.526A pdb=" N ILE 4 537 " --> pdb=" O GLY 4 533 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL 4 540 " --> pdb=" O GLN 4 536 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL 4 541 " --> pdb=" O ILE 4 537 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG 4 543 " --> pdb=" O GLU 4 539 " (cutoff:3.500A) Processing helix chain '4' and resid 548 through 553 removed outlier: 3.862A pdb=" N LEU 4 552 " --> pdb=" O PRO 4 548 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN 4 553 " --> pdb=" O VAL 4 549 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 548 through 553' Processing helix chain '4' and resid 555 through 562 removed outlier: 3.821A pdb=" N LEU 4 561 " --> pdb=" O LYS 4 557 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS 4 562 " --> pdb=" O GLU 4 558 " (cutoff:3.500A) Processing helix chain '4' and resid 562 through 571 removed outlier: 3.757A pdb=" N TYR 4 566 " --> pdb=" O HIS 4 562 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET 4 567 " --> pdb=" O MET 4 563 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS 4 568 " --> pdb=" O GLU 4 564 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN 4 569 " --> pdb=" O GLU 4 565 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS 4 570 " --> pdb=" O TYR 4 566 " (cutoff:3.500A) Processing helix chain '4' and resid 574 through 587 removed outlier: 4.359A pdb=" N LYS 4 579 " --> pdb=" O ASP 4 575 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALA 4 580 " --> pdb=" O GLU 4 576 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA 4 584 " --> pdb=" O ALA 4 580 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE 4 585 " --> pdb=" O ILE 4 581 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG 4 586 " --> pdb=" O CYS 4 582 " (cutoff:3.500A) Processing helix chain '4' and resid 613 through 623 Processing helix chain '4' and resid 646 through 647 No H-bonds generated for 'chain '4' and resid 646 through 647' Processing helix chain '4' and resid 661 through 661 No H-bonds generated for 'chain '4' and resid 661 through 661' Processing helix chain '4' and resid 662 through 667 removed outlier: 3.820A pdb=" N VAL 4 667 " --> pdb=" O LEU 4 663 " (cutoff:3.500A) Processing helix chain '4' and resid 680 through 683 Processing helix chain '4' and resid 686 through 691 removed outlier: 3.798A pdb=" N LEU 4 690 " --> pdb=" O ASP 4 686 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU 4 691 " --> pdb=" O VAL 4 687 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 686 through 691' Processing helix chain '4' and resid 691 through 698 removed outlier: 3.516A pdb=" N LEU 4 695 " --> pdb=" O LEU 4 691 " (cutoff:3.500A) Processing helix chain '4' and resid 739 through 750 removed outlier: 3.789A pdb=" N LEU 4 743 " --> pdb=" O LYS 4 739 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA 4 746 " --> pdb=" O VAL 4 742 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG 4 747 " --> pdb=" O LEU 4 743 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG 4 748 " --> pdb=" O ALA 4 744 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS 4 749 " --> pdb=" O THR 4 745 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE 4 750 " --> pdb=" O ALA 4 746 " (cutoff:3.500A) Processing helix chain '4' and resid 768 through 772 removed outlier: 3.518A pdb=" N ILE 4 772 " --> pdb=" O PRO 4 769 " (cutoff:3.500A) Processing helix chain '4' and resid 774 through 786 removed outlier: 3.849A pdb=" N VAL 4 778 " --> pdb=" O LYS 4 774 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU 4 780 " --> pdb=" O VAL 4 776 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS 4 781 " --> pdb=" O ASP 4 777 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU 4 782 " --> pdb=" O VAL 4 778 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL 4 783 " --> pdb=" O ARG 4 779 " (cutoff:3.500A) Processing helix chain '4' and resid 787 through 791 removed outlier: 3.503A pdb=" N LYS 4 790 " --> pdb=" O LEU 4 787 " (cutoff:3.500A) Processing helix chain '4' and resid 797 through 808 removed outlier: 3.797A pdb=" N LYS 4 801 " --> pdb=" O ASP 4 797 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP 4 802 " --> pdb=" O ASP 4 798 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU 4 803 " --> pdb=" O LYS 4 799 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU 4 804 " --> pdb=" O ALA 4 800 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA 4 805 " --> pdb=" O LYS 4 801 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY 4 808 " --> pdb=" O LEU 4 804 " (cutoff:3.500A) Processing helix chain '4' and resid 815 through 824 removed outlier: 3.963A pdb=" N ASN 4 819 " --> pdb=" O ALA 4 815 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG 4 820 " --> pdb=" O ARG 4 816 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE 4 822 " --> pdb=" O LEU 4 818 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN 4 823 " --> pdb=" O ASN 4 819 " (cutoff:3.500A) Processing helix chain '4' and resid 825 through 834 removed outlier: 3.606A pdb=" N GLN 4 829 " --> pdb=" O ALA 4 825 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG 4 832 " --> pdb=" O THR 4 828 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 4 834 " --> pdb=" O LEU 4 830 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 24 removed outlier: 3.632A pdb=" N GLU 5 12 " --> pdb=" O ASP 5 8 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR 5 13 " --> pdb=" O LYS 5 9 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA 5 16 " --> pdb=" O GLU 5 12 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS 5 19 " --> pdb=" O ASN 5 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA 5 21 " --> pdb=" O ALA 5 17 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA 5 22 " --> pdb=" O ALA 5 18 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU 5 23 " --> pdb=" O LYS 5 19 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN 5 24 " --> pdb=" O TYR 5 20 " (cutoff:3.500A) Processing helix chain '5' and resid 31 through 40 removed outlier: 4.400A pdb=" N ALA 5 35 " --> pdb=" O PRO 5 31 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL 5 36 " --> pdb=" O SER 5 32 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 54 removed outlier: 3.649A pdb=" N LEU 5 50 " --> pdb=" O PHE 5 46 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS 5 52 " --> pdb=" O SER 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 56 through 71 removed outlier: 3.645A pdb=" N ILE 5 67 " --> pdb=" O GLY 5 63 " (cutoff:3.500A) Processing helix chain '5' and resid 84 through 101 removed outlier: 4.155A pdb=" N ALA 5 88 " --> pdb=" O SER 5 84 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS 5 89 " --> pdb=" O PRO 5 85 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS 5 92 " --> pdb=" O ALA 5 88 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR 5 93 " --> pdb=" O LYS 5 89 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU 5 96 " --> pdb=" O HIS 5 92 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS 5 97 " --> pdb=" O TYR 5 93 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET 5 98 " --> pdb=" O ALA 5 94 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS 5 99 " --> pdb=" O HIS 5 95 " (cutoff:3.500A) Processing helix chain '5' and resid 107 through 114 removed outlier: 3.998A pdb=" N LEU 5 111 " --> pdb=" O ALA 5 107 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA 5 114 " --> pdb=" O HIS 5 110 " (cutoff:3.500A) Processing helix chain '5' and resid 115 through 117 No H-bonds generated for 'chain '5' and resid 115 through 117' Processing helix chain '5' and resid 121 through 129 removed outlier: 4.310A pdb=" N LEU 5 125 " --> pdb=" O MET 5 121 " (cutoff:3.500A) Processing helix chain '5' and resid 131 through 144 removed outlier: 3.722A pdb=" N GLU 5 136 " --> pdb=" O LYS 5 132 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN 5 137 " --> pdb=" O LYS 5 133 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL 5 139 " --> pdb=" O LEU 5 135 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR 5 140 " --> pdb=" O GLU 5 136 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS 5 141 " --> pdb=" O ASN 5 137 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL 5 142 " --> pdb=" O ALA 5 138 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG 5 143 " --> pdb=" O VAL 5 139 " (cutoff:3.500A) Processing helix chain '5' and resid 157 through 163 removed outlier: 3.531A pdb=" N TYR 5 163 " --> pdb=" O ALA 5 159 " (cutoff:3.500A) Processing helix chain '5' and resid 167 through 173 Processing helix chain '5' and resid 182 through 194 removed outlier: 3.511A pdb=" N SER 5 187 " --> pdb=" O ASP 5 183 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG 5 188 " --> pdb=" O GLU 5 184 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL 5 189 " --> pdb=" O ILE 5 185 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE 5 190 " --> pdb=" O ILE 5 186 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG 5 191 " --> pdb=" O SER 5 187 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL 5 192 " --> pdb=" O ARG 5 188 " (cutoff:3.500A) Processing helix chain '5' and resid 211 through 224 removed outlier: 4.019A pdb=" N ALA 5 215 " --> pdb=" O LYS 5 211 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA 5 219 " --> pdb=" O ALA 5 215 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN 5 220 " --> pdb=" O GLU 5 216 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG 5 221 " --> pdb=" O GLY 5 217 " (cutoff:3.500A) Processing helix chain '5' and resid 228 through 232 removed outlier: 3.637A pdb=" N GLN 5 232 " --> pdb=" O SER 5 229 " (cutoff:3.500A) Processing helix chain '5' and resid 239 through 245 removed outlier: 3.844A pdb=" N LEU 5 243 " --> pdb=" O ASP 5 239 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA 5 245 " --> pdb=" O GLY 5 241 " (cutoff:3.500A) Processing helix chain '5' and resid 252 through 268 removed outlier: 3.537A pdb=" N LYS 5 258 " --> pdb=" O GLU 5 254 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS 5 265 " --> pdb=" O LEU 5 261 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU 5 266 " --> pdb=" O LYS 5 262 " (cutoff:3.500A) Processing helix chain '5' and resid 339 through 347 removed outlier: 3.640A pdb=" N ILE 5 343 " --> pdb=" O VAL 5 339 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER 5 344 " --> pdb=" O THR 5 340 " (cutoff:3.500A) Processing helix chain '5' and resid 349 through 357 removed outlier: 3.515A pdb=" N THR 5 355 " --> pdb=" O GLU 5 351 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS 5 357 " --> pdb=" O TYR 5 353 " (cutoff:3.500A) Processing helix chain '5' and resid 363 through 374 removed outlier: 3.960A pdb=" N VAL 5 367 " --> pdb=" O ASP 5 363 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA 5 369 " --> pdb=" O ALA 5 365 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA 5 370 " --> pdb=" O ILE 5 366 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA 5 374 " --> pdb=" O ALA 5 370 " (cutoff:3.500A) Processing helix chain '5' and resid 383 through 403 removed outlier: 3.783A pdb=" N ASP 5 388 " --> pdb=" O ASP 5 384 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU 5 389 " --> pdb=" O LYS 5 385 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE 5 390 " --> pdb=" O ALA 5 386 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA 5 393 " --> pdb=" O LEU 5 389 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA 5 395 " --> pdb=" O ASP 5 391 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR 5 397 " --> pdb=" O ALA 5 393 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG 5 398 " --> pdb=" O CYS 5 394 " (cutoff:3.500A) Processing helix chain '5' and resid 405 through 428 removed outlier: 4.693A pdb=" N LEU 5 411 " --> pdb=" O ALA 5 407 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN 5 417 " --> pdb=" O ARG 5 413 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU 5 425 " --> pdb=" O GLU 5 421 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU 5 426 " --> pdb=" O ALA 5 422 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS 5 427 " --> pdb=" O THR 5 423 " (cutoff:3.500A) Processing helix chain '5' and resid 430 through 488 removed outlier: 3.801A pdb=" N LYS 5 434 " --> pdb=" O ASP 5 430 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN 5 435 " --> pdb=" O ALA 5 431 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN 5 438 " --> pdb=" O LYS 5 434 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU 5 439 " --> pdb=" O GLN 5 435 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA 5 442 " --> pdb=" O GLN 5 438 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA 5 445 " --> pdb=" O ARG 5 441 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG 5 446 " --> pdb=" O ALA 5 442 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU 5 450 " --> pdb=" O ARG 5 446 " (cutoff:3.500A) Proline residue: 5 453 - end of helix removed outlier: 3.859A pdb=" N LYS 5 457 " --> pdb=" O PRO 5 453 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG 5 474 " --> pdb=" O ASN 5 470 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP 5 476 " --> pdb=" O SER 5 472 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU 5 477 " --> pdb=" O GLN 5 473 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU 5 483 " --> pdb=" O LYS 5 479 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP 5 484 " --> pdb=" O ALA 5 480 " (cutoff:3.500A) Processing helix chain '5' and resid 490 through 499 removed outlier: 3.636A pdb=" N ALA 5 494 " --> pdb=" O ASP 5 490 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA 5 495 " --> pdb=" O LEU 5 491 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASP 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE 5 497 " --> pdb=" O ARG 5 493 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR 5 499 " --> pdb=" O ALA 5 495 " (cutoff:3.500A) Processing helix chain '5' and resid 500 through 524 removed outlier: 4.089A pdb=" N ARG 5 508 " --> pdb=" O ASP 5 504 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU 5 509 " --> pdb=" O LEU 5 505 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 5 512 " --> pdb=" O ARG 5 508 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA 5 514 " --> pdb=" O ALA 5 510 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU 5 515 " --> pdb=" O GLN 5 511 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA 5 521 " --> pdb=" O SER 5 517 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU 5 522 " --> pdb=" O GLN 5 518 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG 5 523 " --> pdb=" O ALA 5 519 " (cutoff:3.500A) Processing helix chain '5' and resid 533 through 546 removed outlier: 3.585A pdb=" N ILE 5 537 " --> pdb=" O GLY 5 533 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU 5 539 " --> pdb=" O ASP 5 535 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL 5 540 " --> pdb=" O GLN 5 536 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL 5 541 " --> pdb=" O ILE 5 537 " (cutoff:3.500A) Processing helix chain '5' and resid 548 through 553 removed outlier: 3.735A pdb=" N LEU 5 552 " --> pdb=" O PRO 5 548 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN 5 553 " --> pdb=" O VAL 5 549 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 548 through 553' Processing helix chain '5' and resid 556 through 561 removed outlier: 3.619A pdb=" N LEU 5 560 " --> pdb=" O GLU 5 556 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU 5 561 " --> pdb=" O LYS 5 557 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 556 through 561' Processing helix chain '5' and resid 562 through 567 removed outlier: 3.642A pdb=" N TYR 5 566 " --> pdb=" O HIS 5 562 " (cutoff:3.500A) Processing helix chain '5' and resid 574 through 588 removed outlier: 4.302A pdb=" N LYS 5 579 " --> pdb=" O ASP 5 575 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA 5 580 " --> pdb=" O GLU 5 576 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP 5 583 " --> pdb=" O LYS 5 579 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA 5 584 " --> pdb=" O ALA 5 580 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE 5 585 " --> pdb=" O ILE 5 581 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU 5 587 " --> pdb=" O ASP 5 583 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER 5 588 " --> pdb=" O ALA 5 584 " (cutoff:3.500A) Processing helix chain '5' and resid 612 through 620 removed outlier: 3.774A pdb=" N VAL 5 616 " --> pdb=" O LYS 5 612 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA 5 620 " --> pdb=" O VAL 5 616 " (cutoff:3.500A) Processing helix chain '5' and resid 662 through 670 removed outlier: 3.511A pdb=" N VAL 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG 5 669 " --> pdb=" O GLU 5 665 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG 5 670 " --> pdb=" O ALA 5 666 " (cutoff:3.500A) Processing helix chain '5' and resid 684 through 698 removed outlier: 3.978A pdb=" N ASN 5 689 " --> pdb=" O LYS 5 685 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU 5 690 " --> pdb=" O ASP 5 686 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU 5 691 " --> pdb=" O VAL 5 687 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN 5 693 " --> pdb=" O ASN 5 689 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE 5 694 " --> pdb=" O LEU 5 690 " (cutoff:3.500A) Processing helix chain '5' and resid 739 through 748 removed outlier: 3.715A pdb=" N ALA 5 744 " --> pdb=" O ASN 5 740 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR 5 745 " --> pdb=" O ALA 5 741 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA 5 746 " --> pdb=" O VAL 5 742 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG 5 747 " --> pdb=" O LEU 5 743 " (cutoff:3.500A) Processing helix chain '5' and resid 768 through 770 No H-bonds generated for 'chain '5' and resid 768 through 770' Processing helix chain '5' and resid 771 through 788 removed outlier: 3.547A pdb=" N ILE 5 775 " --> pdb=" O ASN 5 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL 5 776 " --> pdb=" O ILE 5 772 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP 5 777 " --> pdb=" O ARG 5 773 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL 5 778 " --> pdb=" O LYS 5 774 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG 5 779 " --> pdb=" O ILE 5 775 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU 5 780 " --> pdb=" O VAL 5 776 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU 5 782 " --> pdb=" O VAL 5 778 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL 5 783 " --> pdb=" O ARG 5 779 " (cutoff:3.500A) Processing helix chain '5' and resid 797 through 805 removed outlier: 3.969A pdb=" N LYS 5 801 " --> pdb=" O ASP 5 797 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP 5 802 " --> pdb=" O ASP 5 798 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU 5 803 " --> pdb=" O LYS 5 799 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU 5 804 " --> pdb=" O ALA 5 800 " (cutoff:3.500A) Processing helix chain '5' and resid 815 through 826 removed outlier: 3.809A pdb=" N ASN 5 819 " --> pdb=" O ALA 5 815 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG 5 820 " --> pdb=" O ARG 5 816 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE 5 822 " --> pdb=" O LEU 5 818 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN 5 823 " --> pdb=" O ASN 5 819 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS 5 824 " --> pdb=" O ARG 5 820 " (cutoff:3.500A) Processing helix chain '5' and resid 826 through 836 removed outlier: 3.714A pdb=" N LEU 5 830 " --> pdb=" O LEU 5 826 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER 5 831 " --> pdb=" O LEU 5 827 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG 5 832 " --> pdb=" O THR 5 828 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU 5 834 " --> pdb=" O LEU 5 830 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU 5 835 " --> pdb=" O SER 5 831 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP 5 836 " --> pdb=" O ARG 5 832 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 24 removed outlier: 3.540A pdb=" N GLU 6 12 " --> pdb=" O ASP 6 8 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU 6 14 " --> pdb=" O ALA 6 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA 6 18 " --> pdb=" O LEU 6 14 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS 6 19 " --> pdb=" O ASN 6 15 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR 6 20 " --> pdb=" O ALA 6 16 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU 6 23 " --> pdb=" O LYS 6 19 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN 6 24 " --> pdb=" O TYR 6 20 " (cutoff:3.500A) Processing helix chain '6' and resid 31 through 40 removed outlier: 4.200A pdb=" N ALA 6 35 " --> pdb=" O PRO 6 31 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL 6 36 " --> pdb=" O SER 6 32 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 54 removed outlier: 3.560A pdb=" N SER 6 48 " --> pdb=" O SER 6 44 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU 6 50 " --> pdb=" O PHE 6 46 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS 6 52 " --> pdb=" O SER 6 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA 6 53 " --> pdb=" O ILE 6 49 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY 6 54 " --> pdb=" O LEU 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 56 through 71 removed outlier: 3.693A pdb=" N ILE 6 60 " --> pdb=" O ASP 6 56 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE 6 64 " --> pdb=" O ILE 6 60 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS 6 65 " --> pdb=" O GLU 6 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS 6 66 " --> pdb=" O ARG 6 62 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE 6 67 " --> pdb=" O GLY 6 63 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET 6 68 " --> pdb=" O PHE 6 64 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL 6 69 " --> pdb=" O LYS 6 65 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG 6 70 " --> pdb=" O LYS 6 66 " (cutoff:3.500A) Processing helix chain '6' and resid 84 through 102 removed outlier: 3.633A pdb=" N ALA 6 88 " --> pdb=" O SER 6 84 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS 6 89 " --> pdb=" O PRO 6 85 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 6 90 " --> pdb=" O GLU 6 86 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU 6 91 " --> pdb=" O LEU 6 87 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU 6 96 " --> pdb=" O HIS 6 92 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS 6 97 " --> pdb=" O TYR 6 93 " (cutoff:3.500A) Processing helix chain '6' and resid 108 through 112 Processing helix chain '6' and resid 121 through 129 removed outlier: 3.919A pdb=" N LEU 6 125 " --> pdb=" O MET 6 121 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY 6 128 " --> pdb=" O VAL 6 124 " (cutoff:3.500A) Processing helix chain '6' and resid 131 through 144 removed outlier: 3.838A pdb=" N GLU 6 136 " --> pdb=" O LYS 6 132 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN 6 137 " --> pdb=" O LYS 6 133 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR 6 140 " --> pdb=" O GLU 6 136 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL 6 142 " --> pdb=" O ALA 6 138 " (cutoff:3.500A) Processing helix chain '6' and resid 158 through 163 Processing helix chain '6' and resid 167 through 173 Processing helix chain '6' and resid 182 through 194 removed outlier: 3.903A pdb=" N SER 6 187 " --> pdb=" O ASP 6 183 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG 6 188 " --> pdb=" O GLU 6 184 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE 6 190 " --> pdb=" O ILE 6 186 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG 6 191 " --> pdb=" O SER 6 187 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER 6 194 " --> pdb=" O ILE 6 190 " (cutoff:3.500A) Processing helix chain '6' and resid 211 through 225 removed outlier: 4.178A pdb=" N ALA 6 215 " --> pdb=" O LYS 6 211 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU 6 218 " --> pdb=" O ILE 6 214 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG 6 221 " --> pdb=" O GLY 6 217 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE 6 222 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL 6 223 " --> pdb=" O ALA 6 219 " (cutoff:3.500A) Processing helix chain '6' and resid 241 through 245 removed outlier: 3.561A pdb=" N ALA 6 245 " --> pdb=" O SER 6 242 " (cutoff:3.500A) Processing helix chain '6' and resid 252 through 268 removed outlier: 3.547A pdb=" N LYS 6 258 " --> pdb=" O GLU 6 254 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU 6 263 " --> pdb=" O ALA 6 259 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU 6 264 " --> pdb=" O VAL 6 260 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS 6 265 " --> pdb=" O LEU 6 261 " (cutoff:3.500A) Processing helix chain '6' and resid 295 through 301 Processing helix chain '6' and resid 312 through 317 removed outlier: 3.570A pdb=" N ARG 6 316 " --> pdb=" O LEU 6 312 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN 6 317 " --> pdb=" O THR 6 313 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 312 through 317' Processing helix chain '6' and resid 322 through 327 removed outlier: 3.551A pdb=" N ARG 6 327 " --> pdb=" O PRO 6 323 " (cutoff:3.500A) Processing helix chain '6' and resid 339 through 349 removed outlier: 3.618A pdb=" N SER 6 344 " --> pdb=" O THR 6 340 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY 6 348 " --> pdb=" O SER 6 344 " (cutoff:3.500A) Processing helix chain '6' and resid 349 through 357 removed outlier: 3.653A pdb=" N TYR 6 353 " --> pdb=" O LEU 6 349 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR 6 355 " --> pdb=" O GLU 6 351 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS 6 356 " --> pdb=" O ARG 6 352 " (cutoff:3.500A) Processing helix chain '6' and resid 363 through 377 removed outlier: 3.925A pdb=" N VAL 6 367 " --> pdb=" O ASP 6 363 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA 6 370 " --> pdb=" O ILE 6 366 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA 6 374 " --> pdb=" O ALA 6 370 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG 6 375 " --> pdb=" O GLN 6 371 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR 6 376 " --> pdb=" O LEU 6 372 " (cutoff:3.500A) Processing helix chain '6' and resid 383 through 403 removed outlier: 3.642A pdb=" N ASP 6 388 " --> pdb=" O ASP 6 384 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU 6 389 " --> pdb=" O LYS 6 385 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE 6 390 " --> pdb=" O ALA 6 386 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA 6 395 " --> pdb=" O ASP 6 391 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN 6 396 " --> pdb=" O GLU 6 392 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR 6 397 " --> pdb=" O ALA 6 393 " (cutoff:3.500A) Processing helix chain '6' and resid 405 through 426 removed outlier: 4.259A pdb=" N LEU 6 411 " --> pdb=" O ALA 6 407 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA 6 424 " --> pdb=" O VAL 6 420 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU 6 426 " --> pdb=" O ALA 6 422 " (cutoff:3.500A) Processing helix chain '6' and resid 433 through 450 removed outlier: 3.519A pdb=" N GLN 6 438 " --> pdb=" O LYS 6 434 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU 6 439 " --> pdb=" O GLN 6 435 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG 6 446 " --> pdb=" O ALA 6 442 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU 6 450 " --> pdb=" O ARG 6 446 " (cutoff:3.500A) Processing helix chain '6' and resid 451 through 488 removed outlier: 4.139A pdb=" N LYS 6 457 " --> pdb=" O PRO 6 453 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU 6 467 " --> pdb=" O GLY 6 463 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG 6 469 " --> pdb=" O LEU 6 465 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG 6 474 " --> pdb=" O ASN 6 470 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP 6 476 " --> pdb=" O SER 6 472 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU 6 477 " --> pdb=" O GLN 6 473 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU 6 483 " --> pdb=" O LYS 6 479 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG 6 487 " --> pdb=" O GLU 6 483 " (cutoff:3.500A) Processing helix chain '6' and resid 490 through 495 removed outlier: 3.642A pdb=" N ALA 6 495 " --> pdb=" O LEU 6 491 " (cutoff:3.500A) Processing helix chain '6' and resid 501 through 524 removed outlier: 3.588A pdb=" N LYS 6 507 " --> pdb=" O PRO 6 503 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN 6 511 " --> pdb=" O LYS 6 507 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU 6 512 " --> pdb=" O ARG 6 508 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER 6 517 " --> pdb=" O GLN 6 513 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN 6 518 " --> pdb=" O ALA 6 514 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP 6 520 " --> pdb=" O LYS 6 516 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA 6 521 " --> pdb=" O SER 6 517 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU 6 522 " --> pdb=" O GLN 6 518 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG 6 523 " --> pdb=" O ALA 6 519 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA 6 524 " --> pdb=" O ASP 6 520 " (cutoff:3.500A) Processing helix chain '6' and resid 533 through 545 removed outlier: 3.552A pdb=" N ILE 6 537 " --> pdb=" O GLY 6 533 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU 6 539 " --> pdb=" O ASP 6 535 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL 6 540 " --> pdb=" O GLN 6 536 " (cutoff:3.500A) Processing helix chain '6' and resid 548 through 552 removed outlier: 3.671A pdb=" N ASN 6 551 " --> pdb=" O PRO 6 548 " (cutoff:3.500A) Processing helix chain '6' and resid 555 through 562 removed outlier: 3.521A pdb=" N LYS 6 559 " --> pdb=" O SER 6 555 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU 6 560 " --> pdb=" O GLU 6 556 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS 6 562 " --> pdb=" O GLU 6 558 " (cutoff:3.500A) Processing helix chain '6' and resid 562 through 568 removed outlier: 3.795A pdb=" N TYR 6 566 " --> pdb=" O HIS 6 562 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS 6 568 " --> pdb=" O GLU 6 564 " (cutoff:3.500A) Processing helix chain '6' and resid 574 through 591 removed outlier: 3.718A pdb=" N ILE 6 578 " --> pdb=" O GLN 6 574 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS 6 579 " --> pdb=" O ASP 6 575 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA 6 580 " --> pdb=" O GLU 6 576 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE 6 581 " --> pdb=" O ALA 6 577 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS 6 582 " --> pdb=" O ILE 6 578 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA 6 584 " --> pdb=" O ALA 6 580 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU 6 587 " --> pdb=" O ASP 6 583 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER 6 588 " --> pdb=" O ALA 6 584 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR 6 590 " --> pdb=" O ARG 6 586 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY 6 591 " --> pdb=" O LEU 6 587 " (cutoff:3.500A) Processing helix chain '6' and resid 613 through 621 removed outlier: 3.580A pdb=" N LYS 6 617 " --> pdb=" O THR 6 613 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA 6 620 " --> pdb=" O VAL 6 616 " (cutoff:3.500A) Processing helix chain '6' and resid 636 through 638 No H-bonds generated for 'chain '6' and resid 636 through 638' Processing helix chain '6' and resid 662 through 667 removed outlier: 3.639A pdb=" N VAL 6 667 " --> pdb=" O LEU 6 663 " (cutoff:3.500A) Processing helix chain '6' and resid 679 through 683 Processing helix chain '6' and resid 684 through 689 removed outlier: 3.644A pdb=" N ASN 6 689 " --> pdb=" O LYS 6 685 " (cutoff:3.500A) Processing helix chain '6' and resid 689 through 698 removed outlier: 3.779A pdb=" N GLN 6 693 " --> pdb=" O ASN 6 689 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE 6 694 " --> pdb=" O LEU 6 690 " (cutoff:3.500A) Processing helix chain '6' and resid 739 through 750 removed outlier: 3.717A pdb=" N LEU 6 743 " --> pdb=" O LYS 6 739 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA 6 744 " --> pdb=" O ASN 6 740 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR 6 745 " --> pdb=" O ALA 6 741 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA 6 746 " --> pdb=" O VAL 6 742 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG 6 747 " --> pdb=" O LEU 6 743 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG 6 748 " --> pdb=" O ALA 6 744 " (cutoff:3.500A) Processing helix chain '6' and resid 751 through 756 removed outlier: 3.923A pdb=" N ASN 6 756 " --> pdb=" O ASN 6 752 " (cutoff:3.500A) Processing helix chain '6' and resid 768 through 770 No H-bonds generated for 'chain '6' and resid 768 through 770' Processing helix chain '6' and resid 771 through 785 removed outlier: 3.547A pdb=" N ILE 6 775 " --> pdb=" O ASN 6 771 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL 6 776 " --> pdb=" O ILE 6 772 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP 6 777 " --> pdb=" O ARG 6 773 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL 6 778 " --> pdb=" O LYS 6 774 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS 6 781 " --> pdb=" O ASP 6 777 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU 6 782 " --> pdb=" O VAL 6 778 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL 6 783 " --> pdb=" O ARG 6 779 " (cutoff:3.500A) Processing helix chain '6' and resid 799 through 807 removed outlier: 3.805A pdb=" N LEU 6 803 " --> pdb=" O LYS 6 799 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU 6 804 " --> pdb=" O ALA 6 800 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA 6 805 " --> pdb=" O LYS 6 801 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN 6 806 " --> pdb=" O ASP 6 802 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN 6 807 " --> pdb=" O LEU 6 803 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 799 through 807' Processing helix chain '6' and resid 817 through 824 removed outlier: 3.631A pdb=" N ILE 6 822 " --> pdb=" O LEU 6 818 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN 6 823 " --> pdb=" O ASN 6 819 " (cutoff:3.500A) Processing helix chain '6' and resid 825 through 834 removed outlier: 3.960A pdb=" N GLN 6 829 " --> pdb=" O ALA 6 825 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU 6 830 " --> pdb=" O LEU 6 826 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER 6 831 " --> pdb=" O LEU 6 827 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU 6 834 " --> pdb=" O LEU 6 830 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 164 through 166 removed outlier: 6.554A pdb=" N TYR 1 236 " --> pdb=" O PHE 1 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 308 through 310 removed outlier: 3.510A pdb=" N THR 1 310 " --> pdb=" O LEU 1 203 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN 1 330 " --> pdb=" O CYS 1 202 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL 1 204 " --> pdb=" O GLN 1 330 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL 1 332 " --> pdb=" O VAL 1 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 360 through 361 removed outlier: 7.383A pdb=" N ARG 1 360 " --> pdb=" O VAL 1 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain '1' and resid 630 through 634 removed outlier: 3.650A pdb=" N LEU 1 676 " --> pdb=" O VAL 1 631 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR 1 673 " --> pdb=" O ILE 1 714 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N VAL 1 716 " --> pdb=" O THR 1 673 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL 1 675 " --> pdb=" O VAL 1 716 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 699 through 701 removed outlier: 3.734A pdb=" N CYS 1 700 " --> pdb=" O VAL 1 708 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL 1 708 " --> pdb=" O CYS 1 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '1' and resid 793 through 796 removed outlier: 6.901A pdb=" N THR 1 793 " --> pdb=" O ALA 1 845 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL 1 847 " --> pdb=" O THR 1 793 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP 1 795 " --> pdb=" O VAL 1 847 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N VAL 1 849 " --> pdb=" O ASP 1 795 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS 1 846 " --> pdb=" O ILE 1 858 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 164 through 166 removed outlier: 6.070A pdb=" N TYR 2 236 " --> pdb=" O PHE 2 272 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 200 through 204 removed outlier: 6.572A pdb=" N GLN 2 330 " --> pdb=" O CYS 2 202 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL 2 204 " --> pdb=" O GLN 2 330 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL 2 332 " --> pdb=" O VAL 2 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '2' and resid 360 through 361 removed outlier: 7.311A pdb=" N ARG 2 360 " --> pdb=" O VAL 2 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '2' and resid 630 through 634 removed outlier: 6.920A pdb=" N VAL 2 631 " --> pdb=" O LEU 2 676 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASP 2 678 " --> pdb=" O VAL 2 631 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE 2 633 " --> pdb=" O ASP 2 678 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL 2 675 " --> pdb=" O VAL 2 716 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain '2' and resid 699 through 701 removed outlier: 4.178A pdb=" N CYS 2 700 " --> pdb=" O VAL 2 708 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL 2 708 " --> pdb=" O CYS 2 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain '2' and resid 794 through 796 removed outlier: 7.203A pdb=" N ASP 2 795 " --> pdb=" O VAL 2 847 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N VAL 2 849 " --> pdb=" O ASP 2 795 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS 2 846 " --> pdb=" O ILE 2 858 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR 2 848 " --> pdb=" O ILE 2 856 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE 2 856 " --> pdb=" O THR 2 848 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 164 through 166 removed outlier: 5.509A pdb=" N LYS 3 234 " --> pdb=" O ILE 3 270 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE 3 272 " --> pdb=" O LYS 3 234 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR 3 236 " --> pdb=" O PHE 3 272 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 308 through 310 removed outlier: 3.638A pdb=" N THR 3 310 " --> pdb=" O LEU 3 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '3' and resid 360 through 361 removed outlier: 6.808A pdb=" N ARG 3 360 " --> pdb=" O VAL 3 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '3' and resid 630 through 633 removed outlier: 6.797A pdb=" N VAL 3 675 " --> pdb=" O VAL 3 716 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '3' and resid 699 through 701 removed outlier: 3.846A pdb=" N CYS 3 700 " --> pdb=" O VAL 3 708 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL 3 708 " --> pdb=" O CYS 3 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain '3' and resid 793 through 796 removed outlier: 6.388A pdb=" N THR 3 793 " --> pdb=" O ALA 3 845 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL 3 847 " --> pdb=" O THR 3 793 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP 3 795 " --> pdb=" O VAL 3 847 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N VAL 3 849 " --> pdb=" O ASP 3 795 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS 3 846 " --> pdb=" O ILE 3 858 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR 3 848 " --> pdb=" O ILE 3 856 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE 3 856 " --> pdb=" O THR 3 848 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 164 through 166 removed outlier: 6.395A pdb=" N TYR 4 236 " --> pdb=" O PHE 4 272 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL 4 271 " --> pdb=" O ILE 4 307 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ALA 4 309 " --> pdb=" O VAL 4 271 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE 4 273 " --> pdb=" O ALA 4 309 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N THR 4 311 " --> pdb=" O ILE 4 273 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY 4 205 " --> pdb=" O THR 4 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 360 through 361 removed outlier: 7.757A pdb=" N ARG 4 360 " --> pdb=" O VAL 4 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain '4' and resid 604 through 605 removed outlier: 3.559A pdb=" N SER 4 719 " --> pdb=" O PHE 4 604 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL 4 675 " --> pdb=" O VAL 4 716 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N THR 4 718 " --> pdb=" O VAL 4 675 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE 4 677 " --> pdb=" O THR 4 718 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 699 through 701 removed outlier: 3.646A pdb=" N VAL 4 708 " --> pdb=" O CYS 4 700 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '4' and resid 793 through 796 removed outlier: 6.267A pdb=" N THR 4 793 " --> pdb=" O ALA 4 845 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL 4 847 " --> pdb=" O THR 4 793 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP 4 795 " --> pdb=" O VAL 4 847 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N VAL 4 849 " --> pdb=" O ASP 4 795 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS 4 846 " --> pdb=" O ILE 4 858 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 164 through 166 removed outlier: 5.732A pdb=" N LYS 5 234 " --> pdb=" O ILE 5 270 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE 5 272 " --> pdb=" O LYS 5 234 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR 5 236 " --> pdb=" O PHE 5 272 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ILE 5 307 " --> pdb=" O ALA 5 269 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL 5 271 " --> pdb=" O ILE 5 307 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 201 through 203 removed outlier: 6.416A pdb=" N CYS 5 202 " --> pdb=" O VAL 5 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '5' and resid 360 through 361 removed outlier: 7.045A pdb=" N ARG 5 360 " --> pdb=" O VAL 5 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '5' and resid 630 through 632 removed outlier: 6.747A pdb=" N VAL 5 675 " --> pdb=" O VAL 5 716 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR 5 718 " --> pdb=" O VAL 5 675 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE 5 677 " --> pdb=" O THR 5 718 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 793 through 796 removed outlier: 6.931A pdb=" N THR 5 793 " --> pdb=" O ALA 5 845 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL 5 847 " --> pdb=" O THR 5 793 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP 5 795 " --> pdb=" O VAL 5 847 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N VAL 5 849 " --> pdb=" O ASP 5 795 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS 5 846 " --> pdb=" O ILE 5 858 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 165 through 166 removed outlier: 3.789A pdb=" N ILE 6 165 " --> pdb=" O SER 6 237 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR 6 236 " --> pdb=" O PHE 6 272 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 308 through 311 removed outlier: 3.700A pdb=" N GLY 6 205 " --> pdb=" O THR 6 310 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS 6 202 " --> pdb=" O GLN 6 330 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 360 through 361 removed outlier: 7.041A pdb=" N ARG 6 360 " --> pdb=" O VAL 6 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain '6' and resid 602 through 605 removed outlier: 4.423A pdb=" N LEU 6 603 " --> pdb=" O GLU 6 760 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE 6 762 " --> pdb=" O LEU 6 603 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 6 605 " --> pdb=" O ILE 6 762 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain '6' and resid 630 through 634 removed outlier: 3.520A pdb=" N ASP 6 678 " --> pdb=" O ILE 6 633 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL 6 675 " --> pdb=" O VAL 6 716 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 794 through 796 removed outlier: 3.552A pdb=" N VAL 6 847 " --> pdb=" O ASP 6 795 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS 6 846 " --> pdb=" O ILE 6 858 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE 6 858 " --> pdb=" O LYS 6 846 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR 6 848 " --> pdb=" O ILE 6 856 " (cutoff:3.500A) 1147 hydrogen bonds defined for protein. 3345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13176 1.34 - 1.46: 7246 1.46 - 1.58: 18104 1.58 - 1.69: 36 1.69 - 1.81: 252 Bond restraints: 38814 Sorted by residual: bond pdb=" C ARG 2 816 " pdb=" N PRO 2 817 " ideal model delta sigma weight residual 1.337 1.351 -0.014 1.11e-02 8.12e+03 1.69e+00 bond pdb=" C4 ADP 6 901 " pdb=" C5 ADP 6 901 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.83e-01 bond pdb=" C4 ADP 4 902 " pdb=" C5 ADP 4 902 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.58e-01 bond pdb=" C4 ADP 5 901 " pdb=" C5 ADP 5 901 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.49e-01 bond pdb=" C4 ADP 3 902 " pdb=" C5 ADP 3 902 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.47e-01 ... (remaining 38809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 51028 1.16 - 2.31: 929 2.31 - 3.47: 223 3.47 - 4.63: 76 4.63 - 5.78: 70 Bond angle restraints: 52326 Sorted by residual: angle pdb=" N ALA 3 386 " pdb=" CA ALA 3 386 " pdb=" C ALA 3 386 " ideal model delta sigma weight residual 114.62 110.70 3.92 1.14e+00 7.69e-01 1.18e+01 angle pdb=" N ILE 6 497 " pdb=" CA ILE 6 497 " pdb=" C ILE 6 497 " ideal model delta sigma weight residual 111.62 109.42 2.20 7.90e-01 1.60e+00 7.79e+00 angle pdb=" N VAL 4 549 " pdb=" CA VAL 4 549 " pdb=" C VAL 4 549 " ideal model delta sigma weight residual 113.07 109.66 3.41 1.36e+00 5.41e-01 6.30e+00 angle pdb=" CA ALA 3 386 " pdb=" C ALA 3 386 " pdb=" N ILE 3 387 " ideal model delta sigma weight residual 119.71 116.82 2.89 1.17e+00 7.31e-01 6.09e+00 angle pdb=" N ILE 2 497 " pdb=" CA ILE 2 497 " pdb=" C ILE 2 497 " ideal model delta sigma weight residual 111.48 109.42 2.06 9.40e-01 1.13e+00 4.80e+00 ... (remaining 52321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.51: 23743 27.51 - 55.03: 394 55.03 - 82.54: 29 82.54 - 110.06: 7 110.06 - 137.57: 13 Dihedral angle restraints: 24186 sinusoidal: 10140 harmonic: 14046 Sorted by residual: dihedral pdb=" C5' ADP 4 901 " pdb=" O5' ADP 4 901 " pdb=" PA ADP 4 901 " pdb=" O2A ADP 4 901 " ideal model delta sinusoidal sigma weight residual 300.00 162.43 137.57 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C5' ADP 4 902 " pdb=" O5' ADP 4 902 " pdb=" PA ADP 4 902 " pdb=" O2A ADP 4 902 " ideal model delta sinusoidal sigma weight residual -60.00 76.23 -136.23 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP 1 901 " pdb=" O3A ADP 1 901 " pdb=" PA ADP 1 901 " pdb=" PB ADP 1 901 " ideal model delta sinusoidal sigma weight residual 300.00 165.27 134.73 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 24183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3456 0.026 - 0.052: 1802 0.052 - 0.078: 404 0.078 - 0.104: 272 0.104 - 0.130: 108 Chirality restraints: 6042 Sorted by residual: chirality pdb=" CA ILE 2 547 " pdb=" N ILE 2 547 " pdb=" C ILE 2 547 " pdb=" CB ILE 2 547 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE 1 547 " pdb=" N ILE 1 547 " pdb=" C ILE 1 547 " pdb=" CB ILE 1 547 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE 5 547 " pdb=" N ILE 5 547 " pdb=" C ILE 5 547 " pdb=" CB ILE 5 547 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 6039 not shown) Planarity restraints: 6756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET 6 382 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.83e+00 pdb=" N PRO 6 383 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO 6 383 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO 6 383 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET 3 382 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO 3 383 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO 3 383 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO 3 383 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET 1 382 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO 1 383 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO 1 383 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO 1 383 " -0.017 5.00e-02 4.00e+02 ... (remaining 6753 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 10438 2.81 - 3.33: 31739 3.33 - 3.85: 56223 3.85 - 4.38: 68484 4.38 - 4.90: 116318 Nonbonded interactions: 283202 Sorted by model distance: nonbonded pdb=" OD2 ASP 3 166 " pdb=" OG1 THR 3 168 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR 3 608 " pdb=" O2B ADP 3 902 " model vdw 2.298 3.040 nonbonded pdb=" O ASP 1 226 " pdb=" OG SER 2 403 " model vdw 2.305 3.040 nonbonded pdb=" OG1 THR 3 768 " pdb=" OD1 ASN 3 771 " model vdw 2.309 3.040 nonbonded pdb=" O SER 4 338 " pdb=" OG1 THR 4 342 " model vdw 2.311 3.040 ... (remaining 283197 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: 0.02 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.550 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4341 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 : 0.001 0.020 38814 Z= 0.083 Angle : 0.453 5.782 52326 Z= 0.251 Chirality : 0.037 0.130 6042 Planarity : 0.003 0.034 6756 Dihedral : 9.421 137.570 15030 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.50 % Favored : 92.83 % Rotamer: Outliers : 0.05 % Allowed : 1.89 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.95 (0.09), residues: 4740 helix: -4.55 (0.04), residues: 2245 sheet: -1.97 (0.30), residues: 309 loop : -1.83 (0.11), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG 4 328 TYR 0.003 0.000 TYR 4 813 PHE 0.002 0.000 PHE 6 329 TRP 0.002 0.000 TRP 3 544 HIS 0.002 0.000 HIS 6 684 Details of bonding type rmsd covalent geometry : bond 0.00133 (38814) covalent geometry : angle 0.45286 (52326) hydrogen bonds : bond 0.38216 ( 1147) hydrogen bonds : angle 8.77393 ( 3345) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1383 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 199 ASN cc_start: 0.5581 (p0) cc_final: 0.5048 (p0) REVERT: 1 461 GLU cc_start: 0.0058 (tt0) cc_final: -0.0397 (tt0) REVERT: 2 630 ILE cc_start: 0.5910 (mt) cc_final: 0.5702 (tt) REVERT: 2 718 THR cc_start: 0.5417 (m) cc_final: 0.5189 (p) REVERT: 2 835 LEU cc_start: 0.5435 (mt) cc_final: 0.5218 (mm) REVERT: 3 278 THR cc_start: 0.6838 (p) cc_final: 0.6394 (p) REVERT: 3 389 LEU cc_start: 0.5447 (mt) cc_final: 0.4942 (mt) REVERT: 3 614 LEU cc_start: 0.5446 (tp) cc_final: 0.5155 (tp) REVERT: 4 383 PRO cc_start: 0.8314 (Cg_endo) cc_final: 0.8089 (Cg_exo) REVERT: 4 471 LEU cc_start: 0.4055 (mt) cc_final: 0.3760 (mt) REVERT: 5 330 GLN cc_start: 0.7562 (tp40) cc_final: 0.7231 (tm-30) REVERT: 6 798 ASP cc_start: 0.4465 (m-30) cc_final: 0.4100 (m-30) outliers start: 2 outliers final: 0 residues processed: 1384 average time/residue: 0.2399 time to fit residues: 502.3484 Evaluate side-chains 743 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 743 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 0.0270 chunk 197 optimal weight: 0.0980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 10.0000 overall best weight: 2.4280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 ASN ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 71 GLN ** 1 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 200 ASN 1 277 HIS ** 1 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 553 GLN 1 693 GLN 1 784 GLN 2 26 HIS ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 95 HIS 2 97 HIS 2 268 GLN ** 2 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 404 GLN 2 415 HIS 2 473 GLN 2 551 ASN 2 740 ASN ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 823 GLN 2 824 HIS 3 24 ASN ** 3 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 97 HIS ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 470 ASN 3 824 HIS 3 860 ASN 4 15 ASN ** 4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 43 ASN 4 83 HIS 4 141 HIS 4 277 HIS 4 293 ASN 4 784 GLN 4 806 GLN 5 137 ASN 5 200 ASN 5 536 GLN 5 594 ASN 5 699 HIS 5 771 ASN 5 860 ASN ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 92 HIS 6 95 HIS 6 200 ASN 6 379 GLN 6 473 GLN ** 6 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 594 ASN ** 6 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 860 ASN 6 861 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.135687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.121885 restraints weight = 177874.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.123674 restraints weight = 123430.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.124744 restraints weight = 90999.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.125773 restraints weight = 72839.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.126213 restraints weight = 59769.873| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 38814 Z= 0.161 Angle : 0.715 9.537 52326 Z= 0.343 Chirality : 0.043 0.167 6042 Planarity : 0.005 0.118 6756 Dihedral : 7.390 151.777 5400 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.31 % Favored : 96.67 % Rotamer: Outliers : 2.80 % Allowed : 12.47 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (0.11), residues: 4740 helix: -2.69 (0.08), residues: 2491 sheet: -1.44 (0.28), residues: 355 loop : -1.12 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG 5 668 TYR 0.015 0.002 TYR 6 458 PHE 0.019 0.002 PHE 4 602 TRP 0.034 0.004 TRP 6 544 HIS 0.011 0.001 HIS 6 684 Details of bonding type rmsd covalent geometry : bond 0.00354 (38814) covalent geometry : angle 0.71520 (52326) hydrogen bonds : bond 0.04889 ( 1147) hydrogen bonds : angle 4.91743 ( 3345) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 845 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 366 ILE cc_start: 0.7710 (mp) cc_final: 0.7095 (mm) REVERT: 1 668 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7817 (mtp-110) REVERT: 2 4 MET cc_start: 0.0161 (ptp) cc_final: -0.0305 (ttp) REVERT: 2 98 MET cc_start: 0.3534 (ptt) cc_final: 0.3235 (ptt) REVERT: 2 260 VAL cc_start: 0.8457 (t) cc_final: 0.8043 (p) REVERT: 2 403 SER cc_start: 0.7136 (m) cc_final: 0.6762 (p) REVERT: 2 670 ARG cc_start: 0.7082 (tpp-160) cc_final: 0.6691 (tpp-160) REVERT: 2 686 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: 2 696 ASP cc_start: 0.7801 (m-30) cc_final: 0.7562 (m-30) REVERT: 2 717 MET cc_start: 0.6877 (mmt) cc_final: 0.6321 (mmt) REVERT: 2 753 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7737 (tm-30) REVERT: 2 770 SER cc_start: 0.8692 (m) cc_final: 0.8344 (t) REVERT: 3 38 MET cc_start: 0.4639 (ppp) cc_final: 0.3883 (ptm) REVERT: 3 68 MET cc_start: -0.0910 (mtm) cc_final: -0.1757 (ttm) REVERT: 3 162 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8681 (mtpt) REVERT: 3 198 LYS cc_start: 0.8492 (mptt) cc_final: 0.8160 (mmtt) REVERT: 3 275 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6835 (mt-10) REVERT: 3 595 ARG cc_start: 0.6401 (mmt180) cc_final: 0.6146 (mmp80) REVERT: 3 709 ASP cc_start: 0.6677 (t0) cc_final: 0.5799 (t0) REVERT: 4 192 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7647 (p) REVERT: 4 473 GLN cc_start: 0.6959 (mt0) cc_final: 0.6548 (mm110) REVERT: 4 474 ARG cc_start: 0.6840 (mmp-170) cc_final: 0.6525 (mmp-170) REVERT: 4 601 SER cc_start: 0.8355 (m) cc_final: 0.7857 (p) REVERT: 5 196 ARG cc_start: 0.7521 (ptt180) cc_final: 0.7125 (ptt180) REVERT: 5 296 LYS cc_start: 0.6821 (mtpt) cc_final: 0.6426 (ttpp) REVERT: 5 449 GLU cc_start: 0.8172 (tp30) cc_final: 0.7886 (tp30) REVERT: 5 483 GLU cc_start: 0.7056 (tp30) cc_final: 0.6617 (tp30) REVERT: 5 639 MET cc_start: 0.7180 (mtm) cc_final: 0.6541 (mtm) REVERT: 5 664 THR cc_start: 0.8243 (m) cc_final: 0.7672 (p) REVERT: 5 775 ILE cc_start: 0.7955 (mt) cc_final: 0.7590 (mm) REVERT: 6 265 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7412 (mmmm) REVERT: 6 275 GLU cc_start: 0.8002 (tp30) cc_final: 0.7139 (tp30) REVERT: 6 798 ASP cc_start: 0.6773 (m-30) cc_final: 0.6541 (m-30) outliers start: 114 outliers final: 55 residues processed: 910 average time/residue: 0.2322 time to fit residues: 323.4476 Evaluate side-chains 699 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 641 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 83 HIS Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 253 PHE Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 763 VAL Chi-restraints excluded: chain 2 residue 183 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 2 residue 280 LEU Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 686 ASP Chi-restraints excluded: chain 3 residue 261 LEU Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 622 PHE Chi-restraints excluded: chain 3 residue 759 ASP Chi-restraints excluded: chain 3 residue 768 THR Chi-restraints excluded: chain 3 residue 778 VAL Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 3 residue 860 ASN Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 345 ILE Chi-restraints excluded: chain 4 residue 367 VAL Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 204 VAL Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 531 VAL Chi-restraints excluded: chain 5 residue 592 LEU Chi-restraints excluded: chain 5 residue 631 VAL Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 714 ILE Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 265 LYS Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 451 LEU Chi-restraints excluded: chain 6 residue 537 ILE Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 776 VAL Chi-restraints excluded: chain 6 residue 787 LEU Chi-restraints excluded: chain 6 residue 828 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 462 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 270 optimal weight: 10.0000 chunk 456 optimal weight: 9.9990 chunk 228 optimal weight: 0.9980 chunk 352 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 408 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 83 HIS 1 101 GLN 1 293 ASN ** 1 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 15 ASN ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 108 GLN ** 2 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 861 HIS 3 30 HIS 3 33 HIS 3 95 HIS 3 356 HIS 3 553 GLN 3 756 ASN 3 861 HIS 4 137 ASN 4 400 GLN 4 511 GLN 4 562 HIS 4 625 ASN 4 752 ASN 4 756 ASN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 829 GLN 5 28 GLN ** 5 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 277 HIS 5 470 ASN 5 574 GLN 5 593 GLN 5 806 GLN 5 829 GLN ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 277 HIS ** 6 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 473 GLN 6 551 ASN 6 562 HIS 6 593 GLN 6 749 HIS 6 824 HIS 6 829 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.123583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.109581 restraints weight = 176042.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.111287 restraints weight = 123881.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.112431 restraints weight = 93501.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.113283 restraints weight = 75073.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.113927 restraints weight = 62878.488| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.7550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 38814 Z= 0.246 Angle : 0.854 14.003 52326 Z= 0.419 Chirality : 0.048 0.290 6042 Planarity : 0.006 0.072 6756 Dihedral : 7.896 136.200 5400 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.64 % Favored : 95.34 % Rotamer: Outliers : 4.66 % Allowed : 14.48 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.11), residues: 4740 helix: -1.84 (0.09), residues: 2672 sheet: -1.63 (0.27), residues: 367 loop : -0.86 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 3 328 TYR 0.027 0.002 TYR 2 638 PHE 0.031 0.003 PHE 1 46 TRP 0.028 0.003 TRP 6 544 HIS 0.011 0.002 HIS 5 699 Details of bonding type rmsd covalent geometry : bond 0.00546 (38814) covalent geometry : angle 0.85425 (52326) hydrogen bonds : bond 0.05294 ( 1147) hydrogen bonds : angle 5.11397 ( 3345) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 720 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 216 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8012 (pp20) REVERT: 1 366 ILE cc_start: 0.8485 (mp) cc_final: 0.8033 (mm) REVERT: 1 563 MET cc_start: 0.6988 (ttm) cc_final: 0.6743 (ttm) REVERT: 1 623 LEU cc_start: 0.8328 (mp) cc_final: 0.8052 (mt) REVERT: 1 672 TYR cc_start: 0.7209 (m-10) cc_final: 0.6973 (m-10) REVERT: 1 714 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8319 (mm) REVERT: 1 773 ARG cc_start: 0.8322 (tpt170) cc_final: 0.8074 (tpt-90) REVERT: 2 195 ARG cc_start: 0.7765 (mtp-110) cc_final: 0.7507 (mtm-85) REVERT: 2 198 LYS cc_start: 0.7328 (mttm) cc_final: 0.6884 (mttm) REVERT: 2 326 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7151 (tm-30) REVERT: 2 403 SER cc_start: 0.7183 (m) cc_final: 0.6904 (p) REVERT: 2 618 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6628 (tm-30) REVERT: 2 623 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7918 (mt) REVERT: 2 685 LYS cc_start: 0.8682 (tttt) cc_final: 0.8473 (tttt) REVERT: 2 717 MET cc_start: 0.7073 (mmt) cc_final: 0.6782 (mmt) REVERT: 3 121 MET cc_start: 0.4295 (tpp) cc_final: 0.4001 (tpt) REVERT: 3 162 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8754 (mtpt) REVERT: 3 198 LYS cc_start: 0.8407 (mptt) cc_final: 0.8130 (mptt) REVERT: 3 682 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8725 (ttpp) REVERT: 3 835 LEU cc_start: 0.7922 (mt) cc_final: 0.7719 (mm) REVERT: 4 234 LYS cc_start: 0.7910 (ttmm) cc_final: 0.7479 (ttmm) REVERT: 4 275 GLU cc_start: 0.7663 (mm-30) cc_final: 0.6432 (mm-30) REVERT: 4 278 THR cc_start: 0.7913 (t) cc_final: 0.7685 (t) REVERT: 4 330 GLN cc_start: 0.7603 (tt0) cc_final: 0.7266 (tp40) REVERT: 4 413 ARG cc_start: 0.8697 (mtm180) cc_final: 0.8491 (mtt180) REVERT: 4 414 ARG cc_start: 0.8345 (mmp80) cc_final: 0.8123 (mmp80) REVERT: 4 473 GLN cc_start: 0.7493 (mt0) cc_final: 0.7114 (mm110) REVERT: 4 474 ARG cc_start: 0.7047 (mmp-170) cc_final: 0.6664 (mmp-170) REVERT: 4 538 MET cc_start: 0.7112 (mtt) cc_final: 0.6900 (mtp) REVERT: 4 601 SER cc_start: 0.8690 (m) cc_final: 0.8388 (p) REVERT: 4 634 ASP cc_start: 0.8183 (t0) cc_final: 0.7914 (t0) REVERT: 4 704 LYS cc_start: 0.8253 (tppp) cc_final: 0.8042 (tppp) REVERT: 5 196 ARG cc_start: 0.7818 (ptt180) cc_final: 0.7554 (ptm160) REVERT: 5 351 GLU cc_start: 0.7426 (tp30) cc_final: 0.7118 (tp30) REVERT: 5 366 ILE cc_start: 0.7981 (mt) cc_final: 0.7755 (mm) REVERT: 5 372 LEU cc_start: 0.9022 (mt) cc_final: 0.8775 (mt) REVERT: 5 483 GLU cc_start: 0.7715 (tp30) cc_final: 0.7281 (mm-30) REVERT: 5 638 TYR cc_start: 0.6740 (m-80) cc_final: 0.6482 (m-80) REVERT: 5 678 ASP cc_start: 0.7327 (t0) cc_final: 0.6866 (p0) REVERT: 6 353 TYR cc_start: 0.7250 (m-80) cc_final: 0.6651 (m-80) REVERT: 6 397 THR cc_start: 0.8025 (m) cc_final: 0.7736 (p) REVERT: 6 596 ASN cc_start: 0.7219 (OUTLIER) cc_final: 0.6983 (t0) REVERT: 6 693 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: 6 759 ASP cc_start: 0.7324 (p0) cc_final: 0.6441 (p0) outliers start: 190 outliers final: 112 residues processed: 842 average time/residue: 0.2232 time to fit residues: 292.3620 Evaluate side-chains 725 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 608 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 68 MET Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 1 residue 216 GLU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 356 HIS Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 583 ASP Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 647 LEU Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 714 ILE Chi-restraints excluded: chain 1 residue 739 LYS Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 771 ASN Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 1 residue 812 VAL Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 338 SER Chi-restraints excluded: chain 2 residue 340 THR Chi-restraints excluded: chain 2 residue 343 ILE Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 563 MET Chi-restraints excluded: chain 2 residue 572 VAL Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 623 LEU Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 669 ARG Chi-restraints excluded: chain 2 residue 673 THR Chi-restraints excluded: chain 2 residue 716 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 235 VAL Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 390 ILE Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 572 VAL Chi-restraints excluded: chain 3 residue 616 VAL Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 716 VAL Chi-restraints excluded: chain 3 residue 768 THR Chi-restraints excluded: chain 3 residue 778 VAL Chi-restraints excluded: chain 3 residue 793 THR Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 3 residue 860 ASN Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 243 LEU Chi-restraints excluded: chain 4 residue 343 ILE Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 387 ILE Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 497 ILE Chi-restraints excluded: chain 4 residue 515 GLU Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 581 ILE Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 623 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 697 ASP Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 767 LEU Chi-restraints excluded: chain 4 residue 776 VAL Chi-restraints excluded: chain 5 residue 164 CYS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 388 ASP Chi-restraints excluded: chain 5 residue 509 LEU Chi-restraints excluded: chain 5 residue 511 GLN Chi-restraints excluded: chain 5 residue 605 LEU Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 713 THR Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 778 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 186 ILE Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 378 THR Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 420 VAL Chi-restraints excluded: chain 6 residue 545 THR Chi-restraints excluded: chain 6 residue 596 ASN Chi-restraints excluded: chain 6 residue 693 GLN Chi-restraints excluded: chain 6 residue 694 ILE Chi-restraints excluded: chain 6 residue 711 LYS Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 776 VAL Chi-restraints excluded: chain 6 residue 785 GLU Chi-restraints excluded: chain 6 residue 790 LYS Chi-restraints excluded: chain 6 residue 803 LEU Chi-restraints excluded: chain 6 residue 826 LEU Chi-restraints excluded: chain 6 residue 829 GLN Chi-restraints excluded: chain 6 residue 852 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 89 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 431 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 chunk 270 optimal weight: 7.9990 chunk 237 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 30 optimal weight: 0.0570 chunk 164 optimal weight: 3.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 43 ASN 1 83 HIS ** 1 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 15 ASN ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 108 GLN ** 2 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 625 ASN 3 26 HIS 3 30 HIS 3 473 GLN 4 756 ASN 4 771 ASN 4 806 GLN 5 400 GLN 5 806 GLN 5 824 HIS ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 473 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.126277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.111740 restraints weight = 176804.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.113570 restraints weight = 122233.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.114772 restraints weight = 91388.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.115699 restraints weight = 72926.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.116225 restraints weight = 60810.542| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.7585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38814 Z= 0.115 Angle : 0.654 9.373 52326 Z= 0.307 Chirality : 0.042 0.156 6042 Planarity : 0.004 0.048 6756 Dihedral : 6.992 129.531 5400 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.91 % Favored : 97.07 % Rotamer: Outliers : 2.48 % Allowed : 17.18 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.12), residues: 4740 helix: -1.10 (0.10), residues: 2688 sheet: -1.40 (0.28), residues: 332 loop : -0.53 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 191 TYR 0.019 0.001 TYR 3 20 PHE 0.018 0.001 PHE 2 381 TRP 0.016 0.001 TRP 6 544 HIS 0.012 0.001 HIS 4 562 Details of bonding type rmsd covalent geometry : bond 0.00257 (38814) covalent geometry : angle 0.65447 (52326) hydrogen bonds : bond 0.03425 ( 1147) hydrogen bonds : angle 4.49348 ( 3345) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 692 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 216 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7943 (pp20) REVERT: 1 276 ILE cc_start: 0.6555 (mm) cc_final: 0.6111 (mt) REVERT: 1 366 ILE cc_start: 0.8426 (mp) cc_final: 0.7855 (mm) REVERT: 1 820 ARG cc_start: 0.7270 (tpp-160) cc_final: 0.7036 (tpp-160) REVERT: 1 824 HIS cc_start: 0.7953 (m-70) cc_final: 0.7633 (m-70) REVERT: 2 198 LYS cc_start: 0.7565 (mttm) cc_final: 0.6912 (mttm) REVERT: 2 260 VAL cc_start: 0.8646 (t) cc_final: 0.8221 (p) REVERT: 2 326 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7042 (tm-30) REVERT: 2 566 TYR cc_start: 0.7672 (t80) cc_final: 0.7443 (t80) REVERT: 2 670 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.8028 (mmm-85) REVERT: 2 685 LYS cc_start: 0.8628 (tttt) cc_final: 0.8411 (tttt) REVERT: 2 696 ASP cc_start: 0.8303 (m-30) cc_final: 0.7863 (m-30) REVERT: 2 753 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7835 (tm-30) REVERT: 2 757 ARG cc_start: 0.7011 (tpp80) cc_final: 0.6684 (tpp80) REVERT: 3 4 MET cc_start: 0.6132 (mmt) cc_final: 0.5926 (mmt) REVERT: 3 38 MET cc_start: 0.3707 (ppp) cc_final: 0.2337 (ptm) REVERT: 3 121 MET cc_start: 0.4639 (tpp) cc_final: 0.4289 (tpt) REVERT: 3 162 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8537 (mtpt) REVERT: 3 198 LYS cc_start: 0.8307 (mptt) cc_final: 0.8080 (mptt) REVERT: 3 682 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8671 (ttpt) REVERT: 4 234 LYS cc_start: 0.7847 (ttmm) cc_final: 0.7451 (ttmm) REVERT: 4 329 PHE cc_start: 0.7731 (m-80) cc_final: 0.7057 (m-10) REVERT: 4 330 GLN cc_start: 0.7225 (tt0) cc_final: 0.7012 (tp40) REVERT: 4 413 ARG cc_start: 0.8743 (mtm180) cc_final: 0.8539 (mtt180) REVERT: 4 473 GLN cc_start: 0.7452 (mt0) cc_final: 0.7167 (mm110) REVERT: 4 474 ARG cc_start: 0.7194 (mmp-170) cc_final: 0.6741 (mmp-170) REVERT: 4 601 SER cc_start: 0.8674 (m) cc_final: 0.8290 (p) REVERT: 5 263 GLU cc_start: 0.7786 (pt0) cc_final: 0.7539 (pp20) REVERT: 5 372 LEU cc_start: 0.9130 (mt) cc_final: 0.8742 (tt) REVERT: 5 382 MET cc_start: 0.7271 (mmm) cc_final: 0.7024 (mtp) REVERT: 5 483 GLU cc_start: 0.7709 (tp30) cc_final: 0.6267 (tp30) REVERT: 5 487 ARG cc_start: 0.7979 (mtt90) cc_final: 0.6114 (mtt90) REVERT: 5 691 LEU cc_start: 0.8944 (tt) cc_final: 0.8537 (mm) REVERT: 6 68 MET cc_start: 0.0211 (mtt) cc_final: -0.0440 (mtt) REVERT: 6 236 TYR cc_start: 0.6869 (m-10) cc_final: 0.6653 (m-80) REVERT: 6 353 TYR cc_start: 0.7294 (m-80) cc_final: 0.7055 (m-80) REVERT: 6 397 THR cc_start: 0.7980 (m) cc_final: 0.7611 (p) REVERT: 6 668 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.6755 (tmm-80) REVERT: 6 782 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7954 (mp0) outliers start: 101 outliers final: 59 residues processed: 753 average time/residue: 0.2290 time to fit residues: 267.0331 Evaluate side-chains 683 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 621 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 83 HIS Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 216 GLU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 547 ILE Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 572 VAL Chi-restraints excluded: chain 2 residue 669 ARG Chi-restraints excluded: chain 3 residue 184 GLU Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 310 THR Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 711 LYS Chi-restraints excluded: chain 3 residue 768 THR Chi-restraints excluded: chain 3 residue 778 VAL Chi-restraints excluded: chain 3 residue 788 ASP Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 416 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 497 ILE Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 692 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 828 THR Chi-restraints excluded: chain 5 residue 164 CYS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 420 VAL Chi-restraints excluded: chain 6 residue 507 LYS Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 668 ARG Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 782 GLU Chi-restraints excluded: chain 6 residue 790 LYS Chi-restraints excluded: chain 6 residue 828 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 442 optimal weight: 6.9990 chunk 318 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 382 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 381 optimal weight: 1.9990 chunk 346 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 771 ASN ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 293 ASN ** 2 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 553 GLN ** 4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 596 ASN 4 699 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 806 GLN ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 357 HIS 6 404 GLN ** 6 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 473 GLN 6 806 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.121438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.107745 restraints weight = 176324.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.109192 restraints weight = 126440.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.110274 restraints weight = 96977.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.111077 restraints weight = 78942.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.111643 restraints weight = 67095.087| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.8439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 38814 Z= 0.201 Angle : 0.758 10.305 52326 Z= 0.365 Chirality : 0.045 0.209 6042 Planarity : 0.005 0.049 6756 Dihedral : 7.285 132.381 5400 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.22 % Favored : 95.76 % Rotamer: Outliers : 4.00 % Allowed : 17.18 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.12), residues: 4740 helix: -1.00 (0.10), residues: 2714 sheet: -1.35 (0.27), residues: 372 loop : -0.54 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 2 586 TYR 0.020 0.002 TYR 2 638 PHE 0.019 0.002 PHE 2 381 TRP 0.012 0.002 TRP 3 544 HIS 0.021 0.002 HIS 1 83 Details of bonding type rmsd covalent geometry : bond 0.00452 (38814) covalent geometry : angle 0.75798 (52326) hydrogen bonds : bond 0.04180 ( 1147) hydrogen bonds : angle 4.85939 ( 3345) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 641 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 38 MET cc_start: 0.5995 (ptt) cc_final: 0.5177 (mtt) REVERT: 1 195 ARG cc_start: 0.6715 (ptm160) cc_final: 0.6431 (ptm160) REVERT: 1 216 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8046 (pp20) REVERT: 1 366 ILE cc_start: 0.8723 (mp) cc_final: 0.8463 (mm) REVERT: 1 382 MET cc_start: 0.7187 (tpp) cc_final: 0.6632 (tpp) REVERT: 1 599 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7444 (mp) REVERT: 1 668 ARG cc_start: 0.8377 (mmm160) cc_final: 0.8062 (mmm-85) REVERT: 1 685 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8090 (ttmm) REVERT: 1 757 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7028 (ttm-80) REVERT: 1 854 GLU cc_start: 0.4110 (OUTLIER) cc_final: 0.3415 (mp0) REVERT: 2 195 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7400 (ptt90) REVERT: 2 338 SER cc_start: 0.7993 (OUTLIER) cc_final: 0.7759 (t) REVERT: 2 696 ASP cc_start: 0.8233 (m-30) cc_final: 0.7960 (m-30) REVERT: 2 753 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7862 (tm-30) REVERT: 3 38 MET cc_start: 0.3145 (ppp) cc_final: 0.1638 (ptm) REVERT: 3 121 MET cc_start: 0.5652 (tpp) cc_final: 0.5391 (tpt) REVERT: 3 198 LYS cc_start: 0.8421 (mptt) cc_final: 0.8130 (mptt) REVERT: 3 274 ASP cc_start: 0.6959 (t0) cc_final: 0.6681 (t0) REVERT: 3 642 HIS cc_start: 0.7852 (t70) cc_final: 0.7437 (t-90) REVERT: 3 662 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8322 (tm-30) REVERT: 3 679 GLU cc_start: 0.7676 (tt0) cc_final: 0.7136 (tt0) REVERT: 3 682 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8506 (ttpp) REVERT: 4 198 LYS cc_start: 0.7564 (mtpt) cc_final: 0.7345 (mtmm) REVERT: 4 234 LYS cc_start: 0.7887 (ttmm) cc_final: 0.7356 (ttmm) REVERT: 4 329 PHE cc_start: 0.7953 (m-80) cc_final: 0.7273 (m-10) REVERT: 4 413 ARG cc_start: 0.8657 (mtm180) cc_final: 0.8423 (mtt180) REVERT: 4 469 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7529 (mtt180) REVERT: 4 474 ARG cc_start: 0.7052 (mmp-170) cc_final: 0.6798 (mmp-170) REVERT: 4 701 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8273 (p) REVERT: 5 372 LEU cc_start: 0.9208 (mt) cc_final: 0.8816 (tt) REVERT: 6 68 MET cc_start: 0.0108 (mtt) cc_final: -0.0292 (mtt) REVERT: 6 236 TYR cc_start: 0.6893 (m-10) cc_final: 0.6625 (m-80) REVERT: 6 397 THR cc_start: 0.8164 (m) cc_final: 0.7885 (p) REVERT: 6 668 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6786 (tmm-80) REVERT: 6 839 VAL cc_start: 0.7719 (m) cc_final: 0.7430 (t) REVERT: 6 855 ILE cc_start: 0.3330 (OUTLIER) cc_final: 0.2927 (tt) outliers start: 163 outliers final: 111 residues processed: 748 average time/residue: 0.2277 time to fit residues: 265.0322 Evaluate side-chains 704 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 585 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 216 GLU Chi-restraints excluded: chain 1 residue 262 LYS Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 339 VAL Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 484 ASP Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 538 MET Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 599 LEU Chi-restraints excluded: chain 1 residue 601 SER Chi-restraints excluded: chain 1 residue 623 LEU Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 757 ARG Chi-restraints excluded: chain 1 residue 771 ASN Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 1 residue 854 GLU Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 2 residue 235 VAL Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 338 SER Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 563 MET Chi-restraints excluded: chain 2 residue 565 GLU Chi-restraints excluded: chain 2 residue 572 VAL Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 619 LEU Chi-restraints excluded: chain 2 residue 623 LEU Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 834 LEU Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 204 VAL Chi-restraints excluded: chain 3 residue 270 ILE Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 310 THR Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 389 LEU Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 711 LYS Chi-restraints excluded: chain 3 residue 742 VAL Chi-restraints excluded: chain 3 residue 759 ASP Chi-restraints excluded: chain 3 residue 768 THR Chi-restraints excluded: chain 3 residue 799 LYS Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 830 LEU Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 42 GLU Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 186 ILE Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 372 LEU Chi-restraints excluded: chain 4 residue 387 ILE Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 497 ILE Chi-restraints excluded: chain 4 residue 515 GLU Chi-restraints excluded: chain 4 residue 547 ILE Chi-restraints excluded: chain 4 residue 581 ILE Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 692 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 824 HIS Chi-restraints excluded: chain 4 residue 828 THR Chi-restraints excluded: chain 5 residue 164 CYS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 231 LEU Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 563 MET Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 378 THR Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 507 LYS Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 539 GLU Chi-restraints excluded: chain 6 residue 544 TRP Chi-restraints excluded: chain 6 residue 585 ILE Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 644 VAL Chi-restraints excluded: chain 6 residue 668 ARG Chi-restraints excluded: chain 6 residue 675 VAL Chi-restraints excluded: chain 6 residue 693 GLN Chi-restraints excluded: chain 6 residue 711 LYS Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 776 VAL Chi-restraints excluded: chain 6 residue 790 LYS Chi-restraints excluded: chain 6 residue 826 LEU Chi-restraints excluded: chain 6 residue 852 GLU Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 381 optimal weight: 9.9990 chunk 465 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 421 optimal weight: 7.9990 chunk 316 optimal weight: 4.9990 chunk 401 optimal weight: 2.9990 chunk 464 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 276 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 200 ASN 1 357 HIS ** 1 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 268 GLN ** 2 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 28 GLN 3 97 HIS 3 553 GLN ** 4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 108 GLN 4 473 GLN 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.121116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.107492 restraints weight = 176386.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.109020 restraints weight = 125139.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.110071 restraints weight = 95750.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 73)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.110884 restraints weight = 77779.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.111445 restraints weight = 66128.753| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.8766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 38814 Z= 0.174 Angle : 0.722 14.000 52326 Z= 0.344 Chirality : 0.044 0.174 6042 Planarity : 0.005 0.049 6756 Dihedral : 7.195 138.860 5400 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 3.51 % Allowed : 18.29 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.12), residues: 4740 helix: -0.84 (0.10), residues: 2740 sheet: -1.32 (0.27), residues: 376 loop : -0.53 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 2 586 TYR 0.018 0.002 TYR 3 20 PHE 0.030 0.002 PHE 2 325 TRP 0.009 0.001 TRP 6 544 HIS 0.009 0.001 HIS 5 699 Details of bonding type rmsd covalent geometry : bond 0.00393 (38814) covalent geometry : angle 0.72213 (52326) hydrogen bonds : bond 0.03814 ( 1147) hydrogen bonds : angle 4.79452 ( 3345) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 621 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 38 MET cc_start: 0.6204 (ptt) cc_final: 0.5281 (mtt) REVERT: 1 216 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8042 (pp20) REVERT: 1 326 GLU cc_start: 0.8019 (mp0) cc_final: 0.7737 (mp0) REVERT: 1 352 ARG cc_start: 0.9021 (tpt90) cc_final: 0.8803 (mmm160) REVERT: 1 366 ILE cc_start: 0.8770 (mp) cc_final: 0.8458 (mm) REVERT: 1 599 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7836 (mp) REVERT: 2 262 LYS cc_start: 0.8893 (tptt) cc_final: 0.8681 (tptt) REVERT: 2 266 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.5893 (pt0) REVERT: 2 693 GLN cc_start: 0.8196 (mp10) cc_final: 0.7852 (mp10) REVERT: 2 706 ARG cc_start: 0.7309 (mpp80) cc_final: 0.6977 (mpt-90) REVERT: 2 753 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7766 (tm-30) REVERT: 3 4 MET cc_start: 0.6118 (mmt) cc_final: 0.5853 (mmt) REVERT: 3 38 MET cc_start: 0.3414 (ppp) cc_final: 0.2069 (ptm) REVERT: 3 121 MET cc_start: 0.5887 (tpp) cc_final: 0.5554 (tpt) REVERT: 3 162 LYS cc_start: 0.8871 (pttp) cc_final: 0.8336 (pttm) REVERT: 3 198 LYS cc_start: 0.8408 (mptt) cc_final: 0.7806 (mtpp) REVERT: 3 505 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5794 (tt) REVERT: 3 642 HIS cc_start: 0.7910 (t70) cc_final: 0.7530 (t-90) REVERT: 3 679 GLU cc_start: 0.7625 (tt0) cc_final: 0.7121 (tt0) REVERT: 3 682 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8681 (ttpp) REVERT: 4 234 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7468 (ttmm) REVERT: 4 329 PHE cc_start: 0.7951 (m-80) cc_final: 0.7262 (m-10) REVERT: 4 352 ARG cc_start: 0.7677 (ttm170) cc_final: 0.7267 (mtp180) REVERT: 4 413 ARG cc_start: 0.8759 (mtm180) cc_final: 0.8542 (mtt180) REVERT: 4 474 ARG cc_start: 0.7050 (mmp-170) cc_final: 0.6810 (mmp-170) REVERT: 4 701 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8341 (p) REVERT: 4 709 ASP cc_start: 0.7375 (t0) cc_final: 0.7169 (m-30) REVERT: 5 372 LEU cc_start: 0.9178 (mt) cc_final: 0.8789 (tt) REVERT: 5 668 ARG cc_start: 0.7723 (mmp80) cc_final: 0.7479 (mmp80) REVERT: 6 68 MET cc_start: -0.0056 (mtt) cc_final: -0.0384 (mtt) REVERT: 6 236 TYR cc_start: 0.6831 (m-10) cc_final: 0.6555 (m-80) REVERT: 6 353 TYR cc_start: 0.7659 (m-80) cc_final: 0.7405 (m-10) REVERT: 6 668 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.6844 (tmm-80) REVERT: 6 839 VAL cc_start: 0.7689 (m) cc_final: 0.7415 (t) REVERT: 6 855 ILE cc_start: 0.3150 (OUTLIER) cc_final: 0.2710 (tt) outliers start: 143 outliers final: 106 residues processed: 713 average time/residue: 0.2342 time to fit residues: 259.5943 Evaluate side-chains 703 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 590 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 216 GLU Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 339 VAL Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 484 ASP Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 538 MET Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 599 LEU Chi-restraints excluded: chain 1 residue 647 LEU Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 739 LYS Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 771 ASN Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 266 GLU Chi-restraints excluded: chain 2 residue 565 GLU Chi-restraints excluded: chain 2 residue 619 LEU Chi-restraints excluded: chain 2 residue 834 LEU Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 204 VAL Chi-restraints excluded: chain 3 residue 270 ILE Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 389 LEU Chi-restraints excluded: chain 3 residue 505 LEU Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 708 VAL Chi-restraints excluded: chain 3 residue 711 LYS Chi-restraints excluded: chain 3 residue 716 VAL Chi-restraints excluded: chain 3 residue 742 VAL Chi-restraints excluded: chain 3 residue 759 ASP Chi-restraints excluded: chain 3 residue 768 THR Chi-restraints excluded: chain 3 residue 799 LYS Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 830 LEU Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 42 GLU Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 186 ILE Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 243 LEU Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 372 LEU Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 497 ILE Chi-restraints excluded: chain 4 residue 547 ILE Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 567 MET Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 692 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 799 LYS Chi-restraints excluded: chain 4 residue 828 THR Chi-restraints excluded: chain 5 residue 164 CYS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 231 LEU Chi-restraints excluded: chain 5 residue 469 ARG Chi-restraints excluded: chain 5 residue 563 MET Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 378 THR Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 507 LYS Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 539 GLU Chi-restraints excluded: chain 6 residue 585 ILE Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 614 LEU Chi-restraints excluded: chain 6 residue 644 VAL Chi-restraints excluded: chain 6 residue 668 ARG Chi-restraints excluded: chain 6 residue 693 GLN Chi-restraints excluded: chain 6 residue 711 LYS Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 776 VAL Chi-restraints excluded: chain 6 residue 783 VAL Chi-restraints excluded: chain 6 residue 844 ILE Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 345 optimal weight: 8.9990 chunk 337 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 440 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 321 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 383 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 271 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 83 HIS ** 1 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 699 HIS ** 1 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 268 GLN 2 574 GLN ** 2 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 28 GLN 3 553 GLN 3 860 ASN ** 4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 30 HIS ** 6 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.120636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.108626 restraints weight = 178180.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.109480 restraints weight = 130397.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.110313 restraints weight = 99490.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.110807 restraints weight = 81898.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.110936 restraints weight = 72853.033| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.8987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 38814 Z= 0.161 Angle : 0.723 20.153 52326 Z= 0.340 Chirality : 0.044 0.172 6042 Planarity : 0.004 0.049 6756 Dihedral : 7.129 136.881 5400 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 3.66 % Allowed : 18.75 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.12), residues: 4740 helix: -0.72 (0.10), residues: 2731 sheet: -1.28 (0.27), residues: 365 loop : -0.43 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 3 328 TYR 0.023 0.002 TYR 4 376 PHE 0.018 0.002 PHE 2 381 TRP 0.036 0.002 TRP 6 544 HIS 0.018 0.001 HIS 4 562 Details of bonding type rmsd covalent geometry : bond 0.00368 (38814) covalent geometry : angle 0.72295 (52326) hydrogen bonds : bond 0.03681 ( 1147) hydrogen bonds : angle 4.77023 ( 3345) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 620 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 38 MET cc_start: 0.6241 (ptt) cc_final: 0.5301 (mtt) REVERT: 1 216 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7971 (pp20) REVERT: 1 366 ILE cc_start: 0.8600 (mp) cc_final: 0.8116 (mm) REVERT: 1 563 MET cc_start: 0.7204 (ttm) cc_final: 0.6898 (ttp) REVERT: 1 757 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7235 (ttm-80) REVERT: 2 262 LYS cc_start: 0.8967 (tptt) cc_final: 0.8280 (tptt) REVERT: 2 266 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6116 (pm20) REVERT: 2 380 ARG cc_start: 0.6354 (tpp80) cc_final: 0.5864 (tpt170) REVERT: 2 488 ARG cc_start: 0.4894 (mmp-170) cc_final: 0.4508 (tpp-160) REVERT: 2 564 GLU cc_start: 0.7583 (pm20) cc_final: 0.7269 (pm20) REVERT: 2 665 GLU cc_start: 0.8678 (pp20) cc_final: 0.7891 (tp30) REVERT: 2 753 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7985 (tm-30) REVERT: 3 4 MET cc_start: 0.6250 (mmt) cc_final: 0.5966 (mmt) REVERT: 3 38 MET cc_start: 0.3324 (ppp) cc_final: 0.2181 (ptm) REVERT: 3 198 LYS cc_start: 0.8434 (mptt) cc_final: 0.7761 (mtpp) REVERT: 3 505 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5719 (tt) REVERT: 3 642 HIS cc_start: 0.8116 (t70) cc_final: 0.7733 (t-90) REVERT: 3 679 GLU cc_start: 0.7727 (tt0) cc_final: 0.7150 (tt0) REVERT: 3 682 LYS cc_start: 0.9113 (ttpt) cc_final: 0.8786 (ttpp) REVERT: 4 234 LYS cc_start: 0.7875 (ttmm) cc_final: 0.7425 (ttmm) REVERT: 4 329 PHE cc_start: 0.7868 (m-80) cc_final: 0.7174 (m-10) REVERT: 4 352 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7309 (mtp180) REVERT: 4 382 MET cc_start: 0.7990 (mmm) cc_final: 0.7772 (mmm) REVERT: 4 413 ARG cc_start: 0.8814 (mtm180) cc_final: 0.8526 (mtt180) REVERT: 4 701 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8302 (p) REVERT: 4 709 ASP cc_start: 0.7506 (t70) cc_final: 0.7283 (m-30) REVERT: 5 372 LEU cc_start: 0.9218 (mt) cc_final: 0.8831 (tt) REVERT: 5 483 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7309 (mm-30) REVERT: 5 487 ARG cc_start: 0.8091 (mtm180) cc_final: 0.7311 (mtm-85) REVERT: 5 668 ARG cc_start: 0.7896 (mmp80) cc_final: 0.7074 (mmp80) REVERT: 6 68 MET cc_start: 0.0015 (mtt) cc_final: -0.0314 (mtt) REVERT: 6 236 TYR cc_start: 0.6691 (m-10) cc_final: 0.6444 (m-80) REVERT: 6 275 GLU cc_start: 0.8273 (tp30) cc_final: 0.8004 (tp30) REVERT: 6 668 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.6964 (tmm-80) REVERT: 6 839 VAL cc_start: 0.7764 (m) cc_final: 0.7474 (t) REVERT: 6 855 ILE cc_start: 0.3052 (OUTLIER) cc_final: 0.2633 (tt) outliers start: 149 outliers final: 113 residues processed: 721 average time/residue: 0.2366 time to fit residues: 265.4128 Evaluate side-chains 697 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 577 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 216 GLU Chi-restraints excluded: chain 1 residue 262 LYS Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 339 VAL Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 406 GLU Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 484 ASP Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 538 MET Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 647 LEU Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 739 LYS Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 757 ARG Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 266 GLU Chi-restraints excluded: chain 2 residue 565 GLU Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 691 LEU Chi-restraints excluded: chain 2 residue 834 LEU Chi-restraints excluded: chain 2 residue 857 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 204 VAL Chi-restraints excluded: chain 3 residue 270 ILE Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 389 LEU Chi-restraints excluded: chain 3 residue 505 LEU Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 556 GLU Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 716 VAL Chi-restraints excluded: chain 3 residue 742 VAL Chi-restraints excluded: chain 3 residue 759 ASP Chi-restraints excluded: chain 3 residue 768 THR Chi-restraints excluded: chain 3 residue 799 LYS Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 830 LEU Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 42 GLU Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 243 LEU Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 372 LEU Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain 4 residue 425 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 497 ILE Chi-restraints excluded: chain 4 residue 515 GLU Chi-restraints excluded: chain 4 residue 567 MET Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 692 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 799 LYS Chi-restraints excluded: chain 4 residue 828 THR Chi-restraints excluded: chain 5 residue 164 CYS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 231 LEU Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 713 THR Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 231 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 378 THR Chi-restraints excluded: chain 6 residue 379 GLN Chi-restraints excluded: chain 6 residue 380 ARG Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 507 LYS Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 585 ILE Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 614 LEU Chi-restraints excluded: chain 6 residue 644 VAL Chi-restraints excluded: chain 6 residue 668 ARG Chi-restraints excluded: chain 6 residue 693 GLN Chi-restraints excluded: chain 6 residue 711 LYS Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 768 THR Chi-restraints excluded: chain 6 residue 776 VAL Chi-restraints excluded: chain 6 residue 783 VAL Chi-restraints excluded: chain 6 residue 844 ILE Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 314 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 260 optimal weight: 4.9990 chunk 467 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 319 optimal weight: 1.9990 chunk 158 optimal weight: 40.0000 chunk 34 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 423 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 83 HIS ** 1 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 268 GLN ** 2 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 553 GLN ** 4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.121256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.108567 restraints weight = 178346.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.110504 restraints weight = 125115.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.112580 restraints weight = 84933.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.112943 restraints weight = 62859.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.112881 restraints weight = 50143.044| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.9075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38814 Z= 0.139 Angle : 0.714 25.961 52326 Z= 0.331 Chirality : 0.043 0.157 6042 Planarity : 0.004 0.056 6756 Dihedral : 6.957 133.036 5400 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.63 % Favored : 96.35 % Rotamer: Outliers : 3.12 % Allowed : 19.66 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.12), residues: 4740 helix: -0.56 (0.10), residues: 2705 sheet: -1.32 (0.27), residues: 360 loop : -0.33 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 706 TYR 0.023 0.002 TYR 3 20 PHE 0.018 0.002 PHE 4 325 TRP 0.039 0.002 TRP 6 544 HIS 0.007 0.001 HIS 5 699 Details of bonding type rmsd covalent geometry : bond 0.00318 (38814) covalent geometry : angle 0.71376 (52326) hydrogen bonds : bond 0.03405 ( 1147) hydrogen bonds : angle 4.66552 ( 3345) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 616 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 38 MET cc_start: 0.6324 (ptt) cc_final: 0.5383 (mtt) REVERT: 1 216 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7988 (pp20) REVERT: 1 270 ILE cc_start: 0.8145 (tp) cc_final: 0.7851 (pt) REVERT: 1 352 ARG cc_start: 0.8756 (tpt90) cc_final: 0.8483 (mmm160) REVERT: 1 366 ILE cc_start: 0.8724 (mp) cc_final: 0.8264 (mm) REVERT: 1 854 GLU cc_start: 0.4381 (OUTLIER) cc_final: 0.3650 (mp0) REVERT: 2 488 ARG cc_start: 0.4779 (mmp-170) cc_final: 0.4416 (tpp-160) REVERT: 2 564 GLU cc_start: 0.7219 (pm20) cc_final: 0.6485 (pm20) REVERT: 2 665 GLU cc_start: 0.8587 (pp20) cc_final: 0.7426 (tp30) REVERT: 2 680 MET cc_start: 0.7432 (mtp) cc_final: 0.7191 (mtp) REVERT: 3 38 MET cc_start: 0.3369 (ppp) cc_final: 0.2290 (ptm) REVERT: 3 198 LYS cc_start: 0.8354 (mptt) cc_final: 0.7663 (mtpp) REVERT: 3 255 GLU cc_start: 0.8461 (pm20) cc_final: 0.8113 (pm20) REVERT: 3 505 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5725 (tt) REVERT: 3 642 HIS cc_start: 0.7897 (t70) cc_final: 0.7586 (t-90) REVERT: 3 662 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8356 (tm-30) REVERT: 3 670 ARG cc_start: 0.7674 (tpt170) cc_final: 0.7317 (tpt170) REVERT: 3 679 GLU cc_start: 0.7599 (tt0) cc_final: 0.7042 (tt0) REVERT: 3 682 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8690 (ttpp) REVERT: 4 234 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7297 (ttmm) REVERT: 4 329 PHE cc_start: 0.7765 (m-80) cc_final: 0.7082 (m-10) REVERT: 4 352 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7360 (mtp180) REVERT: 4 413 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8553 (mtt180) REVERT: 4 701 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8344 (p) REVERT: 5 196 ARG cc_start: 0.7283 (ptt180) cc_final: 0.6776 (ptt90) REVERT: 5 257 LEU cc_start: 0.9069 (mm) cc_final: 0.8804 (mm) REVERT: 5 372 LEU cc_start: 0.9196 (mt) cc_final: 0.8799 (tt) REVERT: 5 483 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7168 (mm-30) REVERT: 5 487 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7248 (mtm-85) REVERT: 5 678 ASP cc_start: 0.7447 (t0) cc_final: 0.6793 (p0) REVERT: 6 68 MET cc_start: 0.0176 (mtt) cc_final: -0.0397 (mtt) REVERT: 6 236 TYR cc_start: 0.6811 (m-10) cc_final: 0.6594 (m-80) REVERT: 6 353 TYR cc_start: 0.7535 (m-10) cc_final: 0.7066 (m-10) REVERT: 6 668 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.6968 (tmm-80) REVERT: 6 839 VAL cc_start: 0.7658 (m) cc_final: 0.7373 (t) REVERT: 6 855 ILE cc_start: 0.2976 (OUTLIER) cc_final: 0.2536 (tt) outliers start: 127 outliers final: 103 residues processed: 704 average time/residue: 0.2293 time to fit residues: 251.1629 Evaluate side-chains 689 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 580 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 83 HIS Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 216 GLU Chi-restraints excluded: chain 1 residue 262 LYS Chi-restraints excluded: chain 1 residue 290 ASP Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 406 GLU Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 484 ASP Chi-restraints excluded: chain 1 residue 490 ASP Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 571 VAL Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 647 LEU Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 739 LYS Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 854 GLU Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 596 ASN Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 691 LEU Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 834 LEU Chi-restraints excluded: chain 2 residue 857 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 204 VAL Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 505 LEU Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 556 GLU Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 716 VAL Chi-restraints excluded: chain 3 residue 742 VAL Chi-restraints excluded: chain 3 residue 753 GLU Chi-restraints excluded: chain 3 residue 799 LYS Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 186 ILE Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 243 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 372 LEU Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain 4 residue 425 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 497 ILE Chi-restraints excluded: chain 4 residue 515 GLU Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 567 MET Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 692 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 799 LYS Chi-restraints excluded: chain 4 residue 828 THR Chi-restraints excluded: chain 5 residue 164 CYS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 231 LEU Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 469 ARG Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 231 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 378 THR Chi-restraints excluded: chain 6 residue 380 ARG Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 585 ILE Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 614 LEU Chi-restraints excluded: chain 6 residue 644 VAL Chi-restraints excluded: chain 6 residue 668 ARG Chi-restraints excluded: chain 6 residue 693 GLN Chi-restraints excluded: chain 6 residue 711 LYS Chi-restraints excluded: chain 6 residue 768 THR Chi-restraints excluded: chain 6 residue 776 VAL Chi-restraints excluded: chain 6 residue 844 ILE Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 89 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 281 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 183 optimal weight: 0.1980 chunk 253 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 342 optimal weight: 7.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 83 HIS ** 1 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 200 ASN 2 268 GLN ** 2 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 553 GLN ** 4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.120835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.108234 restraints weight = 178724.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.110470 restraints weight = 124399.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.111362 restraints weight = 81952.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.111716 restraints weight = 70805.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.111935 restraints weight = 60696.792| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.9199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 38814 Z= 0.146 Angle : 0.732 24.601 52326 Z= 0.342 Chirality : 0.044 0.159 6042 Planarity : 0.004 0.066 6756 Dihedral : 6.891 131.250 5400 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.90 % Favored : 96.08 % Rotamer: Outliers : 2.99 % Allowed : 20.27 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.12), residues: 4740 helix: -0.49 (0.10), residues: 2694 sheet: -1.28 (0.27), residues: 371 loop : -0.29 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 1 328 TYR 0.026 0.002 TYR 3 20 PHE 0.015 0.002 PHE 3 622 TRP 0.045 0.002 TRP 6 544 HIS 0.010 0.001 HIS 4 861 Details of bonding type rmsd covalent geometry : bond 0.00335 (38814) covalent geometry : angle 0.73243 (52326) hydrogen bonds : bond 0.03442 ( 1147) hydrogen bonds : angle 4.68162 ( 3345) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 601 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 38 MET cc_start: 0.6283 (ptt) cc_final: 0.5371 (mtt) REVERT: 1 326 GLU cc_start: 0.8198 (mp0) cc_final: 0.7952 (mp0) REVERT: 1 352 ARG cc_start: 0.8733 (tpt90) cc_final: 0.8479 (mmm160) REVERT: 1 366 ILE cc_start: 0.8702 (mp) cc_final: 0.8198 (mm) REVERT: 1 582 CYS cc_start: 0.7682 (m) cc_final: 0.7135 (t) REVERT: 1 680 MET cc_start: 0.8231 (ptm) cc_final: 0.7872 (ptm) REVERT: 1 820 ARG cc_start: 0.7242 (tpp-160) cc_final: 0.6900 (tpp-160) REVERT: 1 854 GLU cc_start: 0.4467 (OUTLIER) cc_final: 0.3722 (mp0) REVERT: 2 4 MET cc_start: 0.0240 (ttp) cc_final: -0.0054 (tmm) REVERT: 2 266 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6719 (pt0) REVERT: 2 567 MET cc_start: 0.7225 (mtt) cc_final: 0.7013 (ptp) REVERT: 2 665 GLU cc_start: 0.8633 (pp20) cc_final: 0.7673 (tp30) REVERT: 3 38 MET cc_start: 0.3260 (ppp) cc_final: 0.2184 (ptm) REVERT: 3 198 LYS cc_start: 0.8371 (mptt) cc_final: 0.7672 (mtpp) REVERT: 3 255 GLU cc_start: 0.8520 (pm20) cc_final: 0.8258 (pm20) REVERT: 3 412 GLU cc_start: 0.6276 (mm-30) cc_final: 0.5960 (mm-30) REVERT: 3 505 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5787 (tt) REVERT: 3 662 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8486 (tm-30) REVERT: 3 679 GLU cc_start: 0.7669 (tt0) cc_final: 0.7375 (tt0) REVERT: 3 682 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8595 (ttpt) REVERT: 3 757 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7548 (mmm-85) REVERT: 4 234 LYS cc_start: 0.7861 (ttmm) cc_final: 0.7321 (ttmm) REVERT: 4 329 PHE cc_start: 0.7982 (m-80) cc_final: 0.7156 (m-10) REVERT: 4 413 ARG cc_start: 0.8854 (mtm180) cc_final: 0.8618 (mtt180) REVERT: 4 701 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8302 (p) REVERT: 5 257 LEU cc_start: 0.9068 (mm) cc_final: 0.8790 (mm) REVERT: 5 346 LEU cc_start: 0.7848 (mm) cc_final: 0.7579 (mm) REVERT: 5 372 LEU cc_start: 0.9207 (mt) cc_final: 0.8786 (tt) REVERT: 5 483 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7210 (mm-30) REVERT: 5 487 ARG cc_start: 0.7957 (mtm180) cc_final: 0.7238 (mtm180) REVERT: 5 678 ASP cc_start: 0.7361 (t0) cc_final: 0.6839 (p0) REVERT: 6 68 MET cc_start: 0.0223 (mtt) cc_final: -0.0311 (mtt) REVERT: 6 236 TYR cc_start: 0.6783 (m-10) cc_final: 0.6567 (m-80) REVERT: 6 275 GLU cc_start: 0.8186 (tp30) cc_final: 0.7965 (tp30) REVERT: 6 322 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6913 (t70) REVERT: 6 382 MET cc_start: 0.7517 (mmm) cc_final: 0.7195 (mmp) REVERT: 6 426 GLU cc_start: 0.7541 (pm20) cc_final: 0.7337 (mp0) REVERT: 6 668 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7011 (tmm-80) REVERT: 6 782 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: 6 839 VAL cc_start: 0.7791 (m) cc_final: 0.7511 (t) REVERT: 6 855 ILE cc_start: 0.2977 (OUTLIER) cc_final: 0.2574 (tt) outliers start: 122 outliers final: 100 residues processed: 685 average time/residue: 0.2210 time to fit residues: 236.1666 Evaluate side-chains 686 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 578 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 83 HIS Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 262 LYS Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 406 GLU Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 484 ASP Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 571 VAL Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 647 LEU Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 739 LYS Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 854 GLU Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 266 GLU Chi-restraints excluded: chain 2 residue 596 ASN Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 691 LEU Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 834 LEU Chi-restraints excluded: chain 2 residue 857 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 204 VAL Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 505 LEU Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 635 MET Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 716 VAL Chi-restraints excluded: chain 3 residue 742 VAL Chi-restraints excluded: chain 3 residue 759 ASP Chi-restraints excluded: chain 3 residue 799 LYS Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 186 ILE Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 243 LEU Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 372 LEU Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain 4 residue 425 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 497 ILE Chi-restraints excluded: chain 4 residue 515 GLU Chi-restraints excluded: chain 4 residue 547 ILE Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 567 MET Chi-restraints excluded: chain 4 residue 601 SER Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 692 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 799 LYS Chi-restraints excluded: chain 4 residue 828 THR Chi-restraints excluded: chain 5 residue 164 CYS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 231 LEU Chi-restraints excluded: chain 5 residue 469 ARG Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 231 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 322 ASP Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 378 THR Chi-restraints excluded: chain 6 residue 380 ARG Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 585 ILE Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 614 LEU Chi-restraints excluded: chain 6 residue 668 ARG Chi-restraints excluded: chain 6 residue 693 GLN Chi-restraints excluded: chain 6 residue 768 THR Chi-restraints excluded: chain 6 residue 776 VAL Chi-restraints excluded: chain 6 residue 782 GLU Chi-restraints excluded: chain 6 residue 844 ILE Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 402 optimal weight: 7.9990 chunk 416 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 345 optimal weight: 0.0000 chunk 180 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 405 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 469 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 137 ASN 2 268 GLN 2 404 GLN 2 662 GLN ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 553 GLN ** 4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 712 ASN 5 749 HIS ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 513 GLN ** 6 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.122330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.109108 restraints weight = 175180.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.110740 restraints weight = 122955.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.111881 restraints weight = 92453.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.112682 restraints weight = 73839.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.113254 restraints weight = 61937.016| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.9189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38814 Z= 0.121 Angle : 0.719 27.535 52326 Z= 0.331 Chirality : 0.043 0.160 6042 Planarity : 0.004 0.051 6756 Dihedral : 6.573 130.486 5400 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.54 % Rotamer: Outliers : 2.36 % Allowed : 21.18 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.12), residues: 4740 helix: -0.32 (0.10), residues: 2697 sheet: -1.14 (0.28), residues: 346 loop : -0.18 (0.16), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 1 328 TYR 0.024 0.001 TYR 3 20 PHE 0.014 0.001 PHE 2 272 TRP 0.034 0.002 TRP 6 544 HIS 0.016 0.001 HIS 4 562 Details of bonding type rmsd covalent geometry : bond 0.00279 (38814) covalent geometry : angle 0.71904 (52326) hydrogen bonds : bond 0.03151 ( 1147) hydrogen bonds : angle 4.53775 ( 3345) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 622 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 38 MET cc_start: 0.6433 (ptt) cc_final: 0.5483 (mtt) REVERT: 1 98 MET cc_start: 0.5669 (ttm) cc_final: 0.5465 (ttm) REVERT: 1 270 ILE cc_start: 0.8079 (tp) cc_final: 0.7769 (pt) REVERT: 1 326 GLU cc_start: 0.8240 (mp0) cc_final: 0.7919 (mp0) REVERT: 1 352 ARG cc_start: 0.8694 (tpt90) cc_final: 0.8474 (mmm160) REVERT: 1 366 ILE cc_start: 0.8680 (mp) cc_final: 0.8222 (mm) REVERT: 1 757 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7080 (ttm-80) REVERT: 1 854 GLU cc_start: 0.4220 (OUTLIER) cc_final: 0.3502 (mp0) REVERT: 2 266 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6706 (pt0) REVERT: 2 595 ARG cc_start: 0.8300 (mmp80) cc_final: 0.7872 (mmp-170) REVERT: 2 665 GLU cc_start: 0.8273 (pp20) cc_final: 0.7381 (tp30) REVERT: 2 696 ASP cc_start: 0.8193 (m-30) cc_final: 0.7259 (m-30) REVERT: 3 38 MET cc_start: 0.3635 (ppp) cc_final: 0.2614 (ptm) REVERT: 3 198 LYS cc_start: 0.8378 (mptt) cc_final: 0.7688 (mtpp) REVERT: 3 255 GLU cc_start: 0.8374 (pm20) cc_final: 0.8030 (pm20) REVERT: 3 412 GLU cc_start: 0.6221 (mm-30) cc_final: 0.5887 (mm-30) REVERT: 3 553 GLN cc_start: 0.5897 (OUTLIER) cc_final: 0.5670 (pm20) REVERT: 3 639 MET cc_start: 0.8402 (mmm) cc_final: 0.7755 (mmm) REVERT: 3 679 GLU cc_start: 0.7583 (tt0) cc_final: 0.6988 (tt0) REVERT: 3 682 LYS cc_start: 0.8606 (ttpt) cc_final: 0.7744 (ttpp) REVERT: 4 98 MET cc_start: 0.2252 (tmm) cc_final: 0.1073 (tmm) REVERT: 4 234 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7403 (ttmm) REVERT: 4 329 PHE cc_start: 0.7955 (m-80) cc_final: 0.7128 (m-10) REVERT: 4 352 ARG cc_start: 0.7645 (ttm170) cc_final: 0.7058 (mtp180) REVERT: 4 701 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8310 (p) REVERT: 5 157 TYR cc_start: 0.4860 (m-80) cc_final: 0.4657 (m-80) REVERT: 5 196 ARG cc_start: 0.6782 (ptt180) cc_final: 0.6242 (ptt90) REVERT: 5 257 LEU cc_start: 0.9160 (mm) cc_final: 0.8919 (mm) REVERT: 5 346 LEU cc_start: 0.7741 (mm) cc_final: 0.7473 (mm) REVERT: 5 372 LEU cc_start: 0.9232 (mt) cc_final: 0.8865 (mt) REVERT: 5 483 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6976 (mm-30) REVERT: 5 487 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7158 (mtm180) REVERT: 5 668 ARG cc_start: 0.7698 (mmp80) cc_final: 0.7332 (mmp80) REVERT: 5 678 ASP cc_start: 0.7443 (t0) cc_final: 0.6783 (p0) REVERT: 6 68 MET cc_start: -0.0280 (mtt) cc_final: -0.0701 (mtt) REVERT: 6 236 TYR cc_start: 0.6858 (m-10) cc_final: 0.6604 (m-80) REVERT: 6 322 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7218 (t70) REVERT: 6 353 TYR cc_start: 0.7477 (m-10) cc_final: 0.7255 (m-10) REVERT: 6 382 MET cc_start: 0.7423 (mmm) cc_final: 0.7209 (mmp) REVERT: 6 426 GLU cc_start: 0.7546 (pm20) cc_final: 0.7322 (mp0) REVERT: 6 668 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6899 (tmm-80) REVERT: 6 782 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: 6 839 VAL cc_start: 0.7646 (m) cc_final: 0.7374 (t) outliers start: 96 outliers final: 72 residues processed: 689 average time/residue: 0.2278 time to fit residues: 244.0825 Evaluate side-chains 673 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 593 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 262 LYS Chi-restraints excluded: chain 1 residue 290 ASP Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 406 GLU Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 484 ASP Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 571 VAL Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 757 ARG Chi-restraints excluded: chain 1 residue 854 GLU Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 266 GLU Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 662 GLN Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 857 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 204 VAL Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 799 LYS Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 186 ILE Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 243 LEU Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 372 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 497 ILE Chi-restraints excluded: chain 4 residue 547 ILE Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 567 MET Chi-restraints excluded: chain 4 residue 601 SER Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 692 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 799 LYS Chi-restraints excluded: chain 4 residue 828 THR Chi-restraints excluded: chain 5 residue 164 CYS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 469 ARG Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 231 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 322 ASP Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 380 ARG Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 668 ARG Chi-restraints excluded: chain 6 residue 693 GLN Chi-restraints excluded: chain 6 residue 782 GLU Chi-restraints excluded: chain 6 residue 844 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 73 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 367 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 425 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 268 GLN ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 553 GLN ** 4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 26 HIS 6 277 HIS ** 6 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.122874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.109686 restraints weight = 177470.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.111331 restraints weight = 124242.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.112429 restraints weight = 93421.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.113290 restraints weight = 74714.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.113940 restraints weight = 62639.575| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.9209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38814 Z= 0.118 Angle : 0.720 31.126 52326 Z= 0.329 Chirality : 0.043 0.169 6042 Planarity : 0.004 0.048 6756 Dihedral : 6.382 130.303 5400 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 2.11 % Allowed : 21.48 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.13), residues: 4740 helix: -0.13 (0.10), residues: 2671 sheet: -1.14 (0.28), residues: 355 loop : -0.13 (0.16), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 2 748 TYR 0.029 0.001 TYR 4 315 PHE 0.014 0.001 PHE 2 272 TRP 0.032 0.002 TRP 6 544 HIS 0.010 0.001 HIS 2 824 Details of bonding type rmsd covalent geometry : bond 0.00271 (38814) covalent geometry : angle 0.72022 (52326) hydrogen bonds : bond 0.03083 ( 1147) hydrogen bonds : angle 4.45806 ( 3345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7359.85 seconds wall clock time: 127 minutes 14.33 seconds (7634.33 seconds total)