Starting phenix.real_space_refine (version: dev) on Sat Feb 25 14:47:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w1r_8751/02_2023/5w1r_8751.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w1r_8751/02_2023/5w1r_8751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w1r_8751/02_2023/5w1r_8751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w1r_8751/02_2023/5w1r_8751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w1r_8751/02_2023/5w1r_8751.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w1r_8751/02_2023/5w1r_8751.pdb" } resolution = 4.4 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 ------------------------------------------------------------------------------- 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= 0.005 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 Process input model Symmetric amino acids flipped Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 791": "OD1" <-> "OD2" Residue "A TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1002": "OE1" <-> "OE2" Residue "A GLU 1050": "OE1" <-> "OE2" Residue "A PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1090": "NH1" <-> "NH2" Residue "A PHE 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1440": "OD1" <-> "OD2" Residue "A PHE 1519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1711": "NH1" <-> "NH2" Residue "A PHE 1736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1986": "NH1" <-> "NH2" Residue "A PHE 2045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2060": "NH1" <-> "NH2" Residue "A PHE 2218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2872": "OD1" <-> "OD2" Residue "A ARG 2922": "NH1" <-> "NH2" Residue "A TYR 2930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3095": "OD1" <-> "OD2" Residue "A ARG 3125": "NH1" <-> "NH2" Residue "A GLU 3265": "OE1" <-> "OE2" Residue "A ARG 3282": "NH1" <-> "NH2" Residue "A GLU 3352": "OE1" <-> "OE2" Residue "A PHE 3465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3741": "NH1" <-> "NH2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A PHE 3750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3759": "NH1" <-> "NH2" Residue "A PHE 3768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3875": "OE1" <-> "OE2" Residue "A PHE 3887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4113": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 25559 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 25559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3563, 25559 Classifications: {'peptide': 3563} Incomplete info: {'truncation_to_alanine': 713} Link IDs: {'PTRANS': 156, 'TRANS': 3406} Chain breaks: 25 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3069 Unresolved non-hydrogen angles: 3789 Unresolved non-hydrogen dihedrals: 2686 Unresolved non-hydrogen chiralities: 146 Planarities with less than four sites: {'GLN:plan1': 47, 'ASP:plan': 38, 'TYR:plan': 36, 'ASN:plan1': 23, 'TRP:plan': 12, 'HIS:plan': 20, 'PHE:plan': 52, 'GLU:plan': 72, 'ARG:plan': 81} Unresolved non-hydrogen planarities: 1836 Time building chain proxies: 14.03, per 1000 atoms: 0.55 Number of scatterers: 25559 At special positions: 0 Unit cell: (167.61, 138.92, 172.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 4889 8.00 N 4350 7.00 C 16187 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 - 3.50 Amino acid : False - 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: 10.15 Conformation dependent library (CDL) restraints added in 4.4 seconds 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6818 Finding SS restraints... Secondary structure from input PDB file: 221 helices and 3 sheets defined 67.9% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 removed outlier: 3.860A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 50 through 65 Processing helix chain 'A' and resid 74 through 96 removed outlier: 3.689A pdb=" N GLU A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N CYS A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 118 removed outlier: 3.582A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 removed outlier: 4.095A pdb=" N SER A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 162 removed outlier: 3.924A pdb=" N GLU A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.876A pdb=" N VAL A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 206 removed outlier: 3.525A pdb=" N ASN A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 removed outlier: 4.349A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 248 removed outlier: 3.645A pdb=" N GLU A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 265 through 275 removed outlier: 3.648A pdb=" N SER A 269 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 removed outlier: 3.697A pdb=" N GLN A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.572A pdb=" N LEU A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 329 Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.553A pdb=" N VAL A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.626A pdb=" N ILE A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 382 through 398 removed outlier: 3.584A pdb=" N VAL A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 409 through 422 removed outlier: 3.726A pdb=" N PHE A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 414 " --> pdb=" O MET A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.615A pdb=" N LEU A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 472 removed outlier: 3.662A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 462 " --> pdb=" O CYS A 458 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 removed outlier: 4.088A pdb=" N ASN A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 482 " --> pdb=" O CYS A 478 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 539 Processing helix chain 'A' and resid 547 through 564 removed outlier: 3.787A pdb=" N SER A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 582 removed outlier: 4.447A pdb=" N LYS A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 581 " --> pdb=" O GLU A 577 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 611 through 622 removed outlier: 3.841A pdb=" N ALA A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Proline residue: A 617 - end of helix removed outlier: 3.986A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 638 removed outlier: 3.687A pdb=" N GLU A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 649 Proline residue: A 644 - end of helix Processing helix chain 'A' and resid 653 through 660 removed outlier: 3.839A pdb=" N SER A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 removed outlier: 3.673A pdb=" N SER A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 665 " --> pdb=" O PRO A 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 660 through 665' Processing helix chain 'A' and resid 670 through 676 Processing helix chain 'A' and resid 677 through 682 removed outlier: 3.578A pdb=" N TYR A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 713 Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.769A pdb=" N VAL A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 removed outlier: 4.495A pdb=" N MET A 754 " --> pdb=" O PRO A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 782 removed outlier: 3.885A pdb=" N GLU A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TRP A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 801 Proline residue: A 794 - end of helix removed outlier: 3.678A pdb=" N ASP A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR A 799 " --> pdb=" O CYS A 795 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 801 " --> pdb=" O ASP A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 805 removed outlier: 4.033A pdb=" N LEU A 805 " --> pdb=" O THR A 802 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 802 through 805' Processing helix chain 'A' and resid 847 through 860 removed outlier: 3.619A pdb=" N ARG A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 854 " --> pdb=" O GLU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 877 removed outlier: 4.001A pdb=" N LEU A 870 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 871 " --> pdb=" O ASN A 867 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR A 872 " --> pdb=" O LYS A 868 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 877 " --> pdb=" O VAL A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 920 removed outlier: 4.240A pdb=" N ARG A 913 " --> pdb=" O VAL A 909 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 917 " --> pdb=" O ARG A 913 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 918 " --> pdb=" O VAL A 914 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 924 through 945 removed outlier: 4.206A pdb=" N ALA A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 936 " --> pdb=" O GLU A 932 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 943 " --> pdb=" O MET A 939 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS A 944 " --> pdb=" O PHE A 940 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA A 945 " --> pdb=" O MET A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 961 removed outlier: 3.626A pdb=" N LEU A 961 " --> pdb=" O PRO A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 976 removed outlier: 3.952A pdb=" N LEU A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 975 " --> pdb=" O ARG A 971 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 991 removed outlier: 3.747A pdb=" N GLN A 982 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Proline residue: A 986 - end of helix removed outlier: 3.558A pdb=" N MET A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 removed outlier: 3.848A pdb=" N PHE A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1012 removed outlier: 3.676A pdb=" N VAL A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1014 No H-bonds generated for 'chain 'A' and resid 1013 through 1014' Processing helix chain 'A' and resid 1015 through 1019 Processing helix chain 'A' and resid 1021 through 1030 removed outlier: 3.642A pdb=" N LEU A1025 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG A1026 " --> pdb=" O ASP A1022 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A1029 " --> pdb=" O LEU A1025 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1041 Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1068 through 1073 removed outlier: 3.897A pdb=" N ALA A1072 " --> pdb=" O LEU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1092 removed outlier: 3.718A pdb=" N ALA A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN A1083 " --> pdb=" O SER A1079 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N PHE A1089 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1100 removed outlier: 3.977A pdb=" N PHE A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1117 removed outlier: 3.743A pdb=" N VAL A1105 " --> pdb=" O PHE A1101 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N HIS A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A1117 " --> pdb=" O LEU A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1137 removed outlier: 3.606A pdb=" N ASP A1129 " --> pdb=" O GLN A1125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A1131 " --> pdb=" O CYS A1127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A1132 " --> pdb=" O CYS A1128 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1151 removed outlier: 3.556A pdb=" N ARG A1151 " --> pdb=" O LYS A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1156 removed outlier: 3.645A pdb=" N ARG A1155 " --> pdb=" O ARG A1151 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A1156 " --> pdb=" O ARG A1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1151 through 1156' Processing helix chain 'A' and resid 1168 through 1177 Processing helix chain 'A' and resid 1216 through 1225 removed outlier: 4.129A pdb=" N ILE A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN A1222 " --> pdb=" O SER A1218 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A1223 " --> pdb=" O PHE A1219 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A1225 " --> pdb=" O ILE A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1265 removed outlier: 3.603A pdb=" N ALA A1263 " --> pdb=" O LEU A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1270 removed outlier: 4.026A pdb=" N PHE A1270 " --> pdb=" O TYR A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1305 removed outlier: 3.692A pdb=" N ALA A1293 " --> pdb=" O SER A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1350 removed outlier: 3.512A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A1334 " --> pdb=" O TYR A1330 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A1344 " --> pdb=" O ARG A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1373 removed outlier: 3.756A pdb=" N LEU A1372 " --> pdb=" O LEU A1368 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A1373 " --> pdb=" O MET A1369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1368 through 1373' Processing helix chain 'A' and resid 1377 through 1382 removed outlier: 4.142A pdb=" N SER A1381 " --> pdb=" O CYS A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1408 Proline residue: A1396 - end of helix removed outlier: 3.544A pdb=" N LYS A1404 " --> pdb=" O VAL A1400 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1420 removed outlier: 4.081A pdb=" N THR A1417 " --> pdb=" O ASP A1413 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS A1418 " --> pdb=" O ILE A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1428 removed outlier: 4.049A pdb=" N ILE A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1433 removed outlier: 3.833A pdb=" N CYS A1432 " --> pdb=" O ILE A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1457 removed outlier: 3.554A pdb=" N SER A1446 " --> pdb=" O GLN A1442 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A1447 " --> pdb=" O VAL A1443 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A1449 " --> pdb=" O ARG A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1461 Processing helix chain 'A' and resid 1477 through 1486 removed outlier: 4.021A pdb=" N LEU A1486 " --> pdb=" O GLU A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1511 removed outlier: 3.787A pdb=" N LEU A1510 " --> pdb=" O SER A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1521 Processing helix chain 'A' and resid 1522 through 1526 Processing helix chain 'A' and resid 1549 through 1556 removed outlier: 3.541A pdb=" N PHE A1553 " --> pdb=" O SER A1549 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A1554 " --> pdb=" O VAL A1550 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A1555 " --> pdb=" O ILE A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1560 through 1566 removed outlier: 3.719A pdb=" N SER A1564 " --> pdb=" O TYR A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1576 removed outlier: 3.702A pdb=" N LEU A1571 " --> pdb=" O ILE A1567 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A1572 " --> pdb=" O ASN A1568 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A1575 " --> pdb=" O LEU A1571 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A1576 " --> pdb=" O LEU A1572 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1588 removed outlier: 4.146A pdb=" N GLN A1584 " --> pdb=" O LEU A1580 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP A1588 " --> pdb=" O GLN A1584 " (cutoff:3.500A) Processing helix chain 'A' and resid 1593 through 1608 removed outlier: 4.100A pdb=" N GLY A1599 " --> pdb=" O ALA A1595 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A1600 " --> pdb=" O VAL A1596 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A1603 " --> pdb=" O GLY A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1643 Processing helix chain 'A' and resid 1651 through 1656 Processing helix chain 'A' and resid 1677 through 1695 removed outlier: 3.618A pdb=" N ASP A1681 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A1682 " --> pdb=" O LEU A1678 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A1683 " --> pdb=" O LEU A1679 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A1685 " --> pdb=" O ASP A1681 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A1686 " --> pdb=" O THR A1682 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1702 Processing helix chain 'A' and resid 1710 through 1721 removed outlier: 3.776A pdb=" N LEU A1714 " --> pdb=" O LEU A1710 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A1715 " --> pdb=" O ARG A1711 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN A1716 " --> pdb=" O ARG A1712 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A1717 " --> pdb=" O VAL A1713 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A1718 " --> pdb=" O LEU A1714 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A1719 " --> pdb=" O GLU A1715 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A1720 " --> pdb=" O GLN A1716 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS A1721 " --> pdb=" O LEU A1717 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1710 through 1721' Processing helix chain 'A' and resid 1738 through 1752 removed outlier: 3.511A pdb=" N ALA A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1807 Processing helix chain 'A' and resid 1858 through 1872 removed outlier: 3.565A pdb=" N PHE A1863 " --> pdb=" O ASN A1859 " (cutoff:3.500A) Processing helix chain 'A' and resid 1873 through 1877 removed outlier: 3.518A pdb=" N LEU A1877 " --> pdb=" O TYR A1874 " (cutoff:3.500A) Processing helix chain 'A' and resid 1879 through 1881 No H-bonds generated for 'chain 'A' and resid 1879 through 1881' Processing helix chain 'A' and resid 1882 through 1890 removed outlier: 3.672A pdb=" N ASP A1887 " --> pdb=" O ARG A1883 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A1888 " --> pdb=" O LEU A1884 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1909 removed outlier: 4.518A pdb=" N VAL A1899 " --> pdb=" O LYS A1895 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A1905 " --> pdb=" O HIS A1901 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A1906 " --> pdb=" O GLY A1902 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A1907 " --> pdb=" O SER A1903 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A1909 " --> pdb=" O ILE A1905 " (cutoff:3.500A) Processing helix chain 'A' and resid 1915 through 1928 Processing helix chain 'A' and resid 1935 through 1950 removed outlier: 3.627A pdb=" N HIS A1941 " --> pdb=" O ARG A1937 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A1942 " --> pdb=" O ARG A1938 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS A1947 " --> pdb=" O ALA A1943 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A1948 " --> pdb=" O ALA A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1969 removed outlier: 3.576A pdb=" N PHE A1961 " --> pdb=" O ASN A1957 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A1968 " --> pdb=" O GLY A1964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1979 through 1999 Proline residue: A1991 - end of helix removed outlier: 3.679A pdb=" N VAL A1996 " --> pdb=" O VAL A1992 " (cutoff:3.500A) Proline residue: A1997 - end of helix Processing helix chain 'A' and resid 2002 through 2011 removed outlier: 3.688A pdb=" N GLU A2006 " --> pdb=" O LYS A2002 " (cutoff:3.500A) Processing helix chain 'A' and resid 2011 through 2021 Processing helix chain 'A' and resid 2036 through 2044 removed outlier: 3.855A pdb=" N MET A2040 " --> pdb=" O LEU A2036 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A2043 " --> pdb=" O GLU A2039 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A2044 " --> pdb=" O MET A2040 " (cutoff:3.500A) Processing helix chain 'A' and resid 2044 through 2049 Processing helix chain 'A' and resid 2049 through 2054 Processing helix chain 'A' and resid 2074 through 2081 removed outlier: 3.794A pdb=" N ASP A2078 " --> pdb=" O PRO A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2081 through 2090 Processing helix chain 'A' and resid 2093 through 2105 removed outlier: 4.154A pdb=" N LEU A2097 " --> pdb=" O CYS A2093 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A2102 " --> pdb=" O THR A2098 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS A2103 " --> pdb=" O ALA A2099 " (cutoff:3.500A) Processing helix chain 'A' and resid 2118 through 2122 removed outlier: 3.551A pdb=" N LEU A2122 " --> pdb=" O VAL A2118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2118 through 2122' Processing helix chain 'A' and resid 2137 through 2148 removed outlier: 3.708A pdb=" N ASN A2141 " --> pdb=" O ILE A2137 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A2142 " --> pdb=" O VAL A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2156 removed outlier: 3.993A pdb=" N GLU A2155 " --> pdb=" O ASN A2152 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A2156 " --> pdb=" O THR A2153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2152 through 2156' Processing helix chain 'A' and resid 2157 through 2165 removed outlier: 3.623A pdb=" N ALA A2161 " --> pdb=" O PHE A2157 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP A2164 " --> pdb=" O TYR A2160 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A2165 " --> pdb=" O ALA A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2169 through 2174 removed outlier: 4.294A pdb=" N SER A2174 " --> pdb=" O GLN A2170 " (cutoff:3.500A) Processing helix chain 'A' and resid 2181 through 2193 removed outlier: 3.712A pdb=" N MET A2185 " --> pdb=" O GLY A2181 " (cutoff:3.500A) Processing helix chain 'A' and resid 2196 through 2201 removed outlier: 3.784A pdb=" N THR A2201 " --> pdb=" O THR A2197 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2223 Processing helix chain 'A' and resid 2232 through 2245 removed outlier: 3.982A pdb=" N GLU A2236 " --> pdb=" O ARG A2232 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS A2244 " --> pdb=" O THR A2240 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP A2245 " --> pdb=" O LEU A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2250 through 2260 removed outlier: 4.153A pdb=" N ARG A2254 " --> pdb=" O SER A2250 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A2257 " --> pdb=" O TYR A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2270 through 2275 removed outlier: 4.776A pdb=" N GLN A2275 " --> pdb=" O SER A2271 " (cutoff:3.500A) Processing helix chain 'A' and resid 2275 through 2280 removed outlier: 4.172A pdb=" N VAL A2280 " --> pdb=" O LEU A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2288 through 2297 removed outlier: 3.793A pdb=" N GLY A2293 " --> pdb=" O ASP A2289 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A2295 " --> pdb=" O GLN A2291 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A2296 " --> pdb=" O CYS A2292 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A2297 " --> pdb=" O GLY A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2298 through 2308 removed outlier: 3.829A pdb=" N ALA A2302 " --> pdb=" O GLU A2298 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET A2307 " --> pdb=" O LEU A2303 " (cutoff:3.500A) Processing helix chain 'A' and resid 2315 through 2333 removed outlier: 4.141A pdb=" N ALA A2319 " --> pdb=" O VAL A2315 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA A2320 " --> pdb=" O TYR A2316 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A2333 " --> pdb=" O TYR A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2338 through 2351 removed outlier: 3.601A pdb=" N GLU A2343 " --> pdb=" O GLU A2339 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A2344 " --> pdb=" O SER A2340 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2365 removed outlier: 3.586A pdb=" N ILE A2361 " --> pdb=" O GLU A2357 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2366 through 2370 removed outlier: 3.640A pdb=" N SER A2370 " --> pdb=" O VAL A2367 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2385 removed outlier: 3.606A pdb=" N LEU A2385 " --> pdb=" O ALA A2381 " (cutoff:3.500A) Processing helix chain 'A' and resid 2393 through 2407 removed outlier: 3.945A pdb=" N CYS A2397 " --> pdb=" O LEU A2393 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A2399 " --> pdb=" O THR A2395 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A2400 " --> pdb=" O LEU A2396 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A2406 " --> pdb=" O LEU A2402 " (cutoff:3.500A) Processing helix chain 'A' and resid 2415 through 2425 removed outlier: 3.774A pdb=" N ASP A2419 " --> pdb=" O LEU A2415 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A2421 " --> pdb=" O SER A2417 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLN A2422 " --> pdb=" O LYS A2418 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) Processing helix chain 'A' and resid 2430 through 2433 Processing helix chain 'A' and resid 2434 through 2440 removed outlier: 4.067A pdb=" N TYR A2440 " --> pdb=" O LEU A2436 " (cutoff:3.500A) Processing helix chain 'A' and resid 2441 through 2443 No H-bonds generated for 'chain 'A' and resid 2441 through 2443' Processing helix chain 'A' and resid 2447 through 2461 removed outlier: 3.524A pdb=" N ARG A2452 " --> pdb=" O PRO A2448 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A2454 " --> pdb=" O GLU A2450 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix removed outlier: 3.705A pdb=" N GLU A2460 " --> pdb=" O ASN A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2469 through 2483 removed outlier: 4.170A pdb=" N ASN A2475 " --> pdb=" O GLU A2471 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A2477 " --> pdb=" O MET A2473 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2509 removed outlier: 3.772A pdb=" N ILE A2498 " --> pdb=" O ASP A2494 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A2500 " --> pdb=" O GLN A2496 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A2505 " --> pdb=" O LEU A2501 " (cutoff:3.500A) Processing helix chain 'A' and resid 2515 through 2526 removed outlier: 4.102A pdb=" N LEU A2519 " --> pdb=" O PRO A2515 " (cutoff:3.500A) Processing helix chain 'A' and resid 2535 through 2547 removed outlier: 3.875A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A2547 " --> pdb=" O ASN A2543 " (cutoff:3.500A) Processing helix chain 'A' and resid 2554 through 2566 removed outlier: 3.867A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A2566 " --> pdb=" O LEU A2562 " (cutoff:3.500A) Processing helix chain 'A' and resid 2787 through 2792 removed outlier: 3.635A pdb=" N ILE A2791 " --> pdb=" O HIS A2787 " (cutoff:3.500A) Processing helix chain 'A' and resid 2792 through 2801 removed outlier: 4.007A pdb=" N ALA A2796 " --> pdb=" O THR A2792 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A2798 " --> pdb=" O LEU A2794 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A2799 " --> pdb=" O GLN A2795 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A2800 " --> pdb=" O ALA A2796 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP A2801 " --> pdb=" O VAL A2797 " (cutoff:3.500A) Processing helix chain 'A' and resid 2806 through 2818 removed outlier: 4.369A pdb=" N SER A2810 " --> pdb=" O LYS A2806 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLY A2815 " --> pdb=" O SER A2811 " (cutoff:3.500A) Processing helix chain 'A' and resid 2818 through 2823 removed outlier: 3.855A pdb=" N LYS A2822 " --> pdb=" O LYS A2818 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A2823 " --> pdb=" O GLU A2819 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2818 through 2823' Processing helix chain 'A' and resid 2825 through 2842 removed outlier: 3.730A pdb=" N LYS A2829 " --> pdb=" O THR A2825 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A2838 " --> pdb=" O GLN A2834 " (cutoff:3.500A) Processing helix chain 'A' and resid 2842 through 2847 Processing helix chain 'A' and resid 2856 through 2862 removed outlier: 3.966A pdb=" N ASP A2860 " --> pdb=" O SER A2856 " (cutoff:3.500A) Processing helix chain 'A' and resid 2876 through 2883 removed outlier: 3.627A pdb=" N LEU A2881 " --> pdb=" O SER A2877 " (cutoff:3.500A) Processing helix chain 'A' and resid 2887 through 2895 removed outlier: 3.599A pdb=" N LEU A2892 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A2893 " --> pdb=" O GLY A2889 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A2895 " --> pdb=" O ARG A2891 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2922 Processing helix chain 'A' and resid 2930 through 2939 removed outlier: 3.859A pdb=" N ASP A2937 " --> pdb=" O ILE A2933 " (cutoff:3.500A) Processing helix chain 'A' and resid 2946 through 2957 removed outlier: 3.919A pdb=" N GLN A2954 " --> pdb=" O LYS A2950 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A2955 " --> pdb=" O GLN A2951 " (cutoff:3.500A) Processing helix chain 'A' and resid 2960 through 2968 removed outlier: 5.669A pdb=" N SER A2966 " --> pdb=" O ARG A2962 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A2967 " --> pdb=" O SER A2963 " (cutoff:3.500A) Processing helix chain 'A' and resid 2970 through 2975 Processing helix chain 'A' and resid 2985 through 2990 removed outlier: 3.881A pdb=" N ALA A2989 " --> pdb=" O GLU A2985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2990 through 3002 removed outlier: 3.854A pdb=" N LEU A2996 " --> pdb=" O ASP A2992 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP A3000 " --> pdb=" O LEU A2996 " (cutoff:3.500A) Processing helix chain 'A' and resid 3007 through 3017 removed outlier: 3.631A pdb=" N LEU A3011 " --> pdb=" O GLU A3007 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A3012 " --> pdb=" O TRP A3008 " (cutoff:3.500A) Processing helix chain 'A' and resid 3025 through 3032 removed outlier: 3.701A pdb=" N SER A3032 " --> pdb=" O ASN A3028 " (cutoff:3.500A) Processing helix chain 'A' and resid 3037 through 3039 No H-bonds generated for 'chain 'A' and resid 3037 through 3039' Processing helix chain 'A' and resid 3040 through 3047 removed outlier: 3.768A pdb=" N ILE A3045 " --> pdb=" O LEU A3041 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A3047 " --> pdb=" O TYR A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3047 through 3054 removed outlier: 3.621A pdb=" N LEU A3051 " --> pdb=" O SER A3047 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A3054 " --> pdb=" O LYS A3050 " (cutoff:3.500A) Processing helix chain 'A' and resid 3060 through 3071 removed outlier: 4.899A pdb=" N ASP A3066 " --> pdb=" O LEU A3062 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A3067 " --> pdb=" O THR A3063 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET A3069 " --> pdb=" O ILE A3065 " (cutoff:3.500A) Processing helix chain 'A' and resid 3075 through 3080 Processing helix chain 'A' and resid 3083 through 3090 removed outlier: 3.731A pdb=" N TYR A3090 " --> pdb=" O LEU A3086 " (cutoff:3.500A) Processing helix chain 'A' and resid 3096 through 3114 removed outlier: 4.114A pdb=" N GLN A3112 " --> pdb=" O GLN A3108 " (cutoff:3.500A) Processing helix chain 'A' and resid 3119 through 3130 removed outlier: 4.038A pdb=" N GLN A3123 " --> pdb=" O VAL A3119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A3130 " --> pdb=" O LEU A3126 " (cutoff:3.500A) Processing helix chain 'A' and resid 3130 through 3146 removed outlier: 3.942A pdb=" N THR A3136 " --> pdb=" O VAL A3132 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A3141 " --> pdb=" O GLU A3137 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A3146 " --> pdb=" O ILE A3142 " (cutoff:3.500A) Processing helix chain 'A' and resid 3146 through 3155 Processing helix chain 'A' and resid 3156 through 3168 removed outlier: 3.722A pdb=" N LEU A3160 " --> pdb=" O PRO A3156 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A3163 " --> pdb=" O ARG A3159 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A3164 " --> pdb=" O LEU A3160 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A3165 " --> pdb=" O LEU A3161 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A3166 " --> pdb=" O ASN A3162 " (cutoff:3.500A) Processing helix chain 'A' and resid 3177 through 3195 removed outlier: 3.747A pdb=" N ILE A3183 " --> pdb=" O TRP A3179 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR A3184 " --> pdb=" O ASP A3180 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN A3185 " --> pdb=" O ASP A3181 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N CYS A3187 " --> pdb=" O ILE A3183 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A3193 " --> pdb=" O PHE A3189 " (cutoff:3.500A) Processing helix chain 'A' and resid 3228 through 3245 removed outlier: 3.609A pdb=" N MET A3242 " --> pdb=" O MET A3238 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A3243 " --> pdb=" O LYS A3239 " (cutoff:3.500A) Processing helix chain 'A' and resid 3246 through 3249 Processing helix chain 'A' and resid 3253 through 3265 removed outlier: 3.967A pdb=" N LYS A3257 " --> pdb=" O SER A3253 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A3258 " --> pdb=" O LEU A3254 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A3259 " --> pdb=" O ALA A3255 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU A3265 " --> pdb=" O GLU A3261 " (cutoff:3.500A) Processing helix chain 'A' and resid 3268 through 3287 removed outlier: 3.987A pdb=" N TRP A3272 " --> pdb=" O THR A3268 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A3273 " --> pdb=" O ARG A3269 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A3274 " --> pdb=" O ASP A3270 " (cutoff:3.500A) Processing helix chain 'A' and resid 3291 through 3312 removed outlier: 4.075A pdb=" N SER A3305 " --> pdb=" O LEU A3301 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A3306 " --> pdb=" O LYS A3302 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A3307 " --> pdb=" O THR A3303 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A3308 " --> pdb=" O VAL A3304 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU A3309 " --> pdb=" O SER A3305 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN A3310 " --> pdb=" O LEU A3306 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A3312 " --> pdb=" O ASP A3308 " (cutoff:3.500A) Processing helix chain 'A' and resid 3315 through 3334 removed outlier: 3.809A pdb=" N LEU A3329 " --> pdb=" O ASP A3325 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A3330 " --> pdb=" O GLN A3326 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A3331 " --> pdb=" O ASN A3327 " (cutoff:3.500A) Processing helix chain 'A' and resid 3346 through 3353 removed outlier: 3.715A pdb=" N GLU A3350 " --> pdb=" O ALA A3346 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3358 removed outlier: 3.786A pdb=" N ARG A3358 " --> pdb=" O ASP A3354 " (cutoff:3.500A) Processing helix chain 'A' and resid 3380 through 3394 Processing helix chain 'A' and resid 3395 through 3401 Proline residue: A3398 - end of helix Processing helix chain 'A' and resid 3407 through 3427 removed outlier: 3.910A pdb=" N ASP A3411 " --> pdb=" O ALA A3407 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A3412 " --> pdb=" O GLY A3408 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A3415 " --> pdb=" O ASP A3411 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS A3420 " --> pdb=" O LEU A3416 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A3422 " --> pdb=" O ASP A3418 " (cutoff:3.500A) Processing helix chain 'A' and resid 3433 through 3440 Processing helix chain 'A' and resid 3442 through 3444 No H-bonds generated for 'chain 'A' and resid 3442 through 3444' Processing helix chain 'A' and resid 3445 through 3450 removed outlier: 4.237A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A3450 " --> pdb=" O VAL A3446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3445 through 3450' Processing helix chain 'A' and resid 3459 through 3472 removed outlier: 4.023A pdb=" N LEU A3463 " --> pdb=" O ASN A3459 " (cutoff:3.500A) Proline residue: A3466 - end of helix removed outlier: 3.805A pdb=" N ILE A3472 " --> pdb=" O LEU A3468 " (cutoff:3.500A) Processing helix chain 'A' and resid 3475 through 3485 removed outlier: 3.706A pdb=" N MET A3483 " --> pdb=" O THR A3479 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A3484 " --> pdb=" O LEU A3480 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) Processing helix chain 'A' and resid 3498 through 3508 removed outlier: 3.755A pdb=" N MET A3502 " --> pdb=" O TRP A3498 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A3503 " --> pdb=" O ILE A3499 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A3504 " --> pdb=" O SER A3500 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A3505 " --> pdb=" O HIS A3501 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A3508 " --> pdb=" O ALA A3504 " (cutoff:3.500A) Processing helix chain 'A' and resid 3511 through 3523 removed outlier: 3.672A pdb=" N GLN A3515 " --> pdb=" O ALA A3511 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS A3516 " --> pdb=" O VAL A3512 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER A3517 " --> pdb=" O ALA A3513 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A3518 " --> pdb=" O VAL A3514 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A3519 " --> pdb=" O GLN A3515 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3539 removed outlier: 3.994A pdb=" N PHE A3533 " --> pdb=" O ILE A3529 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE A3534 " --> pdb=" O VAL A3530 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A3537 " --> pdb=" O PHE A3533 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3548 through 3561 Processing helix chain 'A' and resid 3568 through 3580 Processing helix chain 'A' and resid 3581 through 3593 removed outlier: 3.722A pdb=" N ASN A3590 " --> pdb=" O LYS A3586 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASP A3591 " --> pdb=" O ASP A3587 " (cutoff:3.500A) Processing helix chain 'A' and resid 3603 through 3613 removed outlier: 3.603A pdb=" N GLU A3607 " --> pdb=" O LYS A3603 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A3610 " --> pdb=" O ILE A3606 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3622 through 3627 removed outlier: 3.853A pdb=" N ALA A3627 " --> pdb=" O PRO A3623 " (cutoff:3.500A) Processing helix chain 'A' and resid 3631 through 3648 removed outlier: 3.567A pdb=" N LYS A3638 " --> pdb=" O GLN A3634 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS A3643 " --> pdb=" O GLU A3639 " (cutoff:3.500A) Processing helix chain 'A' and resid 3658 through 3675 removed outlier: 3.932A pdb=" N ILE A3662 " --> pdb=" O ASP A3658 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN A3664 " --> pdb=" O ASN A3660 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N MET A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3686 through 3690 Processing helix chain 'A' and resid 3693 through 3697 Processing helix chain 'A' and resid 3759 through 3772 Processing helix chain 'A' and resid 3778 through 3784 removed outlier: 3.656A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3818 Processing helix chain 'A' and resid 3820 through 3847 removed outlier: 4.235A pdb=" N SER A3830 " --> pdb=" O ALA A3826 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A3831 " --> pdb=" O ALA A3827 " (cutoff:3.500A) Proline residue: A3832 - end of helix Proline residue: A3835 - end of helix removed outlier: 4.107A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3860 through 3877 removed outlier: 3.897A pdb=" N ARG A3864 " --> pdb=" O LYS A3860 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A3865 " --> pdb=" O GLY A3861 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A3873 " --> pdb=" O THR A3869 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3890 removed outlier: 3.902A pdb=" N ASP A3881 " --> pdb=" O LYS A3877 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A3889 " --> pdb=" O ARG A3885 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET A3890 " --> pdb=" O ALA A3886 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3919 removed outlier: 4.415A pdb=" N SER A3902 " --> pdb=" O LEU A3898 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A3910 " --> pdb=" O SER A3906 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A3911 " --> pdb=" O SER A3907 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A3912 " --> pdb=" O HIS A3908 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A3914 " --> pdb=" O LEU A3910 " (cutoff:3.500A) Processing helix chain 'A' and resid 3947 through 3952 Processing helix chain 'A' and resid 3964 through 3972 removed outlier: 3.833A pdb=" N ILE A3968 " --> pdb=" O THR A3964 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A3969 " --> pdb=" O ARG A3965 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A3970 " --> pdb=" O GLN A3966 " (cutoff:3.500A) Processing helix chain 'A' and resid 3979 through 3993 removed outlier: 3.597A pdb=" N ILE A3983 " --> pdb=" O LEU A3979 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A3985 " --> pdb=" O TYR A3981 " (cutoff:3.500A) Processing helix chain 'A' and resid 3995 through 4006 removed outlier: 3.563A pdb=" N VAL A4004 " --> pdb=" O ASN A4000 " (cutoff:3.500A) Processing helix chain 'A' and resid 4015 through 4020 Processing helix chain 'A' and resid 4041 through 4052 removed outlier: 3.707A pdb=" N CYS A4045 " --> pdb=" O ARG A4041 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR A4046 " --> pdb=" O GLN A4042 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A4051 " --> pdb=" O ALA A4047 " (cutoff:3.500A) Processing helix chain 'A' and resid 4058 through 4066 removed outlier: 3.696A pdb=" N ASP A4062 " --> pdb=" O VAL A4058 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A4063 " --> pdb=" O ILE A4059 " (cutoff:3.500A) Processing helix chain 'A' and resid 4072 through 4082 Processing helix chain 'A' and resid 4082 through 4087 Processing helix chain 'A' and resid 4101 through 4113 removed outlier: 3.538A pdb=" N LYS A4105 " --> pdb=" O GLU A4101 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA A4111 " --> pdb=" O LEU A4107 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A4112 " --> pdb=" O MET A4108 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A4113 " --> pdb=" O ASP A4109 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4119 removed outlier: 4.204A pdb=" N ARG A4119 " --> pdb=" O ASN A4115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 4.705A pdb=" N ARG A3741 " --> pdb=" O ALA A3720 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N PHE A3722 " --> pdb=" O ILE A3739 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE A3739 " --> pdb=" O PHE A3722 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 4.705A pdb=" N ARG A3741 " --> pdb=" O ALA A3720 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N PHE A3722 " --> pdb=" O ILE A3739 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE A3739 " --> pdb=" O PHE A3722 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A3794 " --> pdb=" O LEU A3802 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3809 through 3811 1129 hydrogen bonds defined for protein. 3315 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: 14.88 Time building geometry restraints manager: 11.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 8660 1.36 - 1.51: 6870 1.51 - 1.66: 10272 1.66 - 1.80: 128 1.80 - 1.95: 64 Bond restraints: 25994 Sorted by residual: bond pdb=" CA ILE A3568 " pdb=" C ILE A3568 " ideal model delta sigma weight residual 1.522 1.613 -0.092 1.32e-02 5.74e+03 4.83e+01 bond pdb=" N ASN A3580 " pdb=" CA ASN A3580 " ideal model delta sigma weight residual 1.452 1.551 -0.099 1.54e-02 4.22e+03 4.12e+01 bond pdb=" SD MET A1342 " pdb=" CE MET A1342 " ideal model delta sigma weight residual 1.791 1.950 -0.159 2.50e-02 1.60e+03 4.06e+01 bond pdb=" C ASP A3576 " pdb=" O ASP A3576 " ideal model delta sigma weight residual 1.237 1.303 -0.066 1.17e-02 7.31e+03 3.21e+01 bond pdb=" C GLU A 643 " pdb=" N PRO A 644 " ideal model delta sigma weight residual 1.336 1.405 -0.069 1.23e-02 6.61e+03 3.18e+01 ... (remaining 25989 not shown) Histogram of bond angle deviations from ideal: 94.47 - 104.84: 527 104.84 - 115.22: 16046 115.22 - 125.60: 18491 125.60 - 135.97: 385 135.97 - 146.35: 14 Bond angle restraints: 35463 Sorted by residual: angle pdb=" N PHE A 666 " pdb=" CA PHE A 666 " pdb=" C PHE A 666 " ideal model delta sigma weight residual 111.28 122.80 -11.52 1.09e+00 8.42e-01 1.12e+02 angle pdb=" N LEU A3316 " pdb=" CA LEU A3316 " pdb=" C LEU A3316 " ideal model delta sigma weight residual 111.36 100.62 10.74 1.09e+00 8.42e-01 9.70e+01 angle pdb=" N ASN A3580 " pdb=" CA ASN A3580 " pdb=" C ASN A3580 " ideal model delta sigma weight residual 110.10 125.09 -14.99 1.53e+00 4.27e-01 9.60e+01 angle pdb=" N LEU A3348 " pdb=" CA LEU A3348 " pdb=" C LEU A3348 " ideal model delta sigma weight residual 111.14 121.25 -10.11 1.08e+00 8.57e-01 8.76e+01 angle pdb=" N ILE A 654 " pdb=" CA ILE A 654 " pdb=" C ILE A 654 " ideal model delta sigma weight residual 110.72 119.81 -9.09 1.01e+00 9.80e-01 8.10e+01 ... (remaining 35458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 13919 17.06 - 34.12: 1431 34.12 - 51.18: 335 51.18 - 68.25: 50 68.25 - 85.31: 10 Dihedral angle restraints: 15745 sinusoidal: 5314 harmonic: 10431 Sorted by residual: dihedral pdb=" C PRO A1070 " pdb=" N PRO A1070 " pdb=" CA PRO A1070 " pdb=" CB PRO A1070 " ideal model delta harmonic sigma weight residual -120.70 -136.58 15.88 0 2.50e+00 1.60e-01 4.03e+01 dihedral pdb=" N PRO A1070 " pdb=" C PRO A1070 " pdb=" CA PRO A1070 " pdb=" CB PRO A1070 " ideal model delta harmonic sigma weight residual 115.10 130.01 -14.91 0 2.50e+00 1.60e-01 3.56e+01 dihedral pdb=" CA GLN A3769 " pdb=" C GLN A3769 " pdb=" N VAL A3770 " pdb=" CA VAL A3770 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 15742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 4209 0.159 - 0.319: 67 0.319 - 0.478: 9 0.478 - 0.637: 0 0.637 - 0.797: 1 Chirality restraints: 4286 Sorted by residual: chirality pdb=" CA PRO A1070 " pdb=" N PRO A1070 " pdb=" C PRO A1070 " pdb=" CB PRO A1070 " both_signs ideal model delta sigma weight residual False 2.72 1.92 0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CA TYR A1874 " pdb=" N TYR A1874 " pdb=" C TYR A1874 " pdb=" CB TYR A1874 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CA VAL A3119 " pdb=" N VAL A3119 " pdb=" C VAL A3119 " pdb=" CB VAL A3119 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 4283 not shown) Planarity restraints: 4616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A3580 " 0.113 5.00e-02 4.00e+02 1.73e-01 4.79e+01 pdb=" N PRO A3581 " -0.299 5.00e-02 4.00e+02 pdb=" CA PRO A3581 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO A3581 " 0.098 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 371 " -0.076 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO A 372 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A1069 " -0.077 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A1070 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A1070 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A1070 " -0.064 5.00e-02 4.00e+02 ... (remaining 4613 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 23 1.97 - 2.70: 1340 2.70 - 3.44: 39696 3.44 - 4.17: 56719 4.17 - 4.90: 94304 Nonbonded interactions: 192082 Sorted by model distance: nonbonded pdb=" O GLN A 990 " pdb=" NE1 TRP A 994 " model vdw 1.238 2.520 nonbonded pdb=" O ALA A4081 " pdb=" NE2 GLN A4110 " model vdw 1.572 2.520 nonbonded pdb=" O GLY A3978 " pdb=" N MET A3980 " model vdw 1.612 2.520 nonbonded pdb=" CZ PHE A 995 " pdb=" N SER A1003 " model vdw 1.692 3.420 nonbonded pdb=" OH TYR A1874 " pdb=" CG PRO A1885 " model vdw 1.700 3.440 ... (remaining 192077 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 16187 2.51 5 N 4350 2.21 5 O 4889 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.380 Check model and map are aligned: 0.380 Process input model: 74.070 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.250 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 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 : 0.006 0.159 25994 Z= 0.390 Angle : 1.214 21.351 35463 Z= 0.711 Chirality : 0.059 0.797 4286 Planarity : 0.008 0.173 4616 Dihedral : 14.969 85.307 8927 Min Nonbonded Distance : 1.238 Molprobity Statistics. All-atom Clashscore : 42.66 Ramachandran Plot: Outliers : 5.35 % Allowed : 15.58 % Favored : 79.07 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.31 (0.11), residues: 3511 helix: -3.44 (0.09), residues: 1842 sheet: -4.48 (0.68), residues: 22 loop : -3.59 (0.14), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 755 time to evaluate : 3.319 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 outliers start: 32 outliers final: 8 residues processed: 778 average time/residue: 0.3924 time to fit residues: 480.6458 Evaluate side-chains 397 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 389 time to evaluate : 3.347 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2552 time to fit residues: 8.2354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 182 optimal weight: 40.0000 chunk 144 optimal weight: 5.9990 chunk 279 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 169 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 323 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 HIS A 325 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 442 GLN ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1909 ASN A1957 ASN ** A2222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2234 ASN ** A2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 ASN ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3028 ASN ** A3037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3390 GLN A3494 GLN A3516 HIS A3915 HIS ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 25994 Z= 0.275 Angle : 0.939 15.751 35463 Z= 0.469 Chirality : 0.047 0.267 4286 Planarity : 0.007 0.169 4616 Dihedral : 6.586 36.062 3710 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 1.40 % Allowed : 10.65 % Favored : 87.95 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.12), residues: 3511 helix: -2.27 (0.10), residues: 1995 sheet: -3.96 (0.59), residues: 38 loop : -3.33 (0.15), residues: 1478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 587 time to evaluate : 2.926 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 outliers start: 8 outliers final: 0 residues processed: 594 average time/residue: 0.4159 time to fit residues: 398.3159 Evaluate side-chains 396 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 3.066 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 323 optimal weight: 9.9990 chunk 349 optimal weight: 0.1980 chunk 288 optimal weight: 8.9990 chunk 321 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 259 optimal weight: 0.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN A 611 ASN A 997 ASN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 ASN A1394 HIS ** A1476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2518 GLN ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2865 HIS ** A3327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3515 GLN ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 25994 Z= 0.265 Angle : 0.843 12.030 35463 Z= 0.419 Chirality : 0.045 0.318 4286 Planarity : 0.006 0.143 4616 Dihedral : 6.060 32.126 3710 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 1.08 % Allowed : 11.65 % Favored : 87.27 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.13), residues: 3511 helix: -1.56 (0.10), residues: 2013 sheet: -3.80 (0.70), residues: 28 loop : -3.15 (0.15), residues: 1470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 500 time to evaluate : 3.044 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 outliers start: 3 outliers final: 0 residues processed: 502 average time/residue: 0.3571 time to fit residues: 294.2228 Evaluate side-chains 358 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 7.9990 chunk 243 optimal weight: 20.0000 chunk 168 optimal weight: 30.0000 chunk 35 optimal weight: 40.0000 chunk 154 optimal weight: 20.0000 chunk 217 optimal weight: 3.9990 chunk 325 optimal weight: 4.9990 chunk 344 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 308 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN A 325 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2518 GLN A2831 ASN A3285 HIS A3291 GLN ** A3327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3423 GLN A3494 GLN ** A3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.110 25994 Z= 0.298 Angle : 0.832 10.565 35463 Z= 0.418 Chirality : 0.045 0.351 4286 Planarity : 0.006 0.133 4616 Dihedral : 6.016 29.546 3710 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.02 % Favored : 87.92 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.13), residues: 3511 helix: -1.20 (0.11), residues: 2034 sheet: -3.38 (0.75), residues: 33 loop : -3.04 (0.15), residues: 1444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 469 time to evaluate : 3.440 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 outliers start: 1 outliers final: 1 residues processed: 470 average time/residue: 0.3724 time to fit residues: 283.1231 Evaluate side-chains 332 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 331 time to evaluate : 3.065 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2176 time to fit residues: 4.5597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 256 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 293 optimal weight: 0.0570 chunk 237 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 175 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN A1901 HIS ** A1909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3250 ASN ** A3384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 25994 Z= 0.242 Angle : 0.792 11.077 35463 Z= 0.393 Chirality : 0.044 0.227 4286 Planarity : 0.006 0.123 4616 Dihedral : 5.821 29.478 3710 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.94 % Allowed : 10.28 % Favored : 88.78 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.14), residues: 3511 helix: -0.96 (0.11), residues: 2025 sheet: -2.92 (0.84), residues: 33 loop : -2.89 (0.16), residues: 1453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 463 time to evaluate : 3.149 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 outliers start: 2 outliers final: 1 residues processed: 464 average time/residue: 0.3712 time to fit residues: 281.0936 Evaluate side-chains 330 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 329 time to evaluate : 3.449 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2509 time to fit residues: 4.5625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 50.0000 chunk 309 optimal weight: 10.0000 chunk 68 optimal weight: 0.3980 chunk 202 optimal weight: 20.0000 chunk 84 optimal weight: 0.5980 chunk 344 optimal weight: 7.9990 chunk 285 optimal weight: 0.5980 chunk 159 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 chunk 180 optimal weight: 6.9990 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2830 ASN A3084 GLN A3384 HIS A3787 GLN ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 25994 Z= 0.224 Angle : 0.773 11.183 35463 Z= 0.382 Chirality : 0.043 0.280 4286 Planarity : 0.006 0.114 4616 Dihedral : 5.664 28.461 3710 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.94 % Allowed : 10.11 % Favored : 88.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.14), residues: 3511 helix: -0.76 (0.11), residues: 2034 sheet: -2.17 (0.98), residues: 27 loop : -2.90 (0.16), residues: 1450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 3.350 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 outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.3735 time to fit residues: 272.9743 Evaluate side-chains 326 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 3.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 289 optimal weight: 9.9990 chunk 192 optimal weight: 20.0000 chunk 343 optimal weight: 0.0570 chunk 214 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 HIS A 625 ASN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3285 HIS ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 25994 Z= 0.238 Angle : 0.787 11.945 35463 Z= 0.387 Chirality : 0.043 0.243 4286 Planarity : 0.006 0.105 4616 Dihedral : 5.660 28.321 3710 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.85 % Allowed : 10.65 % Favored : 88.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.14), residues: 3511 helix: -0.63 (0.11), residues: 2049 sheet: -2.11 (0.99), residues: 27 loop : -2.88 (0.16), residues: 1435 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 3.213 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 outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.3709 time to fit residues: 271.2220 Evaluate side-chains 324 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 3.136 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 31 optimal weight: 40.0000 chunk 269 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1866 GLN ** A1909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2141 ASN A2830 ASN ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.7354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 25994 Z= 0.256 Angle : 0.797 10.889 35463 Z= 0.396 Chirality : 0.044 0.262 4286 Planarity : 0.006 0.103 4616 Dihedral : 5.743 29.006 3710 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.91 % Favored : 88.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.14), residues: 3511 helix: -0.63 (0.11), residues: 2070 sheet: -2.28 (0.93), residues: 27 loop : -2.90 (0.16), residues: 1414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 3.556 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 outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.3710 time to fit residues: 261.1526 Evaluate side-chains 311 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 3.099 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 0.0770 chunk 328 optimal weight: 4.9990 chunk 299 optimal weight: 9.9990 chunk 319 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 251 optimal weight: 30.0000 chunk 98 optimal weight: 9.9990 chunk 288 optimal weight: 6.9990 chunk 302 optimal weight: 6.9990 chunk 318 optimal weight: 9.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 HIS A 625 ASN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2493 ASN ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.7659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 25994 Z= 0.253 Angle : 0.800 12.318 35463 Z= 0.395 Chirality : 0.044 0.245 4286 Planarity : 0.006 0.102 4616 Dihedral : 5.745 29.573 3710 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.83 % Allowed : 11.22 % Favored : 87.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.14), residues: 3511 helix: -0.60 (0.11), residues: 2086 sheet: -2.21 (1.01), residues: 29 loop : -3.00 (0.16), residues: 1396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 2.974 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 outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.3763 time to fit residues: 257.9971 Evaluate side-chains 308 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 3.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 5.9990 chunk 338 optimal weight: 0.0470 chunk 206 optimal weight: 0.0970 chunk 160 optimal weight: 7.9990 chunk 235 optimal weight: 30.0000 chunk 354 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 218 optimal weight: 0.0060 chunk 173 optimal weight: 10.0000 overall best weight: 1.8296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.7856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 25994 Z= 0.207 Angle : 0.782 12.354 35463 Z= 0.379 Chirality : 0.043 0.221 4286 Planarity : 0.005 0.099 4616 Dihedral : 5.484 28.866 3710 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.77 % Allowed : 10.03 % Favored : 89.21 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.14), residues: 3511 helix: -0.38 (0.12), residues: 2084 sheet: -2.32 (0.96), residues: 29 loop : -2.88 (0.16), residues: 1398 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7022 Ramachandran restraints generated. 3511 Oldfield, 0 Emsley, 3511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 440 time to evaluate : 3.439 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 outliers start: 1 outliers final: 0 residues processed: 441 average time/residue: 0.3575 time to fit residues: 261.2824 Evaluate side-chains 325 residues out of total 3173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 3.210 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 282 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 290 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 HIS A 625 ASN A1049 GLN ** A1909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3524 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.109462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.095949 restraints weight = 125776.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.097387 restraints weight = 91632.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.098432 restraints weight = 71353.009| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 25994 Z= 0.199 Angle : 0.766 12.537 35463 Z= 0.369 Chirality : 0.042 0.210 4286 Planarity : 0.005 0.095 4616 Dihedral : 5.208 27.230 3710 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.74 % Allowed : 9.34 % Favored : 89.92 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.14), residues: 3511 helix: -0.20 (0.12), residues: 2093 sheet: -2.17 (0.92), residues: 29 loop : -2.89 (0.16), residues: 1389 =============================================================================== Job complete usr+sys time: 5608.38 seconds wall clock time: 102 minutes 49.32 seconds (6169.32 seconds total)