Starting phenix.real_space_refine on Wed Mar 20 20:23:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sen_40422/03_2024/8sen_40422.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sen_40422/03_2024/8sen_40422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sen_40422/03_2024/8sen_40422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sen_40422/03_2024/8sen_40422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sen_40422/03_2024/8sen_40422.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sen_40422/03_2024/8sen_40422.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 960 5.16 5 C 90932 2.51 5 N 24676 2.21 5 O 26388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 4568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 1.50s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 142960 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 34921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35570 Chain: "B" Number of atoms: 34921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35570 Chain: "C" Number of atoms: 34921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35570 Chain: "D" Number of atoms: 34921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 4378, 34858 Classifications: {'peptide': 4378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4161} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35570 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34247 SG CYS A4958 175.967 201.466 87.545 1.00122.21 S ATOM 34272 SG CYS A4961 178.154 202.057 90.557 1.00125.51 S ATOM 69168 SG CYS B4958 179.718 175.966 87.518 1.00122.21 S ATOM 69193 SG CYS B4961 179.135 178.152 90.533 1.00125.51 S ATOM A035L SG CYS C4958 205.282 179.718 87.518 1.00122.21 S ATOM A036A SG CYS C4961 203.096 179.135 90.533 1.00125.51 S ATOM A0U3M SG CYS D4958 201.530 205.282 87.518 1.00122.21 S ATOM A0U4B SG CYS D4961 202.113 203.096 90.533 1.00125.51 S Time building chain proxies: 102.07, per 1000 atoms: 0.71 Number of scatterers: 142960 At special positions: 0 Unit cell: (382.536, 382.536, 215.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 960 16.00 O 26388 8.00 N 24676 7.00 C 90932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A3170 " - pdb=" SG CYS A3240 " distance=2.03 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.02 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 253 " distance=2.02 Simple disulfide: pdb=" SG CYS B3170 " - pdb=" SG CYS B3240 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.02 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 253 " distance=2.02 Simple disulfide: pdb=" SG CYS C3170 " - pdb=" SG CYS C3240 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.02 Simple disulfide: pdb=" SG CYS D 230 " - pdb=" SG CYS D 253 " distance=2.02 Simple disulfide: pdb=" SG CYS D3170 " - pdb=" SG CYS D3240 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.02 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: 42.12 Conformation dependent library (CDL) restraints added in 37.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5101 " pdb="ZN ZN A5101 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5101 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5101 " - pdb=" SG CYS A4958 " pdb="ZN ZN A5101 " - pdb=" SG CYS A4961 " pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4958 " pdb=" ZN C5101 " pdb="ZN ZN C5101 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5101 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5101 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5101 " - pdb=" SG CYS C4958 " pdb=" ZN D5101 " pdb="ZN ZN D5101 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5101 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5101 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5101 " - pdb=" SG CYS D4958 " Number of angles added : 8 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 33688 Finding SS restraints... Secondary structure from input PDB file: 804 helices and 116 sheets defined 56.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 22.70 Creating SS restraints... Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.690A pdb=" N GLN A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.942A pdb=" N LEU A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.587A pdb=" N GLY A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 452 Processing helix chain 'A' and resid 460 through 481 removed outlier: 3.598A pdb=" N SER A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 496 removed outlier: 3.958A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.858A pdb=" N TYR A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 512 through 531 removed outlier: 4.569A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 539 Processing helix chain 'A' and resid 543 through 549 removed outlier: 4.155A pdb=" N VAL A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 553 Processing helix chain 'A' and resid 556 through 571 removed outlier: 4.029A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 removed outlier: 3.918A pdb=" N LEU A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 571 through 576' Processing helix chain 'A' and resid 579 through 593 removed outlier: 3.551A pdb=" N SER A 588 " --> pdb=" O LYS A 584 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.836A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 625 Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.931A pdb=" N GLY A 798 " --> pdb=" O GLY A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 815 removed outlier: 4.094A pdb=" N VAL A 815 " --> pdb=" O HIS A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 812 through 815' Processing helix chain 'A' and resid 847 through 851 Processing helix chain 'A' and resid 864 through 869 Processing helix chain 'A' and resid 872 through 877 Processing helix chain 'A' and resid 880 through 885 removed outlier: 4.386A pdb=" N THR A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 Processing helix chain 'A' and resid 978 through 1003 removed outlier: 3.536A pdb=" N VAL A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1027 Processing helix chain 'A' and resid 1028 through 1049 removed outlier: 4.050A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1082 Processing helix chain 'A' and resid 1423 through 1428 Processing helix chain 'A' and resid 1444 through 1446 No H-bonds generated for 'chain 'A' and resid 1444 through 1446' Processing helix chain 'A' and resid 1465 through 1469 Processing helix chain 'A' and resid 1498 through 1500 No H-bonds generated for 'chain 'A' and resid 1498 through 1500' Processing helix chain 'A' and resid 1574 through 1578 Processing helix chain 'A' and resid 1580 through 1584 removed outlier: 3.720A pdb=" N ARG A1584 " --> pdb=" O LEU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1655 Processing helix chain 'A' and resid 1656 through 1674 removed outlier: 4.006A pdb=" N PHE A1662 " --> pdb=" O ASP A1658 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1689 removed outlier: 3.512A pdb=" N ALA A1684 " --> pdb=" O ARG A1680 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A1686 " --> pdb=" O ALA A1682 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER A1687 " --> pdb=" O HIS A1683 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS A1688 " --> pdb=" O ALA A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1700 Processing helix chain 'A' and resid 1704 through 1720 Processing helix chain 'A' and resid 1720 through 1731 removed outlier: 3.569A pdb=" N MET A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1744 Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.586A pdb=" N GLY A1823 " --> pdb=" O VAL A1819 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A1824 " --> pdb=" O ARG A1820 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1829 through 1832 Processing helix chain 'A' and resid 1833 through 1851 Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1855 through 1867 Processing helix chain 'A' and resid 1925 through 1929 removed outlier: 4.115A pdb=" N MET A1929 " --> pdb=" O LEU A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1932 through 1982 removed outlier: 3.915A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A1982 " --> pdb=" O ALA A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1983 through 1986 Processing helix chain 'A' and resid 1990 through 1995 removed outlier: 4.193A pdb=" N ARG A1994 " --> pdb=" O GLU A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2011 removed outlier: 3.503A pdb=" N GLN A2005 " --> pdb=" O PRO A2001 " (cutoff:3.500A) Processing helix chain 'A' and resid 2024 through 2042 Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 3.537A pdb=" N SER A2099 " --> pdb=" O GLN A2095 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2129 Processing helix chain 'A' and resid 2129 through 2136 removed outlier: 3.693A pdb=" N LEU A2134 " --> pdb=" O GLY A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2137 through 2139 No H-bonds generated for 'chain 'A' and resid 2137 through 2139' Processing helix chain 'A' and resid 2145 through 2147 No H-bonds generated for 'chain 'A' and resid 2145 through 2147' Processing helix chain 'A' and resid 2148 through 2164 removed outlier: 3.714A pdb=" N SER A2154 " --> pdb=" O GLU A2150 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2168 removed outlier: 3.671A pdb=" N VAL A2168 " --> pdb=" O LEU A2165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2165 through 2168' Processing helix chain 'A' and resid 2171 through 2188 Processing helix chain 'A' and resid 2189 through 2194 Processing helix chain 'A' and resid 2194 through 2202 Processing helix chain 'A' and resid 2202 through 2217 Processing helix chain 'A' and resid 2225 through 2241 removed outlier: 3.574A pdb=" N VAL A2229 " --> pdb=" O PHE A2225 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) Processing helix chain 'A' and resid 2243 through 2252 removed outlier: 3.636A pdb=" N ASP A2252 " --> pdb=" O ARG A2248 " (cutoff:3.500A) Processing helix chain 'A' and resid 2253 through 2261 removed outlier: 3.660A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2263 through 2267 removed outlier: 3.752A pdb=" N GLY A2266 " --> pdb=" O ILE A2263 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2280 removed outlier: 3.516A pdb=" N VAL A2275 " --> pdb=" O THR A2271 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A2276 " --> pdb=" O PRO A2272 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2290 Processing helix chain 'A' and resid 2291 through 2306 removed outlier: 3.624A pdb=" N LEU A2295 " --> pdb=" O GLN A2291 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2316 removed outlier: 3.819A pdb=" N LYS A2316 " --> pdb=" O MET A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2339 removed outlier: 3.797A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2360 Processing helix chain 'A' and resid 2361 through 2365 Processing helix chain 'A' and resid 2375 through 2389 Processing helix chain 'A' and resid 2417 through 2437 removed outlier: 3.704A pdb=" N MET A2423 " --> pdb=" O GLY A2419 " (cutoff:3.500A) Processing helix chain 'A' and resid 2439 through 2446 removed outlier: 3.552A pdb=" N ILE A2443 " --> pdb=" O GLU A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2461 Processing helix chain 'A' and resid 2462 through 2471 removed outlier: 3.617A pdb=" N LEU A2466 " --> pdb=" O PRO A2462 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2493 removed outlier: 4.044A pdb=" N SER A2493 " --> pdb=" O MET A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2495 through 2509 removed outlier: 3.898A pdb=" N LYS A2499 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A2505 " --> pdb=" O SER A2501 " (cutoff:3.500A) Processing helix chain 'A' and resid 2514 through 2526 removed outlier: 3.927A pdb=" N VAL A2524 " --> pdb=" O HIS A2520 " (cutoff:3.500A) Processing helix chain 'A' and resid 2526 through 2537 Processing helix chain 'A' and resid 2544 through 2558 Processing helix chain 'A' and resid 2558 through 2565 Processing helix chain 'A' and resid 2566 through 2570 Processing helix chain 'A' and resid 2572 through 2574 No H-bonds generated for 'chain 'A' and resid 2572 through 2574' Processing helix chain 'A' and resid 2575 through 2591 Processing helix chain 'A' and resid 2596 through 2614 removed outlier: 3.681A pdb=" N VAL A2602 " --> pdb=" O ALA A2598 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A2603 " --> pdb=" O GLN A2599 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A2613 " --> pdb=" O ALA A2609 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2618 Processing helix chain 'A' and resid 2619 through 2633 removed outlier: 4.073A pdb=" N PHE A2628 " --> pdb=" O ARG A2624 " (cutoff:3.500A) Proline residue: A2631 - end of helix Processing helix chain 'A' and resid 2637 through 2651 removed outlier: 3.681A pdb=" N LEU A2641 " --> pdb=" O ALA A2637 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A2642 " --> pdb=" O LYS A2638 " (cutoff:3.500A) Processing helix chain 'A' and resid 2651 through 2657 removed outlier: 3.546A pdb=" N TYR A2655 " --> pdb=" O CYS A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2670 through 2689 Processing helix chain 'A' and resid 2692 through 2710 removed outlier: 3.678A pdb=" N MET A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) Proline residue: A2701 - end of helix Processing helix chain 'A' and resid 2751 through 2772 removed outlier: 3.904A pdb=" N LYS A2757 " --> pdb=" O SER A2753 " (cutoff:3.500A) Processing helix chain 'A' and resid 2782 through 2786 removed outlier: 4.083A pdb=" N LEU A2785 " --> pdb=" O ASP A2782 " (cutoff:3.500A) Processing helix chain 'A' and resid 2793 through 2797 removed outlier: 3.756A pdb=" N PHE A2797 " --> pdb=" O TYR A2794 " (cutoff:3.500A) Processing helix chain 'A' and resid 2806 through 2819 removed outlier: 3.612A pdb=" N ILE A2817 " --> pdb=" O LEU A2813 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP A2819 " --> pdb=" O ALA A2815 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2895 removed outlier: 3.648A pdb=" N GLU A2893 " --> pdb=" O LYS A2889 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2934 removed outlier: 3.747A pdb=" N ALA A2917 " --> pdb=" O ALA A2913 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A2918 " --> pdb=" O LYS A2914 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A2922 " --> pdb=" O ARG A2918 " (cutoff:3.500A) Processing helix chain 'A' and resid 2949 through 2954 Processing helix chain 'A' and resid 2954 through 2983 removed outlier: 3.642A pdb=" N GLN A2962 " --> pdb=" O GLY A2958 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A2969 " --> pdb=" O ARG A2965 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A2975 " --> pdb=" O GLN A2971 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS A2976 " --> pdb=" O GLU A2972 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A2982 " --> pdb=" O GLU A2978 " (cutoff:3.500A) Processing helix chain 'A' and resid 2991 through 3013 removed outlier: 4.566A pdb=" N LEU A3003 " --> pdb=" O ALA A2999 " (cutoff:3.500A) Proline residue: A3004 - end of helix Processing helix chain 'A' and resid 3013 through 3019 removed outlier: 3.541A pdb=" N PHE A3017 " --> pdb=" O HIS A3013 " (cutoff:3.500A) Processing helix chain 'A' and resid 3032 through 3051 Processing helix chain 'A' and resid 3053 through 3058 removed outlier: 3.656A pdb=" N PHE A3057 " --> pdb=" O ARG A3053 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A3058 " --> pdb=" O VAL A3054 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3053 through 3058' Processing helix chain 'A' and resid 3060 through 3074 Processing helix chain 'A' and resid 3076 through 3083 Processing helix chain 'A' and resid 3085 through 3111 Processing helix chain 'A' and resid 3124 through 3135 removed outlier: 3.634A pdb=" N VAL A3134 " --> pdb=" O THR A3130 " (cutoff:3.500A) Processing helix chain 'A' and resid 3135 through 3151 Processing helix chain 'A' and resid 3152 through 3157 Processing helix chain 'A' and resid 3160 through 3174 Processing helix chain 'A' and resid 3175 through 3178 Processing helix chain 'A' and resid 3180 through 3201 Proline residue: A3188 - end of helix Processing helix chain 'A' and resid 3207 through 3214 removed outlier: 5.011A pdb=" N GLU A3212 " --> pdb=" O GLN A3209 " (cutoff:3.500A) Processing helix chain 'A' and resid 3217 through 3222 Processing helix chain 'A' and resid 3235 through 3239 Processing helix chain 'A' and resid 3245 through 3260 removed outlier: 3.559A pdb=" N GLU A3258 " --> pdb=" O GLY A3254 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A3260 " --> pdb=" O LEU A3256 " (cutoff:3.500A) Processing helix chain 'A' and resid 3266 through 3272 Processing helix chain 'A' and resid 3272 through 3286 removed outlier: 4.266A pdb=" N MET A3276 " --> pdb=" O ILE A3272 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A3277 " --> pdb=" O THR A3273 " (cutoff:3.500A) Proline residue: A3282 - end of helix removed outlier: 4.382A pdb=" N GLU A3286 " --> pdb=" O PRO A3282 " (cutoff:3.500A) Processing helix chain 'A' and resid 3308 through 3326 removed outlier: 3.789A pdb=" N LEU A3312 " --> pdb=" O THR A3308 " (cutoff:3.500A) Processing helix chain 'A' and resid 3333 through 3343 removed outlier: 4.462A pdb=" N ARG A3337 " --> pdb=" O THR A3333 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A3343 " --> pdb=" O ALA A3339 " (cutoff:3.500A) Processing helix chain 'A' and resid 3344 through 3350 removed outlier: 3.886A pdb=" N SER A3347 " --> pdb=" O PRO A3344 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG A3350 " --> pdb=" O SER A3347 " (cutoff:3.500A) Processing helix chain 'A' and resid 3351 through 3357 removed outlier: 4.332A pdb=" N HIS A3355 " --> pdb=" O PRO A3351 " (cutoff:3.500A) Processing helix chain 'A' and resid 3357 through 3382 removed outlier: 3.729A pdb=" N GLU A3382 " --> pdb=" O GLN A3378 " (cutoff:3.500A) Processing helix chain 'A' and resid 3390 through 3426 Proline residue: A3410 - end of helix removed outlier: 4.938A pdb=" N ALA A3421 " --> pdb=" O ASP A3417 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS A3422 " --> pdb=" O ASN A3418 " (cutoff:3.500A) Processing helix chain 'A' and resid 3428 through 3448 Processing helix chain 'A' and resid 3448 through 3463 removed outlier: 3.671A pdb=" N GLN A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A3457 " --> pdb=" O ARG A3453 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A3459 " --> pdb=" O GLU A3455 " (cutoff:3.500A) Processing helix chain 'A' and resid 3467 through 3477 removed outlier: 3.575A pdb=" N THR A3471 " --> pdb=" O MET A3467 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP A3473 " --> pdb=" O PHE A3469 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER A3474 " --> pdb=" O LEU A3470 " (cutoff:3.500A) Processing helix chain 'A' and resid 3504 through 3507 Processing helix chain 'A' and resid 3508 through 3525 Proline residue: A3519 - end of helix removed outlier: 3.741A pdb=" N MET A3524 " --> pdb=" O ILE A3520 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS A3525 " --> pdb=" O GLY A3521 " (cutoff:3.500A) Processing helix chain 'A' and resid 3526 through 3528 No H-bonds generated for 'chain 'A' and resid 3526 through 3528' Processing helix chain 'A' and resid 3529 through 3542 removed outlier: 3.583A pdb=" N MET A3534 " --> pdb=" O GLN A3530 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A3535 " --> pdb=" O ASP A3531 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3556 Processing helix chain 'A' and resid 3557 through 3560 removed outlier: 3.721A pdb=" N GLN A3560 " --> pdb=" O LEU A3557 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3557 through 3560' Processing helix chain 'A' and resid 3566 through 3578 removed outlier: 3.758A pdb=" N TRP A3571 " --> pdb=" O PRO A3567 " (cutoff:3.500A) Processing helix chain 'A' and resid 3588 through 3611 Processing helix chain 'A' and resid 3624 through 3638 removed outlier: 3.525A pdb=" N ARG A3629 " --> pdb=" O SER A3625 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA A3631 " --> pdb=" O GLN A3627 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A3632 " --> pdb=" O ARG A3628 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A3633 " --> pdb=" O ARG A3629 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE A3636 " --> pdb=" O VAL A3632 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG A3637 " --> pdb=" O VAL A3633 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3644 Processing helix chain 'A' and resid 3645 through 3662 Processing helix chain 'A' and resid 3669 through 3678 removed outlier: 3.664A pdb=" N ASP A3676 " --> pdb=" O ARG A3672 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3711 Processing helix chain 'A' and resid 3719 through 3732 Processing helix chain 'A' and resid 3752 through 3772 removed outlier: 3.541A pdb=" N MET A3758 " --> pdb=" O GLU A3754 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A3759 " --> pdb=" O GLU A3755 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A3760 " --> pdb=" O LYS A3756 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A3765 " --> pdb=" O GLN A3761 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A3770 " --> pdb=" O GLN A3766 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A3772 " --> pdb=" O SER A3768 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3786 removed outlier: 3.522A pdb=" N LEU A3780 " --> pdb=" O ALA A3776 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3804 Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3826 through 3838 Processing helix chain 'A' and resid 3843 through 3857 Processing helix chain 'A' and resid 3877 through 3893 Processing helix chain 'A' and resid 3896 through 3905 removed outlier: 3.687A pdb=" N TYR A3902 " --> pdb=" O ASP A3898 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3937 removed outlier: 3.516A pdb=" N TRP A3935 " --> pdb=" O SER A3931 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR A3936 " --> pdb=" O ASP A3932 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A3937 " --> pdb=" O PHE A3933 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 3.738A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3983 Processing helix chain 'A' and resid 3984 through 4004 removed outlier: 3.723A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) Processing helix chain 'A' and resid 4006 through 4008 No H-bonds generated for 'chain 'A' and resid 4006 through 4008' Processing helix chain 'A' and resid 4009 through 4031 removed outlier: 3.552A pdb=" N LEU A4019 " --> pdb=" O GLU A4015 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4051 Processing helix chain 'A' and resid 4051 through 4072 removed outlier: 3.625A pdb=" N PHE A4065 " --> pdb=" O PHE A4061 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A4068 " --> pdb=" O MET A4064 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A4070 " --> pdb=" O LEU A4066 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4081 Processing helix chain 'A' and resid 4090 through 4098 removed outlier: 3.711A pdb=" N ASP A4098 " --> pdb=" O GLN A4094 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4104 through 4115 Processing helix chain 'A' and resid 4124 through 4129 removed outlier: 3.615A pdb=" N PHE A4128 " --> pdb=" O ASN A4124 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A4129 " --> pdb=" O PHE A4125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4124 through 4129' Processing helix chain 'A' and resid 4132 through 4154 removed outlier: 4.098A pdb=" N ASP A4138 " --> pdb=" O GLU A4134 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4157 through 4167 removed outlier: 3.842A pdb=" N PHE A4163 " --> pdb=" O ARG A4159 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A4164 " --> pdb=" O LEU A4160 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A4165 " --> pdb=" O ARG A4161 " (cutoff:3.500A) Processing helix chain 'A' and resid 4167 through 4175 Processing helix chain 'A' and resid 4198 through 4206 Processing helix chain 'A' and resid 4207 through 4224 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4541 through 4558 Processing helix chain 'A' and resid 4558 through 4578 Processing helix chain 'A' and resid 4638 through 4665 removed outlier: 3.699A pdb=" N TRP A4644 " --> pdb=" O GLU A4640 " (cutoff:3.500A) Processing helix chain 'A' and resid 4665 through 4685 removed outlier: 3.729A pdb=" N VAL A4669 " --> pdb=" O LYS A4665 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A4685 " --> pdb=" O LEU A4681 " (cutoff:3.500A) Processing helix chain 'A' and resid 4696 through 4703 Processing helix chain 'A' and resid 4704 through 4706 No H-bonds generated for 'chain 'A' and resid 4704 through 4706' Processing helix chain 'A' and resid 4719 through 4733 removed outlier: 4.712A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4741 Processing helix chain 'A' and resid 4773 through 4785 Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 3.752A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4809 removed outlier: 3.684A pdb=" N PHE A4809 " --> pdb=" O ASN A4806 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4806 through 4809' Processing helix chain 'A' and resid 4812 through 4814 No H-bonds generated for 'chain 'A' and resid 4812 through 4814' Processing helix chain 'A' and resid 4815 through 4820 Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.521A pdb=" N ARG A4824 " --> pdb=" O VAL A4820 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4859 removed outlier: 3.933A pdb=" N ALA A4845 " --> pdb=" O VAL A4841 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A4846 " --> pdb=" O GLY A4842 " (cutoff:3.500A) Processing helix chain 'A' and resid 4860 through 4863 removed outlier: 3.686A pdb=" N TYR A4863 " --> pdb=" O ARG A4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4860 through 4863' Processing helix chain 'A' and resid 4878 through 4890 Processing helix chain 'A' and resid 4896 through 4901 removed outlier: 4.227A pdb=" N GLU A4900 " --> pdb=" O GLY A4896 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4926 through 4957 removed outlier: 3.957A pdb=" N ILE A4936 " --> pdb=" O ILE A4932 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 3.967A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4998 Processing helix chain 'A' and resid 4999 through 5003 Processing helix chain 'A' and resid 5004 through 5016 Processing helix chain 'A' and resid 5027 through 5032 Processing helix chain 'A' and resid 5032 through 5037 Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.690A pdb=" N GLN B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.942A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 421 removed outlier: 3.587A pdb=" N GLY B 409 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 Processing helix chain 'B' and resid 460 through 481 removed outlier: 3.599A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 496 removed outlier: 3.959A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 508 removed outlier: 3.858A pdb=" N TYR B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 511 No H-bonds generated for 'chain 'B' and resid 509 through 511' Processing helix chain 'B' and resid 512 through 531 removed outlier: 4.569A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 Processing helix chain 'B' and resid 543 through 549 removed outlier: 4.154A pdb=" N VAL B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 553 Processing helix chain 'B' and resid 556 through 571 removed outlier: 4.029A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 removed outlier: 3.919A pdb=" N LEU B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 576 " --> pdb=" O PRO B 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 571 through 576' Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.552A pdb=" N SER B 588 " --> pdb=" O LYS B 584 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 607 removed outlier: 3.836A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 Processing helix chain 'B' and resid 794 through 798 removed outlier: 3.931A pdb=" N GLY B 798 " --> pdb=" O GLY B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 815 removed outlier: 4.094A pdb=" N VAL B 815 " --> pdb=" O HIS B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 812 through 815' Processing helix chain 'B' and resid 847 through 851 Processing helix chain 'B' and resid 864 through 869 Processing helix chain 'B' and resid 872 through 877 Processing helix chain 'B' and resid 880 through 885 removed outlier: 4.385A pdb=" N THR B 885 " --> pdb=" O LEU B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 Processing helix chain 'B' and resid 978 through 1003 removed outlier: 3.536A pdb=" N VAL B 995 " --> pdb=" O ASN B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1027 Processing helix chain 'B' and resid 1028 through 1049 removed outlier: 4.050A pdb=" N SER B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR B1049 " --> pdb=" O THR B1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1082 Processing helix chain 'B' and resid 1423 through 1428 Processing helix chain 'B' and resid 1444 through 1446 No H-bonds generated for 'chain 'B' and resid 1444 through 1446' Processing helix chain 'B' and resid 1465 through 1469 Processing helix chain 'B' and resid 1498 through 1500 No H-bonds generated for 'chain 'B' and resid 1498 through 1500' Processing helix chain 'B' and resid 1574 through 1578 Processing helix chain 'B' and resid 1580 through 1584 removed outlier: 3.719A pdb=" N ARG B1584 " --> pdb=" O LEU B1581 " (cutoff:3.500A) Processing helix chain 'B' and resid 1651 through 1655 Processing helix chain 'B' and resid 1656 through 1674 removed outlier: 4.006A pdb=" N PHE B1662 " --> pdb=" O ASP B1658 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1689 removed outlier: 3.511A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B1686 " --> pdb=" O ALA B1682 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER B1687 " --> pdb=" O HIS B1683 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS B1688 " --> pdb=" O ALA B1684 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1700 Processing helix chain 'B' and resid 1704 through 1720 Processing helix chain 'B' and resid 1720 through 1731 removed outlier: 3.568A pdb=" N MET B1730 " --> pdb=" O SER B1726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1744 Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.586A pdb=" N GLY B1823 " --> pdb=" O VAL B1819 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B1824 " --> pdb=" O ARG B1820 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS B1825 " --> pdb=" O ASP B1821 " (cutoff:3.500A) Processing helix chain 'B' and resid 1829 through 1832 Processing helix chain 'B' and resid 1833 through 1851 Proline residue: B1840 - end of helix Processing helix chain 'B' and resid 1855 through 1867 Processing helix chain 'B' and resid 1925 through 1929 removed outlier: 4.115A pdb=" N MET B1929 " --> pdb=" O LEU B1926 " (cutoff:3.500A) Processing helix chain 'B' and resid 1932 through 1982 removed outlier: 3.915A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP B1967 " --> pdb=" O GLU B1963 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG B1982 " --> pdb=" O ALA B1978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1983 through 1986 Processing helix chain 'B' and resid 1990 through 1995 removed outlier: 4.192A pdb=" N ARG B1994 " --> pdb=" O GLU B1990 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2011 removed outlier: 3.503A pdb=" N GLN B2005 " --> pdb=" O PRO B2001 " (cutoff:3.500A) Processing helix chain 'B' and resid 2024 through 2042 Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 3.538A pdb=" N SER B2099 " --> pdb=" O GLN B2095 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2129 Processing helix chain 'B' and resid 2129 through 2136 removed outlier: 3.694A pdb=" N LEU B2134 " --> pdb=" O GLY B2130 " (cutoff:3.500A) Processing helix chain 'B' and resid 2137 through 2139 No H-bonds generated for 'chain 'B' and resid 2137 through 2139' Processing helix chain 'B' and resid 2145 through 2147 No H-bonds generated for 'chain 'B' and resid 2145 through 2147' Processing helix chain 'B' and resid 2148 through 2164 removed outlier: 3.715A pdb=" N SER B2154 " --> pdb=" O GLU B2150 " (cutoff:3.500A) Processing helix chain 'B' and resid 2165 through 2168 removed outlier: 3.671A pdb=" N VAL B2168 " --> pdb=" O LEU B2165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2165 through 2168' Processing helix chain 'B' and resid 2171 through 2188 Processing helix chain 'B' and resid 2189 through 2194 Processing helix chain 'B' and resid 2194 through 2202 Processing helix chain 'B' and resid 2202 through 2217 Processing helix chain 'B' and resid 2225 through 2241 removed outlier: 3.574A pdb=" N VAL B2229 " --> pdb=" O PHE B2225 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B2231 " --> pdb=" O LYS B2227 " (cutoff:3.500A) Processing helix chain 'B' and resid 2243 through 2252 removed outlier: 3.636A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2253 through 2261 removed outlier: 3.661A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) Processing helix chain 'B' and resid 2263 through 2267 removed outlier: 3.752A pdb=" N GLY B2266 " --> pdb=" O ILE B2263 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2280 removed outlier: 3.516A pdb=" N VAL B2275 " --> pdb=" O THR B2271 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B2276 " --> pdb=" O PRO B2272 " (cutoff:3.500A) Processing helix chain 'B' and resid 2283 through 2290 Processing helix chain 'B' and resid 2291 through 2306 removed outlier: 3.623A pdb=" N LEU B2295 " --> pdb=" O GLN B2291 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2316 removed outlier: 3.819A pdb=" N LYS B2316 " --> pdb=" O MET B2312 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2339 removed outlier: 3.797A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2360 Processing helix chain 'B' and resid 2361 through 2365 Processing helix chain 'B' and resid 2375 through 2389 Processing helix chain 'B' and resid 2417 through 2437 removed outlier: 3.703A pdb=" N MET B2423 " --> pdb=" O GLY B2419 " (cutoff:3.500A) Processing helix chain 'B' and resid 2439 through 2446 removed outlier: 3.550A pdb=" N ILE B2443 " --> pdb=" O GLU B2439 " (cutoff:3.500A) Processing helix chain 'B' and resid 2447 through 2461 Processing helix chain 'B' and resid 2462 through 2471 removed outlier: 3.617A pdb=" N LEU B2466 " --> pdb=" O PRO B2462 " (cutoff:3.500A) Processing helix chain 'B' and resid 2489 through 2493 removed outlier: 4.044A pdb=" N SER B2493 " --> pdb=" O MET B2490 " (cutoff:3.500A) Processing helix chain 'B' and resid 2495 through 2509 removed outlier: 3.899A pdb=" N LYS B2499 " --> pdb=" O VAL B2495 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B2505 " --> pdb=" O SER B2501 " (cutoff:3.500A) Processing helix chain 'B' and resid 2514 through 2526 removed outlier: 3.927A pdb=" N VAL B2524 " --> pdb=" O HIS B2520 " (cutoff:3.500A) Processing helix chain 'B' and resid 2526 through 2537 Processing helix chain 'B' and resid 2544 through 2558 Processing helix chain 'B' and resid 2558 through 2565 Processing helix chain 'B' and resid 2566 through 2570 Processing helix chain 'B' and resid 2572 through 2574 No H-bonds generated for 'chain 'B' and resid 2572 through 2574' Processing helix chain 'B' and resid 2575 through 2591 Processing helix chain 'B' and resid 2596 through 2614 removed outlier: 3.680A pdb=" N VAL B2602 " --> pdb=" O ALA B2598 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B2603 " --> pdb=" O GLN B2599 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B2613 " --> pdb=" O ALA B2609 " (cutoff:3.500A) Processing helix chain 'B' and resid 2615 through 2618 Processing helix chain 'B' and resid 2619 through 2633 removed outlier: 4.073A pdb=" N PHE B2628 " --> pdb=" O ARG B2624 " (cutoff:3.500A) Proline residue: B2631 - end of helix Processing helix chain 'B' and resid 2637 through 2651 removed outlier: 3.681A pdb=" N LEU B2641 " --> pdb=" O ALA B2637 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B2642 " --> pdb=" O LYS B2638 " (cutoff:3.500A) Processing helix chain 'B' and resid 2651 through 2657 removed outlier: 3.546A pdb=" N TYR B2655 " --> pdb=" O CYS B2651 " (cutoff:3.500A) Processing helix chain 'B' and resid 2670 through 2689 Processing helix chain 'B' and resid 2692 through 2710 removed outlier: 3.678A pdb=" N MET B2698 " --> pdb=" O GLU B2694 " (cutoff:3.500A) Proline residue: B2701 - end of helix Processing helix chain 'B' and resid 2751 through 2772 removed outlier: 3.904A pdb=" N LYS B2757 " --> pdb=" O SER B2753 " (cutoff:3.500A) Processing helix chain 'B' and resid 2782 through 2786 removed outlier: 4.083A pdb=" N LEU B2785 " --> pdb=" O ASP B2782 " (cutoff:3.500A) Processing helix chain 'B' and resid 2793 through 2797 removed outlier: 3.757A pdb=" N PHE B2797 " --> pdb=" O TYR B2794 " (cutoff:3.500A) Processing helix chain 'B' and resid 2806 through 2819 removed outlier: 3.613A pdb=" N ILE B2817 " --> pdb=" O LEU B2813 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TRP B2819 " --> pdb=" O ALA B2815 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 3.647A pdb=" N GLU B2893 " --> pdb=" O LYS B2889 " (cutoff:3.500A) Processing helix chain 'B' and resid 2912 through 2934 removed outlier: 3.746A pdb=" N ALA B2917 " --> pdb=" O ALA B2913 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG B2918 " --> pdb=" O LYS B2914 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B2922 " --> pdb=" O ARG B2918 " (cutoff:3.500A) Processing helix chain 'B' and resid 2949 through 2954 Processing helix chain 'B' and resid 2954 through 2983 removed outlier: 3.642A pdb=" N GLN B2962 " --> pdb=" O GLY B2958 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B2969 " --> pdb=" O ARG B2965 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B2975 " --> pdb=" O GLN B2971 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS B2976 " --> pdb=" O GLU B2972 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B2982 " --> pdb=" O GLU B2978 " (cutoff:3.500A) Processing helix chain 'B' and resid 2991 through 3013 removed outlier: 4.567A pdb=" N LEU B3003 " --> pdb=" O ALA B2999 " (cutoff:3.500A) Proline residue: B3004 - end of helix Processing helix chain 'B' and resid 3013 through 3019 removed outlier: 3.540A pdb=" N PHE B3017 " --> pdb=" O HIS B3013 " (cutoff:3.500A) Processing helix chain 'B' and resid 3032 through 3051 Processing helix chain 'B' and resid 3053 through 3058 removed outlier: 3.657A pdb=" N PHE B3057 " --> pdb=" O ARG B3053 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B3058 " --> pdb=" O VAL B3054 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3053 through 3058' Processing helix chain 'B' and resid 3060 through 3074 Processing helix chain 'B' and resid 3076 through 3083 Processing helix chain 'B' and resid 3085 through 3111 Processing helix chain 'B' and resid 3124 through 3135 removed outlier: 3.634A pdb=" N VAL B3134 " --> pdb=" O THR B3130 " (cutoff:3.500A) Processing helix chain 'B' and resid 3135 through 3151 Processing helix chain 'B' and resid 3152 through 3157 Processing helix chain 'B' and resid 3160 through 3174 Processing helix chain 'B' and resid 3175 through 3178 Processing helix chain 'B' and resid 3180 through 3201 Proline residue: B3188 - end of helix Processing helix chain 'B' and resid 3207 through 3214 removed outlier: 5.011A pdb=" N GLU B3212 " --> pdb=" O GLN B3209 " (cutoff:3.500A) Processing helix chain 'B' and resid 3217 through 3222 Processing helix chain 'B' and resid 3235 through 3239 Processing helix chain 'B' and resid 3245 through 3260 removed outlier: 3.559A pdb=" N GLU B3258 " --> pdb=" O GLY B3254 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B3260 " --> pdb=" O LEU B3256 " (cutoff:3.500A) Processing helix chain 'B' and resid 3266 through 3272 Processing helix chain 'B' and resid 3272 through 3286 removed outlier: 4.266A pdb=" N MET B3276 " --> pdb=" O ILE B3272 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B3277 " --> pdb=" O THR B3273 " (cutoff:3.500A) Proline residue: B3282 - end of helix removed outlier: 4.382A pdb=" N GLU B3286 " --> pdb=" O PRO B3282 " (cutoff:3.500A) Processing helix chain 'B' and resid 3308 through 3326 removed outlier: 3.789A pdb=" N LEU B3312 " --> pdb=" O THR B3308 " (cutoff:3.500A) Processing helix chain 'B' and resid 3333 through 3343 removed outlier: 4.462A pdb=" N ARG B3337 " --> pdb=" O THR B3333 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B3343 " --> pdb=" O ALA B3339 " (cutoff:3.500A) Processing helix chain 'B' and resid 3344 through 3350 removed outlier: 3.886A pdb=" N SER B3347 " --> pdb=" O PRO B3344 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG B3350 " --> pdb=" O SER B3347 " (cutoff:3.500A) Processing helix chain 'B' and resid 3351 through 3357 removed outlier: 4.332A pdb=" N HIS B3355 " --> pdb=" O PRO B3351 " (cutoff:3.500A) Processing helix chain 'B' and resid 3357 through 3382 removed outlier: 3.729A pdb=" N GLU B3382 " --> pdb=" O GLN B3378 " (cutoff:3.500A) Processing helix chain 'B' and resid 3390 through 3426 Proline residue: B3410 - end of helix removed outlier: 4.939A pdb=" N ALA B3421 " --> pdb=" O ASP B3417 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS B3422 " --> pdb=" O ASN B3418 " (cutoff:3.500A) Processing helix chain 'B' and resid 3428 through 3448 Processing helix chain 'B' and resid 3448 through 3463 removed outlier: 3.670A pdb=" N GLN B3456 " --> pdb=" O LYS B3452 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B3457 " --> pdb=" O ARG B3453 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B3459 " --> pdb=" O GLU B3455 " (cutoff:3.500A) Processing helix chain 'B' and resid 3467 through 3477 removed outlier: 3.575A pdb=" N THR B3471 " --> pdb=" O MET B3467 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP B3473 " --> pdb=" O PHE B3469 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER B3474 " --> pdb=" O LEU B3470 " (cutoff:3.500A) Processing helix chain 'B' and resid 3504 through 3507 Processing helix chain 'B' and resid 3508 through 3525 Proline residue: B3519 - end of helix removed outlier: 3.741A pdb=" N MET B3524 " --> pdb=" O ILE B3520 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS B3525 " --> pdb=" O GLY B3521 " (cutoff:3.500A) Processing helix chain 'B' and resid 3526 through 3528 No H-bonds generated for 'chain 'B' and resid 3526 through 3528' Processing helix chain 'B' and resid 3529 through 3542 removed outlier: 3.583A pdb=" N MET B3534 " --> pdb=" O GLN B3530 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B3535 " --> pdb=" O ASP B3531 " (cutoff:3.500A) Processing helix chain 'B' and resid 3545 through 3556 Processing helix chain 'B' and resid 3557 through 3560 removed outlier: 3.722A pdb=" N GLN B3560 " --> pdb=" O LEU B3557 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3557 through 3560' Processing helix chain 'B' and resid 3566 through 3578 removed outlier: 3.758A pdb=" N TRP B3571 " --> pdb=" O PRO B3567 " (cutoff:3.500A) Processing helix chain 'B' and resid 3588 through 3611 Processing helix chain 'B' and resid 3624 through 3638 removed outlier: 3.525A pdb=" N ARG B3629 " --> pdb=" O SER B3625 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B3631 " --> pdb=" O GLN B3627 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B3632 " --> pdb=" O ARG B3628 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B3633 " --> pdb=" O ARG B3629 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE B3636 " --> pdb=" O VAL B3632 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG B3637 " --> pdb=" O VAL B3633 " (cutoff:3.500A) Processing helix chain 'B' and resid 3640 through 3644 Processing helix chain 'B' and resid 3645 through 3662 Processing helix chain 'B' and resid 3669 through 3678 removed outlier: 3.664A pdb=" N ASP B3676 " --> pdb=" O ARG B3672 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3711 Processing helix chain 'B' and resid 3719 through 3732 Processing helix chain 'B' and resid 3752 through 3772 removed outlier: 3.542A pdb=" N MET B3758 " --> pdb=" O GLU B3754 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B3759 " --> pdb=" O GLU B3755 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B3760 " --> pdb=" O LYS B3756 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR B3765 " --> pdb=" O GLN B3761 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU B3770 " --> pdb=" O GLN B3766 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B3772 " --> pdb=" O SER B3768 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3786 removed outlier: 3.521A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3804 Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3826 through 3838 Processing helix chain 'B' and resid 3843 through 3857 Processing helix chain 'B' and resid 3877 through 3893 Processing helix chain 'B' and resid 3896 through 3905 removed outlier: 3.687A pdb=" N TYR B3902 " --> pdb=" O ASP B3898 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3937 removed outlier: 3.517A pdb=" N TRP B3935 " --> pdb=" O SER B3931 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR B3936 " --> pdb=" O ASP B3932 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 removed outlier: 3.738A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3983 Processing helix chain 'B' and resid 3984 through 4004 removed outlier: 3.722A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) Processing helix chain 'B' and resid 4006 through 4008 No H-bonds generated for 'chain 'B' and resid 4006 through 4008' Processing helix chain 'B' and resid 4009 through 4031 removed outlier: 3.551A pdb=" N LEU B4019 " --> pdb=" O GLU B4015 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4051 Processing helix chain 'B' and resid 4051 through 4072 removed outlier: 3.625A pdb=" N PHE B4065 " --> pdb=" O PHE B4061 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B4068 " --> pdb=" O MET B4064 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4081 Processing helix chain 'B' and resid 4090 through 4098 removed outlier: 3.711A pdb=" N ASP B4098 " --> pdb=" O GLN B4094 " (cutoff:3.500A) Processing helix chain 'B' and resid 4099 through 4101 No H-bonds generated for 'chain 'B' and resid 4099 through 4101' Processing helix chain 'B' and resid 4104 through 4115 Processing helix chain 'B' and resid 4124 through 4129 removed outlier: 3.615A pdb=" N PHE B4128 " --> pdb=" O ASN B4124 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA B4129 " --> pdb=" O PHE B4125 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4124 through 4129' Processing helix chain 'B' and resid 4132 through 4154 removed outlier: 4.097A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) Processing helix chain 'B' and resid 4157 through 4167 removed outlier: 3.842A pdb=" N PHE B4163 " --> pdb=" O ARG B4159 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B4164 " --> pdb=" O LEU B4160 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B4165 " --> pdb=" O ARG B4161 " (cutoff:3.500A) Processing helix chain 'B' and resid 4167 through 4175 Processing helix chain 'B' and resid 4198 through 4206 Processing helix chain 'B' and resid 4207 through 4224 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4541 through 4558 Processing helix chain 'B' and resid 4558 through 4578 Processing helix chain 'B' and resid 4638 through 4665 removed outlier: 3.699A pdb=" N TRP B4644 " --> pdb=" O GLU B4640 " (cutoff:3.500A) Processing helix chain 'B' and resid 4665 through 4685 removed outlier: 3.729A pdb=" N VAL B4669 " --> pdb=" O LYS B4665 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B4685 " --> pdb=" O LEU B4681 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4703 Processing helix chain 'B' and resid 4704 through 4706 No H-bonds generated for 'chain 'B' and resid 4704 through 4706' Processing helix chain 'B' and resid 4719 through 4733 removed outlier: 4.712A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4741 Processing helix chain 'B' and resid 4773 through 4785 Processing helix chain 'B' and resid 4786 through 4805 removed outlier: 3.751A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4809 removed outlier: 3.683A pdb=" N PHE B4809 " --> pdb=" O ASN B4806 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4806 through 4809' Processing helix chain 'B' and resid 4812 through 4814 No H-bonds generated for 'chain 'B' and resid 4812 through 4814' Processing helix chain 'B' and resid 4815 through 4820 Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.521A pdb=" N ARG B4824 " --> pdb=" O VAL B4820 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4859 removed outlier: 3.933A pdb=" N ALA B4845 " --> pdb=" O VAL B4841 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B4846 " --> pdb=" O GLY B4842 " (cutoff:3.500A) Processing helix chain 'B' and resid 4860 through 4863 removed outlier: 3.686A pdb=" N TYR B4863 " --> pdb=" O ARG B4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4860 through 4863' Processing helix chain 'B' and resid 4878 through 4890 Processing helix chain 'B' and resid 4896 through 4901 removed outlier: 4.226A pdb=" N GLU B4900 " --> pdb=" O GLY B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4924 Processing helix chain 'B' and resid 4926 through 4957 removed outlier: 3.957A pdb=" N ILE B4936 " --> pdb=" O ILE B4932 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 3.966A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4984 through 4998 Processing helix chain 'B' and resid 4999 through 5003 Processing helix chain 'B' and resid 5004 through 5016 Processing helix chain 'B' and resid 5027 through 5032 Processing helix chain 'B' and resid 5032 through 5037 Processing helix chain 'C' and resid 75 through 84 removed outlier: 3.690A pdb=" N GLN C 79 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.942A pdb=" N LEU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 421 removed outlier: 3.587A pdb=" N GLY C 409 " --> pdb=" O HIS C 405 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 452 Processing helix chain 'C' and resid 460 through 481 removed outlier: 3.599A pdb=" N SER C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 496 removed outlier: 3.959A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.858A pdb=" N TYR C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 511 No H-bonds generated for 'chain 'C' and resid 509 through 511' Processing helix chain 'C' and resid 512 through 531 removed outlier: 4.568A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 539 Processing helix chain 'C' and resid 543 through 549 removed outlier: 4.154A pdb=" N VAL C 547 " --> pdb=" O ASN C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 553 Processing helix chain 'C' and resid 556 through 571 removed outlier: 4.029A pdb=" N ILE C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 576 removed outlier: 3.919A pdb=" N LEU C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 571 through 576' Processing helix chain 'C' and resid 579 through 593 removed outlier: 3.552A pdb=" N SER C 588 " --> pdb=" O LYS C 584 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 590 " --> pdb=" O ILE C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 607 removed outlier: 3.837A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 625 Processing helix chain 'C' and resid 794 through 798 removed outlier: 3.931A pdb=" N GLY C 798 " --> pdb=" O GLY C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 815 removed outlier: 4.094A pdb=" N VAL C 815 " --> pdb=" O HIS C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 812 through 815' Processing helix chain 'C' and resid 847 through 851 Processing helix chain 'C' and resid 864 through 869 Processing helix chain 'C' and resid 872 through 877 Processing helix chain 'C' and resid 880 through 885 removed outlier: 4.385A pdb=" N THR C 885 " --> pdb=" O LEU C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 936 Processing helix chain 'C' and resid 978 through 1003 removed outlier: 3.537A pdb=" N VAL C 995 " --> pdb=" O ASN C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1027 Processing helix chain 'C' and resid 1028 through 1049 removed outlier: 4.050A pdb=" N SER C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR C1049 " --> pdb=" O THR C1045 " (cutoff:3.500A) Processing helix chain 'C' and resid 1079 through 1082 Processing helix chain 'C' and resid 1423 through 1428 Processing helix chain 'C' and resid 1444 through 1446 No H-bonds generated for 'chain 'C' and resid 1444 through 1446' Processing helix chain 'C' and resid 1465 through 1469 Processing helix chain 'C' and resid 1498 through 1500 No H-bonds generated for 'chain 'C' and resid 1498 through 1500' Processing helix chain 'C' and resid 1574 through 1578 Processing helix chain 'C' and resid 1580 through 1584 removed outlier: 3.719A pdb=" N ARG C1584 " --> pdb=" O LEU C1581 " (cutoff:3.500A) Processing helix chain 'C' and resid 1651 through 1655 Processing helix chain 'C' and resid 1656 through 1674 removed outlier: 4.005A pdb=" N PHE C1662 " --> pdb=" O ASP C1658 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1689 removed outlier: 3.511A pdb=" N ALA C1684 " --> pdb=" O ARG C1680 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS C1686 " --> pdb=" O ALA C1682 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER C1687 " --> pdb=" O HIS C1683 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS C1688 " --> pdb=" O ALA C1684 " (cutoff:3.500A) Processing helix chain 'C' and resid 1690 through 1700 Processing helix chain 'C' and resid 1704 through 1720 Processing helix chain 'C' and resid 1720 through 1731 removed outlier: 3.569A pdb=" N MET C1730 " --> pdb=" O SER C1726 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1744 Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.586A pdb=" N GLY C1823 " --> pdb=" O VAL C1819 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN C1824 " --> pdb=" O ARG C1820 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS C1825 " --> pdb=" O ASP C1821 " (cutoff:3.500A) Processing helix chain 'C' and resid 1829 through 1832 Processing helix chain 'C' and resid 1833 through 1851 Proline residue: C1840 - end of helix Processing helix chain 'C' and resid 1855 through 1867 Processing helix chain 'C' and resid 1925 through 1929 removed outlier: 4.115A pdb=" N MET C1929 " --> pdb=" O LEU C1926 " (cutoff:3.500A) Processing helix chain 'C' and resid 1932 through 1982 removed outlier: 3.915A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C1967 " --> pdb=" O GLU C1963 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C1982 " --> pdb=" O ALA C1978 " (cutoff:3.500A) Processing helix chain 'C' and resid 1983 through 1986 Processing helix chain 'C' and resid 1990 through 1995 removed outlier: 4.192A pdb=" N ARG C1994 " --> pdb=" O GLU C1990 " (cutoff:3.500A) Processing helix chain 'C' and resid 2001 through 2011 removed outlier: 3.503A pdb=" N GLN C2005 " --> pdb=" O PRO C2001 " (cutoff:3.500A) Processing helix chain 'C' and resid 2024 through 2042 Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 3.538A pdb=" N SER C2099 " --> pdb=" O GLN C2095 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2129 Processing helix chain 'C' and resid 2129 through 2136 removed outlier: 3.694A pdb=" N LEU C2134 " --> pdb=" O GLY C2130 " (cutoff:3.500A) Processing helix chain 'C' and resid 2137 through 2139 No H-bonds generated for 'chain 'C' and resid 2137 through 2139' Processing helix chain 'C' and resid 2145 through 2147 No H-bonds generated for 'chain 'C' and resid 2145 through 2147' Processing helix chain 'C' and resid 2148 through 2164 removed outlier: 3.715A pdb=" N SER C2154 " --> pdb=" O GLU C2150 " (cutoff:3.500A) Processing helix chain 'C' and resid 2165 through 2168 removed outlier: 3.671A pdb=" N VAL C2168 " --> pdb=" O LEU C2165 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2165 through 2168' Processing helix chain 'C' and resid 2171 through 2188 Processing helix chain 'C' and resid 2189 through 2194 Processing helix chain 'C' and resid 2194 through 2202 Processing helix chain 'C' and resid 2202 through 2217 Processing helix chain 'C' and resid 2225 through 2241 removed outlier: 3.574A pdb=" N VAL C2229 " --> pdb=" O PHE C2225 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C2231 " --> pdb=" O LYS C2227 " (cutoff:3.500A) Processing helix chain 'C' and resid 2243 through 2252 removed outlier: 3.636A pdb=" N ASP C2252 " --> pdb=" O ARG C2248 " (cutoff:3.500A) Processing helix chain 'C' and resid 2253 through 2261 removed outlier: 3.661A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) Processing helix chain 'C' and resid 2263 through 2267 removed outlier: 3.752A pdb=" N GLY C2266 " --> pdb=" O ILE C2263 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2280 removed outlier: 3.516A pdb=" N VAL C2275 " --> pdb=" O THR C2271 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C2276 " --> pdb=" O PRO C2272 " (cutoff:3.500A) Processing helix chain 'C' and resid 2283 through 2290 Processing helix chain 'C' and resid 2291 through 2306 removed outlier: 3.623A pdb=" N LEU C2295 " --> pdb=" O GLN C2291 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2316 removed outlier: 3.819A pdb=" N LYS C2316 " --> pdb=" O MET C2312 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2339 removed outlier: 3.797A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2360 Processing helix chain 'C' and resid 2361 through 2365 Processing helix chain 'C' and resid 2375 through 2389 Processing helix chain 'C' and resid 2417 through 2437 removed outlier: 3.703A pdb=" N MET C2423 " --> pdb=" O GLY C2419 " (cutoff:3.500A) Processing helix chain 'C' and resid 2439 through 2446 removed outlier: 3.550A pdb=" N ILE C2443 " --> pdb=" O GLU C2439 " (cutoff:3.500A) Processing helix chain 'C' and resid 2447 through 2461 Processing helix chain 'C' and resid 2462 through 2471 removed outlier: 3.617A pdb=" N LEU C2466 " --> pdb=" O PRO C2462 " (cutoff:3.500A) Processing helix chain 'C' and resid 2489 through 2493 removed outlier: 4.044A pdb=" N SER C2493 " --> pdb=" O MET C2490 " (cutoff:3.500A) Processing helix chain 'C' and resid 2495 through 2509 removed outlier: 3.898A pdb=" N LYS C2499 " --> pdb=" O VAL C2495 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C2505 " --> pdb=" O SER C2501 " (cutoff:3.500A) Processing helix chain 'C' and resid 2514 through 2526 removed outlier: 3.927A pdb=" N VAL C2524 " --> pdb=" O HIS C2520 " (cutoff:3.500A) Processing helix chain 'C' and resid 2526 through 2537 Processing helix chain 'C' and resid 2544 through 2558 Processing helix chain 'C' and resid 2558 through 2565 Processing helix chain 'C' and resid 2566 through 2570 Processing helix chain 'C' and resid 2572 through 2574 No H-bonds generated for 'chain 'C' and resid 2572 through 2574' Processing helix chain 'C' and resid 2575 through 2591 Processing helix chain 'C' and resid 2596 through 2614 removed outlier: 3.680A pdb=" N VAL C2602 " --> pdb=" O ALA C2598 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C2603 " --> pdb=" O GLN C2599 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C2613 " --> pdb=" O ALA C2609 " (cutoff:3.500A) Processing helix chain 'C' and resid 2615 through 2618 Processing helix chain 'C' and resid 2619 through 2633 removed outlier: 4.073A pdb=" N PHE C2628 " --> pdb=" O ARG C2624 " (cutoff:3.500A) Proline residue: C2631 - end of helix Processing helix chain 'C' and resid 2637 through 2651 removed outlier: 3.681A pdb=" N LEU C2641 " --> pdb=" O ALA C2637 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C2642 " --> pdb=" O LYS C2638 " (cutoff:3.500A) Processing helix chain 'C' and resid 2651 through 2657 removed outlier: 3.546A pdb=" N TYR C2655 " --> pdb=" O CYS C2651 " (cutoff:3.500A) Processing helix chain 'C' and resid 2670 through 2689 Processing helix chain 'C' and resid 2692 through 2710 removed outlier: 3.678A pdb=" N MET C2698 " --> pdb=" O GLU C2694 " (cutoff:3.500A) Proline residue: C2701 - end of helix Processing helix chain 'C' and resid 2751 through 2772 removed outlier: 3.904A pdb=" N LYS C2757 " --> pdb=" O SER C2753 " (cutoff:3.500A) Processing helix chain 'C' and resid 2782 through 2786 removed outlier: 4.083A pdb=" N LEU C2785 " --> pdb=" O ASP C2782 " (cutoff:3.500A) Processing helix chain 'C' and resid 2793 through 2797 removed outlier: 3.757A pdb=" N PHE C2797 " --> pdb=" O TYR C2794 " (cutoff:3.500A) Processing helix chain 'C' and resid 2806 through 2819 removed outlier: 3.613A pdb=" N ILE C2817 " --> pdb=" O LEU C2813 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TRP C2819 " --> pdb=" O ALA C2815 " (cutoff:3.500A) Processing helix chain 'C' and resid 2868 through 2895 removed outlier: 3.647A pdb=" N GLU C2893 " --> pdb=" O LYS C2889 " (cutoff:3.500A) Processing helix chain 'C' and resid 2912 through 2934 removed outlier: 3.746A pdb=" N ALA C2917 " --> pdb=" O ALA C2913 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG C2918 " --> pdb=" O LYS C2914 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C2922 " --> pdb=" O ARG C2918 " (cutoff:3.500A) Processing helix chain 'C' and resid 2949 through 2954 Processing helix chain 'C' and resid 2954 through 2983 removed outlier: 3.642A pdb=" N GLN C2962 " --> pdb=" O GLY C2958 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C2969 " --> pdb=" O ARG C2965 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA C2975 " --> pdb=" O GLN C2971 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS C2976 " --> pdb=" O GLU C2972 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C2982 " --> pdb=" O GLU C2978 " (cutoff:3.500A) Processing helix chain 'C' and resid 2991 through 3013 removed outlier: 4.567A pdb=" N LEU C3003 " --> pdb=" O ALA C2999 " (cutoff:3.500A) Proline residue: C3004 - end of helix Processing helix chain 'C' and resid 3013 through 3019 removed outlier: 3.540A pdb=" N PHE C3017 " --> pdb=" O HIS C3013 " (cutoff:3.500A) Processing helix chain 'C' and resid 3032 through 3051 Processing helix chain 'C' and resid 3053 through 3058 removed outlier: 3.657A pdb=" N PHE C3057 " --> pdb=" O ARG C3053 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY C3058 " --> pdb=" O VAL C3054 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3053 through 3058' Processing helix chain 'C' and resid 3060 through 3074 Processing helix chain 'C' and resid 3076 through 3083 Processing helix chain 'C' and resid 3085 through 3111 Processing helix chain 'C' and resid 3124 through 3135 removed outlier: 3.634A pdb=" N VAL C3134 " --> pdb=" O THR C3130 " (cutoff:3.500A) Processing helix chain 'C' and resid 3135 through 3151 Processing helix chain 'C' and resid 3152 through 3157 Processing helix chain 'C' and resid 3160 through 3174 Processing helix chain 'C' and resid 3175 through 3178 Processing helix chain 'C' and resid 3180 through 3201 Proline residue: C3188 - end of helix Processing helix chain 'C' and resid 3207 through 3214 removed outlier: 5.011A pdb=" N GLU C3212 " --> pdb=" O GLN C3209 " (cutoff:3.500A) Processing helix chain 'C' and resid 3217 through 3222 Processing helix chain 'C' and resid 3235 through 3239 Processing helix chain 'C' and resid 3245 through 3260 removed outlier: 3.559A pdb=" N GLU C3258 " --> pdb=" O GLY C3254 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C3260 " --> pdb=" O LEU C3256 " (cutoff:3.500A) Processing helix chain 'C' and resid 3266 through 3272 Processing helix chain 'C' and resid 3272 through 3286 removed outlier: 4.266A pdb=" N MET C3276 " --> pdb=" O ILE C3272 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C3277 " --> pdb=" O THR C3273 " (cutoff:3.500A) Proline residue: C3282 - end of helix removed outlier: 4.382A pdb=" N GLU C3286 " --> pdb=" O PRO C3282 " (cutoff:3.500A) Processing helix chain 'C' and resid 3308 through 3326 removed outlier: 3.789A pdb=" N LEU C3312 " --> pdb=" O THR C3308 " (cutoff:3.500A) Processing helix chain 'C' and resid 3333 through 3343 removed outlier: 4.462A pdb=" N ARG C3337 " --> pdb=" O THR C3333 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C3343 " --> pdb=" O ALA C3339 " (cutoff:3.500A) Processing helix chain 'C' and resid 3344 through 3350 removed outlier: 3.886A pdb=" N SER C3347 " --> pdb=" O PRO C3344 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG C3350 " --> pdb=" O SER C3347 " (cutoff:3.500A) Processing helix chain 'C' and resid 3351 through 3357 removed outlier: 4.332A pdb=" N HIS C3355 " --> pdb=" O PRO C3351 " (cutoff:3.500A) Processing helix chain 'C' and resid 3357 through 3382 removed outlier: 3.729A pdb=" N GLU C3382 " --> pdb=" O GLN C3378 " (cutoff:3.500A) Processing helix chain 'C' and resid 3390 through 3426 Proline residue: C3410 - end of helix removed outlier: 4.939A pdb=" N ALA C3421 " --> pdb=" O ASP C3417 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS C3422 " --> pdb=" O ASN C3418 " (cutoff:3.500A) Processing helix chain 'C' and resid 3428 through 3448 Processing helix chain 'C' and resid 3448 through 3463 removed outlier: 3.670A pdb=" N GLN C3456 " --> pdb=" O LYS C3452 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN C3457 " --> pdb=" O ARG C3453 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C3459 " --> pdb=" O GLU C3455 " (cutoff:3.500A) Processing helix chain 'C' and resid 3467 through 3477 removed outlier: 3.575A pdb=" N THR C3471 " --> pdb=" O MET C3467 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP C3473 " --> pdb=" O PHE C3469 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER C3474 " --> pdb=" O LEU C3470 " (cutoff:3.500A) Processing helix chain 'C' and resid 3504 through 3507 Processing helix chain 'C' and resid 3508 through 3525 Proline residue: C3519 - end of helix removed outlier: 3.741A pdb=" N MET C3524 " --> pdb=" O ILE C3520 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS C3525 " --> pdb=" O GLY C3521 " (cutoff:3.500A) Processing helix chain 'C' and resid 3526 through 3528 No H-bonds generated for 'chain 'C' and resid 3526 through 3528' Processing helix chain 'C' and resid 3529 through 3542 removed outlier: 3.583A pdb=" N MET C3534 " --> pdb=" O GLN C3530 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C3535 " --> pdb=" O ASP C3531 " (cutoff:3.500A) Processing helix chain 'C' and resid 3545 through 3556 Processing helix chain 'C' and resid 3557 through 3560 removed outlier: 3.722A pdb=" N GLN C3560 " --> pdb=" O LEU C3557 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3557 through 3560' Processing helix chain 'C' and resid 3566 through 3578 removed outlier: 3.758A pdb=" N TRP C3571 " --> pdb=" O PRO C3567 " (cutoff:3.500A) Processing helix chain 'C' and resid 3588 through 3611 Processing helix chain 'C' and resid 3624 through 3638 removed outlier: 3.525A pdb=" N ARG C3629 " --> pdb=" O SER C3625 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA C3631 " --> pdb=" O GLN C3627 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C3632 " --> pdb=" O ARG C3628 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C3633 " --> pdb=" O ARG C3629 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE C3636 " --> pdb=" O VAL C3632 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG C3637 " --> pdb=" O VAL C3633 " (cutoff:3.500A) Processing helix chain 'C' and resid 3640 through 3644 Processing helix chain 'C' and resid 3645 through 3662 Processing helix chain 'C' and resid 3669 through 3678 removed outlier: 3.664A pdb=" N ASP C3676 " --> pdb=" O ARG C3672 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3711 Processing helix chain 'C' and resid 3719 through 3732 Processing helix chain 'C' and resid 3752 through 3772 removed outlier: 3.542A pdb=" N MET C3758 " --> pdb=" O GLU C3754 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU C3759 " --> pdb=" O GLU C3755 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C3760 " --> pdb=" O LYS C3756 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR C3765 " --> pdb=" O GLN C3761 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU C3770 " --> pdb=" O GLN C3766 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR C3772 " --> pdb=" O SER C3768 " (cutoff:3.500A) Processing helix chain 'C' and resid 3774 through 3786 removed outlier: 3.521A pdb=" N LEU C3780 " --> pdb=" O ALA C3776 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3804 Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3826 through 3838 Processing helix chain 'C' and resid 3843 through 3857 Processing helix chain 'C' and resid 3877 through 3893 Processing helix chain 'C' and resid 3896 through 3905 removed outlier: 3.687A pdb=" N TYR C3902 " --> pdb=" O ASP C3898 " (cutoff:3.500A) Processing helix chain 'C' and resid 3914 through 3937 removed outlier: 3.517A pdb=" N TRP C3935 " --> pdb=" O SER C3931 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR C3936 " --> pdb=" O ASP C3932 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C3937 " --> pdb=" O PHE C3933 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 3.738A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3983 Processing helix chain 'C' and resid 3984 through 4004 removed outlier: 3.722A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) Processing helix chain 'C' and resid 4006 through 4008 No H-bonds generated for 'chain 'C' and resid 4006 through 4008' Processing helix chain 'C' and resid 4009 through 4031 removed outlier: 3.551A pdb=" N LEU C4019 " --> pdb=" O GLU C4015 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4051 Processing helix chain 'C' and resid 4051 through 4072 removed outlier: 3.625A pdb=" N PHE C4065 " --> pdb=" O PHE C4061 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C4068 " --> pdb=" O MET C4064 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C4070 " --> pdb=" O LEU C4066 " (cutoff:3.500A) Processing helix chain 'C' and resid 4074 through 4081 Processing helix chain 'C' and resid 4090 through 4098 removed outlier: 3.711A pdb=" N ASP C4098 " --> pdb=" O GLN C4094 " (cutoff:3.500A) Processing helix chain 'C' and resid 4099 through 4101 No H-bonds generated for 'chain 'C' and resid 4099 through 4101' Processing helix chain 'C' and resid 4104 through 4115 Processing helix chain 'C' and resid 4124 through 4129 removed outlier: 3.615A pdb=" N PHE C4128 " --> pdb=" O ASN C4124 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA C4129 " --> pdb=" O PHE C4125 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4124 through 4129' Processing helix chain 'C' and resid 4132 through 4154 removed outlier: 4.097A pdb=" N ASP C4138 " --> pdb=" O GLU C4134 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C4139 " --> pdb=" O PRO C4135 " (cutoff:3.500A) Processing helix chain 'C' and resid 4157 through 4167 removed outlier: 3.842A pdb=" N PHE C4163 " --> pdb=" O ARG C4159 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C4164 " --> pdb=" O LEU C4160 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C4165 " --> pdb=" O ARG C4161 " (cutoff:3.500A) Processing helix chain 'C' and resid 4167 through 4175 Processing helix chain 'C' and resid 4198 through 4206 Processing helix chain 'C' and resid 4207 through 4224 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4541 through 4558 Processing helix chain 'C' and resid 4558 through 4578 Processing helix chain 'C' and resid 4638 through 4665 removed outlier: 3.699A pdb=" N TRP C4644 " --> pdb=" O GLU C4640 " (cutoff:3.500A) Processing helix chain 'C' and resid 4665 through 4685 removed outlier: 3.729A pdb=" N VAL C4669 " --> pdb=" O LYS C4665 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C4685 " --> pdb=" O LEU C4681 " (cutoff:3.500A) Processing helix chain 'C' and resid 4696 through 4703 Processing helix chain 'C' and resid 4704 through 4706 No H-bonds generated for 'chain 'C' and resid 4704 through 4706' Processing helix chain 'C' and resid 4719 through 4733 removed outlier: 4.712A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4741 Processing helix chain 'C' and resid 4773 through 4785 Processing helix chain 'C' and resid 4786 through 4805 removed outlier: 3.751A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4809 removed outlier: 3.683A pdb=" N PHE C4809 " --> pdb=" O ASN C4806 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4806 through 4809' Processing helix chain 'C' and resid 4812 through 4814 No H-bonds generated for 'chain 'C' and resid 4812 through 4814' Processing helix chain 'C' and resid 4815 through 4820 Processing helix chain 'C' and resid 4820 through 4833 removed outlier: 3.521A pdb=" N ARG C4824 " --> pdb=" O VAL C4820 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4859 removed outlier: 3.933A pdb=" N ALA C4845 " --> pdb=" O VAL C4841 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C4846 " --> pdb=" O GLY C4842 " (cutoff:3.500A) Processing helix chain 'C' and resid 4860 through 4863 removed outlier: 3.686A pdb=" N TYR C4863 " --> pdb=" O ARG C4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4860 through 4863' Processing helix chain 'C' and resid 4878 through 4890 Processing helix chain 'C' and resid 4896 through 4901 removed outlier: 4.226A pdb=" N GLU C4900 " --> pdb=" O GLY C4896 " (cutoff:3.500A) Processing helix chain 'C' and resid 4909 through 4924 Processing helix chain 'C' and resid 4926 through 4957 removed outlier: 3.957A pdb=" N ILE C4936 " --> pdb=" O ILE C4932 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 3.966A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4998 Processing helix chain 'C' and resid 4999 through 5003 Processing helix chain 'C' and resid 5004 through 5016 Processing helix chain 'C' and resid 5027 through 5032 Processing helix chain 'C' and resid 5032 through 5037 Processing helix chain 'D' and resid 75 through 84 removed outlier: 3.690A pdb=" N GLN D 79 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 305 through 307 No H-bonds generated for 'chain 'D' and resid 305 through 307' Processing helix chain 'D' and resid 364 through 370 removed outlier: 3.942A pdb=" N LEU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 421 removed outlier: 3.587A pdb=" N GLY D 409 " --> pdb=" O HIS D 405 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 452 Processing helix chain 'D' and resid 460 through 481 removed outlier: 3.599A pdb=" N SER D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 496 removed outlier: 3.959A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 508 removed outlier: 3.858A pdb=" N TYR D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 511 No H-bonds generated for 'chain 'D' and resid 509 through 511' Processing helix chain 'D' and resid 512 through 531 removed outlier: 4.568A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 539 Processing helix chain 'D' and resid 543 through 549 removed outlier: 4.154A pdb=" N VAL D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 553 Processing helix chain 'D' and resid 556 through 571 removed outlier: 4.029A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 576 removed outlier: 3.919A pdb=" N LEU D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D 576 " --> pdb=" O PRO D 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 571 through 576' Processing helix chain 'D' and resid 579 through 593 removed outlier: 3.552A pdb=" N SER D 588 " --> pdb=" O LYS D 584 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 607 removed outlier: 3.837A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 Processing helix chain 'D' and resid 794 through 798 removed outlier: 3.931A pdb=" N GLY D 798 " --> pdb=" O GLY D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 815 removed outlier: 4.094A pdb=" N VAL D 815 " --> pdb=" O HIS D 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 812 through 815' Processing helix chain 'D' and resid 847 through 851 Processing helix chain 'D' and resid 864 through 869 Processing helix chain 'D' and resid 872 through 877 Processing helix chain 'D' and resid 880 through 885 removed outlier: 4.385A pdb=" N THR D 885 " --> pdb=" O LEU D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 936 Processing helix chain 'D' and resid 978 through 1003 removed outlier: 3.537A pdb=" N VAL D 995 " --> pdb=" O ASN D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1023 through 1027 Processing helix chain 'D' and resid 1028 through 1049 removed outlier: 4.050A pdb=" N SER D1038 " --> pdb=" O SER D1034 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D1039 " --> pdb=" O ASN D1035 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D1049 " --> pdb=" O THR D1045 " (cutoff:3.500A) Processing helix chain 'D' and resid 1079 through 1082 Processing helix chain 'D' and resid 1423 through 1428 Processing helix chain 'D' and resid 1444 through 1446 No H-bonds generated for 'chain 'D' and resid 1444 through 1446' Processing helix chain 'D' and resid 1465 through 1469 Processing helix chain 'D' and resid 1498 through 1500 No H-bonds generated for 'chain 'D' and resid 1498 through 1500' Processing helix chain 'D' and resid 1574 through 1578 Processing helix chain 'D' and resid 1580 through 1584 removed outlier: 3.719A pdb=" N ARG D1584 " --> pdb=" O LEU D1581 " (cutoff:3.500A) Processing helix chain 'D' and resid 1651 through 1655 Processing helix chain 'D' and resid 1656 through 1674 removed outlier: 4.005A pdb=" N PHE D1662 " --> pdb=" O ASP D1658 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1689 removed outlier: 3.511A pdb=" N ALA D1684 " --> pdb=" O ARG D1680 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS D1686 " --> pdb=" O ALA D1682 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER D1687 " --> pdb=" O HIS D1683 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS D1688 " --> pdb=" O ALA D1684 " (cutoff:3.500A) Processing helix chain 'D' and resid 1690 through 1700 Processing helix chain 'D' and resid 1704 through 1720 Processing helix chain 'D' and resid 1720 through 1731 removed outlier: 3.569A pdb=" N MET D1730 " --> pdb=" O SER D1726 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1744 Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 3.586A pdb=" N GLY D1823 " --> pdb=" O VAL D1819 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN D1824 " --> pdb=" O ARG D1820 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS D1825 " --> pdb=" O ASP D1821 " (cutoff:3.500A) Processing helix chain 'D' and resid 1829 through 1832 Processing helix chain 'D' and resid 1833 through 1851 Proline residue: D1840 - end of helix Processing helix chain 'D' and resid 1855 through 1867 Processing helix chain 'D' and resid 1925 through 1929 removed outlier: 4.115A pdb=" N MET D1929 " --> pdb=" O LEU D1926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1932 through 1982 removed outlier: 3.915A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP D1967 " --> pdb=" O GLU D1963 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG D1982 " --> pdb=" O ALA D1978 " (cutoff:3.500A) Processing helix chain 'D' and resid 1983 through 1986 Processing helix chain 'D' and resid 1990 through 1995 removed outlier: 4.192A pdb=" N ARG D1994 " --> pdb=" O GLU D1990 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2011 removed outlier: 3.503A pdb=" N GLN D2005 " --> pdb=" O PRO D2001 " (cutoff:3.500A) Processing helix chain 'D' and resid 2024 through 2042 Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 3.538A pdb=" N SER D2099 " --> pdb=" O GLN D2095 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2129 Processing helix chain 'D' and resid 2129 through 2136 removed outlier: 3.693A pdb=" N LEU D2134 " --> pdb=" O GLY D2130 " (cutoff:3.500A) Processing helix chain 'D' and resid 2137 through 2139 No H-bonds generated for 'chain 'D' and resid 2137 through 2139' Processing helix chain 'D' and resid 2145 through 2147 No H-bonds generated for 'chain 'D' and resid 2145 through 2147' Processing helix chain 'D' and resid 2148 through 2164 removed outlier: 3.715A pdb=" N SER D2154 " --> pdb=" O GLU D2150 " (cutoff:3.500A) Processing helix chain 'D' and resid 2165 through 2168 removed outlier: 3.671A pdb=" N VAL D2168 " --> pdb=" O LEU D2165 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2165 through 2168' Processing helix chain 'D' and resid 2171 through 2188 Processing helix chain 'D' and resid 2189 through 2194 Processing helix chain 'D' and resid 2194 through 2202 Processing helix chain 'D' and resid 2202 through 2217 Processing helix chain 'D' and resid 2225 through 2241 removed outlier: 3.574A pdb=" N VAL D2229 " --> pdb=" O PHE D2225 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D2231 " --> pdb=" O LYS D2227 " (cutoff:3.500A) Processing helix chain 'D' and resid 2243 through 2252 removed outlier: 3.636A pdb=" N ASP D2252 " --> pdb=" O ARG D2248 " (cutoff:3.500A) Processing helix chain 'D' and resid 2253 through 2261 removed outlier: 3.661A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) Processing helix chain 'D' and resid 2263 through 2267 removed outlier: 3.752A pdb=" N GLY D2266 " --> pdb=" O ILE D2263 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2280 removed outlier: 3.516A pdb=" N VAL D2275 " --> pdb=" O THR D2271 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D2276 " --> pdb=" O PRO D2272 " (cutoff:3.500A) Processing helix chain 'D' and resid 2283 through 2290 Processing helix chain 'D' and resid 2291 through 2306 removed outlier: 3.623A pdb=" N LEU D2295 " --> pdb=" O GLN D2291 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2316 removed outlier: 3.819A pdb=" N LYS D2316 " --> pdb=" O MET D2312 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2339 removed outlier: 3.797A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2360 Processing helix chain 'D' and resid 2361 through 2365 Processing helix chain 'D' and resid 2375 through 2389 Processing helix chain 'D' and resid 2417 through 2437 removed outlier: 3.703A pdb=" N MET D2423 " --> pdb=" O GLY D2419 " (cutoff:3.500A) Processing helix chain 'D' and resid 2439 through 2446 removed outlier: 3.550A pdb=" N ILE D2443 " --> pdb=" O GLU D2439 " (cutoff:3.500A) Processing helix chain 'D' and resid 2447 through 2461 Processing helix chain 'D' and resid 2462 through 2471 removed outlier: 3.617A pdb=" N LEU D2466 " --> pdb=" O PRO D2462 " (cutoff:3.500A) Processing helix chain 'D' and resid 2489 through 2493 removed outlier: 4.044A pdb=" N SER D2493 " --> pdb=" O MET D2490 " (cutoff:3.500A) Processing helix chain 'D' and resid 2495 through 2509 removed outlier: 3.898A pdb=" N LYS D2499 " --> pdb=" O VAL D2495 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE D2505 " --> pdb=" O SER D2501 " (cutoff:3.500A) Processing helix chain 'D' and resid 2514 through 2526 removed outlier: 3.927A pdb=" N VAL D2524 " --> pdb=" O HIS D2520 " (cutoff:3.500A) Processing helix chain 'D' and resid 2526 through 2537 Processing helix chain 'D' and resid 2544 through 2558 Processing helix chain 'D' and resid 2558 through 2565 Processing helix chain 'D' and resid 2566 through 2570 Processing helix chain 'D' and resid 2572 through 2574 No H-bonds generated for 'chain 'D' and resid 2572 through 2574' Processing helix chain 'D' and resid 2575 through 2591 Processing helix chain 'D' and resid 2596 through 2614 removed outlier: 3.680A pdb=" N VAL D2602 " --> pdb=" O ALA D2598 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D2603 " --> pdb=" O GLN D2599 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR D2613 " --> pdb=" O ALA D2609 " (cutoff:3.500A) Processing helix chain 'D' and resid 2615 through 2618 Processing helix chain 'D' and resid 2619 through 2633 removed outlier: 4.073A pdb=" N PHE D2628 " --> pdb=" O ARG D2624 " (cutoff:3.500A) Proline residue: D2631 - end of helix Processing helix chain 'D' and resid 2637 through 2651 removed outlier: 3.681A pdb=" N LEU D2641 " --> pdb=" O ALA D2637 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS D2642 " --> pdb=" O LYS D2638 " (cutoff:3.500A) Processing helix chain 'D' and resid 2651 through 2657 removed outlier: 3.546A pdb=" N TYR D2655 " --> pdb=" O CYS D2651 " (cutoff:3.500A) Processing helix chain 'D' and resid 2670 through 2689 Processing helix chain 'D' and resid 2692 through 2710 removed outlier: 3.678A pdb=" N MET D2698 " --> pdb=" O GLU D2694 " (cutoff:3.500A) Proline residue: D2701 - end of helix Processing helix chain 'D' and resid 2751 through 2772 removed outlier: 3.904A pdb=" N LYS D2757 " --> pdb=" O SER D2753 " (cutoff:3.500A) Processing helix chain 'D' and resid 2782 through 2786 removed outlier: 4.083A pdb=" N LEU D2785 " --> pdb=" O ASP D2782 " (cutoff:3.500A) Processing helix chain 'D' and resid 2793 through 2797 removed outlier: 3.757A pdb=" N PHE D2797 " --> pdb=" O TYR D2794 " (cutoff:3.500A) Processing helix chain 'D' and resid 2806 through 2819 removed outlier: 3.613A pdb=" N ILE D2817 " --> pdb=" O LEU D2813 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TRP D2819 " --> pdb=" O ALA D2815 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2895 removed outlier: 3.647A pdb=" N GLU D2893 " --> pdb=" O LYS D2889 " (cutoff:3.500A) Processing helix chain 'D' and resid 2912 through 2934 removed outlier: 3.746A pdb=" N ALA D2917 " --> pdb=" O ALA D2913 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG D2918 " --> pdb=" O LYS D2914 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP D2919 " --> pdb=" O GLU D2915 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D2922 " --> pdb=" O ARG D2918 " (cutoff:3.500A) Processing helix chain 'D' and resid 2949 through 2954 Processing helix chain 'D' and resid 2954 through 2983 removed outlier: 3.642A pdb=" N GLN D2962 " --> pdb=" O GLY D2958 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D2969 " --> pdb=" O ARG D2965 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA D2975 " --> pdb=" O GLN D2971 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS D2976 " --> pdb=" O GLU D2972 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D2982 " --> pdb=" O GLU D2978 " (cutoff:3.500A) Processing helix chain 'D' and resid 2991 through 3013 removed outlier: 4.567A pdb=" N LEU D3003 " --> pdb=" O ALA D2999 " (cutoff:3.500A) Proline residue: D3004 - end of helix Processing helix chain 'D' and resid 3013 through 3019 removed outlier: 3.540A pdb=" N PHE D3017 " --> pdb=" O HIS D3013 " (cutoff:3.500A) Processing helix chain 'D' and resid 3032 through 3051 Processing helix chain 'D' and resid 3053 through 3058 removed outlier: 3.657A pdb=" N PHE D3057 " --> pdb=" O ARG D3053 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY D3058 " --> pdb=" O VAL D3054 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3053 through 3058' Processing helix chain 'D' and resid 3060 through 3074 Processing helix chain 'D' and resid 3076 through 3083 Processing helix chain 'D' and resid 3085 through 3111 Processing helix chain 'D' and resid 3124 through 3135 removed outlier: 3.634A pdb=" N VAL D3134 " --> pdb=" O THR D3130 " (cutoff:3.500A) Processing helix chain 'D' and resid 3135 through 3151 Processing helix chain 'D' and resid 3152 through 3157 Processing helix chain 'D' and resid 3160 through 3174 Processing helix chain 'D' and resid 3175 through 3178 Processing helix chain 'D' and resid 3180 through 3201 Proline residue: D3188 - end of helix Processing helix chain 'D' and resid 3207 through 3214 removed outlier: 5.011A pdb=" N GLU D3212 " --> pdb=" O GLN D3209 " (cutoff:3.500A) Processing helix chain 'D' and resid 3217 through 3222 Processing helix chain 'D' and resid 3235 through 3239 Processing helix chain 'D' and resid 3245 through 3260 removed outlier: 3.559A pdb=" N GLU D3258 " --> pdb=" O GLY D3254 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY D3260 " --> pdb=" O LEU D3256 " (cutoff:3.500A) Processing helix chain 'D' and resid 3266 through 3272 Processing helix chain 'D' and resid 3272 through 3286 removed outlier: 4.266A pdb=" N MET D3276 " --> pdb=" O ILE D3272 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU D3277 " --> pdb=" O THR D3273 " (cutoff:3.500A) Proline residue: D3282 - end of helix removed outlier: 4.382A pdb=" N GLU D3286 " --> pdb=" O PRO D3282 " (cutoff:3.500A) Processing helix chain 'D' and resid 3308 through 3326 removed outlier: 3.789A pdb=" N LEU D3312 " --> pdb=" O THR D3308 " (cutoff:3.500A) Processing helix chain 'D' and resid 3333 through 3343 removed outlier: 4.462A pdb=" N ARG D3337 " --> pdb=" O THR D3333 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D3343 " --> pdb=" O ALA D3339 " (cutoff:3.500A) Processing helix chain 'D' and resid 3344 through 3350 removed outlier: 3.886A pdb=" N SER D3347 " --> pdb=" O PRO D3344 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG D3350 " --> pdb=" O SER D3347 " (cutoff:3.500A) Processing helix chain 'D' and resid 3351 through 3357 removed outlier: 4.332A pdb=" N HIS D3355 " --> pdb=" O PRO D3351 " (cutoff:3.500A) Processing helix chain 'D' and resid 3357 through 3382 removed outlier: 3.729A pdb=" N GLU D3382 " --> pdb=" O GLN D3378 " (cutoff:3.500A) Processing helix chain 'D' and resid 3390 through 3426 Proline residue: D3410 - end of helix removed outlier: 4.939A pdb=" N ALA D3421 " --> pdb=" O ASP D3417 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS D3422 " --> pdb=" O ASN D3418 " (cutoff:3.500A) Processing helix chain 'D' and resid 3428 through 3448 Processing helix chain 'D' and resid 3448 through 3463 removed outlier: 3.671A pdb=" N GLN D3456 " --> pdb=" O LYS D3452 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN D3457 " --> pdb=" O ARG D3453 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D3459 " --> pdb=" O GLU D3455 " (cutoff:3.500A) Processing helix chain 'D' and resid 3467 through 3477 removed outlier: 3.575A pdb=" N THR D3471 " --> pdb=" O MET D3467 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP D3473 " --> pdb=" O PHE D3469 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER D3474 " --> pdb=" O LEU D3470 " (cutoff:3.500A) Processing helix chain 'D' and resid 3504 through 3507 Processing helix chain 'D' and resid 3508 through 3525 Proline residue: D3519 - end of helix removed outlier: 3.741A pdb=" N MET D3524 " --> pdb=" O ILE D3520 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS D3525 " --> pdb=" O GLY D3521 " (cutoff:3.500A) Processing helix chain 'D' and resid 3526 through 3528 No H-bonds generated for 'chain 'D' and resid 3526 through 3528' Processing helix chain 'D' and resid 3529 through 3542 removed outlier: 3.583A pdb=" N MET D3534 " --> pdb=" O GLN D3530 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D3535 " --> pdb=" O ASP D3531 " (cutoff:3.500A) Processing helix chain 'D' and resid 3545 through 3556 Processing helix chain 'D' and resid 3557 through 3560 removed outlier: 3.722A pdb=" N GLN D3560 " --> pdb=" O LEU D3557 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3557 through 3560' Processing helix chain 'D' and resid 3566 through 3578 removed outlier: 3.758A pdb=" N TRP D3571 " --> pdb=" O PRO D3567 " (cutoff:3.500A) Processing helix chain 'D' and resid 3588 through 3611 Processing helix chain 'D' and resid 3624 through 3638 removed outlier: 3.525A pdb=" N ARG D3629 " --> pdb=" O SER D3625 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D3631 " --> pdb=" O GLN D3627 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL D3632 " --> pdb=" O ARG D3628 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D3633 " --> pdb=" O ARG D3629 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE D3636 " --> pdb=" O VAL D3632 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG D3637 " --> pdb=" O VAL D3633 " (cutoff:3.500A) Processing helix chain 'D' and resid 3640 through 3644 Processing helix chain 'D' and resid 3645 through 3662 Processing helix chain 'D' and resid 3669 through 3678 removed outlier: 3.664A pdb=" N ASP D3676 " --> pdb=" O ARG D3672 " (cutoff:3.500A) Processing helix chain 'D' and resid 3696 through 3711 Processing helix chain 'D' and resid 3719 through 3732 Processing helix chain 'D' and resid 3752 through 3772 removed outlier: 3.542A pdb=" N MET D3758 " --> pdb=" O GLU D3754 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D3759 " --> pdb=" O GLU D3755 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D3760 " --> pdb=" O LYS D3756 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D3765 " --> pdb=" O GLN D3761 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU D3770 " --> pdb=" O GLN D3766 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D3772 " --> pdb=" O SER D3768 " (cutoff:3.500A) Processing helix chain 'D' and resid 3774 through 3786 removed outlier: 3.521A pdb=" N LEU D3780 " --> pdb=" O ALA D3776 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3804 Processing helix chain 'D' and resid 3809 through 3824 Processing helix chain 'D' and resid 3826 through 3838 Processing helix chain 'D' and resid 3843 through 3857 Processing helix chain 'D' and resid 3877 through 3893 Processing helix chain 'D' and resid 3896 through 3905 removed outlier: 3.687A pdb=" N TYR D3902 " --> pdb=" O ASP D3898 " (cutoff:3.500A) Processing helix chain 'D' and resid 3914 through 3937 removed outlier: 3.517A pdb=" N TRP D3935 " --> pdb=" O SER D3931 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR D3936 " --> pdb=" O ASP D3932 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D3937 " --> pdb=" O PHE D3933 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 removed outlier: 3.738A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3983 Processing helix chain 'D' and resid 3984 through 4004 removed outlier: 3.722A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) Processing helix chain 'D' and resid 4006 through 4008 No H-bonds generated for 'chain 'D' and resid 4006 through 4008' Processing helix chain 'D' and resid 4009 through 4031 removed outlier: 3.551A pdb=" N LEU D4019 " --> pdb=" O GLU D4015 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4051 Processing helix chain 'D' and resid 4051 through 4072 removed outlier: 3.625A pdb=" N PHE D4065 " --> pdb=" O PHE D4061 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU D4068 " --> pdb=" O MET D4064 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP D4070 " --> pdb=" O LEU D4066 " (cutoff:3.500A) Processing helix chain 'D' and resid 4074 through 4081 Processing helix chain 'D' and resid 4090 through 4098 removed outlier: 3.711A pdb=" N ASP D4098 " --> pdb=" O GLN D4094 " (cutoff:3.500A) Processing helix chain 'D' and resid 4099 through 4101 No H-bonds generated for 'chain 'D' and resid 4099 through 4101' Processing helix chain 'D' and resid 4104 through 4115 Processing helix chain 'D' and resid 4124 through 4129 removed outlier: 3.615A pdb=" N PHE D4128 " --> pdb=" O ASN D4124 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA D4129 " --> pdb=" O PHE D4125 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4124 through 4129' Processing helix chain 'D' and resid 4132 through 4154 removed outlier: 4.097A pdb=" N ASP D4138 " --> pdb=" O GLU D4134 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE D4139 " --> pdb=" O PRO D4135 " (cutoff:3.500A) Processing helix chain 'D' and resid 4157 through 4167 removed outlier: 3.842A pdb=" N PHE D4163 " --> pdb=" O ARG D4159 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D4164 " --> pdb=" O LEU D4160 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU D4165 " --> pdb=" O ARG D4161 " (cutoff:3.500A) Processing helix chain 'D' and resid 4167 through 4175 Processing helix chain 'D' and resid 4198 through 4206 Processing helix chain 'D' and resid 4207 through 4224 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4541 through 4558 Processing helix chain 'D' and resid 4558 through 4578 Processing helix chain 'D' and resid 4638 through 4665 removed outlier: 3.699A pdb=" N TRP D4644 " --> pdb=" O GLU D4640 " (cutoff:3.500A) Processing helix chain 'D' and resid 4665 through 4685 removed outlier: 3.729A pdb=" N VAL D4669 " --> pdb=" O LYS D4665 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY D4685 " --> pdb=" O LEU D4681 " (cutoff:3.500A) Processing helix chain 'D' and resid 4696 through 4703 Processing helix chain 'D' and resid 4704 through 4706 No H-bonds generated for 'chain 'D' and resid 4704 through 4706' Processing helix chain 'D' and resid 4719 through 4733 removed outlier: 4.712A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4733 through 4741 Processing helix chain 'D' and resid 4773 through 4785 Processing helix chain 'D' and resid 4786 through 4805 removed outlier: 3.751A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4809 removed outlier: 3.683A pdb=" N PHE D4809 " --> pdb=" O ASN D4806 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4806 through 4809' Processing helix chain 'D' and resid 4812 through 4814 No H-bonds generated for 'chain 'D' and resid 4812 through 4814' Processing helix chain 'D' and resid 4815 through 4820 Processing helix chain 'D' and resid 4820 through 4833 removed outlier: 3.521A pdb=" N ARG D4824 " --> pdb=" O VAL D4820 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 removed outlier: 3.933A pdb=" N ALA D4845 " --> pdb=" O VAL D4841 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL D4846 " --> pdb=" O GLY D4842 " (cutoff:3.500A) Processing helix chain 'D' and resid 4860 through 4863 removed outlier: 3.686A pdb=" N TYR D4863 " --> pdb=" O ARG D4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4860 through 4863' Processing helix chain 'D' and resid 4878 through 4890 Processing helix chain 'D' and resid 4896 through 4901 removed outlier: 4.226A pdb=" N GLU D4900 " --> pdb=" O GLY D4896 " (cutoff:3.500A) Processing helix chain 'D' and resid 4909 through 4924 Processing helix chain 'D' and resid 4926 through 4957 removed outlier: 3.957A pdb=" N ILE D4936 " --> pdb=" O ILE D4932 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 3.966A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4998 Processing helix chain 'D' and resid 4999 through 5003 Processing helix chain 'D' and resid 5004 through 5016 Processing helix chain 'D' and resid 5027 through 5032 Processing helix chain 'D' and resid 5032 through 5037 Processing helix chain 'E' and resid 56 through 64 removed outlier: 3.538A pdb=" N ALA E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 64 removed outlier: 3.538A pdb=" N ALA F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 64 removed outlier: 3.538A pdb=" N ALA G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 64 removed outlier: 3.538A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 5.761A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A 206 " --> pdb=" O GLU A 19 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL A 21 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLN A 23 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N MET A 202 " --> pdb=" O GLN A 23 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N SER A 25 " --> pdb=" O TRP A 200 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N TRP A 200 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS A 105 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN A 71 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG A 110 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU A 69 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 120 Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 303 removed outlier: 3.607A pdb=" N ARG A 289 " --> pdb=" O HIS A 284 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE A 282 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N LEU A 293 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 14.668A pdb=" N LEU A 280 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 229 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 314 through 317 Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 359 Processing sheet with id=AA8, first strand: chain 'A' and resid 608 through 609 Processing sheet with id=AA9, first strand: chain 'A' and resid 634 through 639 removed outlier: 3.615A pdb=" N ARG A1646 " --> pdb=" O ILE A1641 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 726 through 729 Processing sheet with id=AB2, first strand: chain 'A' and resid 809 through 810 removed outlier: 6.796A pdb=" N LYS A 661 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 754 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 755 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY A 766 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE A 757 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN A 765 " --> pdb=" O GLY A1477 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY A1477 " --> pdb=" O GLN A 765 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 809 through 810 removed outlier: 6.796A pdb=" N LYS A 661 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY A1625 " --> pdb=" O ALA A1620 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 830 through 832 removed outlier: 4.594A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A1147 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1006 through 1007 removed outlier: 6.454A pdb=" N SER A1006 " --> pdb=" O ASN A1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1136 through 1138 removed outlier: 3.504A pdb=" N ALA A1077 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1088 through 1089 Processing sheet with id=AB8, first strand: chain 'A' and resid 1159 through 1160 Processing sheet with id=AB9, first strand: chain 'A' and resid 1244 through 1247 removed outlier: 5.927A pdb=" N PHE A1288 " --> pdb=" O LEU A1600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1244 through 1247 removed outlier: 5.927A pdb=" N PHE A1288 " --> pdb=" O LEU A1600 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A1450 " --> pdb=" O VAL A1495 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1255 through 1260 removed outlier: 3.724A pdb=" N ILE A1562 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N HIS A1274 " --> pdb=" O ASN A1560 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASN A1560 " --> pdb=" O HIS A1274 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A1514 " --> pdb=" O VAL A1439 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE A1529 " --> pdb=" O THR A1538 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR A1538 " --> pdb=" O PHE A1529 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1734 through 1737 Processing sheet with id=AC4, first strand: chain 'A' and resid 1777 through 1778 Processing sheet with id=AC5, first strand: chain 'A' and resid 2340 through 2341 Processing sheet with id=AC6, first strand: chain 'A' and resid 2822 through 2825 removed outlier: 4.125A pdb=" N THR A2822 " --> pdb=" O THR A2938 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR A2938 " --> pdb=" O THR A2822 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU A2824 " --> pdb=" O ALA A2936 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A2936 " --> pdb=" O GLU A2824 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 4088 through 4089 Processing sheet with id=AC8, first strand: chain 'A' and resid 4178 through 4184 Processing sheet with id=AC9, first strand: chain 'A' and resid 4580 through 4583 Processing sheet with id=AD1, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.761A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS B 206 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL B 21 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLN B 23 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N MET B 202 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N SER B 25 " --> pdb=" O TRP B 200 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N TRP B 200 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS B 105 " --> pdb=" O MET B 150 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN B 71 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARG B 110 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 69 " --> pdb=" O ARG B 110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 117 through 120 Processing sheet with id=AD3, first strand: chain 'B' and resid 179 through 181 Processing sheet with id=AD4, first strand: chain 'B' and resid 298 through 303 removed outlier: 3.607A pdb=" N ARG B 289 " --> pdb=" O HIS B 284 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE B 282 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N LEU B 293 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 14.668A pdb=" N LEU B 280 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 229 through 233 Processing sheet with id=AD6, first strand: chain 'B' and resid 314 through 317 Processing sheet with id=AD7, first strand: chain 'B' and resid 356 through 359 Processing sheet with id=AD8, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD9, first strand: chain 'B' and resid 634 through 639 removed outlier: 3.615A pdb=" N ARG B1646 " --> pdb=" O ILE B1641 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 726 through 729 Processing sheet with id=AE2, first strand: chain 'B' and resid 809 through 810 removed outlier: 6.796A pdb=" N LYS B 661 " --> pdb=" O ALA B 809 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 754 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 755 " --> pdb=" O GLY B 766 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY B 766 " --> pdb=" O ILE B 755 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE B 757 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN B 765 " --> pdb=" O GLY B1477 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY B1477 " --> pdb=" O GLN B 765 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 809 through 810 removed outlier: 6.796A pdb=" N LYS B 661 " --> pdb=" O ALA B 809 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY B1625 " --> pdb=" O ALA B1620 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 830 through 832 removed outlier: 4.593A pdb=" N LEU B1202 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B1147 " --> pdb=" O ALA B1094 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1006 through 1007 removed outlier: 6.453A pdb=" N SER B1006 " --> pdb=" O ASN B1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 1136 through 1138 removed outlier: 3.504A pdb=" N ALA B1077 " --> pdb=" O PRO B1190 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1088 through 1089 Processing sheet with id=AE8, first strand: chain 'B' and resid 1159 through 1160 Processing sheet with id=AE9, first strand: chain 'B' and resid 1244 through 1247 removed outlier: 5.926A pdb=" N PHE B1288 " --> pdb=" O LEU B1600 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1244 through 1247 removed outlier: 5.926A pdb=" N PHE B1288 " --> pdb=" O LEU B1600 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B1450 " --> pdb=" O VAL B1495 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 1255 through 1260 removed outlier: 3.724A pdb=" N ILE B1562 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS B1274 " --> pdb=" O ASN B1560 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN B1560 " --> pdb=" O HIS B1274 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B1514 " --> pdb=" O VAL B1439 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE B1529 " --> pdb=" O THR B1538 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR B1538 " --> pdb=" O PHE B1529 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 1734 through 1737 Processing sheet with id=AF4, first strand: chain 'B' and resid 1777 through 1778 Processing sheet with id=AF5, first strand: chain 'B' and resid 2340 through 2341 Processing sheet with id=AF6, first strand: chain 'B' and resid 2822 through 2825 removed outlier: 4.126A pdb=" N THR B2822 " --> pdb=" O THR B2938 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR B2938 " --> pdb=" O THR B2822 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU B2824 " --> pdb=" O ALA B2936 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B2936 " --> pdb=" O GLU B2824 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'B' and resid 4088 through 4089 Processing sheet with id=AF8, first strand: chain 'B' and resid 4178 through 4184 Processing sheet with id=AF9, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id=AG1, first strand: chain 'C' and resid 48 through 51 removed outlier: 5.761A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS C 206 " --> pdb=" O GLU C 19 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL C 21 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLN C 23 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N MET C 202 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N SER C 25 " --> pdb=" O TRP C 200 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N TRP C 200 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS C 105 " --> pdb=" O MET C 150 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN C 71 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARG C 110 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU C 69 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 117 through 120 Processing sheet with id=AG3, first strand: chain 'C' and resid 179 through 181 Processing sheet with id=AG4, first strand: chain 'C' and resid 298 through 303 removed outlier: 3.607A pdb=" N ARG C 289 " --> pdb=" O HIS C 284 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE C 282 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N LEU C 293 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 14.668A pdb=" N LEU C 280 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 229 through 233 Processing sheet with id=AG6, first strand: chain 'C' and resid 314 through 317 Processing sheet with id=AG7, first strand: chain 'C' and resid 356 through 359 Processing sheet with id=AG8, first strand: chain 'C' and resid 608 through 609 Processing sheet with id=AG9, first strand: chain 'C' and resid 634 through 639 removed outlier: 3.615A pdb=" N ARG C1646 " --> pdb=" O ILE C1641 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 726 through 729 Processing sheet with id=AH2, first strand: chain 'C' and resid 809 through 810 removed outlier: 6.796A pdb=" N LYS C 661 " --> pdb=" O ALA C 809 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 754 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE C 755 " --> pdb=" O GLY C 766 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY C 766 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE C 757 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN C 765 " --> pdb=" O GLY C1477 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY C1477 " --> pdb=" O GLN C 765 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 809 through 810 removed outlier: 6.796A pdb=" N LYS C 661 " --> pdb=" O ALA C 809 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY C1625 " --> pdb=" O ALA C1620 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 830 through 832 removed outlier: 4.593A pdb=" N LEU C1202 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C1147 " --> pdb=" O ALA C1094 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 1006 through 1007 removed outlier: 6.453A pdb=" N SER C1006 " --> pdb=" O ASN C1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.504A pdb=" N ALA C1077 " --> pdb=" O PRO C1190 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 1088 through 1089 Processing sheet with id=AH8, first strand: chain 'C' and resid 1159 through 1160 Processing sheet with id=AH9, first strand: chain 'C' and resid 1244 through 1247 removed outlier: 5.926A pdb=" N PHE C1288 " --> pdb=" O LEU C1600 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 1244 through 1247 removed outlier: 5.926A pdb=" N PHE C1288 " --> pdb=" O LEU C1600 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C1450 " --> pdb=" O VAL C1495 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 1255 through 1260 removed outlier: 3.724A pdb=" N ILE C1562 " --> pdb=" O LEU C1272 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS C1274 " --> pdb=" O ASN C1560 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN C1560 " --> pdb=" O HIS C1274 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C1514 " --> pdb=" O VAL C1439 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE C1529 " --> pdb=" O THR C1538 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR C1538 " --> pdb=" O PHE C1529 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 1734 through 1737 Processing sheet with id=AI4, first strand: chain 'C' and resid 1777 through 1778 Processing sheet with id=AI5, first strand: chain 'C' and resid 2340 through 2341 Processing sheet with id=AI6, first strand: chain 'C' and resid 2822 through 2825 removed outlier: 4.126A pdb=" N THR C2822 " --> pdb=" O THR C2938 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR C2938 " --> pdb=" O THR C2822 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C2824 " --> pdb=" O ALA C2936 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA C2936 " --> pdb=" O GLU C2824 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'C' and resid 4088 through 4089 Processing sheet with id=AI8, first strand: chain 'C' and resid 4178 through 4184 Processing sheet with id=AI9, first strand: chain 'C' and resid 4580 through 4583 Processing sheet with id=AJ1, first strand: chain 'D' and resid 48 through 51 removed outlier: 5.761A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS D 206 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL D 21 " --> pdb=" O PRO D 204 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLN D 23 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N MET D 202 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N SER D 25 " --> pdb=" O TRP D 200 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N TRP D 200 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS D 105 " --> pdb=" O MET D 150 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN D 71 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARG D 110 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU D 69 " --> pdb=" O ARG D 110 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 117 through 120 Processing sheet with id=AJ3, first strand: chain 'D' and resid 179 through 181 Processing sheet with id=AJ4, first strand: chain 'D' and resid 298 through 303 removed outlier: 3.607A pdb=" N ARG D 289 " --> pdb=" O HIS D 284 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE D 282 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N LEU D 293 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 14.668A pdb=" N LEU D 280 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'D' and resid 229 through 233 Processing sheet with id=AJ6, first strand: chain 'D' and resid 314 through 317 Processing sheet with id=AJ7, first strand: chain 'D' and resid 356 through 359 Processing sheet with id=AJ8, first strand: chain 'D' and resid 608 through 609 Processing sheet with id=AJ9, first strand: chain 'D' and resid 634 through 639 removed outlier: 3.615A pdb=" N ARG D1646 " --> pdb=" O ILE D1641 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'D' and resid 726 through 729 Processing sheet with id=AK2, first strand: chain 'D' and resid 809 through 810 removed outlier: 6.796A pdb=" N LYS D 661 " --> pdb=" O ALA D 809 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER D 754 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE D 755 " --> pdb=" O GLY D 766 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY D 766 " --> pdb=" O ILE D 755 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE D 757 " --> pdb=" O VAL D 764 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN D 765 " --> pdb=" O GLY D1477 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY D1477 " --> pdb=" O GLN D 765 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'D' and resid 809 through 810 removed outlier: 6.796A pdb=" N LYS D 661 " --> pdb=" O ALA D 809 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY D1625 " --> pdb=" O ALA D1620 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'D' and resid 830 through 832 removed outlier: 4.593A pdb=" N LEU D1202 " --> pdb=" O PRO D 837 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D1147 " --> pdb=" O ALA D1094 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'D' and resid 1006 through 1007 removed outlier: 6.453A pdb=" N SER D1006 " --> pdb=" O ASN D1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'D' and resid 1136 through 1138 removed outlier: 3.504A pdb=" N ALA D1077 " --> pdb=" O PRO D1190 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'D' and resid 1088 through 1089 Processing sheet with id=AK8, first strand: chain 'D' and resid 1159 through 1160 Processing sheet with id=AK9, first strand: chain 'D' and resid 1244 through 1247 removed outlier: 5.926A pdb=" N PHE D1288 " --> pdb=" O LEU D1600 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'D' and resid 1244 through 1247 removed outlier: 5.926A pdb=" N PHE D1288 " --> pdb=" O LEU D1600 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D1450 " --> pdb=" O VAL D1495 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'D' and resid 1255 through 1260 removed outlier: 3.724A pdb=" N ILE D1562 " --> pdb=" O LEU D1272 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS D1274 " --> pdb=" O ASN D1560 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN D1560 " --> pdb=" O HIS D1274 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D1514 " --> pdb=" O VAL D1439 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE D1529 " --> pdb=" O THR D1538 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR D1538 " --> pdb=" O PHE D1529 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'D' and resid 1734 through 1737 Processing sheet with id=AL4, first strand: chain 'D' and resid 1777 through 1778 Processing sheet with id=AL5, first strand: chain 'D' and resid 2340 through 2341 Processing sheet with id=AL6, first strand: chain 'D' and resid 2822 through 2825 removed outlier: 4.126A pdb=" N THR D2822 " --> pdb=" O THR D2938 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR D2938 " --> pdb=" O THR D2822 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU D2824 " --> pdb=" O ALA D2936 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA D2936 " --> pdb=" O GLU D2824 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL6 Processing sheet with id=AL7, first strand: chain 'D' and resid 4088 through 4089 Processing sheet with id=AL8, first strand: chain 'D' and resid 4178 through 4184 Processing sheet with id=AL9, first strand: chain 'D' and resid 4580 through 4583 Processing sheet with id=AM1, first strand: chain 'E' and resid 5 through 8 removed outlier: 6.687A pdb=" N ARG E 71 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR E 27 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU E 30 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS E 35 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'E' and resid 5 through 8 removed outlier: 6.687A pdb=" N ARG E 71 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 104 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL E 23 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'F' and resid 5 through 8 removed outlier: 6.687A pdb=" N ARG F 71 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 27 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU F 30 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS F 35 " --> pdb=" O LEU F 30 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'F' and resid 5 through 8 removed outlier: 6.687A pdb=" N ARG F 71 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 104 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL F 23 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'G' and resid 5 through 8 removed outlier: 6.687A pdb=" N ARG G 71 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR G 27 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU G 30 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS G 35 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'G' and resid 5 through 8 removed outlier: 6.687A pdb=" N ARG G 71 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU G 104 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL G 23 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'H' and resid 5 through 8 removed outlier: 6.687A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR H 27 " --> pdb=" O ASP H 100 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU H 30 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS H 35 " --> pdb=" O LEU H 30 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'H' and resid 5 through 8 removed outlier: 6.687A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU H 104 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL H 23 " --> pdb=" O LEU H 104 " (cutoff:3.500A) 7444 hydrogen bonds defined for protein. 21344 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: 132.33 Time building geometry restraints manager: 46.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 34483 1.33 - 1.46: 32137 1.46 - 1.58: 78080 1.58 - 1.70: 4 1.70 - 1.83: 1512 Bond restraints: 146216 Sorted by residual: bond pdb=" CG PRO D3301 " pdb=" CD PRO D3301 " ideal model delta sigma weight residual 1.503 1.344 0.159 3.40e-02 8.65e+02 2.18e+01 bond pdb=" CG PRO C3301 " pdb=" CD PRO C3301 " ideal model delta sigma weight residual 1.503 1.344 0.159 3.40e-02 8.65e+02 2.18e+01 bond pdb=" CG PRO B3301 " pdb=" CD PRO B3301 " ideal model delta sigma weight residual 1.503 1.344 0.159 3.40e-02 8.65e+02 2.18e+01 bond pdb=" CG PRO A3301 " pdb=" CD PRO A3301 " ideal model delta sigma weight residual 1.503 1.345 0.158 3.40e-02 8.65e+02 2.17e+01 bond pdb=" C HIS B 904 " pdb=" N PRO B 905 " ideal model delta sigma weight residual 1.334 1.428 -0.094 2.34e-02 1.83e+03 1.61e+01 ... (remaining 146211 not shown) Histogram of bond angle deviations from ideal: 92.12 - 100.96: 369 100.96 - 109.81: 20799 109.81 - 118.65: 95760 118.65 - 127.49: 79400 127.49 - 136.33: 1720 Bond angle restraints: 198048 Sorted by residual: angle pdb=" N PRO A3301 " pdb=" CD PRO A3301 " pdb=" CG PRO A3301 " ideal model delta sigma weight residual 103.20 92.12 11.08 1.50e+00 4.44e-01 5.45e+01 angle pdb=" N PRO C3301 " pdb=" CD PRO C3301 " pdb=" CG PRO C3301 " ideal model delta sigma weight residual 103.20 92.13 11.07 1.50e+00 4.44e-01 5.44e+01 angle pdb=" N PRO D3301 " pdb=" CD PRO D3301 " pdb=" CG PRO D3301 " ideal model delta sigma weight residual 103.20 92.13 11.07 1.50e+00 4.44e-01 5.44e+01 angle pdb=" N PRO B3301 " pdb=" CD PRO B3301 " pdb=" CG PRO B3301 " ideal model delta sigma weight residual 103.20 92.13 11.07 1.50e+00 4.44e-01 5.44e+01 angle pdb=" CA PRO A3301 " pdb=" N PRO A3301 " pdb=" CD PRO A3301 " ideal model delta sigma weight residual 112.00 101.85 10.15 1.40e+00 5.10e-01 5.26e+01 ... (remaining 198043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 79736 17.98 - 35.97: 6671 35.97 - 53.95: 1457 53.95 - 71.93: 344 71.93 - 89.91: 100 Dihedral angle restraints: 88308 sinusoidal: 36116 harmonic: 52192 Sorted by residual: dihedral pdb=" CA CYS D 253 " pdb=" C CYS D 253 " pdb=" N THR D 254 " pdb=" CA THR D 254 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA CYS C 253 " pdb=" C CYS C 253 " pdb=" N THR C 254 " pdb=" CA THR C 254 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA CYS B 253 " pdb=" C CYS B 253 " pdb=" N THR B 254 " pdb=" CA THR B 254 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 88305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 17841 0.071 - 0.142: 3384 0.142 - 0.213: 463 0.213 - 0.284: 52 0.284 - 0.355: 28 Chirality restraints: 21768 Sorted by residual: chirality pdb=" CB VAL A2280 " pdb=" CA VAL A2280 " pdb=" CG1 VAL A2280 " pdb=" CG2 VAL A2280 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB VAL D2280 " pdb=" CA VAL D2280 " pdb=" CG1 VAL D2280 " pdb=" CG2 VAL D2280 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB VAL C2280 " pdb=" CA VAL C2280 " pdb=" CG1 VAL C2280 " pdb=" CG2 VAL C2280 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 21765 not shown) Planarity restraints: 25764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C2230 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C THR C2230 " 0.081 2.00e-02 2.50e+03 pdb=" O THR C2230 " -0.030 2.00e-02 2.50e+03 pdb=" N SER C2231 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B2230 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C THR B2230 " 0.081 2.00e-02 2.50e+03 pdb=" O THR B2230 " -0.030 2.00e-02 2.50e+03 pdb=" N SER B2231 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D2230 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C THR D2230 " 0.081 2.00e-02 2.50e+03 pdb=" O THR D2230 " -0.030 2.00e-02 2.50e+03 pdb=" N SER D2231 " -0.028 2.00e-02 2.50e+03 ... (remaining 25761 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 6218 2.73 - 3.27: 142974 3.27 - 3.81: 239136 3.81 - 4.36: 290519 4.36 - 4.90: 487623 Nonbonded interactions: 1166470 Sorted by model distance: nonbonded pdb=" OG1 THR A 978 " pdb=" OE1 GLN A 981 " model vdw 2.182 2.440 nonbonded pdb=" OG1 THR D 978 " pdb=" OE1 GLN D 981 " model vdw 2.182 2.440 nonbonded pdb=" OG1 THR C 978 " pdb=" OE1 GLN C 981 " model vdw 2.182 2.440 nonbonded pdb=" OG1 THR B 978 " pdb=" OE1 GLN B 981 " model vdw 2.182 2.440 nonbonded pdb=" OG SER A2093 " pdb=" OE1 GLU A2096 " model vdw 2.214 2.440 ... (remaining 1166465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101)) selection = (chain 'B' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101)) selection = (chain 'C' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101)) selection = (chain 'D' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 18.630 Check model and map are aligned: 1.600 Set scattering table: 1.010 Process input model: 473.370 Find NCS groups from input model: 8.320 Set up NCS constraints: 0.960 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 510.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 : 0.005 0.159 146216 Z= 0.357 Angle : 0.999 14.586 198048 Z= 0.546 Chirality : 0.057 0.355 21768 Planarity : 0.007 0.071 25764 Dihedral : 14.407 89.913 54584 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.74 % Favored : 97.15 % Rotamer: Outliers : 2.75 % Allowed : 1.91 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % 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: -0.09 (0.06), residues: 17840 helix: 0.58 (0.05), residues: 8740 sheet: -0.72 (0.12), residues: 1888 loop : -0.53 (0.08), residues: 7212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP C1143 HIS 0.015 0.002 HIS A3771 PHE 0.046 0.003 PHE D4141 TYR 0.044 0.002 TYR D1712 ARG 0.019 0.001 ARG A4913 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 416 poor density : 923 time to evaluate : 12.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.9377 (ptpt) cc_final: 0.9030 (ptpp) REVERT: A 227 MET cc_start: 0.9041 (mmm) cc_final: 0.8600 (mmp) REVERT: A 343 GLU cc_start: 0.8345 (mp0) cc_final: 0.7675 (mp0) REVERT: A 345 LEU cc_start: 0.9421 (mp) cc_final: 0.9117 (mt) REVERT: A 483 MET cc_start: 0.8685 (mmm) cc_final: 0.8130 (mmm) REVERT: A 846 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7999 (tp) REVERT: A 960 MET cc_start: -0.0505 (mmm) cc_final: -0.2610 (ptp) REVERT: A 961 MET cc_start: 0.7374 (pmm) cc_final: 0.6827 (pmm) REVERT: A 1599 MET cc_start: 0.8921 (ppp) cc_final: 0.8527 (ppp) REVERT: A 1601 MET cc_start: 0.8773 (mmm) cc_final: 0.8220 (mmt) REVERT: A 2186 MET cc_start: 0.9162 (mmm) cc_final: 0.8887 (mmt) REVERT: A 2293 GLN cc_start: 0.9399 (pt0) cc_final: 0.9142 (pp30) REVERT: A 2294 ASP cc_start: 0.9390 (m-30) cc_final: 0.8475 (m-30) REVERT: A 2546 MET cc_start: 0.9079 (tpt) cc_final: 0.8794 (tpp) REVERT: A 2578 MET cc_start: 0.9268 (ppp) cc_final: 0.9019 (ppp) REVERT: A 2618 MET cc_start: 0.9208 (mpp) cc_final: 0.8906 (mpp) REVERT: A 2932 MET cc_start: 0.7894 (ptm) cc_final: 0.7460 (ppp) REVERT: A 3437 MET cc_start: 0.8686 (mtt) cc_final: 0.8184 (mtm) REVERT: A 3467 MET cc_start: 0.9238 (ptt) cc_final: 0.8896 (ppp) REVERT: A 3478 MET cc_start: 0.5227 (mmm) cc_final: 0.4454 (mpp) REVERT: A 3517 MET cc_start: 0.9444 (tpt) cc_final: 0.9150 (tpp) REVERT: A 3652 MET cc_start: 0.9206 (mmt) cc_final: 0.8673 (mmm) REVERT: A 3760 LYS cc_start: 0.9428 (mtpp) cc_final: 0.9186 (ptpp) REVERT: A 4047 MET cc_start: 0.9502 (tmm) cc_final: 0.9229 (tmm) REVERT: A 4059 LEU cc_start: 0.9614 (mt) cc_final: 0.9219 (pp) REVERT: A 4064 MET cc_start: 0.9185 (ppp) cc_final: 0.8927 (ppp) REVERT: A 4213 SER cc_start: 0.9780 (OUTLIER) cc_final: 0.9487 (p) REVERT: A 4224 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8752 (pp20) REVERT: A 4580 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8305 (t80) REVERT: A 4628 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8738 (m) REVERT: A 4689 THR cc_start: 0.9519 (OUTLIER) cc_final: 0.9289 (p) REVERT: A 4708 THR cc_start: 0.9471 (OUTLIER) cc_final: 0.9191 (t) REVERT: A 4737 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9016 (mm) REVERT: A 4798 MET cc_start: 0.9124 (mmm) cc_final: 0.8904 (mmm) REVERT: A 4839 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8274 (mtp) REVERT: A 4952 GLU cc_start: 0.9055 (tt0) cc_final: 0.8755 (tm-30) REVERT: A 4953 ASP cc_start: 0.9464 (OUTLIER) cc_final: 0.8915 (m-30) REVERT: A 4956 THR cc_start: 0.8494 (p) cc_final: 0.8206 (t) REVERT: A 4966 ASP cc_start: 0.9463 (OUTLIER) cc_final: 0.9237 (p0) REVERT: A 4971 THR cc_start: 0.9696 (OUTLIER) cc_final: 0.9422 (p) REVERT: A 4980 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9381 (mm) REVERT: A 5030 LYS cc_start: 0.9599 (ttmt) cc_final: 0.9169 (ttmm) REVERT: A 5034 ASP cc_start: 0.9466 (OUTLIER) cc_final: 0.9118 (p0) REVERT: B 227 MET cc_start: 0.8929 (mmm) cc_final: 0.8502 (mmp) REVERT: B 343 GLU cc_start: 0.8397 (mp0) cc_final: 0.7767 (mp0) REVERT: B 345 LEU cc_start: 0.9387 (mp) cc_final: 0.9069 (mt) REVERT: B 483 MET cc_start: 0.8633 (mmm) cc_final: 0.8319 (mmm) REVERT: B 846 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7441 (tm) REVERT: B 960 MET cc_start: -0.0014 (mmm) cc_final: -0.2089 (ptp) REVERT: B 961 MET cc_start: 0.7597 (pmm) cc_final: 0.6922 (pmm) REVERT: B 1599 MET cc_start: 0.8970 (ppp) cc_final: 0.8501 (ppp) REVERT: B 1601 MET cc_start: 0.8797 (mmm) cc_final: 0.8244 (mmt) REVERT: B 2153 MET cc_start: 0.9277 (mmt) cc_final: 0.9075 (mmt) REVERT: B 2186 MET cc_start: 0.9222 (mmm) cc_final: 0.8910 (mmt) REVERT: B 2293 GLN cc_start: 0.9410 (pt0) cc_final: 0.9138 (pp30) REVERT: B 2546 MET cc_start: 0.9114 (tpt) cc_final: 0.8814 (tpp) REVERT: B 2618 MET cc_start: 0.9213 (mpp) cc_final: 0.8918 (mpp) REVERT: B 2932 MET cc_start: 0.7777 (ptm) cc_final: 0.7270 (ppp) REVERT: B 3266 MET cc_start: 0.7615 (mmt) cc_final: 0.7078 (mmt) REVERT: B 3467 MET cc_start: 0.9248 (ptt) cc_final: 0.8910 (ppp) REVERT: B 3478 MET cc_start: 0.5136 (mmm) cc_final: 0.4437 (mpp) REVERT: B 3517 MET cc_start: 0.9425 (tpt) cc_final: 0.9101 (tpp) REVERT: B 3652 MET cc_start: 0.9176 (mmt) cc_final: 0.8959 (mpp) REVERT: B 3760 LYS cc_start: 0.9441 (mtpp) cc_final: 0.9166 (ptpp) REVERT: B 4047 MET cc_start: 0.9459 (tmm) cc_final: 0.9179 (tmm) REVERT: B 4059 LEU cc_start: 0.9654 (mt) cc_final: 0.9275 (pp) REVERT: B 4064 MET cc_start: 0.9185 (ppp) cc_final: 0.8932 (ppp) REVERT: B 4213 SER cc_start: 0.9786 (OUTLIER) cc_final: 0.9482 (p) REVERT: B 4557 ARG cc_start: 0.9413 (OUTLIER) cc_final: 0.9045 (mtm110) REVERT: B 4580 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.8258 (t80) REVERT: B 4628 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8558 (m) REVERT: B 4689 THR cc_start: 0.9561 (OUTLIER) cc_final: 0.9333 (p) REVERT: B 4737 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.8819 (mm) REVERT: B 4798 MET cc_start: 0.9118 (mmm) cc_final: 0.8907 (mmm) REVERT: B 4818 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7412 (mmt) REVERT: B 4839 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8119 (mtm) REVERT: B 4866 SER cc_start: 0.7766 (OUTLIER) cc_final: 0.7546 (p) REVERT: B 4875 LYS cc_start: 0.9572 (OUTLIER) cc_final: 0.9350 (mmmm) REVERT: B 4887 MET cc_start: 0.9126 (mmm) cc_final: 0.8879 (tpp) REVERT: B 4952 GLU cc_start: 0.9098 (tt0) cc_final: 0.8873 (tm-30) REVERT: B 4953 ASP cc_start: 0.9483 (OUTLIER) cc_final: 0.8955 (m-30) REVERT: B 4980 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9393 (mm) REVERT: B 5030 LYS cc_start: 0.9604 (ttmt) cc_final: 0.9179 (ttmm) REVERT: B 5034 ASP cc_start: 0.9463 (OUTLIER) cc_final: 0.9115 (p0) REVERT: C 227 MET cc_start: 0.8930 (mmm) cc_final: 0.8503 (mmp) REVERT: C 343 GLU cc_start: 0.8395 (mp0) cc_final: 0.7765 (mp0) REVERT: C 345 LEU cc_start: 0.9388 (mp) cc_final: 0.9069 (mt) REVERT: C 483 MET cc_start: 0.8634 (mmm) cc_final: 0.8318 (mmm) REVERT: C 846 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7441 (tm) REVERT: C 960 MET cc_start: -0.0016 (mmm) cc_final: -0.2090 (ptp) REVERT: C 961 MET cc_start: 0.7599 (pmm) cc_final: 0.6926 (pmm) REVERT: C 1599 MET cc_start: 0.8971 (ppp) cc_final: 0.8503 (ppp) REVERT: C 1601 MET cc_start: 0.8797 (mmm) cc_final: 0.8245 (mmt) REVERT: C 2153 MET cc_start: 0.9280 (mmt) cc_final: 0.9076 (mmt) REVERT: C 2186 MET cc_start: 0.9222 (mmm) cc_final: 0.8908 (mmt) REVERT: C 2293 GLN cc_start: 0.9410 (pt0) cc_final: 0.9138 (pp30) REVERT: C 2546 MET cc_start: 0.9114 (tpt) cc_final: 0.8814 (tpp) REVERT: C 2618 MET cc_start: 0.9213 (mpp) cc_final: 0.8919 (mpp) REVERT: C 2932 MET cc_start: 0.7778 (ptm) cc_final: 0.7271 (ppp) REVERT: C 3266 MET cc_start: 0.7615 (mmt) cc_final: 0.7079 (mmt) REVERT: C 3467 MET cc_start: 0.9247 (ptt) cc_final: 0.8910 (ppp) REVERT: C 3478 MET cc_start: 0.5136 (mmm) cc_final: 0.4437 (mpp) REVERT: C 3517 MET cc_start: 0.9426 (tpt) cc_final: 0.9103 (tpp) REVERT: C 3652 MET cc_start: 0.9175 (mmt) cc_final: 0.8960 (mpp) REVERT: C 3760 LYS cc_start: 0.9441 (mtpp) cc_final: 0.9167 (ptpp) REVERT: C 4047 MET cc_start: 0.9460 (tmm) cc_final: 0.9180 (tmm) REVERT: C 4059 LEU cc_start: 0.9655 (mt) cc_final: 0.9276 (pp) REVERT: C 4064 MET cc_start: 0.9185 (ppp) cc_final: 0.8933 (ppp) REVERT: C 4213 SER cc_start: 0.9786 (OUTLIER) cc_final: 0.9482 (p) REVERT: C 4557 ARG cc_start: 0.9411 (OUTLIER) cc_final: 0.9044 (mtm110) REVERT: C 4580 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8259 (t80) REVERT: C 4628 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8559 (m) REVERT: C 4689 THR cc_start: 0.9561 (OUTLIER) cc_final: 0.9332 (p) REVERT: C 4737 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.8820 (mm) REVERT: C 4798 MET cc_start: 0.9119 (mmm) cc_final: 0.8910 (mmm) REVERT: C 4818 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7413 (mmt) REVERT: C 4839 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8167 (mtm) REVERT: C 4866 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7544 (p) REVERT: C 4875 LYS cc_start: 0.9572 (OUTLIER) cc_final: 0.9351 (mmmm) REVERT: C 4887 MET cc_start: 0.9124 (mmm) cc_final: 0.8872 (tpp) REVERT: C 4952 GLU cc_start: 0.9098 (tt0) cc_final: 0.8870 (tm-30) REVERT: C 4953 ASP cc_start: 0.9479 (OUTLIER) cc_final: 0.8955 (m-30) REVERT: C 4980 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9393 (mm) REVERT: C 5030 LYS cc_start: 0.9604 (ttmt) cc_final: 0.9180 (ttmm) REVERT: C 5034 ASP cc_start: 0.9464 (OUTLIER) cc_final: 0.9115 (p0) REVERT: D 227 MET cc_start: 0.8930 (mmm) cc_final: 0.8506 (mmp) REVERT: D 343 GLU cc_start: 0.8395 (mp0) cc_final: 0.7765 (mp0) REVERT: D 345 LEU cc_start: 0.9388 (mp) cc_final: 0.9069 (mt) REVERT: D 483 MET cc_start: 0.8634 (mmm) cc_final: 0.8319 (mmm) REVERT: D 846 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7442 (tm) REVERT: D 960 MET cc_start: -0.0016 (mmm) cc_final: -0.2088 (ptp) REVERT: D 961 MET cc_start: 0.7601 (pmm) cc_final: 0.6929 (pmm) REVERT: D 1599 MET cc_start: 0.8972 (ppp) cc_final: 0.8466 (ppp) REVERT: D 1601 MET cc_start: 0.8801 (mmm) cc_final: 0.8255 (mmt) REVERT: D 2153 MET cc_start: 0.9280 (mmt) cc_final: 0.9076 (mmt) REVERT: D 2186 MET cc_start: 0.9222 (mmm) cc_final: 0.8910 (mmt) REVERT: D 2293 GLN cc_start: 0.9411 (pt0) cc_final: 0.9138 (pp30) REVERT: D 2546 MET cc_start: 0.9113 (tpt) cc_final: 0.8814 (tpp) REVERT: D 2618 MET cc_start: 0.9212 (mpp) cc_final: 0.8918 (mpp) REVERT: D 2932 MET cc_start: 0.7778 (ptm) cc_final: 0.7271 (ppp) REVERT: D 3266 MET cc_start: 0.7611 (mmt) cc_final: 0.7074 (mmt) REVERT: D 3467 MET cc_start: 0.9249 (ptt) cc_final: 0.8909 (ppp) REVERT: D 3478 MET cc_start: 0.5145 (mmm) cc_final: 0.4444 (mpp) REVERT: D 3517 MET cc_start: 0.9425 (tpt) cc_final: 0.9101 (tpp) REVERT: D 3652 MET cc_start: 0.9176 (mmt) cc_final: 0.8961 (mpp) REVERT: D 3760 LYS cc_start: 0.9441 (mtpp) cc_final: 0.9166 (ptpp) REVERT: D 4047 MET cc_start: 0.9458 (tmm) cc_final: 0.9178 (tmm) REVERT: D 4059 LEU cc_start: 0.9655 (mt) cc_final: 0.9275 (pp) REVERT: D 4064 MET cc_start: 0.9185 (ppp) cc_final: 0.8933 (ppp) REVERT: D 4213 SER cc_start: 0.9786 (OUTLIER) cc_final: 0.9481 (p) REVERT: D 4557 ARG cc_start: 0.9413 (OUTLIER) cc_final: 0.9044 (mtm110) REVERT: D 4580 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8306 (t80) REVERT: D 4628 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8569 (m) REVERT: D 4689 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9332 (p) REVERT: D 4737 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.8820 (mm) REVERT: D 4798 MET cc_start: 0.9118 (mmm) cc_final: 0.8910 (mmm) REVERT: D 4818 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7413 (mmt) REVERT: D 4839 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8172 (mtm) REVERT: D 4866 SER cc_start: 0.7758 (OUTLIER) cc_final: 0.7538 (p) REVERT: D 4875 LYS cc_start: 0.9570 (OUTLIER) cc_final: 0.9352 (mmmm) REVERT: D 4887 MET cc_start: 0.9130 (mmm) cc_final: 0.8876 (tpp) REVERT: D 4952 GLU cc_start: 0.9099 (tt0) cc_final: 0.8874 (tm-30) REVERT: D 4953 ASP cc_start: 0.9480 (OUTLIER) cc_final: 0.8954 (m-30) REVERT: D 4980 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9393 (mm) REVERT: D 5030 LYS cc_start: 0.9605 (ttmt) cc_final: 0.9179 (ttmm) REVERT: D 5034 ASP cc_start: 0.9463 (OUTLIER) cc_final: 0.9114 (p0) REVERT: E 47 LYS cc_start: 0.9404 (mttt) cc_final: 0.9155 (mttp) REVERT: E 66 MET cc_start: 0.8589 (ptm) cc_final: 0.8307 (tmm) REVERT: F 47 LYS cc_start: 0.9406 (mttt) cc_final: 0.9156 (mttp) REVERT: F 66 MET cc_start: 0.8585 (ptm) cc_final: 0.8304 (tmm) REVERT: G 47 LYS cc_start: 0.9406 (mttt) cc_final: 0.9156 (mttp) REVERT: G 66 MET cc_start: 0.8591 (ptm) cc_final: 0.8307 (tmm) REVERT: H 47 LYS cc_start: 0.9407 (mttt) cc_final: 0.9157 (mttp) REVERT: H 66 MET cc_start: 0.8594 (ptm) cc_final: 0.8306 (tmm) outliers start: 416 outliers final: 76 residues processed: 1275 average time/residue: 1.2038 time to fit residues: 2730.7660 Evaluate side-chains 889 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 758 time to evaluate : 12.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4202 ARG Chi-restraints excluded: chain A residue 4213 SER Chi-restraints excluded: chain A residue 4557 ARG Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4635 SER Chi-restraints excluded: chain A residue 4647 SER Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4695 ASP Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4708 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4788 SER Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4823 LEU Chi-restraints excluded: chain A residue 4839 MET Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4966 ASP Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain A residue 5035 GLN Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4202 ARG Chi-restraints excluded: chain B residue 4213 SER Chi-restraints excluded: chain B residue 4557 ARG Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4628 VAL Chi-restraints excluded: chain B residue 4635 SER Chi-restraints excluded: chain B residue 4647 SER Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4695 ASP Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4773 VAL Chi-restraints excluded: chain B residue 4788 SER Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4839 MET Chi-restraints excluded: chain B residue 4866 SER Chi-restraints excluded: chain B residue 4875 LYS Chi-restraints excluded: chain B residue 4882 CYS Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5015 GLN Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain B residue 5035 GLN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4202 ARG Chi-restraints excluded: chain C residue 4213 SER Chi-restraints excluded: chain C residue 4557 ARG Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4628 VAL Chi-restraints excluded: chain C residue 4635 SER Chi-restraints excluded: chain C residue 4647 SER Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4695 ASP Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4773 VAL Chi-restraints excluded: chain C residue 4788 SER Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4839 MET Chi-restraints excluded: chain C residue 4866 SER Chi-restraints excluded: chain C residue 4875 LYS Chi-restraints excluded: chain C residue 4882 CYS Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain C residue 5015 GLN Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain C residue 5035 GLN Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4202 ARG Chi-restraints excluded: chain D residue 4213 SER Chi-restraints excluded: chain D residue 4557 ARG Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4628 VAL Chi-restraints excluded: chain D residue 4635 SER Chi-restraints excluded: chain D residue 4647 SER Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4695 ASP Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4773 VAL Chi-restraints excluded: chain D residue 4788 SER Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4823 LEU Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4866 SER Chi-restraints excluded: chain D residue 4875 LYS Chi-restraints excluded: chain D residue 4882 CYS Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain D residue 5015 GLN Chi-restraints excluded: chain D residue 5034 ASP Chi-restraints excluded: chain D residue 5035 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1509 optimal weight: 8.9990 chunk 1355 optimal weight: 5.9990 chunk 751 optimal weight: 20.0000 chunk 462 optimal weight: 10.0000 chunk 914 optimal weight: 0.9980 chunk 724 optimal weight: 30.0000 chunk 1401 optimal weight: 6.9990 chunk 542 optimal weight: 8.9990 chunk 852 optimal weight: 3.9990 chunk 1043 optimal weight: 2.9990 chunk 1623 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1563 GLN ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3766 GLN A3895 HIS A3978 GLN A4094 GLN A4216 GLN ** A4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5015 GLN A5035 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 HIS B1563 GLN ** B3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3766 GLN B3895 HIS B3978 GLN B4094 GLN B4216 GLN ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5035 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 HIS ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 HIS C1563 GLN ** C3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3766 GLN C3895 HIS C3978 GLN C4094 GLN C4216 GLN ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5035 GLN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 HIS ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1563 GLN D2772 GLN ** D3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3895 HIS D3978 GLN D4094 GLN D4216 GLN ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5035 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 146216 Z= 0.250 Angle : 0.631 11.338 198048 Z= 0.323 Chirality : 0.041 0.195 21768 Planarity : 0.004 0.068 25764 Dihedral : 5.740 80.737 19803 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.81 % Favored : 97.16 % Rotamer: Outliers : 1.00 % Allowed : 6.30 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.65 (0.06), residues: 17840 helix: 1.40 (0.06), residues: 8948 sheet: -0.60 (0.12), residues: 1848 loop : -0.45 (0.08), residues: 7044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D1143 HIS 0.010 0.001 HIS B2498 PHE 0.028 0.001 PHE B2973 TYR 0.021 0.001 TYR A1051 ARG 0.010 0.000 ARG A1068 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 759 time to evaluate : 12.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.9469 (ptpt) cc_final: 0.9225 (ptpp) REVERT: A 343 GLU cc_start: 0.8204 (mp0) cc_final: 0.7848 (mp0) REVERT: A 345 LEU cc_start: 0.9475 (mp) cc_final: 0.9187 (mt) REVERT: A 404 ILE cc_start: 0.9651 (OUTLIER) cc_final: 0.8924 (mm) REVERT: A 483 MET cc_start: 0.8756 (mmm) cc_final: 0.8309 (mmt) REVERT: A 846 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8272 (tm) REVERT: A 961 MET cc_start: 0.7418 (pmm) cc_final: 0.7073 (pmm) REVERT: A 1494 MET cc_start: 0.7722 (mpp) cc_final: 0.7406 (mpp) REVERT: A 2294 ASP cc_start: 0.9327 (m-30) cc_final: 0.9000 (m-30) REVERT: A 2546 MET cc_start: 0.9149 (tpt) cc_final: 0.8735 (tpp) REVERT: A 2578 MET cc_start: 0.9179 (ppp) cc_final: 0.8906 (ppp) REVERT: A 2582 MET cc_start: 0.9478 (ptt) cc_final: 0.9149 (mtt) REVERT: A 2608 MET cc_start: 0.9183 (mpp) cc_final: 0.8794 (mpp) REVERT: A 2618 MET cc_start: 0.9249 (mpp) cc_final: 0.8857 (mpp) REVERT: A 2932 MET cc_start: 0.7921 (ptm) cc_final: 0.7377 (ppp) REVERT: A 3437 MET cc_start: 0.8737 (mtt) cc_final: 0.8476 (mtm) REVERT: A 3467 MET cc_start: 0.9264 (ptt) cc_final: 0.8881 (ppp) REVERT: A 3478 MET cc_start: 0.5025 (mmm) cc_final: 0.4373 (mpp) REVERT: A 3517 MET cc_start: 0.9459 (tpt) cc_final: 0.9017 (tpp) REVERT: A 3534 MET cc_start: 0.9495 (mpp) cc_final: 0.9147 (pmm) REVERT: A 3652 MET cc_start: 0.9196 (mmt) cc_final: 0.8780 (mmm) REVERT: A 3760 LYS cc_start: 0.9402 (mtpp) cc_final: 0.9111 (ptpp) REVERT: A 3875 MET cc_start: 0.8930 (mmm) cc_final: 0.8294 (mmt) REVERT: A 4014 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8986 (ptpp) REVERT: A 4023 MET cc_start: 0.9021 (ttt) cc_final: 0.8785 (ttt) REVERT: A 4047 MET cc_start: 0.9479 (tmm) cc_final: 0.9210 (tmm) REVERT: A 4059 LEU cc_start: 0.9615 (mt) cc_final: 0.9274 (pp) REVERT: A 4213 SER cc_start: 0.9791 (OUTLIER) cc_final: 0.9542 (p) REVERT: A 4580 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8309 (t80) REVERT: A 4798 MET cc_start: 0.9249 (mmm) cc_final: 0.9035 (mmm) REVERT: A 4839 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8344 (mpp) REVERT: A 4952 GLU cc_start: 0.9067 (tt0) cc_final: 0.8798 (tm-30) REVERT: A 4953 ASP cc_start: 0.9449 (OUTLIER) cc_final: 0.8812 (m-30) REVERT: A 4956 THR cc_start: 0.8660 (p) cc_final: 0.8436 (t) REVERT: A 4980 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9404 (mm) REVERT: A 5013 MET cc_start: 0.9141 (mtm) cc_final: 0.8863 (mtt) REVERT: B 343 GLU cc_start: 0.8227 (mp0) cc_final: 0.7896 (mp0) REVERT: B 345 LEU cc_start: 0.9478 (mp) cc_final: 0.9198 (mt) REVERT: B 483 MET cc_start: 0.8705 (mmm) cc_final: 0.8463 (mmt) REVERT: B 846 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7808 (tm) REVERT: B 960 MET cc_start: 0.0140 (mmm) cc_final: -0.2068 (ttp) REVERT: B 961 MET cc_start: 0.7312 (pmm) cc_final: 0.6779 (pmm) REVERT: B 1152 MET cc_start: 0.8299 (mmp) cc_final: 0.7945 (mmp) REVERT: B 1494 MET cc_start: 0.7588 (mpp) cc_final: 0.7374 (mpp) REVERT: B 2294 ASP cc_start: 0.9361 (m-30) cc_final: 0.9087 (m-30) REVERT: B 2423 MET cc_start: 0.9065 (ptp) cc_final: 0.8825 (ptp) REVERT: B 2582 MET cc_start: 0.9479 (ptt) cc_final: 0.9157 (ttm) REVERT: B 2608 MET cc_start: 0.9160 (mpp) cc_final: 0.8871 (mpp) REVERT: B 2618 MET cc_start: 0.9204 (mpp) cc_final: 0.8824 (mpp) REVERT: B 2932 MET cc_start: 0.7951 (ptm) cc_final: 0.7586 (ppp) REVERT: B 3437 MET cc_start: 0.8830 (mtt) cc_final: 0.8445 (mtm) REVERT: B 3467 MET cc_start: 0.9271 (ptt) cc_final: 0.8882 (ppp) REVERT: B 3517 MET cc_start: 0.9479 (tpt) cc_final: 0.8965 (tpp) REVERT: B 3534 MET cc_start: 0.9582 (mpp) cc_final: 0.9226 (pmm) REVERT: B 3760 LYS cc_start: 0.9425 (mtpp) cc_final: 0.9177 (ptpp) REVERT: B 3875 MET cc_start: 0.8918 (mmm) cc_final: 0.8225 (mmt) REVERT: B 3999 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8765 (mmm) REVERT: B 4014 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9001 (ptpp) REVERT: B 4023 MET cc_start: 0.9033 (ttt) cc_final: 0.8802 (ttt) REVERT: B 4047 MET cc_start: 0.9450 (tmm) cc_final: 0.9190 (tmm) REVERT: B 4059 LEU cc_start: 0.9666 (mt) cc_final: 0.9310 (pp) REVERT: B 4213 SER cc_start: 0.9791 (OUTLIER) cc_final: 0.9526 (p) REVERT: B 4798 MET cc_start: 0.9259 (mmm) cc_final: 0.9032 (mmm) REVERT: B 4818 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7360 (mmt) REVERT: B 4839 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8384 (mpp) REVERT: B 4952 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8813 (tm-30) REVERT: B 4953 ASP cc_start: 0.9438 (OUTLIER) cc_final: 0.8840 (m-30) REVERT: B 4980 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9410 (mm) REVERT: B 5013 MET cc_start: 0.9089 (mtm) cc_final: 0.8887 (mtm) REVERT: C 343 GLU cc_start: 0.8226 (mp0) cc_final: 0.7894 (mp0) REVERT: C 345 LEU cc_start: 0.9479 (mp) cc_final: 0.9199 (mt) REVERT: C 483 MET cc_start: 0.8702 (mmm) cc_final: 0.8464 (mmt) REVERT: C 846 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7809 (tm) REVERT: C 960 MET cc_start: 0.0126 (mmm) cc_final: -0.2074 (ttp) REVERT: C 961 MET cc_start: 0.7266 (pmm) cc_final: 0.6739 (pmm) REVERT: C 1152 MET cc_start: 0.8304 (mmp) cc_final: 0.7948 (mmp) REVERT: C 1494 MET cc_start: 0.7587 (mpp) cc_final: 0.7372 (mpp) REVERT: C 2294 ASP cc_start: 0.9362 (m-30) cc_final: 0.9089 (m-30) REVERT: C 2423 MET cc_start: 0.9063 (ptp) cc_final: 0.8827 (ptp) REVERT: C 2582 MET cc_start: 0.9479 (ptt) cc_final: 0.9158 (ttm) REVERT: C 2608 MET cc_start: 0.9160 (mpp) cc_final: 0.8871 (mpp) REVERT: C 2618 MET cc_start: 0.9206 (mpp) cc_final: 0.8826 (mpp) REVERT: C 2932 MET cc_start: 0.7953 (ptm) cc_final: 0.7589 (ppp) REVERT: C 3437 MET cc_start: 0.8831 (mtt) cc_final: 0.8448 (mtm) REVERT: C 3467 MET cc_start: 0.9270 (ptt) cc_final: 0.8881 (ppp) REVERT: C 3517 MET cc_start: 0.9481 (tpt) cc_final: 0.8967 (tpp) REVERT: C 3534 MET cc_start: 0.9583 (mpp) cc_final: 0.9226 (pmm) REVERT: C 3760 LYS cc_start: 0.9425 (mtpp) cc_final: 0.9178 (ptpp) REVERT: C 3875 MET cc_start: 0.8915 (mmm) cc_final: 0.8222 (mmt) REVERT: C 3999 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8766 (mmm) REVERT: C 4014 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9002 (ptpp) REVERT: C 4023 MET cc_start: 0.9032 (ttt) cc_final: 0.8800 (ttt) REVERT: C 4047 MET cc_start: 0.9452 (tmm) cc_final: 0.9189 (tmm) REVERT: C 4059 LEU cc_start: 0.9666 (mt) cc_final: 0.9310 (pp) REVERT: C 4213 SER cc_start: 0.9791 (OUTLIER) cc_final: 0.9526 (p) REVERT: C 4798 MET cc_start: 0.9259 (mmm) cc_final: 0.9032 (mmm) REVERT: C 4818 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7360 (mmt) REVERT: C 4839 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8333 (mtt) REVERT: C 4952 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8811 (tm-30) REVERT: C 4953 ASP cc_start: 0.9434 (OUTLIER) cc_final: 0.8839 (m-30) REVERT: C 4980 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9410 (mm) REVERT: C 5013 MET cc_start: 0.9093 (mtm) cc_final: 0.8892 (mtm) REVERT: D 343 GLU cc_start: 0.8226 (mp0) cc_final: 0.7894 (mp0) REVERT: D 345 LEU cc_start: 0.9479 (mp) cc_final: 0.9199 (mt) REVERT: D 483 MET cc_start: 0.8703 (mmm) cc_final: 0.8466 (mmt) REVERT: D 846 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7807 (tm) REVERT: D 960 MET cc_start: 0.0127 (mmm) cc_final: -0.2074 (ttp) REVERT: D 961 MET cc_start: 0.7269 (pmm) cc_final: 0.6743 (pmm) REVERT: D 1152 MET cc_start: 0.8300 (mmp) cc_final: 0.7945 (mmp) REVERT: D 1494 MET cc_start: 0.7585 (mpp) cc_final: 0.7370 (mpp) REVERT: D 2294 ASP cc_start: 0.9362 (m-30) cc_final: 0.9088 (m-30) REVERT: D 2423 MET cc_start: 0.9067 (ptp) cc_final: 0.8828 (ptp) REVERT: D 2582 MET cc_start: 0.9480 (ptt) cc_final: 0.9159 (ttm) REVERT: D 2608 MET cc_start: 0.9161 (mpp) cc_final: 0.8871 (mpp) REVERT: D 2618 MET cc_start: 0.9205 (mpp) cc_final: 0.8825 (mpp) REVERT: D 2932 MET cc_start: 0.7953 (ptm) cc_final: 0.7591 (ppp) REVERT: D 3437 MET cc_start: 0.8833 (mtt) cc_final: 0.8449 (mtm) REVERT: D 3467 MET cc_start: 0.9269 (ptt) cc_final: 0.8877 (ppp) REVERT: D 3517 MET cc_start: 0.9480 (tpt) cc_final: 0.8962 (tpp) REVERT: D 3534 MET cc_start: 0.9582 (mpp) cc_final: 0.9225 (pmm) REVERT: D 3760 LYS cc_start: 0.9425 (mtpp) cc_final: 0.9177 (ptpp) REVERT: D 3875 MET cc_start: 0.8916 (mmm) cc_final: 0.8221 (mmt) REVERT: D 3999 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8767 (mmm) REVERT: D 4014 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9002 (ptpp) REVERT: D 4023 MET cc_start: 0.9032 (ttt) cc_final: 0.8802 (ttt) REVERT: D 4047 MET cc_start: 0.9453 (tmm) cc_final: 0.9191 (tmm) REVERT: D 4059 LEU cc_start: 0.9666 (mt) cc_final: 0.9309 (pp) REVERT: D 4213 SER cc_start: 0.9791 (OUTLIER) cc_final: 0.9526 (p) REVERT: D 4798 MET cc_start: 0.9262 (mmm) cc_final: 0.9031 (mmm) REVERT: D 4818 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7451 (mmt) REVERT: D 4839 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8337 (mtt) REVERT: D 4952 GLU cc_start: 0.9225 (tm-30) cc_final: 0.8811 (tm-30) REVERT: D 4953 ASP cc_start: 0.9435 (OUTLIER) cc_final: 0.8841 (m-30) REVERT: D 4980 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9409 (mm) REVERT: E 5 GLU cc_start: 0.8374 (mp0) cc_final: 0.8144 (mp0) REVERT: E 29 MET cc_start: 0.8462 (mtp) cc_final: 0.8088 (mpp) REVERT: E 47 LYS cc_start: 0.9356 (mttt) cc_final: 0.9087 (mtmm) REVERT: E 66 MET cc_start: 0.8725 (ptm) cc_final: 0.8180 (tmm) REVERT: F 5 GLU cc_start: 0.8374 (mp0) cc_final: 0.8145 (mp0) REVERT: F 29 MET cc_start: 0.8458 (mtp) cc_final: 0.8086 (mpp) REVERT: F 47 LYS cc_start: 0.9356 (mttt) cc_final: 0.9087 (mtmm) REVERT: F 66 MET cc_start: 0.8722 (ptm) cc_final: 0.8177 (tmm) REVERT: G 5 GLU cc_start: 0.8372 (mp0) cc_final: 0.8142 (mp0) REVERT: G 29 MET cc_start: 0.8459 (mtp) cc_final: 0.8087 (mpp) REVERT: G 47 LYS cc_start: 0.9356 (mttt) cc_final: 0.9088 (mtmm) REVERT: G 66 MET cc_start: 0.8726 (ptm) cc_final: 0.8180 (tmm) REVERT: H 5 GLU cc_start: 0.8372 (mp0) cc_final: 0.8142 (mp0) REVERT: H 29 MET cc_start: 0.8457 (mtp) cc_final: 0.8085 (mpp) REVERT: H 47 LYS cc_start: 0.9356 (mttt) cc_final: 0.9087 (mtmm) REVERT: H 66 MET cc_start: 0.8723 (ptm) cc_final: 0.8178 (tmm) outliers start: 140 outliers final: 72 residues processed: 876 average time/residue: 1.1602 time to fit residues: 1841.7333 Evaluate side-chains 815 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 711 time to evaluate : 12.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 4014 LYS Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4213 SER Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4585 SER Chi-restraints excluded: chain A residue 4635 SER Chi-restraints excluded: chain A residue 4647 SER Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4822 THR Chi-restraints excluded: chain A residue 4823 LEU Chi-restraints excluded: chain A residue 4839 MET Chi-restraints excluded: chain A residue 4866 SER Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4985 LEU Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain A residue 5016 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4014 LYS Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4202 ARG Chi-restraints excluded: chain B residue 4213 SER Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4585 SER Chi-restraints excluded: chain B residue 4635 SER Chi-restraints excluded: chain B residue 4647 SER Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4822 THR Chi-restraints excluded: chain B residue 4839 MET Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4985 LEU Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 3999 MET Chi-restraints excluded: chain C residue 4014 LYS Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4202 ARG Chi-restraints excluded: chain C residue 4213 SER Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4585 SER Chi-restraints excluded: chain C residue 4635 SER Chi-restraints excluded: chain C residue 4647 SER Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4822 THR Chi-restraints excluded: chain C residue 4839 MET Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4985 LEU Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 3999 MET Chi-restraints excluded: chain D residue 4014 LYS Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4202 ARG Chi-restraints excluded: chain D residue 4213 SER Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4585 SER Chi-restraints excluded: chain D residue 4635 SER Chi-restraints excluded: chain D residue 4647 SER Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4985 LEU Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 902 optimal weight: 20.0000 chunk 503 optimal weight: 0.6980 chunk 1351 optimal weight: 30.0000 chunk 1105 optimal weight: 9.9990 chunk 447 optimal weight: 30.0000 chunk 1626 optimal weight: 30.0000 chunk 1757 optimal weight: 5.9990 chunk 1448 optimal weight: 20.0000 chunk 1613 optimal weight: 20.0000 chunk 554 optimal weight: 7.9990 chunk 1304 optimal weight: 7.9990 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1563 GLN A2194 HIS ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 GLN ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3608 GLN ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN C 634 GLN ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN D 634 GLN ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3211 ASN ** D3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 146216 Z= 0.354 Angle : 0.670 11.927 198048 Z= 0.338 Chirality : 0.042 0.335 21768 Planarity : 0.004 0.061 25764 Dihedral : 4.945 59.772 19695 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.82 % Allowed : 7.71 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.67 (0.06), residues: 17840 helix: 1.47 (0.06), residues: 8892 sheet: -0.72 (0.12), residues: 1844 loop : -0.48 (0.08), residues: 7104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1143 HIS 0.011 0.001 HIS A 226 PHE 0.024 0.002 PHE A4141 TYR 0.031 0.002 TYR C1712 ARG 0.007 0.001 ARG B 869 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 727 time to evaluate : 12.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8221 (mmp) cc_final: 0.7936 (mmp) REVERT: A 343 GLU cc_start: 0.8275 (mp0) cc_final: 0.7982 (mp0) REVERT: A 345 LEU cc_start: 0.9559 (mp) cc_final: 0.9277 (mt) REVERT: A 384 MET cc_start: 0.6402 (ptp) cc_final: 0.5144 (tmm) REVERT: A 483 MET cc_start: 0.8759 (mmm) cc_final: 0.8503 (mmt) REVERT: A 846 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7992 (tp) REVERT: A 941 MET cc_start: 0.6590 (tpt) cc_final: 0.5922 (mmm) REVERT: A 960 MET cc_start: -0.0751 (mmm) cc_final: -0.3304 (ptp) REVERT: A 1152 MET cc_start: 0.8755 (mmp) cc_final: 0.8375 (mmp) REVERT: A 1170 MET cc_start: 0.7972 (tpp) cc_final: 0.7432 (tpp) REVERT: A 1494 MET cc_start: 0.8077 (mpp) cc_final: 0.7826 (tpp) REVERT: A 2618 MET cc_start: 0.9305 (mpp) cc_final: 0.8963 (mpp) REVERT: A 3106 MET cc_start: 0.8237 (mmm) cc_final: 0.8023 (mmm) REVERT: A 3437 MET cc_start: 0.8692 (mtt) cc_final: 0.8471 (mtm) REVERT: A 3467 MET cc_start: 0.9269 (ptt) cc_final: 0.8859 (ppp) REVERT: A 3478 MET cc_start: 0.5407 (mmm) cc_final: 0.4835 (mpp) REVERT: A 3517 MET cc_start: 0.9428 (tpt) cc_final: 0.8904 (tpp) REVERT: A 3573 MET cc_start: 0.9315 (mmt) cc_final: 0.9007 (mmm) REVERT: A 3760 LYS cc_start: 0.9395 (mtpp) cc_final: 0.9111 (ptpp) REVERT: A 4014 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.8663 (ptpp) REVERT: A 4015 GLU cc_start: 0.9417 (OUTLIER) cc_final: 0.8979 (mm-30) REVERT: A 4023 MET cc_start: 0.8998 (ttt) cc_final: 0.8726 (ttt) REVERT: A 4047 MET cc_start: 0.9430 (tmm) cc_final: 0.9163 (tmm) REVERT: A 4245 MET cc_start: 0.9142 (mtp) cc_final: 0.8905 (mtp) REVERT: A 4798 MET cc_start: 0.9275 (mmm) cc_final: 0.9014 (mmm) REVERT: A 4839 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8030 (mpp) REVERT: A 4887 MET cc_start: 0.9122 (mmm) cc_final: 0.8887 (tpp) REVERT: A 4948 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8790 (mp0) REVERT: A 4952 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8771 (pp20) REVERT: A 4953 ASP cc_start: 0.9457 (OUTLIER) cc_final: 0.8815 (m-30) REVERT: B 227 MET cc_start: 0.8154 (mmp) cc_final: 0.7900 (mmp) REVERT: B 343 GLU cc_start: 0.8307 (mp0) cc_final: 0.7989 (mp0) REVERT: B 345 LEU cc_start: 0.9571 (mp) cc_final: 0.9299 (mt) REVERT: B 961 MET cc_start: 0.7574 (pmm) cc_final: 0.7233 (pmm) REVERT: B 1152 MET cc_start: 0.8827 (mmp) cc_final: 0.8445 (mmp) REVERT: B 1170 MET cc_start: 0.7851 (tpp) cc_final: 0.7370 (tpp) REVERT: B 1494 MET cc_start: 0.7703 (mpp) cc_final: 0.7470 (mpp) REVERT: B 2423 MET cc_start: 0.9101 (ptp) cc_final: 0.8873 (ptp) REVERT: B 2618 MET cc_start: 0.9235 (mpp) cc_final: 0.8893 (mpp) REVERT: B 2698 MET cc_start: 0.8515 (ppp) cc_final: 0.8183 (ppp) REVERT: B 2932 MET cc_start: 0.7881 (ptm) cc_final: 0.7025 (ppp) REVERT: B 3437 MET cc_start: 0.8849 (mtt) cc_final: 0.8478 (mtm) REVERT: B 3467 MET cc_start: 0.9270 (ptt) cc_final: 0.8878 (ppp) REVERT: B 3517 MET cc_start: 0.9502 (tpt) cc_final: 0.8948 (tpp) REVERT: B 3573 MET cc_start: 0.9289 (mmt) cc_final: 0.9019 (mmm) REVERT: B 3652 MET cc_start: 0.9164 (mmm) cc_final: 0.8740 (mpp) REVERT: B 3760 LYS cc_start: 0.9415 (mtpp) cc_final: 0.8917 (ptpp) REVERT: B 4014 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.8766 (ptpp) REVERT: B 4015 GLU cc_start: 0.9422 (OUTLIER) cc_final: 0.8966 (mm-30) REVERT: B 4023 MET cc_start: 0.9003 (ttt) cc_final: 0.8736 (ttt) REVERT: B 4047 MET cc_start: 0.9418 (tmm) cc_final: 0.9160 (tmm) REVERT: B 4798 MET cc_start: 0.9293 (mmm) cc_final: 0.9003 (mmm) REVERT: B 4839 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8446 (mpp) REVERT: B 4879 MET cc_start: 0.9095 (tpt) cc_final: 0.8862 (tpt) REVERT: B 4887 MET cc_start: 0.9215 (mmm) cc_final: 0.8862 (tpp) REVERT: B 4952 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8878 (tm-30) REVERT: B 4953 ASP cc_start: 0.9443 (OUTLIER) cc_final: 0.8881 (m-30) REVERT: C 227 MET cc_start: 0.8153 (mmp) cc_final: 0.7896 (mmp) REVERT: C 343 GLU cc_start: 0.8307 (mp0) cc_final: 0.7989 (mp0) REVERT: C 345 LEU cc_start: 0.9572 (mp) cc_final: 0.9300 (mt) REVERT: C 961 MET cc_start: 0.7530 (pmm) cc_final: 0.7193 (pmm) REVERT: C 1152 MET cc_start: 0.8827 (mmp) cc_final: 0.8445 (mmp) REVERT: C 1170 MET cc_start: 0.7840 (tpp) cc_final: 0.7371 (tpp) REVERT: C 1494 MET cc_start: 0.7706 (mpp) cc_final: 0.7494 (mpp) REVERT: C 2423 MET cc_start: 0.9102 (ptp) cc_final: 0.8872 (ptp) REVERT: C 2618 MET cc_start: 0.9235 (mpp) cc_final: 0.8892 (mpp) REVERT: C 2698 MET cc_start: 0.8515 (ppp) cc_final: 0.8183 (ppp) REVERT: C 2932 MET cc_start: 0.7883 (ptm) cc_final: 0.7027 (ppp) REVERT: C 3106 MET cc_start: 0.8312 (mmm) cc_final: 0.8099 (mmm) REVERT: C 3437 MET cc_start: 0.8847 (mtt) cc_final: 0.8474 (mtm) REVERT: C 3467 MET cc_start: 0.9269 (ptt) cc_final: 0.8878 (ppp) REVERT: C 3517 MET cc_start: 0.9504 (tpt) cc_final: 0.8951 (tpp) REVERT: C 3573 MET cc_start: 0.9291 (mmt) cc_final: 0.9020 (mmm) REVERT: C 3652 MET cc_start: 0.9166 (mmm) cc_final: 0.8741 (mpp) REVERT: C 3760 LYS cc_start: 0.9415 (mtpp) cc_final: 0.8917 (ptpp) REVERT: C 4014 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.8766 (ptpp) REVERT: C 4015 GLU cc_start: 0.9422 (OUTLIER) cc_final: 0.8967 (mm-30) REVERT: C 4023 MET cc_start: 0.9004 (ttt) cc_final: 0.8735 (ttt) REVERT: C 4047 MET cc_start: 0.9418 (tmm) cc_final: 0.9160 (tmm) REVERT: C 4798 MET cc_start: 0.9292 (mmm) cc_final: 0.9003 (mmm) REVERT: C 4839 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8313 (mtt) REVERT: C 4879 MET cc_start: 0.9118 (tpt) cc_final: 0.8885 (tpt) REVERT: C 4887 MET cc_start: 0.9192 (mmm) cc_final: 0.8875 (tpp) REVERT: C 4952 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8878 (tm-30) REVERT: C 4953 ASP cc_start: 0.9442 (OUTLIER) cc_final: 0.8878 (m-30) REVERT: D 227 MET cc_start: 0.8153 (mmp) cc_final: 0.7897 (mmp) REVERT: D 343 GLU cc_start: 0.8305 (mp0) cc_final: 0.7987 (mp0) REVERT: D 345 LEU cc_start: 0.9572 (mp) cc_final: 0.9299 (mt) REVERT: D 961 MET cc_start: 0.7531 (pmm) cc_final: 0.7192 (pmm) REVERT: D 1152 MET cc_start: 0.8829 (mmp) cc_final: 0.8445 (mmp) REVERT: D 1170 MET cc_start: 0.7844 (tpp) cc_final: 0.7373 (tpp) REVERT: D 1494 MET cc_start: 0.7705 (mpp) cc_final: 0.7492 (mpp) REVERT: D 2423 MET cc_start: 0.9104 (ptp) cc_final: 0.8876 (ptp) REVERT: D 2618 MET cc_start: 0.9234 (mpp) cc_final: 0.8891 (mpp) REVERT: D 2698 MET cc_start: 0.8515 (ppp) cc_final: 0.8182 (ppp) REVERT: D 2932 MET cc_start: 0.7881 (ptm) cc_final: 0.7023 (ppp) REVERT: D 3106 MET cc_start: 0.8308 (mmm) cc_final: 0.8096 (mmm) REVERT: D 3437 MET cc_start: 0.8852 (mtt) cc_final: 0.8480 (mtm) REVERT: D 3467 MET cc_start: 0.9270 (ptt) cc_final: 0.8876 (ppp) REVERT: D 3517 MET cc_start: 0.9503 (tpt) cc_final: 0.8942 (tpp) REVERT: D 3573 MET cc_start: 0.9288 (mmt) cc_final: 0.9017 (mmm) REVERT: D 3652 MET cc_start: 0.9168 (mmm) cc_final: 0.8742 (mpp) REVERT: D 3760 LYS cc_start: 0.9415 (mtpp) cc_final: 0.8916 (ptpp) REVERT: D 4014 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.8765 (ptpp) REVERT: D 4015 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.8966 (mm-30) REVERT: D 4023 MET cc_start: 0.9004 (ttt) cc_final: 0.8738 (ttt) REVERT: D 4047 MET cc_start: 0.9419 (tmm) cc_final: 0.9159 (tmm) REVERT: D 4798 MET cc_start: 0.9293 (mmm) cc_final: 0.9004 (mmm) REVERT: D 4839 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8314 (mtt) REVERT: D 4879 MET cc_start: 0.9118 (tpt) cc_final: 0.8887 (tpt) REVERT: D 4887 MET cc_start: 0.9212 (mmm) cc_final: 0.8872 (tpp) REVERT: D 4952 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8878 (tm-30) REVERT: D 4953 ASP cc_start: 0.9441 (OUTLIER) cc_final: 0.8878 (m-30) REVERT: E 47 LYS cc_start: 0.9317 (mttt) cc_final: 0.9039 (mtmm) REVERT: E 66 MET cc_start: 0.8900 (ptm) cc_final: 0.8357 (tmm) REVERT: F 47 LYS cc_start: 0.9318 (mttt) cc_final: 0.9041 (mtmm) REVERT: F 66 MET cc_start: 0.8900 (ptm) cc_final: 0.8355 (tmm) REVERT: G 47 LYS cc_start: 0.9318 (mttt) cc_final: 0.9041 (mtmm) REVERT: G 66 MET cc_start: 0.8901 (ptm) cc_final: 0.8355 (tmm) REVERT: H 47 LYS cc_start: 0.9319 (mttt) cc_final: 0.9040 (mtmm) REVERT: H 66 MET cc_start: 0.8901 (ptm) cc_final: 0.8358 (tmm) outliers start: 115 outliers final: 67 residues processed: 814 average time/residue: 1.1390 time to fit residues: 1687.4461 Evaluate side-chains 777 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 693 time to evaluate : 12.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 4014 LYS Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4585 SER Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4822 THR Chi-restraints excluded: chain A residue 4839 MET Chi-restraints excluded: chain A residue 4866 SER Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain A residue 5030 LYS Chi-restraints excluded: chain B residue 4014 LYS Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4585 SER Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4822 THR Chi-restraints excluded: chain B residue 4839 MET Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5030 LYS Chi-restraints excluded: chain C residue 4014 LYS Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4585 SER Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4822 THR Chi-restraints excluded: chain C residue 4839 MET Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain C residue 5030 LYS Chi-restraints excluded: chain D residue 4014 LYS Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4585 SER Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain D residue 5030 LYS Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1607 optimal weight: 20.0000 chunk 1222 optimal weight: 5.9990 chunk 844 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 776 optimal weight: 0.9980 chunk 1092 optimal weight: 10.0000 chunk 1632 optimal weight: 6.9990 chunk 1728 optimal weight: 4.9990 chunk 852 optimal weight: 3.9990 chunk 1547 optimal weight: 7.9990 chunk 465 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3211 ASN ** A3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4223 ASN A5003 HIS ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3211 ASN ** B3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3211 ASN ** C3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3211 ASN ** D3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5003 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 146216 Z= 0.251 Angle : 0.603 15.671 198048 Z= 0.303 Chirality : 0.040 0.236 21768 Planarity : 0.004 0.060 25764 Dihedral : 4.617 58.956 19646 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.73 % Allowed : 8.85 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.82 (0.07), residues: 17840 helix: 1.62 (0.06), residues: 8908 sheet: -0.68 (0.12), residues: 1772 loop : -0.45 (0.08), residues: 7160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A5011 HIS 0.009 0.001 HIS C 226 PHE 0.028 0.001 PHE A3753 TYR 0.028 0.001 TYR A1712 ARG 0.003 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 715 time to evaluate : 12.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8254 (mmp) cc_final: 0.7958 (mmp) REVERT: A 343 GLU cc_start: 0.8278 (mp0) cc_final: 0.7990 (mp0) REVERT: A 345 LEU cc_start: 0.9558 (mp) cc_final: 0.9285 (mt) REVERT: A 384 MET cc_start: 0.5808 (ptp) cc_final: 0.5062 (tmm) REVERT: A 403 MET cc_start: 0.8728 (mtp) cc_final: 0.8349 (mpp) REVERT: A 846 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7994 (tp) REVERT: A 960 MET cc_start: -0.0780 (mmm) cc_final: -0.3065 (ptp) REVERT: A 1152 MET cc_start: 0.8759 (mmp) cc_final: 0.8442 (mmp) REVERT: A 1494 MET cc_start: 0.8246 (mpp) cc_final: 0.8039 (tpp) REVERT: A 1601 MET cc_start: 0.8877 (tpp) cc_final: 0.8621 (tpp) REVERT: A 2582 MET cc_start: 0.9489 (ptt) cc_final: 0.9121 (mtt) REVERT: A 2618 MET cc_start: 0.9281 (mpp) cc_final: 0.8831 (mpp) REVERT: A 2698 MET cc_start: 0.8509 (ppp) cc_final: 0.8184 (ppp) REVERT: A 3106 MET cc_start: 0.8204 (mmm) cc_final: 0.7906 (mmm) REVERT: A 3437 MET cc_start: 0.8697 (mtt) cc_final: 0.8482 (mtm) REVERT: A 3467 MET cc_start: 0.9273 (ptt) cc_final: 0.8855 (ppp) REVERT: A 3478 MET cc_start: 0.5432 (mmm) cc_final: 0.4863 (mpp) REVERT: A 3517 MET cc_start: 0.9435 (tpt) cc_final: 0.8859 (tpp) REVERT: A 3534 MET cc_start: 0.9538 (mpp) cc_final: 0.9239 (pmm) REVERT: A 3652 MET cc_start: 0.9185 (mmm) cc_final: 0.8682 (mpp) REVERT: A 3760 LYS cc_start: 0.9385 (mtpp) cc_final: 0.9088 (ptpp) REVERT: A 3999 MET cc_start: 0.8855 (mmm) cc_final: 0.8474 (mmm) REVERT: A 4014 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.8689 (ptpp) REVERT: A 4015 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.8973 (mm-30) REVERT: A 4023 MET cc_start: 0.8962 (ttt) cc_final: 0.8697 (ttt) REVERT: A 4047 MET cc_start: 0.9409 (tmm) cc_final: 0.9134 (tmm) REVERT: A 4057 MET cc_start: 0.9174 (mtm) cc_final: 0.8920 (mtm) REVERT: A 4059 LEU cc_start: 0.9618 (mt) cc_final: 0.9301 (pp) REVERT: A 4798 MET cc_start: 0.9265 (mmm) cc_final: 0.9005 (mmm) REVERT: A 4839 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8123 (mtt) REVERT: A 4879 MET cc_start: 0.9089 (tpt) cc_final: 0.8838 (tpp) REVERT: A 4887 MET cc_start: 0.9099 (mmm) cc_final: 0.8855 (tpp) REVERT: A 4952 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8798 (pp20) REVERT: A 4953 ASP cc_start: 0.9447 (OUTLIER) cc_final: 0.8763 (m-30) REVERT: A 5035 GLN cc_start: 0.9457 (mp10) cc_final: 0.9224 (mp10) REVERT: B 227 MET cc_start: 0.8046 (mmp) cc_final: 0.7810 (mmp) REVERT: B 343 GLU cc_start: 0.8300 (mp0) cc_final: 0.7991 (mp0) REVERT: B 345 LEU cc_start: 0.9544 (mp) cc_final: 0.9268 (mt) REVERT: B 403 MET cc_start: 0.8708 (mtp) cc_final: 0.8279 (mpp) REVERT: B 1601 MET cc_start: 0.8926 (tpp) cc_final: 0.8721 (tpp) REVERT: B 1636 MET cc_start: 0.8082 (tmm) cc_final: 0.7469 (tmm) REVERT: B 2170 MET cc_start: 0.8436 (tpp) cc_final: 0.7695 (tpp) REVERT: B 2423 MET cc_start: 0.9147 (ptp) cc_final: 0.8832 (ptp) REVERT: B 2582 MET cc_start: 0.9439 (ptt) cc_final: 0.9134 (mtt) REVERT: B 2618 MET cc_start: 0.9289 (mpp) cc_final: 0.8827 (mpp) REVERT: B 2698 MET cc_start: 0.8548 (ppp) cc_final: 0.8239 (ppp) REVERT: B 2874 MET cc_start: -0.3378 (ttt) cc_final: -0.3917 (mtp) REVERT: B 2932 MET cc_start: 0.7874 (ptm) cc_final: 0.7023 (ppp) REVERT: B 3437 MET cc_start: 0.8827 (mtt) cc_final: 0.8561 (mtm) REVERT: B 3467 MET cc_start: 0.9258 (ptt) cc_final: 0.8869 (ppp) REVERT: B 3517 MET cc_start: 0.9440 (tpt) cc_final: 0.8863 (tpp) REVERT: B 3534 MET cc_start: 0.9572 (mpp) cc_final: 0.9278 (pmm) REVERT: B 3652 MET cc_start: 0.9188 (mmm) cc_final: 0.8716 (mpp) REVERT: B 3760 LYS cc_start: 0.9403 (mtpp) cc_final: 0.8912 (ptpp) REVERT: B 4014 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.8787 (ptpp) REVERT: B 4015 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.8974 (mm-30) REVERT: B 4023 MET cc_start: 0.9006 (ttt) cc_final: 0.8732 (ttt) REVERT: B 4047 MET cc_start: 0.9410 (tmm) cc_final: 0.9135 (tmm) REVERT: B 4057 MET cc_start: 0.9221 (mtm) cc_final: 0.8947 (mtm) REVERT: B 4059 LEU cc_start: 0.9634 (mt) cc_final: 0.9314 (pp) REVERT: B 4798 MET cc_start: 0.9254 (mmm) cc_final: 0.8989 (mmm) REVERT: B 4839 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8415 (mpp) REVERT: B 4879 MET cc_start: 0.9105 (tpt) cc_final: 0.8897 (tpt) REVERT: B 4880 MET cc_start: 0.8972 (tpp) cc_final: 0.8672 (tpt) REVERT: B 4887 MET cc_start: 0.9204 (mmm) cc_final: 0.8953 (tpp) REVERT: B 4952 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8813 (pp20) REVERT: B 4953 ASP cc_start: 0.9431 (t0) cc_final: 0.8881 (m-30) REVERT: B 5035 GLN cc_start: 0.9449 (mp10) cc_final: 0.9218 (mp10) REVERT: C 227 MET cc_start: 0.8048 (mmp) cc_final: 0.7810 (mmp) REVERT: C 343 GLU cc_start: 0.8300 (mp0) cc_final: 0.7990 (mp0) REVERT: C 345 LEU cc_start: 0.9545 (mp) cc_final: 0.9268 (mt) REVERT: C 403 MET cc_start: 0.8754 (mtp) cc_final: 0.8288 (mpp) REVERT: C 1601 MET cc_start: 0.8924 (tpp) cc_final: 0.8721 (tpp) REVERT: C 1636 MET cc_start: 0.8087 (tmm) cc_final: 0.7471 (tmm) REVERT: C 2170 MET cc_start: 0.8437 (tpp) cc_final: 0.7693 (tpp) REVERT: C 2423 MET cc_start: 0.9146 (ptp) cc_final: 0.8832 (ptp) REVERT: C 2582 MET cc_start: 0.9439 (ptt) cc_final: 0.9134 (mtt) REVERT: C 2618 MET cc_start: 0.9287 (mpp) cc_final: 0.8824 (mpp) REVERT: C 2698 MET cc_start: 0.8547 (ppp) cc_final: 0.8238 (ppp) REVERT: C 2874 MET cc_start: -0.3375 (ttt) cc_final: -0.3916 (mtp) REVERT: C 2932 MET cc_start: 0.7877 (ptm) cc_final: 0.7027 (ppp) REVERT: C 3106 MET cc_start: 0.8293 (mmm) cc_final: 0.8000 (mmm) REVERT: C 3437 MET cc_start: 0.8825 (mtt) cc_final: 0.8558 (mtm) REVERT: C 3467 MET cc_start: 0.9257 (ptt) cc_final: 0.8868 (ppp) REVERT: C 3517 MET cc_start: 0.9442 (tpt) cc_final: 0.8865 (tpp) REVERT: C 3534 MET cc_start: 0.9571 (mpp) cc_final: 0.9277 (pmm) REVERT: C 3652 MET cc_start: 0.9188 (mmm) cc_final: 0.8713 (mpp) REVERT: C 3760 LYS cc_start: 0.9402 (mtpp) cc_final: 0.8911 (ptpp) REVERT: C 4014 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.8788 (ptpp) REVERT: C 4015 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.8975 (mm-30) REVERT: C 4023 MET cc_start: 0.9007 (ttt) cc_final: 0.8747 (ttt) REVERT: C 4047 MET cc_start: 0.9409 (tmm) cc_final: 0.9135 (tmm) REVERT: C 4057 MET cc_start: 0.9222 (mtm) cc_final: 0.8948 (mtm) REVERT: C 4059 LEU cc_start: 0.9634 (mt) cc_final: 0.9314 (pp) REVERT: C 4798 MET cc_start: 0.9254 (mmm) cc_final: 0.8985 (mmm) REVERT: C 4839 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8319 (mtt) REVERT: C 4952 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8812 (pp20) REVERT: C 4953 ASP cc_start: 0.9430 (t0) cc_final: 0.8879 (m-30) REVERT: C 5035 GLN cc_start: 0.9448 (mp10) cc_final: 0.9217 (mp10) REVERT: D 227 MET cc_start: 0.8042 (mmp) cc_final: 0.7807 (mmp) REVERT: D 343 GLU cc_start: 0.8300 (mp0) cc_final: 0.7990 (mp0) REVERT: D 345 LEU cc_start: 0.9546 (mp) cc_final: 0.9268 (mt) REVERT: D 403 MET cc_start: 0.8756 (mtp) cc_final: 0.8290 (mpp) REVERT: D 960 MET cc_start: 0.0511 (mmm) cc_final: 0.0299 (mmm) REVERT: D 1601 MET cc_start: 0.8924 (tpp) cc_final: 0.8723 (tpp) REVERT: D 1636 MET cc_start: 0.8083 (tmm) cc_final: 0.7469 (tmm) REVERT: D 2170 MET cc_start: 0.8432 (tpp) cc_final: 0.7695 (tpp) REVERT: D 2423 MET cc_start: 0.9149 (ptp) cc_final: 0.8834 (ptp) REVERT: D 2582 MET cc_start: 0.9441 (ptt) cc_final: 0.9135 (mtt) REVERT: D 2618 MET cc_start: 0.9285 (mpp) cc_final: 0.8824 (mpp) REVERT: D 2698 MET cc_start: 0.8546 (ppp) cc_final: 0.8238 (ppp) REVERT: D 2874 MET cc_start: -0.3367 (ttt) cc_final: -0.3910 (mtp) REVERT: D 2932 MET cc_start: 0.7876 (ptm) cc_final: 0.7024 (ppp) REVERT: D 3106 MET cc_start: 0.8289 (mmm) cc_final: 0.7997 (mmm) REVERT: D 3437 MET cc_start: 0.8830 (mtt) cc_final: 0.8563 (mtm) REVERT: D 3467 MET cc_start: 0.9258 (ptt) cc_final: 0.8868 (ppp) REVERT: D 3517 MET cc_start: 0.9442 (tpt) cc_final: 0.8857 (tpp) REVERT: D 3534 MET cc_start: 0.9571 (mpp) cc_final: 0.9277 (pmm) REVERT: D 3652 MET cc_start: 0.9188 (mmm) cc_final: 0.8715 (mpp) REVERT: D 3760 LYS cc_start: 0.9403 (mtpp) cc_final: 0.8912 (ptpp) REVERT: D 4014 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.8787 (ptpp) REVERT: D 4015 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.8975 (mm-30) REVERT: D 4023 MET cc_start: 0.9007 (ttt) cc_final: 0.8734 (ttt) REVERT: D 4047 MET cc_start: 0.9411 (tmm) cc_final: 0.9135 (tmm) REVERT: D 4057 MET cc_start: 0.9220 (mtm) cc_final: 0.8947 (mtm) REVERT: D 4059 LEU cc_start: 0.9634 (mt) cc_final: 0.9314 (pp) REVERT: D 4798 MET cc_start: 0.9255 (mmm) cc_final: 0.8986 (mmm) REVERT: D 4839 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8321 (mtt) REVERT: D 4887 MET cc_start: 0.9199 (mmm) cc_final: 0.8952 (tpp) REVERT: D 4952 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8811 (pp20) REVERT: D 4953 ASP cc_start: 0.9431 (t0) cc_final: 0.8877 (m-30) REVERT: D 5035 GLN cc_start: 0.9451 (mp10) cc_final: 0.9215 (mp10) REVERT: E 47 LYS cc_start: 0.9308 (mttt) cc_final: 0.9027 (mtmm) REVERT: E 66 MET cc_start: 0.8898 (ptm) cc_final: 0.8307 (ppp) REVERT: F 47 LYS cc_start: 0.9308 (mttt) cc_final: 0.9028 (mtmm) REVERT: F 66 MET cc_start: 0.8897 (ptm) cc_final: 0.8307 (ppp) REVERT: G 47 LYS cc_start: 0.9309 (mttt) cc_final: 0.9028 (mtmm) REVERT: G 66 MET cc_start: 0.8896 (ptm) cc_final: 0.8305 (ppp) REVERT: H 47 LYS cc_start: 0.9310 (mttt) cc_final: 0.9028 (mtmm) REVERT: H 66 MET cc_start: 0.8897 (ptm) cc_final: 0.8307 (ppp) outliers start: 100 outliers final: 69 residues processed: 796 average time/residue: 1.1626 time to fit residues: 1683.5119 Evaluate side-chains 781 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 698 time to evaluate : 12.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 4014 LYS Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4223 ASN Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4585 SER Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4822 THR Chi-restraints excluded: chain A residue 4829 SER Chi-restraints excluded: chain A residue 4839 MET Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2382 GLU Chi-restraints excluded: chain B residue 4014 LYS Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4585 SER Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4822 THR Chi-restraints excluded: chain B residue 4839 MET Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2382 GLU Chi-restraints excluded: chain C residue 4014 LYS Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4585 SER Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4822 THR Chi-restraints excluded: chain C residue 4839 MET Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2382 GLU Chi-restraints excluded: chain D residue 4014 LYS Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4585 SER Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1439 optimal weight: 0.0870 chunk 981 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 1286 optimal weight: 0.9990 chunk 713 optimal weight: 10.0000 chunk 1474 optimal weight: 6.9990 chunk 1194 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 882 optimal weight: 9.9990 chunk 1551 optimal weight: 20.0000 chunk 436 optimal weight: 0.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1563 GLN A2003 GLN ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3211 ASN ** A3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4223 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2003 GLN ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3211 ASN ** B3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3457 ASN ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2003 GLN ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3211 ASN ** C3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3457 ASN ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2003 GLN ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3211 ASN ** D3378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 146216 Z= 0.229 Angle : 0.587 11.221 198048 Z= 0.294 Chirality : 0.040 0.267 21768 Planarity : 0.004 0.058 25764 Dihedral : 4.459 58.403 19634 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.76 % Allowed : 9.75 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.91 (0.07), residues: 17840 helix: 1.71 (0.06), residues: 8896 sheet: -0.69 (0.12), residues: 1784 loop : -0.40 (0.08), residues: 7160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A5011 HIS 0.008 0.001 HIS A3771 PHE 0.025 0.001 PHE A2973 TYR 0.027 0.001 TYR A1712 ARG 0.004 0.000 ARG A3672 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 713 time to evaluate : 12.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8277 (mmp) cc_final: 0.8061 (mmp) REVERT: A 343 GLU cc_start: 0.8176 (mp0) cc_final: 0.7895 (mp0) REVERT: A 345 LEU cc_start: 0.9569 (mp) cc_final: 0.9296 (mt) REVERT: A 384 MET cc_start: 0.5632 (ptp) cc_final: 0.4808 (tmm) REVERT: A 403 MET cc_start: 0.8678 (mtp) cc_final: 0.8274 (mpp) REVERT: A 960 MET cc_start: -0.0467 (mmm) cc_final: -0.2929 (ptp) REVERT: A 1152 MET cc_start: 0.8752 (mmp) cc_final: 0.8383 (mmp) REVERT: A 1170 MET cc_start: 0.8004 (tpp) cc_final: 0.7405 (tpp) REVERT: A 1186 ASP cc_start: 0.9432 (OUTLIER) cc_final: 0.9077 (p0) REVERT: A 1494 MET cc_start: 0.8321 (mpp) cc_final: 0.8046 (tpp) REVERT: A 1601 MET cc_start: 0.8918 (tpp) cc_final: 0.8663 (tpp) REVERT: A 2170 MET cc_start: 0.8372 (tpp) cc_final: 0.7652 (tpp) REVERT: A 2178 MET cc_start: 0.8744 (ppp) cc_final: 0.8464 (ppp) REVERT: A 2618 MET cc_start: 0.9276 (mpp) cc_final: 0.8812 (mpp) REVERT: A 2698 MET cc_start: 0.8600 (ppp) cc_final: 0.8304 (ppp) REVERT: A 2874 MET cc_start: -0.3237 (ttt) cc_final: -0.3829 (mtp) REVERT: A 3106 MET cc_start: 0.8306 (mmm) cc_final: 0.7948 (mmm) REVERT: A 3437 MET cc_start: 0.8846 (mtt) cc_final: 0.8594 (mtm) REVERT: A 3467 MET cc_start: 0.9271 (ptt) cc_final: 0.8874 (ppp) REVERT: A 3478 MET cc_start: 0.5450 (mmm) cc_final: 0.4881 (mpp) REVERT: A 3517 MET cc_start: 0.9446 (tpt) cc_final: 0.8863 (tpp) REVERT: A 3534 MET cc_start: 0.9543 (mpp) cc_final: 0.9233 (pmm) REVERT: A 3652 MET cc_start: 0.9204 (mmm) cc_final: 0.8685 (mpp) REVERT: A 3760 LYS cc_start: 0.9373 (mtpp) cc_final: 0.9082 (ptpp) REVERT: A 3999 MET cc_start: 0.8971 (mmm) cc_final: 0.8592 (mmm) REVERT: A 4014 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.8664 (ptpp) REVERT: A 4015 GLU cc_start: 0.9401 (OUTLIER) cc_final: 0.8996 (mm-30) REVERT: A 4023 MET cc_start: 0.8979 (ttt) cc_final: 0.8710 (ttt) REVERT: A 4047 MET cc_start: 0.9383 (tmm) cc_final: 0.9100 (tmm) REVERT: A 4057 MET cc_start: 0.9171 (mtm) cc_final: 0.8881 (mtm) REVERT: A 4798 MET cc_start: 0.9250 (mmm) cc_final: 0.9005 (mmm) REVERT: A 4839 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8081 (mtt) REVERT: A 4879 MET cc_start: 0.9141 (tpt) cc_final: 0.8866 (tpp) REVERT: A 4887 MET cc_start: 0.9089 (mmm) cc_final: 0.8844 (tpp) REVERT: A 4952 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8782 (pp20) REVERT: A 4953 ASP cc_start: 0.9418 (t0) cc_final: 0.8852 (m-30) REVERT: A 5035 GLN cc_start: 0.9467 (mt0) cc_final: 0.9219 (mp10) REVERT: B 343 GLU cc_start: 0.8199 (mp0) cc_final: 0.7923 (mp0) REVERT: B 345 LEU cc_start: 0.9567 (mp) cc_final: 0.9286 (mt) REVERT: B 403 MET cc_start: 0.8749 (mtp) cc_final: 0.8306 (mpp) REVERT: B 960 MET cc_start: 0.0279 (mmm) cc_final: -0.2076 (ptp) REVERT: B 1170 MET cc_start: 0.7883 (tpp) cc_final: 0.7390 (tpp) REVERT: B 1186 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.9118 (p0) REVERT: B 1494 MET cc_start: 0.8224 (mpp) cc_final: 0.7958 (tpp) REVERT: B 1601 MET cc_start: 0.8971 (tpp) cc_final: 0.8711 (tpp) REVERT: B 1636 MET cc_start: 0.8065 (tmm) cc_final: 0.7428 (tmm) REVERT: B 2423 MET cc_start: 0.9151 (ptp) cc_final: 0.8833 (ptp) REVERT: B 2582 MET cc_start: 0.9421 (ptt) cc_final: 0.9101 (ttm) REVERT: B 2618 MET cc_start: 0.9282 (mpp) cc_final: 0.8807 (mpp) REVERT: B 2698 MET cc_start: 0.8595 (ppp) cc_final: 0.8283 (ppp) REVERT: B 2932 MET cc_start: 0.7937 (ptm) cc_final: 0.7103 (ppp) REVERT: B 3437 MET cc_start: 0.8809 (mtt) cc_final: 0.8542 (mtm) REVERT: B 3467 MET cc_start: 0.9327 (ptt) cc_final: 0.8903 (ppp) REVERT: B 3517 MET cc_start: 0.9427 (tpt) cc_final: 0.8824 (tpp) REVERT: B 3534 MET cc_start: 0.9573 (mpp) cc_final: 0.9263 (pmm) REVERT: B 3652 MET cc_start: 0.9187 (mmm) cc_final: 0.8703 (mpp) REVERT: B 3760 LYS cc_start: 0.9387 (mtpp) cc_final: 0.8890 (ptpp) REVERT: B 3836 MET cc_start: 0.9245 (ttt) cc_final: 0.8994 (ttt) REVERT: B 4014 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.8763 (ptpp) REVERT: B 4015 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.8983 (mm-30) REVERT: B 4023 MET cc_start: 0.8984 (ttt) cc_final: 0.8714 (ttt) REVERT: B 4047 MET cc_start: 0.9384 (tmm) cc_final: 0.9164 (tmm) REVERT: B 4048 LEU cc_start: 0.9744 (mt) cc_final: 0.9437 (mt) REVERT: B 4057 MET cc_start: 0.9199 (mtm) cc_final: 0.8912 (mtm) REVERT: B 4798 MET cc_start: 0.9235 (mmm) cc_final: 0.8964 (mmm) REVERT: B 4879 MET cc_start: 0.9126 (tpt) cc_final: 0.8916 (tpt) REVERT: B 4880 MET cc_start: 0.8985 (tpp) cc_final: 0.8774 (tpp) REVERT: B 4952 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8827 (pp20) REVERT: B 4953 ASP cc_start: 0.9435 (t0) cc_final: 0.8900 (m-30) REVERT: B 5035 GLN cc_start: 0.9464 (mt0) cc_final: 0.9216 (mp10) REVERT: C 343 GLU cc_start: 0.8197 (mp0) cc_final: 0.7921 (mp0) REVERT: C 345 LEU cc_start: 0.9568 (mp) cc_final: 0.9286 (mt) REVERT: C 403 MET cc_start: 0.8701 (mtp) cc_final: 0.8168 (mpp) REVERT: C 960 MET cc_start: 0.0284 (mmm) cc_final: -0.2074 (ptp) REVERT: C 1170 MET cc_start: 0.7877 (tpp) cc_final: 0.7391 (tpp) REVERT: C 1186 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.9120 (p0) REVERT: C 1494 MET cc_start: 0.8224 (mpp) cc_final: 0.7956 (tpp) REVERT: C 1601 MET cc_start: 0.8970 (tpp) cc_final: 0.8708 (tpp) REVERT: C 1636 MET cc_start: 0.8062 (tmm) cc_final: 0.7427 (tmm) REVERT: C 2423 MET cc_start: 0.9151 (ptp) cc_final: 0.8834 (ptp) REVERT: C 2582 MET cc_start: 0.9421 (ptt) cc_final: 0.9102 (ttm) REVERT: C 2618 MET cc_start: 0.9282 (mpp) cc_final: 0.8805 (mpp) REVERT: C 2698 MET cc_start: 0.8596 (ppp) cc_final: 0.8284 (ppp) REVERT: C 2932 MET cc_start: 0.7940 (ptm) cc_final: 0.7105 (ppp) REVERT: C 3106 MET cc_start: 0.8340 (mmm) cc_final: 0.7986 (mmm) REVERT: C 3437 MET cc_start: 0.8806 (mtt) cc_final: 0.8539 (mtm) REVERT: C 3467 MET cc_start: 0.9327 (ptt) cc_final: 0.8903 (ppp) REVERT: C 3517 MET cc_start: 0.9430 (tpt) cc_final: 0.8828 (tpp) REVERT: C 3534 MET cc_start: 0.9573 (mpp) cc_final: 0.9263 (pmm) REVERT: C 3652 MET cc_start: 0.9189 (mmm) cc_final: 0.8704 (mpp) REVERT: C 3760 LYS cc_start: 0.9389 (mtpp) cc_final: 0.8890 (ptpp) REVERT: C 3836 MET cc_start: 0.9243 (ttt) cc_final: 0.8992 (ttt) REVERT: C 4014 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.8763 (ptpp) REVERT: C 4015 GLU cc_start: 0.9413 (OUTLIER) cc_final: 0.8983 (mm-30) REVERT: C 4023 MET cc_start: 0.8984 (ttt) cc_final: 0.8714 (ttt) REVERT: C 4047 MET cc_start: 0.9385 (tmm) cc_final: 0.9164 (tmm) REVERT: C 4048 LEU cc_start: 0.9743 (mt) cc_final: 0.9436 (mt) REVERT: C 4057 MET cc_start: 0.9200 (mtm) cc_final: 0.8912 (mtm) REVERT: C 4798 MET cc_start: 0.9235 (mmm) cc_final: 0.8965 (mmm) REVERT: C 4839 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8102 (mtt) REVERT: C 4879 MET cc_start: 0.9087 (tpt) cc_final: 0.8845 (tpp) REVERT: C 4887 MET cc_start: 0.9059 (mmm) cc_final: 0.8844 (tpp) REVERT: C 4952 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8828 (pp20) REVERT: C 4953 ASP cc_start: 0.9436 (t0) cc_final: 0.8898 (m-30) REVERT: C 5035 GLN cc_start: 0.9465 (mt0) cc_final: 0.9218 (mp10) REVERT: D 343 GLU cc_start: 0.8198 (mp0) cc_final: 0.7922 (mp0) REVERT: D 345 LEU cc_start: 0.9567 (mp) cc_final: 0.9287 (mt) REVERT: D 403 MET cc_start: 0.8704 (mtp) cc_final: 0.8169 (mpp) REVERT: D 1170 MET cc_start: 0.7881 (tpp) cc_final: 0.7393 (tpp) REVERT: D 1186 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.9119 (p0) REVERT: D 1494 MET cc_start: 0.8222 (mpp) cc_final: 0.7953 (tpp) REVERT: D 1601 MET cc_start: 0.8970 (tpp) cc_final: 0.8710 (tpp) REVERT: D 1636 MET cc_start: 0.8062 (tmm) cc_final: 0.7426 (tmm) REVERT: D 2423 MET cc_start: 0.9152 (ptp) cc_final: 0.8836 (ptp) REVERT: D 2582 MET cc_start: 0.9422 (ptt) cc_final: 0.9103 (ttm) REVERT: D 2618 MET cc_start: 0.9280 (mpp) cc_final: 0.8806 (mpp) REVERT: D 2698 MET cc_start: 0.8595 (ppp) cc_final: 0.8283 (ppp) REVERT: D 2932 MET cc_start: 0.7938 (ptm) cc_final: 0.7102 (ppp) REVERT: D 3106 MET cc_start: 0.8336 (mmm) cc_final: 0.7982 (mmm) REVERT: D 3437 MET cc_start: 0.8810 (mtt) cc_final: 0.8543 (mtm) REVERT: D 3467 MET cc_start: 0.9309 (ptt) cc_final: 0.8872 (ppp) REVERT: D 3517 MET cc_start: 0.9427 (tpt) cc_final: 0.8817 (tpp) REVERT: D 3534 MET cc_start: 0.9572 (mpp) cc_final: 0.9263 (pmm) REVERT: D 3652 MET cc_start: 0.9190 (mmm) cc_final: 0.8705 (mpp) REVERT: D 3760 LYS cc_start: 0.9387 (mtpp) cc_final: 0.8888 (ptpp) REVERT: D 3836 MET cc_start: 0.9244 (ttt) cc_final: 0.8994 (ttt) REVERT: D 4014 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.8763 (ptpp) REVERT: D 4015 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.8983 (mm-30) REVERT: D 4023 MET cc_start: 0.8987 (ttt) cc_final: 0.8716 (ttt) REVERT: D 4047 MET cc_start: 0.9385 (tmm) cc_final: 0.9165 (tmm) REVERT: D 4048 LEU cc_start: 0.9744 (mt) cc_final: 0.9437 (mt) REVERT: D 4057 MET cc_start: 0.9198 (mtm) cc_final: 0.8912 (mtm) REVERT: D 4798 MET cc_start: 0.9236 (mmm) cc_final: 0.8963 (mmm) REVERT: D 4818 MET cc_start: 0.7928 (ttt) cc_final: 0.7591 (ttt) REVERT: D 4839 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8103 (mtt) REVERT: D 4879 MET cc_start: 0.9090 (tpt) cc_final: 0.8846 (tpp) REVERT: D 4887 MET cc_start: 0.9185 (mmm) cc_final: 0.8966 (tpp) REVERT: D 4952 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8826 (pp20) REVERT: D 4953 ASP cc_start: 0.9436 (t0) cc_final: 0.8898 (m-30) REVERT: D 5035 GLN cc_start: 0.9466 (mt0) cc_final: 0.9217 (mp10) REVERT: E 47 LYS cc_start: 0.9301 (mttt) cc_final: 0.9031 (mttp) REVERT: E 66 MET cc_start: 0.8937 (ptm) cc_final: 0.8463 (ppp) REVERT: F 47 LYS cc_start: 0.9302 (mttt) cc_final: 0.9030 (mttp) REVERT: F 66 MET cc_start: 0.9034 (ptm) cc_final: 0.8496 (ppp) REVERT: G 47 LYS cc_start: 0.9302 (mttt) cc_final: 0.9031 (mttp) REVERT: G 66 MET cc_start: 0.9031 (ptm) cc_final: 0.8494 (ppp) REVERT: H 47 LYS cc_start: 0.9302 (mttt) cc_final: 0.9031 (mttp) REVERT: H 66 MET cc_start: 0.9033 (ptm) cc_final: 0.8495 (ppp) outliers start: 106 outliers final: 64 residues processed: 800 average time/residue: 1.2385 time to fit residues: 1811.2289 Evaluate side-chains 776 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 697 time to evaluate : 12.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 4014 LYS Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4585 SER Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4747 SER Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4822 THR Chi-restraints excluded: chain A residue 4829 SER Chi-restraints excluded: chain A residue 4839 MET Chi-restraints excluded: chain A residue 4866 SER Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 4014 LYS Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4097 MET Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4585 SER Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4747 SER Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4822 THR Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1186 ASP Chi-restraints excluded: chain C residue 4014 LYS Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4097 MET Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4585 SER Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4747 SER Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4822 THR Chi-restraints excluded: chain C residue 4839 MET Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1186 ASP Chi-restraints excluded: chain D residue 4014 LYS Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4097 MET Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4585 SER Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4747 SER Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 581 optimal weight: 5.9990 chunk 1556 optimal weight: 30.0000 chunk 341 optimal weight: 0.0570 chunk 1014 optimal weight: 20.0000 chunk 426 optimal weight: 5.9990 chunk 1729 optimal weight: 4.9990 chunk 1436 optimal weight: 10.0000 chunk 800 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 572 optimal weight: 20.0000 chunk 908 optimal weight: 6.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3211 ASN ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3378 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3211 ASN ** B3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3378 GLN ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3211 ASN ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3378 GLN ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3211 ASN ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3378 GLN ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 146216 Z= 0.228 Angle : 0.591 12.310 198048 Z= 0.294 Chirality : 0.040 0.435 21768 Planarity : 0.004 0.058 25764 Dihedral : 4.373 58.087 19619 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.91 % Allowed : 10.00 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.96 (0.07), residues: 17840 helix: 1.77 (0.06), residues: 8908 sheet: -0.70 (0.12), residues: 1784 loop : -0.40 (0.08), residues: 7148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1143 HIS 0.007 0.001 HIS A3771 PHE 0.026 0.001 PHE A2973 TYR 0.025 0.001 TYR D1712 ARG 0.005 0.000 ARG D3672 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 703 time to evaluate : 12.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.8195 (mp0) cc_final: 0.7922 (mp0) REVERT: A 345 LEU cc_start: 0.9578 (mp) cc_final: 0.9304 (mt) REVERT: A 384 MET cc_start: 0.5330 (ptp) cc_final: 0.4674 (tmm) REVERT: A 403 MET cc_start: 0.8703 (mtp) cc_final: 0.8264 (mpp) REVERT: A 483 MET cc_start: 0.8687 (mmt) cc_final: 0.8459 (mmm) REVERT: A 960 MET cc_start: 0.0057 (mmm) cc_final: -0.2506 (ptp) REVERT: A 1152 MET cc_start: 0.8760 (mmp) cc_final: 0.8440 (mmp) REVERT: A 1170 MET cc_start: 0.7962 (tpp) cc_final: 0.7457 (tpp) REVERT: A 1186 ASP cc_start: 0.9431 (OUTLIER) cc_final: 0.9051 (p0) REVERT: A 1601 MET cc_start: 0.8975 (tpp) cc_final: 0.8688 (tpp) REVERT: A 1981 MET cc_start: 0.8577 (mmm) cc_final: 0.8153 (mmm) REVERT: A 2178 MET cc_start: 0.8730 (ppp) cc_final: 0.8453 (ppp) REVERT: A 2618 MET cc_start: 0.9273 (mpp) cc_final: 0.8792 (mpp) REVERT: A 3046 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9241 (mm) REVERT: A 3437 MET cc_start: 0.8857 (mtt) cc_final: 0.8353 (mtm) REVERT: A 3467 MET cc_start: 0.9328 (ptt) cc_final: 0.8889 (ppp) REVERT: A 3478 MET cc_start: 0.5462 (mmm) cc_final: 0.4893 (mpp) REVERT: A 3517 MET cc_start: 0.9445 (tpt) cc_final: 0.8828 (tpp) REVERT: A 3652 MET cc_start: 0.9226 (mmm) cc_final: 0.8701 (mpp) REVERT: A 3999 MET cc_start: 0.9064 (mmm) cc_final: 0.8628 (mmm) REVERT: A 4014 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.8691 (ptpp) REVERT: A 4015 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.9016 (mm-30) REVERT: A 4047 MET cc_start: 0.9362 (tmm) cc_final: 0.9080 (tmm) REVERT: A 4798 MET cc_start: 0.9240 (mmm) cc_final: 0.9000 (mmm) REVERT: A 4839 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8149 (mtt) REVERT: A 4879 MET cc_start: 0.9247 (tpt) cc_final: 0.9033 (tpp) REVERT: A 4887 MET cc_start: 0.9087 (mmm) cc_final: 0.8849 (tpp) REVERT: A 4952 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8783 (pp20) REVERT: A 4953 ASP cc_start: 0.9417 (t0) cc_final: 0.8855 (m-30) REVERT: A 5035 GLN cc_start: 0.9473 (mt0) cc_final: 0.9217 (mp10) REVERT: B 31 GLU cc_start: 0.9397 (OUTLIER) cc_final: 0.8913 (pm20) REVERT: B 343 GLU cc_start: 0.8211 (mp0) cc_final: 0.7938 (mp0) REVERT: B 345 LEU cc_start: 0.9562 (mp) cc_final: 0.9270 (mt) REVERT: B 403 MET cc_start: 0.8781 (mtp) cc_final: 0.8367 (mpp) REVERT: B 960 MET cc_start: 0.0469 (mmm) cc_final: -0.1990 (ptp) REVERT: B 1170 MET cc_start: 0.7972 (tpp) cc_final: 0.7500 (tpp) REVERT: B 1186 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.9103 (p0) REVERT: B 1494 MET cc_start: 0.8368 (mpp) cc_final: 0.8155 (tpp) REVERT: B 1601 MET cc_start: 0.9024 (tpp) cc_final: 0.8717 (tpp) REVERT: B 1636 MET cc_start: 0.8070 (tmm) cc_final: 0.7436 (tmm) REVERT: B 2170 MET cc_start: 0.8425 (tpp) cc_final: 0.7761 (tpp) REVERT: B 2423 MET cc_start: 0.9157 (ptp) cc_final: 0.8899 (ptp) REVERT: B 2582 MET cc_start: 0.9437 (ptt) cc_final: 0.9128 (ttm) REVERT: B 2618 MET cc_start: 0.9276 (mpp) cc_final: 0.8798 (mpp) REVERT: B 2932 MET cc_start: 0.8149 (ptm) cc_final: 0.7268 (ppp) REVERT: B 3046 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9240 (mm) REVERT: B 3437 MET cc_start: 0.8816 (mtt) cc_final: 0.8550 (mtm) REVERT: B 3467 MET cc_start: 0.9312 (ptt) cc_final: 0.8880 (ppp) REVERT: B 3517 MET cc_start: 0.9434 (tpt) cc_final: 0.8834 (tpp) REVERT: B 3652 MET cc_start: 0.9202 (mmm) cc_final: 0.8809 (mpp) REVERT: B 3836 MET cc_start: 0.9270 (ttt) cc_final: 0.9026 (ttt) REVERT: B 4000 MET cc_start: 0.9043 (mmm) cc_final: 0.8842 (mtm) REVERT: B 4014 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.8815 (ptpp) REVERT: B 4015 GLU cc_start: 0.9419 (OUTLIER) cc_final: 0.9005 (mm-30) REVERT: B 4047 MET cc_start: 0.9350 (tmm) cc_final: 0.9134 (tmm) REVERT: B 4048 LEU cc_start: 0.9752 (mt) cc_final: 0.9444 (mt) REVERT: B 4798 MET cc_start: 0.9243 (mmm) cc_final: 0.8986 (mmm) REVERT: B 4879 MET cc_start: 0.9140 (tpt) cc_final: 0.8937 (tpt) REVERT: B 4880 MET cc_start: 0.8970 (tpp) cc_final: 0.8759 (tpp) REVERT: B 4952 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8813 (pp20) REVERT: B 4953 ASP cc_start: 0.9443 (t0) cc_final: 0.8912 (m-30) REVERT: B 5013 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8727 (mpp) REVERT: B 5035 GLN cc_start: 0.9466 (mt0) cc_final: 0.9208 (mp10) REVERT: C 31 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.8913 (pm20) REVERT: C 343 GLU cc_start: 0.8210 (mp0) cc_final: 0.7937 (mp0) REVERT: C 345 LEU cc_start: 0.9564 (mp) cc_final: 0.9272 (mt) REVERT: C 403 MET cc_start: 0.8736 (mtp) cc_final: 0.8221 (mpp) REVERT: C 960 MET cc_start: 0.0476 (mmm) cc_final: -0.1988 (ptp) REVERT: C 1170 MET cc_start: 0.7967 (tpp) cc_final: 0.7503 (tpp) REVERT: C 1186 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.9104 (p0) REVERT: C 1494 MET cc_start: 0.8369 (mpp) cc_final: 0.8155 (tpp) REVERT: C 1601 MET cc_start: 0.9022 (tpp) cc_final: 0.8715 (tpp) REVERT: C 1636 MET cc_start: 0.8076 (tmm) cc_final: 0.7439 (tmm) REVERT: C 2170 MET cc_start: 0.8427 (tpp) cc_final: 0.7760 (tpp) REVERT: C 2423 MET cc_start: 0.9156 (ptp) cc_final: 0.8899 (ptp) REVERT: C 2582 MET cc_start: 0.9437 (ptt) cc_final: 0.9128 (ttm) REVERT: C 2618 MET cc_start: 0.9275 (mpp) cc_final: 0.8797 (mpp) REVERT: C 2932 MET cc_start: 0.8153 (ptm) cc_final: 0.7271 (ppp) REVERT: C 3046 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9239 (mm) REVERT: C 3437 MET cc_start: 0.8814 (mtt) cc_final: 0.8546 (mtm) REVERT: C 3467 MET cc_start: 0.9312 (ptt) cc_final: 0.8880 (ppp) REVERT: C 3517 MET cc_start: 0.9437 (tpt) cc_final: 0.8836 (tpp) REVERT: C 3652 MET cc_start: 0.9203 (mmm) cc_final: 0.8811 (mpp) REVERT: C 3836 MET cc_start: 0.9268 (ttt) cc_final: 0.9024 (ttt) REVERT: C 4000 MET cc_start: 0.9043 (mmm) cc_final: 0.8842 (mtm) REVERT: C 4014 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.8814 (ptpp) REVERT: C 4015 GLU cc_start: 0.9420 (OUTLIER) cc_final: 0.9005 (mm-30) REVERT: C 4047 MET cc_start: 0.9350 (tmm) cc_final: 0.9135 (tmm) REVERT: C 4048 LEU cc_start: 0.9752 (mt) cc_final: 0.9444 (mt) REVERT: C 4798 MET cc_start: 0.9241 (mmm) cc_final: 0.8984 (mmm) REVERT: C 4879 MET cc_start: 0.9144 (tpt) cc_final: 0.8866 (tpp) REVERT: C 4887 MET cc_start: 0.9071 (mmm) cc_final: 0.8850 (tpp) REVERT: C 4952 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8816 (pp20) REVERT: C 4953 ASP cc_start: 0.9445 (t0) cc_final: 0.8914 (m-30) REVERT: C 5013 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8725 (mpp) REVERT: C 5035 GLN cc_start: 0.9467 (mt0) cc_final: 0.9209 (mp10) REVERT: D 31 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.8912 (pm20) REVERT: D 343 GLU cc_start: 0.8245 (mp0) cc_final: 0.7969 (mp0) REVERT: D 345 LEU cc_start: 0.9554 (mp) cc_final: 0.9284 (mt) REVERT: D 403 MET cc_start: 0.8777 (mtp) cc_final: 0.8246 (mpp) REVERT: D 960 MET cc_start: 0.0690 (mmm) cc_final: -0.1928 (ptp) REVERT: D 1170 MET cc_start: 0.7970 (tpp) cc_final: 0.7505 (tpp) REVERT: D 1186 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.9105 (p0) REVERT: D 1494 MET cc_start: 0.8367 (mpp) cc_final: 0.8154 (tpp) REVERT: D 1601 MET cc_start: 0.9024 (tpp) cc_final: 0.8716 (tpp) REVERT: D 1636 MET cc_start: 0.8070 (tmm) cc_final: 0.7437 (tmm) REVERT: D 2170 MET cc_start: 0.8427 (tpp) cc_final: 0.7762 (tpp) REVERT: D 2423 MET cc_start: 0.9158 (ptp) cc_final: 0.8899 (ptp) REVERT: D 2582 MET cc_start: 0.9438 (ptt) cc_final: 0.9129 (ttm) REVERT: D 2618 MET cc_start: 0.9274 (mpp) cc_final: 0.8797 (mpp) REVERT: D 2932 MET cc_start: 0.8151 (ptm) cc_final: 0.7269 (ppp) REVERT: D 3046 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9239 (mm) REVERT: D 3437 MET cc_start: 0.8818 (mtt) cc_final: 0.8550 (mtm) REVERT: D 3467 MET cc_start: 0.9312 (ptt) cc_final: 0.8879 (ppp) REVERT: D 3517 MET cc_start: 0.9433 (tpt) cc_final: 0.8826 (tpp) REVERT: D 3652 MET cc_start: 0.9203 (mmm) cc_final: 0.8809 (mpp) REVERT: D 3836 MET cc_start: 0.9271 (ttt) cc_final: 0.9027 (ttt) REVERT: D 4000 MET cc_start: 0.9044 (mmm) cc_final: 0.8844 (mtm) REVERT: D 4014 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.8814 (ptpp) REVERT: D 4015 GLU cc_start: 0.9419 (OUTLIER) cc_final: 0.9004 (mm-30) REVERT: D 4047 MET cc_start: 0.9352 (tmm) cc_final: 0.9135 (tmm) REVERT: D 4048 LEU cc_start: 0.9753 (mt) cc_final: 0.9444 (mt) REVERT: D 4798 MET cc_start: 0.9241 (mmm) cc_final: 0.8985 (mmm) REVERT: D 4818 MET cc_start: 0.7958 (ttt) cc_final: 0.7520 (ttm) REVERT: D 4879 MET cc_start: 0.9144 (tpt) cc_final: 0.8867 (tpp) REVERT: D 4887 MET cc_start: 0.9183 (mmm) cc_final: 0.8972 (tpp) REVERT: D 4952 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8814 (pp20) REVERT: D 4953 ASP cc_start: 0.9444 (t0) cc_final: 0.8911 (m-30) REVERT: D 5035 GLN cc_start: 0.9469 (mt0) cc_final: 0.9206 (mp10) REVERT: E 47 LYS cc_start: 0.9297 (mttt) cc_final: 0.8933 (mptt) REVERT: E 66 MET cc_start: 0.9044 (ptm) cc_final: 0.8203 (ttp) REVERT: F 47 LYS cc_start: 0.9297 (mttt) cc_final: 0.9025 (mttp) REVERT: F 66 MET cc_start: 0.9050 (ptm) cc_final: 0.8209 (ttp) REVERT: G 47 LYS cc_start: 0.9297 (mttt) cc_final: 0.9026 (mttp) REVERT: G 66 MET cc_start: 0.9048 (ptm) cc_final: 0.8205 (ttp) REVERT: H 47 LYS cc_start: 0.9297 (mttt) cc_final: 0.9025 (mttp) REVERT: H 66 MET cc_start: 0.9048 (ptm) cc_final: 0.8206 (ttp) outliers start: 128 outliers final: 74 residues processed: 806 average time/residue: 1.1767 time to fit residues: 1725.5367 Evaluate side-chains 792 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 696 time to evaluate : 11.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2296 GLU Chi-restraints excluded: chain A residue 3046 LEU Chi-restraints excluded: chain A residue 4014 LYS Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4097 MET Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4585 SER Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4747 SER Chi-restraints excluded: chain A residue 4748 LEU Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4822 THR Chi-restraints excluded: chain A residue 4829 SER Chi-restraints excluded: chain A residue 4839 MET Chi-restraints excluded: chain A residue 4866 SER Chi-restraints excluded: chain A residue 4948 GLU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 3046 LEU Chi-restraints excluded: chain B residue 4014 LYS Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4097 MET Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4585 SER Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4747 SER Chi-restraints excluded: chain B residue 4748 LEU Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4822 THR Chi-restraints excluded: chain B residue 5013 MET Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1186 ASP Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 3046 LEU Chi-restraints excluded: chain C residue 4014 LYS Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4097 MET Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4585 SER Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4747 SER Chi-restraints excluded: chain C residue 4748 LEU Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4822 THR Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 5013 MET Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1186 ASP Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 3046 LEU Chi-restraints excluded: chain D residue 4014 LYS Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4097 MET Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4585 SER Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4747 SER Chi-restraints excluded: chain D residue 4748 LEU Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4829 SER Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1667 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 985 optimal weight: 5.9990 chunk 1263 optimal weight: 10.0000 chunk 978 optimal weight: 9.9990 chunk 1456 optimal weight: 0.7980 chunk 966 optimal weight: 50.0000 chunk 1723 optimal weight: 1.9990 chunk 1078 optimal weight: 0.6980 chunk 1050 optimal weight: 3.9990 chunk 795 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN A 765 GLN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3457 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3608 GLN ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3211 ASN ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3457 ASN D3608 GLN ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 146216 Z= 0.158 Angle : 0.571 12.315 198048 Z= 0.282 Chirality : 0.039 0.261 21768 Planarity : 0.004 0.058 25764 Dihedral : 4.248 57.960 19607 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.69 % Allowed : 10.37 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 1.08 (0.07), residues: 17840 helix: 1.87 (0.06), residues: 8864 sheet: -0.59 (0.12), residues: 1828 loop : -0.33 (0.08), residues: 7148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1143 HIS 0.008 0.001 HIS A3771 PHE 0.029 0.001 PHE A2973 TYR 0.022 0.001 TYR B5009 ARG 0.004 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 716 time to evaluate : 12.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.8802 (pm20) REVERT: A 343 GLU cc_start: 0.8147 (mp0) cc_final: 0.7859 (mp0) REVERT: A 345 LEU cc_start: 0.9545 (mp) cc_final: 0.9293 (mt) REVERT: A 384 MET cc_start: 0.5219 (ptp) cc_final: 0.4620 (tmm) REVERT: A 403 MET cc_start: 0.8744 (mtp) cc_final: 0.8278 (mpp) REVERT: A 960 MET cc_start: -0.0173 (mmm) cc_final: -0.2677 (ptp) REVERT: A 1152 MET cc_start: 0.8598 (mmp) cc_final: 0.8251 (mmp) REVERT: A 1186 ASP cc_start: 0.9428 (OUTLIER) cc_final: 0.9044 (p0) REVERT: A 1494 MET cc_start: 0.8551 (tpp) cc_final: 0.7786 (mpp) REVERT: A 1601 MET cc_start: 0.8963 (tpp) cc_final: 0.8674 (tpp) REVERT: A 1981 MET cc_start: 0.8648 (mmm) cc_final: 0.8221 (mmm) REVERT: A 2170 MET cc_start: 0.8137 (tpp) cc_final: 0.7551 (tpp) REVERT: A 2178 MET cc_start: 0.8674 (ppp) cc_final: 0.8401 (ppp) REVERT: A 2618 MET cc_start: 0.9256 (mpp) cc_final: 0.8866 (mpp) REVERT: A 2698 MET cc_start: 0.8581 (ppp) cc_final: 0.8274 (ppp) REVERT: A 3106 MET cc_start: 0.8914 (mmt) cc_final: 0.8214 (mmm) REVERT: A 3437 MET cc_start: 0.8849 (mtt) cc_final: 0.8594 (mtm) REVERT: A 3467 MET cc_start: 0.9324 (ptt) cc_final: 0.8888 (ppp) REVERT: A 3517 MET cc_start: 0.9439 (tpt) cc_final: 0.8794 (tpp) REVERT: A 3534 MET cc_start: 0.9533 (mpp) cc_final: 0.9249 (pmm) REVERT: A 3652 MET cc_start: 0.9196 (mmm) cc_final: 0.8680 (mpp) REVERT: A 4000 MET cc_start: 0.8753 (mmm) cc_final: 0.8397 (mmm) REVERT: A 4014 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.8863 (ptpp) REVERT: A 4015 GLU cc_start: 0.9407 (OUTLIER) cc_final: 0.9001 (mm-30) REVERT: A 4047 MET cc_start: 0.9357 (tmm) cc_final: 0.9094 (tmm) REVERT: A 4048 LEU cc_start: 0.9722 (mt) cc_final: 0.9348 (mt) REVERT: A 4798 MET cc_start: 0.9223 (mmm) cc_final: 0.9006 (mmm) REVERT: A 4879 MET cc_start: 0.9240 (tpt) cc_final: 0.9029 (tpp) REVERT: A 4887 MET cc_start: 0.9063 (mmm) cc_final: 0.8824 (tpp) REVERT: A 4952 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8813 (pp20) REVERT: A 5035 GLN cc_start: 0.9470 (mt0) cc_final: 0.9202 (mp10) REVERT: B 31 GLU cc_start: 0.9390 (OUTLIER) cc_final: 0.8890 (pm20) REVERT: B 343 GLU cc_start: 0.8187 (mp0) cc_final: 0.7905 (mp0) REVERT: B 345 LEU cc_start: 0.9530 (mp) cc_final: 0.9274 (mt) REVERT: B 403 MET cc_start: 0.8826 (mtp) cc_final: 0.8390 (mpp) REVERT: B 483 MET cc_start: 0.8611 (mmt) cc_final: 0.8215 (mmm) REVERT: B 960 MET cc_start: 0.0405 (mmm) cc_final: -0.2166 (ptp) REVERT: B 1186 ASP cc_start: 0.9428 (OUTLIER) cc_final: 0.9053 (p0) REVERT: B 1601 MET cc_start: 0.8999 (tpp) cc_final: 0.8671 (tpp) REVERT: B 1731 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9337 (mt) REVERT: B 1981 MET cc_start: 0.8299 (mmp) cc_final: 0.7999 (mmm) REVERT: B 2170 MET cc_start: 0.8419 (tpp) cc_final: 0.7552 (tpp) REVERT: B 2178 MET cc_start: 0.8662 (ppp) cc_final: 0.8459 (ppp) REVERT: B 2423 MET cc_start: 0.9143 (ptp) cc_final: 0.8862 (ptp) REVERT: B 2618 MET cc_start: 0.9266 (mpp) cc_final: 0.8846 (mpp) REVERT: B 2932 MET cc_start: 0.8199 (ptm) cc_final: 0.7368 (ppp) REVERT: B 3106 MET cc_start: 0.8293 (mmm) cc_final: 0.8069 (mmm) REVERT: B 3437 MET cc_start: 0.8795 (mtt) cc_final: 0.8538 (mtm) REVERT: B 3467 MET cc_start: 0.9306 (ptt) cc_final: 0.8878 (ppp) REVERT: B 3517 MET cc_start: 0.9298 (tpt) cc_final: 0.8784 (tpp) REVERT: B 3652 MET cc_start: 0.9174 (mmm) cc_final: 0.8919 (mpp) REVERT: B 3673 MET cc_start: 0.9407 (mmm) cc_final: 0.8980 (mpp) REVERT: B 4014 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.8901 (ptpp) REVERT: B 4015 GLU cc_start: 0.9405 (OUTLIER) cc_final: 0.8992 (mm-30) REVERT: B 4047 MET cc_start: 0.9347 (tmm) cc_final: 0.9137 (tmm) REVERT: B 4048 LEU cc_start: 0.9739 (mt) cc_final: 0.9448 (mt) REVERT: B 4798 MET cc_start: 0.9190 (mmm) cc_final: 0.8951 (mmm) REVERT: B 4952 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8918 (tm-30) REVERT: B 4953 ASP cc_start: 0.9448 (t0) cc_final: 0.9024 (m-30) REVERT: B 5012 LYS cc_start: 0.9233 (ttpt) cc_final: 0.8611 (ttpp) REVERT: B 5013 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8636 (mpp) REVERT: B 5035 GLN cc_start: 0.9467 (mt0) cc_final: 0.9195 (mp10) REVERT: C 31 GLU cc_start: 0.9390 (OUTLIER) cc_final: 0.8890 (pm20) REVERT: C 343 GLU cc_start: 0.8188 (mp0) cc_final: 0.7905 (mp0) REVERT: C 345 LEU cc_start: 0.9531 (mp) cc_final: 0.9276 (mt) REVERT: C 403 MET cc_start: 0.8705 (mtp) cc_final: 0.8242 (mpp) REVERT: C 483 MET cc_start: 0.8610 (mmt) cc_final: 0.8217 (mmm) REVERT: C 960 MET cc_start: 0.0414 (mmm) cc_final: -0.2164 (ptp) REVERT: C 1186 ASP cc_start: 0.9426 (OUTLIER) cc_final: 0.9054 (p0) REVERT: C 1601 MET cc_start: 0.8997 (tpp) cc_final: 0.8666 (tpp) REVERT: C 1731 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9336 (mt) REVERT: C 1981 MET cc_start: 0.8297 (mmp) cc_final: 0.7999 (mmm) REVERT: C 2170 MET cc_start: 0.8418 (tpp) cc_final: 0.7551 (tpp) REVERT: C 2178 MET cc_start: 0.8662 (ppp) cc_final: 0.8460 (ppp) REVERT: C 2423 MET cc_start: 0.9144 (ptp) cc_final: 0.8861 (ptp) REVERT: C 2618 MET cc_start: 0.9263 (mpp) cc_final: 0.8843 (mpp) REVERT: C 2932 MET cc_start: 0.8200 (ptm) cc_final: 0.7370 (ppp) REVERT: C 3106 MET cc_start: 0.8928 (mmt) cc_final: 0.8232 (mmm) REVERT: C 3437 MET cc_start: 0.8791 (mtt) cc_final: 0.8535 (mtm) REVERT: C 3467 MET cc_start: 0.9307 (ptt) cc_final: 0.8878 (ppp) REVERT: C 3517 MET cc_start: 0.9302 (tpt) cc_final: 0.8787 (tpp) REVERT: C 3652 MET cc_start: 0.9174 (mmm) cc_final: 0.8919 (mpp) REVERT: C 3673 MET cc_start: 0.9407 (mmm) cc_final: 0.8982 (mpp) REVERT: C 4014 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.8902 (ptpp) REVERT: C 4015 GLU cc_start: 0.9405 (OUTLIER) cc_final: 0.8992 (mm-30) REVERT: C 4047 MET cc_start: 0.9348 (tmm) cc_final: 0.9138 (tmm) REVERT: C 4048 LEU cc_start: 0.9740 (mt) cc_final: 0.9448 (mt) REVERT: C 4798 MET cc_start: 0.9188 (mmm) cc_final: 0.8950 (mmm) REVERT: C 4879 MET cc_start: 0.9108 (tpt) cc_final: 0.8862 (tpp) REVERT: C 4887 MET cc_start: 0.9060 (mmm) cc_final: 0.8835 (tpp) REVERT: C 4952 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8920 (tm-30) REVERT: C 4953 ASP cc_start: 0.9450 (t0) cc_final: 0.9021 (m-30) REVERT: C 5012 LYS cc_start: 0.9231 (ttpt) cc_final: 0.8610 (ttpp) REVERT: C 5013 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8636 (mpp) REVERT: C 5035 GLN cc_start: 0.9468 (mt0) cc_final: 0.9196 (mp10) REVERT: D 31 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.8889 (pm20) REVERT: D 343 GLU cc_start: 0.8187 (mp0) cc_final: 0.7898 (mp0) REVERT: D 345 LEU cc_start: 0.9524 (mp) cc_final: 0.9247 (mt) REVERT: D 403 MET cc_start: 0.8706 (mtp) cc_final: 0.8241 (mpp) REVERT: D 483 MET cc_start: 0.8611 (mmt) cc_final: 0.8217 (mmm) REVERT: D 960 MET cc_start: 0.0441 (mmm) cc_final: -0.2109 (ptp) REVERT: D 1186 ASP cc_start: 0.9427 (OUTLIER) cc_final: 0.9054 (p0) REVERT: D 1601 MET cc_start: 0.8997 (tpp) cc_final: 0.8668 (tpp) REVERT: D 1731 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9336 (mt) REVERT: D 1981 MET cc_start: 0.8296 (mmp) cc_final: 0.7997 (mmm) REVERT: D 2170 MET cc_start: 0.8415 (tpp) cc_final: 0.7560 (tpp) REVERT: D 2178 MET cc_start: 0.8666 (ppp) cc_final: 0.8461 (ppp) REVERT: D 2423 MET cc_start: 0.9144 (ptp) cc_final: 0.8863 (ptp) REVERT: D 2618 MET cc_start: 0.9262 (mpp) cc_final: 0.8842 (mpp) REVERT: D 2932 MET cc_start: 0.8197 (ptm) cc_final: 0.7366 (ppp) REVERT: D 3106 MET cc_start: 0.8923 (mmt) cc_final: 0.8226 (mmm) REVERT: D 3437 MET cc_start: 0.8795 (mtt) cc_final: 0.8539 (mtm) REVERT: D 3467 MET cc_start: 0.9307 (ptt) cc_final: 0.8877 (ppp) REVERT: D 3517 MET cc_start: 0.9298 (tpt) cc_final: 0.8778 (tpp) REVERT: D 3652 MET cc_start: 0.9175 (mmm) cc_final: 0.8918 (mpp) REVERT: D 3673 MET cc_start: 0.9407 (mmm) cc_final: 0.8980 (mpp) REVERT: D 4014 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.8902 (ptpp) REVERT: D 4015 GLU cc_start: 0.9404 (OUTLIER) cc_final: 0.8992 (mm-30) REVERT: D 4047 MET cc_start: 0.9350 (tmm) cc_final: 0.9138 (tmm) REVERT: D 4048 LEU cc_start: 0.9739 (mt) cc_final: 0.9447 (mt) REVERT: D 4798 MET cc_start: 0.9188 (mmm) cc_final: 0.8950 (mmm) REVERT: D 4818 MET cc_start: 0.7816 (ttt) cc_final: 0.7360 (ttm) REVERT: D 4879 MET cc_start: 0.9107 (tpt) cc_final: 0.8865 (tpp) REVERT: D 4952 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8919 (tm-30) REVERT: D 4953 ASP cc_start: 0.9448 (t0) cc_final: 0.9023 (m-30) REVERT: D 5013 MET cc_start: 0.9045 (mtm) cc_final: 0.8460 (mtm) REVERT: D 5035 GLN cc_start: 0.9469 (mt0) cc_final: 0.9199 (mp10) REVERT: E 29 MET cc_start: 0.7467 (mpp) cc_final: 0.7187 (mpp) REVERT: E 47 LYS cc_start: 0.9296 (mttt) cc_final: 0.8930 (mptt) REVERT: E 66 MET cc_start: 0.9022 (ptm) cc_final: 0.8194 (ttp) REVERT: F 47 LYS cc_start: 0.9296 (mttt) cc_final: 0.8932 (mptt) REVERT: F 66 MET cc_start: 0.9026 (ptm) cc_final: 0.8199 (ttp) REVERT: G 47 LYS cc_start: 0.9297 (mttt) cc_final: 0.8932 (mptt) REVERT: G 66 MET cc_start: 0.9024 (ptm) cc_final: 0.8196 (ttp) REVERT: H 47 LYS cc_start: 0.9296 (mttt) cc_final: 0.8932 (mptt) REVERT: H 66 MET cc_start: 0.9026 (ptm) cc_final: 0.8195 (ttp) outliers start: 94 outliers final: 62 residues processed: 795 average time/residue: 1.1837 time to fit residues: 1705.9294 Evaluate side-chains 781 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 698 time to evaluate : 12.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2296 GLU Chi-restraints excluded: chain A residue 3440 GLU Chi-restraints excluded: chain A residue 4014 LYS Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4748 LEU Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4822 THR Chi-restraints excluded: chain A residue 4866 SER Chi-restraints excluded: chain A residue 4948 GLU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 3440 GLU Chi-restraints excluded: chain B residue 4014 LYS Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4097 MET Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4748 LEU Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4822 THR Chi-restraints excluded: chain B residue 5013 MET Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1186 ASP Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 3440 GLU Chi-restraints excluded: chain C residue 4014 LYS Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4097 MET Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4748 LEU Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4822 THR Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 5013 MET Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1186 ASP Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 3440 GLU Chi-restraints excluded: chain D residue 4014 LYS Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4097 MET Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4748 LEU Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1066 optimal weight: 6.9990 chunk 688 optimal weight: 20.0000 chunk 1029 optimal weight: 7.9990 chunk 519 optimal weight: 0.0980 chunk 338 optimal weight: 8.9990 chunk 333 optimal weight: 20.0000 chunk 1095 optimal weight: 10.0000 chunk 1174 optimal weight: 0.8980 chunk 852 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 1354 optimal weight: 10.0000 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 GLN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3211 ASN ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3608 GLN ** A3683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3211 ASN ** B3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 146216 Z= 0.262 Angle : 0.617 13.475 198048 Z= 0.305 Chirality : 0.040 0.171 21768 Planarity : 0.004 0.057 25764 Dihedral : 4.250 57.824 19603 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.82 % Allowed : 10.43 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 1.02 (0.07), residues: 17840 helix: 1.82 (0.06), residues: 8904 sheet: -0.65 (0.12), residues: 1784 loop : -0.36 (0.08), residues: 7152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1143 HIS 0.007 0.001 HIS B3771 PHE 0.027 0.001 PHE D2973 TYR 0.025 0.001 TYR A5009 ARG 0.005 0.000 ARG D 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 717 time to evaluate : 12.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.8239 (mp0) cc_final: 0.7970 (mp0) REVERT: A 345 LEU cc_start: 0.9586 (mp) cc_final: 0.9339 (mt) REVERT: A 384 MET cc_start: 0.5306 (ptp) cc_final: 0.4613 (tmm) REVERT: A 403 MET cc_start: 0.8707 (mtp) cc_final: 0.8291 (mpp) REVERT: A 960 MET cc_start: 0.0234 (mmm) cc_final: -0.2470 (ptp) REVERT: A 1057 ASP cc_start: 0.8239 (m-30) cc_final: 0.7780 (t0) REVERT: A 1152 MET cc_start: 0.8757 (mmp) cc_final: 0.8381 (mmp) REVERT: A 1186 ASP cc_start: 0.9469 (OUTLIER) cc_final: 0.9036 (p0) REVERT: A 1601 MET cc_start: 0.8949 (tpp) cc_final: 0.8670 (tpp) REVERT: A 1731 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9335 (mt) REVERT: A 2170 MET cc_start: 0.8393 (tpp) cc_final: 0.7818 (tpp) REVERT: A 2178 MET cc_start: 0.8742 (ppp) cc_final: 0.8507 (ppp) REVERT: A 2198 MET cc_start: 0.9231 (mmp) cc_final: 0.8611 (mpp) REVERT: A 2618 MET cc_start: 0.9263 (mpp) cc_final: 0.8663 (mpp) REVERT: A 3437 MET cc_start: 0.8869 (mtt) cc_final: 0.8622 (mtm) REVERT: A 3467 MET cc_start: 0.9310 (ptt) cc_final: 0.8868 (ppp) REVERT: A 3517 MET cc_start: 0.9325 (tpt) cc_final: 0.8692 (tpp) REVERT: A 3652 MET cc_start: 0.9222 (mmm) cc_final: 0.8816 (mpp) REVERT: A 3673 MET cc_start: 0.9320 (tpp) cc_final: 0.8781 (mpp) REVERT: A 3758 MET cc_start: 0.9155 (tmm) cc_final: 0.8813 (tmm) REVERT: A 3875 MET cc_start: 0.8149 (mmt) cc_final: 0.7664 (mmt) REVERT: A 4014 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8828 (ptpp) REVERT: A 4015 GLU cc_start: 0.9428 (OUTLIER) cc_final: 0.9037 (mm-30) REVERT: A 4047 MET cc_start: 0.9351 (tmm) cc_final: 0.9071 (tmm) REVERT: A 4732 PHE cc_start: 0.8827 (m-80) cc_final: 0.8388 (m-80) REVERT: A 4798 MET cc_start: 0.9234 (mmm) cc_final: 0.8995 (mmm) REVERT: A 4879 MET cc_start: 0.9256 (tpt) cc_final: 0.9004 (tpp) REVERT: A 4880 MET cc_start: 0.9018 (mmm) cc_final: 0.8729 (tpp) REVERT: A 4887 MET cc_start: 0.9071 (mmm) cc_final: 0.8851 (tpp) REVERT: A 4952 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8872 (pp20) REVERT: A 5013 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8589 (mpp) REVERT: A 5035 GLN cc_start: 0.9472 (mt0) cc_final: 0.9214 (mp10) REVERT: B 31 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.8910 (pm20) REVERT: B 343 GLU cc_start: 0.8252 (mp0) cc_final: 0.7980 (mp0) REVERT: B 345 LEU cc_start: 0.9582 (mp) cc_final: 0.9303 (mt) REVERT: B 403 MET cc_start: 0.8759 (mtp) cc_final: 0.8349 (mpp) REVERT: B 483 MET cc_start: 0.8603 (mmt) cc_final: 0.8222 (mmm) REVERT: B 960 MET cc_start: 0.0770 (mmm) cc_final: -0.1967 (ptp) REVERT: B 1186 ASP cc_start: 0.9467 (OUTLIER) cc_final: 0.9066 (p0) REVERT: B 1601 MET cc_start: 0.9071 (tpp) cc_final: 0.8739 (tpp) REVERT: B 1731 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9320 (mt) REVERT: B 1981 MET cc_start: 0.8237 (mmp) cc_final: 0.7922 (mmm) REVERT: B 2198 MET cc_start: 0.9247 (mmp) cc_final: 0.8611 (mpp) REVERT: B 2423 MET cc_start: 0.9156 (ptp) cc_final: 0.8876 (ptp) REVERT: B 2582 MET cc_start: 0.9446 (ptt) cc_final: 0.9132 (ttm) REVERT: B 2618 MET cc_start: 0.9250 (mpp) cc_final: 0.8753 (mpp) REVERT: B 2932 MET cc_start: 0.7949 (ptm) cc_final: 0.7117 (ppp) REVERT: B 2966 TRP cc_start: 0.8804 (OUTLIER) cc_final: 0.8310 (t-100) REVERT: B 2967 MET cc_start: 0.4902 (ptm) cc_final: 0.4457 (ptm) REVERT: B 3106 MET cc_start: 0.8319 (mmm) cc_final: 0.8072 (mmm) REVERT: B 3437 MET cc_start: 0.8813 (mtt) cc_final: 0.8562 (mtm) REVERT: B 3467 MET cc_start: 0.9314 (ptt) cc_final: 0.8903 (ppp) REVERT: B 3517 MET cc_start: 0.9315 (tpt) cc_final: 0.8704 (tpp) REVERT: B 3652 MET cc_start: 0.9193 (mmm) cc_final: 0.8901 (mpp) REVERT: B 3875 MET cc_start: 0.8172 (mmt) cc_final: 0.7685 (mmt) REVERT: B 4000 MET cc_start: 0.9077 (mmm) cc_final: 0.8783 (mmm) REVERT: B 4014 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.8745 (ptpp) REVERT: B 4015 GLU cc_start: 0.9421 (OUTLIER) cc_final: 0.8900 (mm-30) REVERT: B 4047 MET cc_start: 0.9336 (tmm) cc_final: 0.9063 (tmm) REVERT: B 4732 PHE cc_start: 0.8857 (m-80) cc_final: 0.8415 (m-80) REVERT: B 4798 MET cc_start: 0.9229 (mmm) cc_final: 0.8969 (mmm) REVERT: B 4879 MET cc_start: 0.9198 (tpt) cc_final: 0.8901 (tpp) REVERT: B 4952 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8875 (tm-30) REVERT: B 4953 ASP cc_start: 0.9440 (t0) cc_final: 0.8847 (m-30) REVERT: B 5006 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8813 (pm20) REVERT: B 5013 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8686 (mpp) REVERT: B 5035 GLN cc_start: 0.9470 (mt0) cc_final: 0.9209 (mp10) REVERT: C 31 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.8909 (pm20) REVERT: C 343 GLU cc_start: 0.8250 (mp0) cc_final: 0.7978 (mp0) REVERT: C 345 LEU cc_start: 0.9584 (mp) cc_final: 0.9303 (mt) REVERT: C 403 MET cc_start: 0.8731 (mtp) cc_final: 0.8159 (mpp) REVERT: C 483 MET cc_start: 0.8603 (mmt) cc_final: 0.8220 (mmm) REVERT: C 960 MET cc_start: 0.0774 (mmm) cc_final: -0.1969 (ptp) REVERT: C 1186 ASP cc_start: 0.9465 (OUTLIER) cc_final: 0.9067 (p0) REVERT: C 1601 MET cc_start: 0.9099 (tpp) cc_final: 0.8774 (tpp) REVERT: C 1731 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9319 (mt) REVERT: C 1981 MET cc_start: 0.8235 (mmp) cc_final: 0.7922 (mmm) REVERT: C 2198 MET cc_start: 0.9248 (mmp) cc_final: 0.8610 (mpp) REVERT: C 2423 MET cc_start: 0.9155 (ptp) cc_final: 0.8874 (ptp) REVERT: C 2582 MET cc_start: 0.9446 (ptt) cc_final: 0.9129 (ttm) REVERT: C 2618 MET cc_start: 0.9247 (mpp) cc_final: 0.8752 (mpp) REVERT: C 2932 MET cc_start: 0.7950 (ptm) cc_final: 0.7118 (ppp) REVERT: C 2966 TRP cc_start: 0.8804 (OUTLIER) cc_final: 0.8310 (t-100) REVERT: C 2967 MET cc_start: 0.4906 (ptm) cc_final: 0.4459 (ptm) REVERT: C 3437 MET cc_start: 0.8809 (mtt) cc_final: 0.8559 (mtm) REVERT: C 3467 MET cc_start: 0.9313 (ptt) cc_final: 0.8902 (ppp) REVERT: C 3517 MET cc_start: 0.9320 (tpt) cc_final: 0.8707 (tpp) REVERT: C 3652 MET cc_start: 0.9193 (mmm) cc_final: 0.8900 (mpp) REVERT: C 3875 MET cc_start: 0.8173 (mmt) cc_final: 0.7686 (mmt) REVERT: C 4000 MET cc_start: 0.9077 (mmm) cc_final: 0.8783 (mmm) REVERT: C 4014 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.8742 (ptpp) REVERT: C 4015 GLU cc_start: 0.9420 (OUTLIER) cc_final: 0.8898 (mm-30) REVERT: C 4047 MET cc_start: 0.9337 (tmm) cc_final: 0.9063 (tmm) REVERT: C 4732 PHE cc_start: 0.8859 (m-80) cc_final: 0.8413 (m-80) REVERT: C 4798 MET cc_start: 0.9226 (mmm) cc_final: 0.8967 (mmm) REVERT: C 4879 MET cc_start: 0.9169 (tpt) cc_final: 0.8878 (tpp) REVERT: C 4952 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8876 (tm-30) REVERT: C 4953 ASP cc_start: 0.9441 (t0) cc_final: 0.8843 (m-30) REVERT: C 5006 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8814 (pm20) REVERT: C 5013 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8684 (mpp) REVERT: C 5035 GLN cc_start: 0.9470 (mt0) cc_final: 0.9210 (mp10) REVERT: D 31 GLU cc_start: 0.9390 (OUTLIER) cc_final: 0.8907 (pm20) REVERT: D 343 GLU cc_start: 0.8275 (mp0) cc_final: 0.7983 (mp0) REVERT: D 345 LEU cc_start: 0.9579 (mp) cc_final: 0.9303 (mt) REVERT: D 403 MET cc_start: 0.8731 (mtp) cc_final: 0.8162 (mpp) REVERT: D 483 MET cc_start: 0.8607 (mmt) cc_final: 0.8222 (mmm) REVERT: D 960 MET cc_start: 0.0810 (mmm) cc_final: -0.1891 (ptp) REVERT: D 1186 ASP cc_start: 0.9466 (OUTLIER) cc_final: 0.9066 (p0) REVERT: D 1601 MET cc_start: 0.9101 (tpp) cc_final: 0.8777 (tpp) REVERT: D 1731 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9319 (mt) REVERT: D 1981 MET cc_start: 0.8234 (mmp) cc_final: 0.7920 (mmm) REVERT: D 2198 MET cc_start: 0.9251 (mmp) cc_final: 0.8613 (mpp) REVERT: D 2423 MET cc_start: 0.9156 (ptp) cc_final: 0.8876 (ptp) REVERT: D 2582 MET cc_start: 0.9448 (ptt) cc_final: 0.9134 (ttm) REVERT: D 2618 MET cc_start: 0.9247 (mpp) cc_final: 0.8751 (mpp) REVERT: D 2932 MET cc_start: 0.7949 (ptm) cc_final: 0.7115 (ppp) REVERT: D 2966 TRP cc_start: 0.8762 (OUTLIER) cc_final: 0.8361 (t-100) REVERT: D 3437 MET cc_start: 0.8813 (mtt) cc_final: 0.8564 (mtm) REVERT: D 3467 MET cc_start: 0.9294 (ptt) cc_final: 0.8871 (ppp) REVERT: D 3517 MET cc_start: 0.9315 (tpt) cc_final: 0.8697 (tpp) REVERT: D 3652 MET cc_start: 0.9194 (mmm) cc_final: 0.8900 (mpp) REVERT: D 3875 MET cc_start: 0.8174 (mmt) cc_final: 0.7685 (mmt) REVERT: D 4000 MET cc_start: 0.9078 (mmm) cc_final: 0.8783 (mmm) REVERT: D 4014 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.8743 (ptpp) REVERT: D 4015 GLU cc_start: 0.9420 (OUTLIER) cc_final: 0.8900 (mm-30) REVERT: D 4047 MET cc_start: 0.9337 (tmm) cc_final: 0.9063 (tmm) REVERT: D 4732 PHE cc_start: 0.8857 (m-80) cc_final: 0.8412 (m-80) REVERT: D 4798 MET cc_start: 0.9229 (mmm) cc_final: 0.8968 (mmm) REVERT: D 4818 MET cc_start: 0.7992 (ttt) cc_final: 0.7558 (ttm) REVERT: D 4879 MET cc_start: 0.9163 (tpt) cc_final: 0.8878 (tpp) REVERT: D 4952 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8875 (tm-30) REVERT: D 4953 ASP cc_start: 0.9440 (t0) cc_final: 0.8844 (m-30) REVERT: D 5006 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8801 (pm20) REVERT: D 5013 MET cc_start: 0.9037 (mtm) cc_final: 0.8594 (mtm) REVERT: D 5035 GLN cc_start: 0.9471 (mt0) cc_final: 0.9209 (mp10) REVERT: E 29 MET cc_start: 0.7663 (mpp) cc_final: 0.7442 (mpp) REVERT: E 47 LYS cc_start: 0.9293 (mttt) cc_final: 0.9059 (mttp) REVERT: E 66 MET cc_start: 0.9068 (ptm) cc_final: 0.8193 (ttp) REVERT: F 47 LYS cc_start: 0.9293 (mttt) cc_final: 0.9024 (mttp) REVERT: F 66 MET cc_start: 0.9073 (ptm) cc_final: 0.8197 (ttp) REVERT: G 47 LYS cc_start: 0.9294 (mttt) cc_final: 0.9026 (mttp) REVERT: G 66 MET cc_start: 0.9072 (ptm) cc_final: 0.8195 (ttp) REVERT: H 47 LYS cc_start: 0.9302 (mttt) cc_final: 0.9017 (mttp) REVERT: H 66 MET cc_start: 0.9072 (ptm) cc_final: 0.8194 (ttp) outliers start: 116 outliers final: 78 residues processed: 809 average time/residue: 1.2254 time to fit residues: 1780.6756 Evaluate side-chains 813 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 707 time to evaluate : 14.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2296 GLU Chi-restraints excluded: chain A residue 3440 GLU Chi-restraints excluded: chain A residue 4014 LYS Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4097 MET Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4747 SER Chi-restraints excluded: chain A residue 4748 LEU Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4822 THR Chi-restraints excluded: chain A residue 4866 SER Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4948 GLU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain A residue 5013 MET Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2296 GLU Chi-restraints excluded: chain B residue 2966 TRP Chi-restraints excluded: chain B residue 3440 GLU Chi-restraints excluded: chain B residue 3836 MET Chi-restraints excluded: chain B residue 4014 LYS Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4097 MET Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4747 SER Chi-restraints excluded: chain B residue 4748 LEU Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4822 THR Chi-restraints excluded: chain B residue 4829 SER Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain B residue 5013 MET Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1186 ASP Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2296 GLU Chi-restraints excluded: chain C residue 2966 TRP Chi-restraints excluded: chain C residue 3440 GLU Chi-restraints excluded: chain C residue 3836 MET Chi-restraints excluded: chain C residue 4014 LYS Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4097 MET Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4747 SER Chi-restraints excluded: chain C residue 4748 LEU Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4822 THR Chi-restraints excluded: chain C residue 4829 SER Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain C residue 5013 MET Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1186 ASP Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2296 GLU Chi-restraints excluded: chain D residue 2966 TRP Chi-restraints excluded: chain D residue 3440 GLU Chi-restraints excluded: chain D residue 3836 MET Chi-restraints excluded: chain D residue 4014 LYS Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4097 MET Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4747 SER Chi-restraints excluded: chain D residue 4748 LEU Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4829 SER Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4993 MET Chi-restraints excluded: chain D residue 5006 GLN Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1567 optimal weight: 30.0000 chunk 1651 optimal weight: 0.9990 chunk 1506 optimal weight: 9.9990 chunk 1605 optimal weight: 40.0000 chunk 1650 optimal weight: 4.9990 chunk 966 optimal weight: 0.7980 chunk 699 optimal weight: 0.0570 chunk 1261 optimal weight: 6.9990 chunk 492 optimal weight: 0.7980 chunk 1451 optimal weight: 20.0000 chunk 1518 optimal weight: 8.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3211 ASN ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3211 ASN ** B3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 146216 Z= 0.154 Angle : 0.589 14.633 198048 Z= 0.288 Chirality : 0.040 0.172 21768 Planarity : 0.004 0.058 25764 Dihedral : 4.187 58.686 19600 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.69 % Allowed : 10.90 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 1.12 (0.07), residues: 17840 helix: 1.87 (0.06), residues: 8920 sheet: -0.53 (0.12), residues: 1836 loop : -0.30 (0.08), residues: 7084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1143 HIS 0.008 0.001 HIS B3771 PHE 0.030 0.001 PHE A2973 TYR 0.025 0.001 TYR A5009 ARG 0.007 0.000 ARG C3248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 719 time to evaluate : 12.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.8796 (pm20) REVERT: A 343 GLU cc_start: 0.8165 (mp0) cc_final: 0.7871 (mp0) REVERT: A 345 LEU cc_start: 0.9549 (mp) cc_final: 0.9295 (mt) REVERT: A 384 MET cc_start: 0.5110 (ptp) cc_final: 0.4573 (tmm) REVERT: A 403 MET cc_start: 0.8770 (mtp) cc_final: 0.8297 (mpp) REVERT: A 960 MET cc_start: 0.0982 (mmm) cc_final: -0.2013 (ptp) REVERT: A 1057 ASP cc_start: 0.8223 (m-30) cc_final: 0.7760 (t0) REVERT: A 1601 MET cc_start: 0.8898 (tpp) cc_final: 0.8595 (tpp) REVERT: A 1731 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9355 (mt) REVERT: A 1981 MET cc_start: 0.8228 (mmp) cc_final: 0.7934 (mmm) REVERT: A 2170 MET cc_start: 0.8299 (tpp) cc_final: 0.7502 (tpp) REVERT: A 2178 MET cc_start: 0.8671 (ppp) cc_final: 0.8393 (ppp) REVERT: A 2582 MET cc_start: 0.9517 (ptt) cc_final: 0.9098 (ttm) REVERT: A 2618 MET cc_start: 0.9244 (mpp) cc_final: 0.8835 (mpp) REVERT: A 2966 TRP cc_start: 0.8676 (OUTLIER) cc_final: 0.8258 (t-100) REVERT: A 3106 MET cc_start: 0.8953 (mmt) cc_final: 0.8258 (mmm) REVERT: A 3437 MET cc_start: 0.8823 (mtt) cc_final: 0.8579 (mtm) REVERT: A 3467 MET cc_start: 0.9324 (ptt) cc_final: 0.8903 (ppp) REVERT: A 3517 MET cc_start: 0.9310 (tpt) cc_final: 0.8651 (tpp) REVERT: A 3534 MET cc_start: 0.9553 (mpp) cc_final: 0.9301 (pmm) REVERT: A 3652 MET cc_start: 0.9187 (mmm) cc_final: 0.8786 (mpp) REVERT: A 3758 MET cc_start: 0.9197 (tmm) cc_final: 0.8834 (tmm) REVERT: A 4014 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.8909 (ptpp) REVERT: A 4015 GLU cc_start: 0.9436 (OUTLIER) cc_final: 0.9057 (mm-30) REVERT: A 4047 MET cc_start: 0.9338 (tmm) cc_final: 0.9118 (tmm) REVERT: A 4048 LEU cc_start: 0.9732 (mt) cc_final: 0.9466 (mt) REVERT: A 4732 PHE cc_start: 0.8942 (m-80) cc_final: 0.8440 (m-80) REVERT: A 4798 MET cc_start: 0.9196 (mmm) cc_final: 0.8978 (mmm) REVERT: A 4879 MET cc_start: 0.9212 (tpt) cc_final: 0.8976 (tpp) REVERT: A 4880 MET cc_start: 0.8957 (mmm) cc_final: 0.8740 (tpp) REVERT: A 4887 MET cc_start: 0.9054 (mmm) cc_final: 0.8816 (tpp) REVERT: A 4952 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8847 (pp20) REVERT: A 4989 MET cc_start: 0.8941 (tmm) cc_final: 0.8700 (tmm) REVERT: A 5013 MET cc_start: 0.8896 (mpp) cc_final: 0.8480 (mpp) REVERT: A 5035 GLN cc_start: 0.9471 (mt0) cc_final: 0.9205 (mp10) REVERT: B 31 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.8895 (pm20) REVERT: B 343 GLU cc_start: 0.8171 (mp0) cc_final: 0.7882 (mp0) REVERT: B 345 LEU cc_start: 0.9535 (mp) cc_final: 0.9275 (mt) REVERT: B 403 MET cc_start: 0.8766 (mtp) cc_final: 0.8336 (mpp) REVERT: B 483 MET cc_start: 0.8621 (mmt) cc_final: 0.8271 (mmm) REVERT: B 960 MET cc_start: 0.0532 (mmm) cc_final: -0.2111 (ptp) REVERT: B 1186 ASP cc_start: 0.9447 (OUTLIER) cc_final: 0.9112 (p0) REVERT: B 1601 MET cc_start: 0.8955 (tpp) cc_final: 0.8617 (tpp) REVERT: B 1731 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9340 (mt) REVERT: B 1981 MET cc_start: 0.8441 (mmp) cc_final: 0.8178 (mmm) REVERT: B 2170 MET cc_start: 0.8130 (tpp) cc_final: 0.7699 (tpp) REVERT: B 2423 MET cc_start: 0.9105 (ptp) cc_final: 0.8808 (ptp) REVERT: B 2582 MET cc_start: 0.9430 (ptt) cc_final: 0.9139 (ttm) REVERT: B 2618 MET cc_start: 0.9279 (mpp) cc_final: 0.8848 (mpp) REVERT: B 2932 MET cc_start: 0.8198 (ptm) cc_final: 0.7362 (ppp) REVERT: B 3106 MET cc_start: 0.8310 (mmm) cc_final: 0.8037 (mmm) REVERT: B 3437 MET cc_start: 0.8827 (mtt) cc_final: 0.8562 (mtm) REVERT: B 3467 MET cc_start: 0.9294 (ptt) cc_final: 0.8871 (ppp) REVERT: B 3517 MET cc_start: 0.9307 (tpt) cc_final: 0.8675 (tpp) REVERT: B 3652 MET cc_start: 0.9167 (mmm) cc_final: 0.8928 (mpp) REVERT: B 3673 MET cc_start: 0.9427 (mmm) cc_final: 0.9200 (mmm) REVERT: B 4000 MET cc_start: 0.9036 (mmm) cc_final: 0.8741 (mmm) REVERT: B 4014 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8910 (ptpp) REVERT: B 4015 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.8922 (mm-30) REVERT: B 4047 MET cc_start: 0.9318 (tmm) cc_final: 0.9109 (tmm) REVERT: B 4048 LEU cc_start: 0.9738 (mt) cc_final: 0.9430 (mt) REVERT: B 4732 PHE cc_start: 0.8764 (m-80) cc_final: 0.8340 (m-80) REVERT: B 4798 MET cc_start: 0.9256 (mmm) cc_final: 0.9016 (mmm) REVERT: B 4879 MET cc_start: 0.9157 (tpt) cc_final: 0.8908 (tpp) REVERT: B 4952 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8901 (tm-30) REVERT: B 4953 ASP cc_start: 0.9450 (t0) cc_final: 0.9027 (m-30) REVERT: B 4989 MET cc_start: 0.8944 (tmm) cc_final: 0.8697 (tmm) REVERT: B 5006 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8760 (pm20) REVERT: B 5013 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8685 (mpp) REVERT: B 5035 GLN cc_start: 0.9468 (mt0) cc_final: 0.9197 (mp10) REVERT: C 31 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.8895 (pm20) REVERT: C 343 GLU cc_start: 0.8168 (mp0) cc_final: 0.7881 (mp0) REVERT: C 345 LEU cc_start: 0.9536 (mp) cc_final: 0.9276 (mt) REVERT: C 403 MET cc_start: 0.8672 (mtp) cc_final: 0.8197 (mpp) REVERT: C 483 MET cc_start: 0.8621 (mmt) cc_final: 0.8270 (mmm) REVERT: C 960 MET cc_start: 0.0523 (mmm) cc_final: -0.2120 (ptp) REVERT: C 1186 ASP cc_start: 0.9446 (OUTLIER) cc_final: 0.9114 (p0) REVERT: C 1601 MET cc_start: 0.8953 (tpp) cc_final: 0.8614 (tpp) REVERT: C 1731 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9338 (mt) REVERT: C 1981 MET cc_start: 0.8440 (mmp) cc_final: 0.8045 (mmp) REVERT: C 2170 MET cc_start: 0.8128 (tpp) cc_final: 0.7699 (tpp) REVERT: C 2423 MET cc_start: 0.9105 (ptp) cc_final: 0.8808 (ptp) REVERT: C 2582 MET cc_start: 0.9428 (ptt) cc_final: 0.9141 (ttm) REVERT: C 2618 MET cc_start: 0.9276 (mpp) cc_final: 0.8845 (mpp) REVERT: C 2932 MET cc_start: 0.8198 (ptm) cc_final: 0.7362 (ppp) REVERT: C 3437 MET cc_start: 0.8824 (mtt) cc_final: 0.8559 (mtm) REVERT: C 3467 MET cc_start: 0.9295 (ptt) cc_final: 0.8872 (ppp) REVERT: C 3517 MET cc_start: 0.9311 (tpt) cc_final: 0.8677 (tpp) REVERT: C 3652 MET cc_start: 0.9168 (mmm) cc_final: 0.8928 (mpp) REVERT: C 3673 MET cc_start: 0.9427 (mmm) cc_final: 0.9200 (mmm) REVERT: C 4000 MET cc_start: 0.9037 (mmm) cc_final: 0.8740 (mmm) REVERT: C 4014 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8910 (ptpp) REVERT: C 4015 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.8922 (mm-30) REVERT: C 4047 MET cc_start: 0.9319 (tmm) cc_final: 0.9110 (tmm) REVERT: C 4048 LEU cc_start: 0.9739 (mt) cc_final: 0.9430 (mt) REVERT: C 4732 PHE cc_start: 0.8769 (m-80) cc_final: 0.8341 (m-80) REVERT: C 4798 MET cc_start: 0.9252 (mmm) cc_final: 0.9014 (mmm) REVERT: C 4879 MET cc_start: 0.9121 (tpt) cc_final: 0.8868 (tpp) REVERT: C 4952 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8904 (tm-30) REVERT: C 4953 ASP cc_start: 0.9449 (t0) cc_final: 0.9025 (m-30) REVERT: C 4989 MET cc_start: 0.8946 (tmm) cc_final: 0.8698 (tmm) REVERT: C 5006 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8762 (pm20) REVERT: C 5013 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8684 (mpp) REVERT: C 5035 GLN cc_start: 0.9469 (mt0) cc_final: 0.9199 (mp10) REVERT: D 31 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.8893 (pm20) REVERT: D 343 GLU cc_start: 0.8170 (mp0) cc_final: 0.7886 (mp0) REVERT: D 345 LEU cc_start: 0.9531 (mp) cc_final: 0.9274 (mt) REVERT: D 403 MET cc_start: 0.8669 (mtp) cc_final: 0.8200 (mpp) REVERT: D 483 MET cc_start: 0.8621 (mmt) cc_final: 0.8272 (mmm) REVERT: D 960 MET cc_start: 0.0628 (mmm) cc_final: -0.2067 (ptp) REVERT: D 1186 ASP cc_start: 0.9446 (OUTLIER) cc_final: 0.9112 (p0) REVERT: D 1601 MET cc_start: 0.8956 (tpp) cc_final: 0.8614 (tpp) REVERT: D 1731 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9339 (mt) REVERT: D 1981 MET cc_start: 0.8440 (mmp) cc_final: 0.8044 (mmp) REVERT: D 2170 MET cc_start: 0.8131 (tpp) cc_final: 0.7700 (tpp) REVERT: D 2423 MET cc_start: 0.9107 (ptp) cc_final: 0.8809 (ptp) REVERT: D 2582 MET cc_start: 0.9430 (ptt) cc_final: 0.9141 (ttm) REVERT: D 2618 MET cc_start: 0.9276 (mpp) cc_final: 0.8844 (mpp) REVERT: D 2932 MET cc_start: 0.8196 (ptm) cc_final: 0.7359 (ppp) REVERT: D 3437 MET cc_start: 0.8828 (mtt) cc_final: 0.8564 (mtm) REVERT: D 3467 MET cc_start: 0.9293 (ptt) cc_final: 0.8870 (ppp) REVERT: D 3517 MET cc_start: 0.9305 (tpt) cc_final: 0.8666 (tpp) REVERT: D 3652 MET cc_start: 0.9168 (mmm) cc_final: 0.8926 (mpp) REVERT: D 3673 MET cc_start: 0.9429 (mmm) cc_final: 0.9199 (mmm) REVERT: D 4000 MET cc_start: 0.9039 (mmm) cc_final: 0.8742 (mmm) REVERT: D 4014 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.8908 (ptpp) REVERT: D 4015 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.8922 (mm-30) REVERT: D 4047 MET cc_start: 0.9319 (tmm) cc_final: 0.9109 (tmm) REVERT: D 4048 LEU cc_start: 0.9739 (mt) cc_final: 0.9429 (mt) REVERT: D 4732 PHE cc_start: 0.8768 (m-80) cc_final: 0.8340 (m-80) REVERT: D 4798 MET cc_start: 0.9256 (mmm) cc_final: 0.9016 (mmm) REVERT: D 4818 MET cc_start: 0.7847 (ttt) cc_final: 0.7389 (ttm) REVERT: D 4879 MET cc_start: 0.9123 (tpt) cc_final: 0.8875 (tpp) REVERT: D 4952 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8899 (tm-30) REVERT: D 4953 ASP cc_start: 0.9448 (t0) cc_final: 0.9026 (m-30) REVERT: D 4989 MET cc_start: 0.8946 (tmm) cc_final: 0.8699 (tmm) REVERT: D 5006 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8750 (pm20) REVERT: D 5013 MET cc_start: 0.8907 (mtm) cc_final: 0.8673 (mpp) REVERT: D 5035 GLN cc_start: 0.9469 (mt0) cc_final: 0.9197 (mp10) REVERT: E 29 MET cc_start: 0.7623 (mpp) cc_final: 0.7403 (mpp) REVERT: E 47 LYS cc_start: 0.9294 (mttt) cc_final: 0.8933 (mptt) REVERT: E 66 MET cc_start: 0.9044 (ptm) cc_final: 0.8209 (ttp) REVERT: F 47 LYS cc_start: 0.9295 (mttt) cc_final: 0.8935 (mptt) REVERT: F 66 MET cc_start: 0.9048 (ptm) cc_final: 0.8501 (ppp) REVERT: G 47 LYS cc_start: 0.9294 (mttt) cc_final: 0.8934 (mptt) REVERT: G 66 MET cc_start: 0.9046 (ptm) cc_final: 0.8498 (ppp) REVERT: H 47 LYS cc_start: 0.9294 (mttt) cc_final: 0.8934 (mptt) REVERT: H 66 MET cc_start: 0.9047 (ptm) cc_final: 0.8498 (ppp) outliers start: 96 outliers final: 66 residues processed: 793 average time/residue: 1.1798 time to fit residues: 1706.9078 Evaluate side-chains 802 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 711 time to evaluate : 12.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2296 GLU Chi-restraints excluded: chain A residue 2966 TRP Chi-restraints excluded: chain A residue 3440 GLU Chi-restraints excluded: chain A residue 4014 LYS Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4585 SER Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4748 LEU Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4866 SER Chi-restraints excluded: chain A residue 4948 GLU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2296 GLU Chi-restraints excluded: chain B residue 3440 GLU Chi-restraints excluded: chain B residue 4014 LYS Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4097 MET Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4585 SER Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4748 LEU Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4822 THR Chi-restraints excluded: chain B residue 4829 SER Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain B residue 5013 MET Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1186 ASP Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2296 GLU Chi-restraints excluded: chain C residue 3440 GLU Chi-restraints excluded: chain C residue 4014 LYS Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4097 MET Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4585 SER Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4748 LEU Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4822 THR Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain C residue 5013 MET Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1186 ASP Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2296 GLU Chi-restraints excluded: chain D residue 3440 GLU Chi-restraints excluded: chain D residue 4014 LYS Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4097 MET Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4748 LEU Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4829 SER Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 5006 GLN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1600 optimal weight: 8.9990 chunk 1054 optimal weight: 0.8980 chunk 1698 optimal weight: 9.9990 chunk 1036 optimal weight: 3.9990 chunk 805 optimal weight: 6.9990 chunk 1180 optimal weight: 5.9990 chunk 1781 optimal weight: 9.9990 chunk 1639 optimal weight: 8.9990 chunk 1418 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 1095 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 146216 Z= 0.235 Angle : 0.615 13.402 198048 Z= 0.301 Chirality : 0.040 0.195 21768 Planarity : 0.004 0.057 25764 Dihedral : 4.201 55.888 19600 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.71 % Allowed : 10.95 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 1.07 (0.07), residues: 17840 helix: 1.84 (0.06), residues: 8940 sheet: -0.59 (0.12), residues: 1836 loop : -0.33 (0.08), residues: 7064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1143 HIS 0.007 0.001 HIS D3771 PHE 0.028 0.001 PHE B2973 TYR 0.028 0.001 TYR A5009 ARG 0.004 0.000 ARG D 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35680 Ramachandran restraints generated. 17840 Oldfield, 0 Emsley, 17840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 708 time to evaluate : 12.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9344 (OUTLIER) cc_final: 0.8829 (pm20) REVERT: A 343 GLU cc_start: 0.8222 (mp0) cc_final: 0.7944 (mp0) REVERT: A 345 LEU cc_start: 0.9579 (mp) cc_final: 0.9331 (mt) REVERT: A 384 MET cc_start: 0.5225 (ptp) cc_final: 0.4600 (tmm) REVERT: A 403 MET cc_start: 0.8775 (mtp) cc_final: 0.8354 (mpp) REVERT: A 960 MET cc_start: 0.0177 (mmm) cc_final: -0.2409 (ptp) REVERT: A 1057 ASP cc_start: 0.8236 (m-30) cc_final: 0.7774 (t0) REVERT: A 1170 MET cc_start: 0.7852 (tpp) cc_final: 0.7257 (tpp) REVERT: A 1186 ASP cc_start: 0.9467 (OUTLIER) cc_final: 0.9007 (p0) REVERT: A 1601 MET cc_start: 0.8963 (tpp) cc_final: 0.8690 (tpp) REVERT: A 1731 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9331 (mt) REVERT: A 1981 MET cc_start: 0.8230 (mmp) cc_final: 0.7790 (mmp) REVERT: A 2170 MET cc_start: 0.8378 (tpp) cc_final: 0.7616 (tpp) REVERT: A 2178 MET cc_start: 0.8745 (ppp) cc_final: 0.8462 (ppp) REVERT: A 2198 MET cc_start: 0.9187 (mmp) cc_final: 0.8562 (mpp) REVERT: A 2582 MET cc_start: 0.9518 (ptt) cc_final: 0.9104 (ttm) REVERT: A 2618 MET cc_start: 0.9243 (mpp) cc_final: 0.8641 (mpp) REVERT: A 2698 MET cc_start: 0.8601 (ppp) cc_final: 0.8263 (ppp) REVERT: A 2966 TRP cc_start: 0.8737 (OUTLIER) cc_final: 0.8316 (t-100) REVERT: A 3437 MET cc_start: 0.8838 (mtt) cc_final: 0.8597 (mtm) REVERT: A 3467 MET cc_start: 0.9310 (ptt) cc_final: 0.8877 (ppp) REVERT: A 3517 MET cc_start: 0.9314 (tpt) cc_final: 0.8657 (tpp) REVERT: A 3534 MET cc_start: 0.9560 (mpp) cc_final: 0.9322 (pmm) REVERT: A 3652 MET cc_start: 0.9211 (mmm) cc_final: 0.8807 (mpp) REVERT: A 3673 MET cc_start: 0.9332 (tpp) cc_final: 0.8874 (mpp) REVERT: A 3758 MET cc_start: 0.9136 (tmm) cc_final: 0.8786 (tmm) REVERT: A 4014 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.8949 (ptpp) REVERT: A 4015 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.9003 (mm-30) REVERT: A 4047 MET cc_start: 0.9337 (tmm) cc_final: 0.9071 (tmm) REVERT: A 4048 LEU cc_start: 0.9736 (mt) cc_final: 0.9330 (mt) REVERT: A 4732 PHE cc_start: 0.9109 (m-80) cc_final: 0.8537 (m-80) REVERT: A 4798 MET cc_start: 0.9283 (mmm) cc_final: 0.9038 (mmm) REVERT: A 4879 MET cc_start: 0.9249 (tpt) cc_final: 0.8982 (tpp) REVERT: A 4880 MET cc_start: 0.8971 (mmm) cc_final: 0.8749 (tpp) REVERT: A 4887 MET cc_start: 0.9065 (mmm) cc_final: 0.8837 (tpp) REVERT: A 4952 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8884 (pp20) REVERT: A 4953 ASP cc_start: 0.9443 (t0) cc_final: 0.9192 (t0) REVERT: A 5013 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8578 (mpp) REVERT: A 5035 GLN cc_start: 0.9465 (mt0) cc_final: 0.9203 (mp10) REVERT: B 31 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.8909 (pm20) REVERT: B 343 GLU cc_start: 0.8223 (mp0) cc_final: 0.7950 (mp0) REVERT: B 345 LEU cc_start: 0.9564 (mp) cc_final: 0.9304 (mt) REVERT: B 403 MET cc_start: 0.8751 (mtp) cc_final: 0.8325 (mpp) REVERT: B 483 MET cc_start: 0.8644 (mmt) cc_final: 0.8254 (mmm) REVERT: B 960 MET cc_start: 0.0191 (mmm) cc_final: -0.2313 (ptp) REVERT: B 1170 MET cc_start: 0.7743 (tpp) cc_final: 0.7263 (tpp) REVERT: B 1186 ASP cc_start: 0.9489 (OUTLIER) cc_final: 0.9125 (p0) REVERT: B 1494 MET cc_start: 0.7976 (mmm) cc_final: 0.7752 (mmp) REVERT: B 1601 MET cc_start: 0.9003 (tpp) cc_final: 0.8668 (tpp) REVERT: B 1731 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9331 (mt) REVERT: B 1981 MET cc_start: 0.8448 (mmp) cc_final: 0.8043 (mmp) REVERT: B 2170 MET cc_start: 0.8350 (tpp) cc_final: 0.7859 (tpp) REVERT: B 2198 MET cc_start: 0.9201 (mmp) cc_final: 0.8561 (mpp) REVERT: B 2423 MET cc_start: 0.9110 (ptp) cc_final: 0.8808 (ptp) REVERT: B 2582 MET cc_start: 0.9445 (ptt) cc_final: 0.9141 (ttm) REVERT: B 2618 MET cc_start: 0.9218 (mpp) cc_final: 0.8750 (mpp) REVERT: B 2932 MET cc_start: 0.7894 (ptm) cc_final: 0.7043 (ppp) REVERT: B 3106 MET cc_start: 0.8326 (mmm) cc_final: 0.8052 (mmm) REVERT: B 3437 MET cc_start: 0.8832 (mtt) cc_final: 0.8576 (mtm) REVERT: B 3467 MET cc_start: 0.9279 (ptt) cc_final: 0.8844 (ppp) REVERT: B 3517 MET cc_start: 0.9314 (tpt) cc_final: 0.8682 (tpp) REVERT: B 3652 MET cc_start: 0.9182 (mmm) cc_final: 0.8938 (mpp) REVERT: B 3673 MET cc_start: 0.9452 (mmm) cc_final: 0.9191 (mmm) REVERT: B 4000 MET cc_start: 0.9044 (mmm) cc_final: 0.8641 (mmm) REVERT: B 4014 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.8908 (ptpp) REVERT: B 4015 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.8912 (mm-30) REVERT: B 4047 MET cc_start: 0.9323 (tmm) cc_final: 0.9046 (tmm) REVERT: B 4732 PHE cc_start: 0.8980 (m-80) cc_final: 0.8448 (m-80) REVERT: B 4798 MET cc_start: 0.9281 (mmm) cc_final: 0.9025 (mmm) REVERT: B 4879 MET cc_start: 0.9195 (tpt) cc_final: 0.8956 (tpp) REVERT: B 4880 MET cc_start: 0.9111 (tpp) cc_final: 0.8874 (tpp) REVERT: B 4952 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8855 (tm-30) REVERT: B 4953 ASP cc_start: 0.9445 (t0) cc_final: 0.8848 (m-30) REVERT: B 5006 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8806 (pm20) REVERT: B 5013 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8776 (mpp) REVERT: B 5035 GLN cc_start: 0.9462 (mt0) cc_final: 0.9201 (mp10) REVERT: C 31 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.8909 (pm20) REVERT: C 343 GLU cc_start: 0.8223 (mp0) cc_final: 0.7950 (mp0) REVERT: C 345 LEU cc_start: 0.9564 (mp) cc_final: 0.9304 (mt) REVERT: C 403 MET cc_start: 0.8706 (mtp) cc_final: 0.8255 (mpp) REVERT: C 483 MET cc_start: 0.8641 (mmt) cc_final: 0.8252 (mmm) REVERT: C 960 MET cc_start: 0.0719 (mmm) cc_final: -0.2017 (ptp) REVERT: C 1170 MET cc_start: 0.7739 (tpp) cc_final: 0.7266 (tpp) REVERT: C 1186 ASP cc_start: 0.9488 (OUTLIER) cc_final: 0.9127 (p0) REVERT: C 1494 MET cc_start: 0.7987 (mmm) cc_final: 0.7760 (mmp) REVERT: C 1601 MET cc_start: 0.9003 (tpp) cc_final: 0.8669 (tpp) REVERT: C 1731 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9330 (mt) REVERT: C 1981 MET cc_start: 0.8445 (mmp) cc_final: 0.8042 (mmp) REVERT: C 2170 MET cc_start: 0.8347 (tpp) cc_final: 0.7858 (tpp) REVERT: C 2198 MET cc_start: 0.9200 (mmp) cc_final: 0.8560 (mpp) REVERT: C 2423 MET cc_start: 0.9110 (ptp) cc_final: 0.8808 (ptp) REVERT: C 2582 MET cc_start: 0.9444 (ptt) cc_final: 0.9142 (ttm) REVERT: C 2618 MET cc_start: 0.9215 (mpp) cc_final: 0.8747 (mpp) REVERT: C 2932 MET cc_start: 0.7894 (ptm) cc_final: 0.7043 (ppp) REVERT: C 3437 MET cc_start: 0.8828 (mtt) cc_final: 0.8574 (mtm) REVERT: C 3467 MET cc_start: 0.9279 (ptt) cc_final: 0.8845 (ppp) REVERT: C 3517 MET cc_start: 0.9317 (tpt) cc_final: 0.8683 (tpp) REVERT: C 3652 MET cc_start: 0.9182 (mmm) cc_final: 0.8937 (mpp) REVERT: C 3673 MET cc_start: 0.9453 (mmm) cc_final: 0.9194 (mmm) REVERT: C 4000 MET cc_start: 0.9044 (mmm) cc_final: 0.8639 (mmm) REVERT: C 4014 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.8908 (ptpp) REVERT: C 4015 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.8911 (mm-30) REVERT: C 4047 MET cc_start: 0.9323 (tmm) cc_final: 0.9047 (tmm) REVERT: C 4732 PHE cc_start: 0.8983 (m-80) cc_final: 0.8447 (m-80) REVERT: C 4798 MET cc_start: 0.9280 (mmm) cc_final: 0.9023 (mmm) REVERT: C 4879 MET cc_start: 0.9161 (tpt) cc_final: 0.8873 (tpp) REVERT: C 4952 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8857 (tm-30) REVERT: C 4953 ASP cc_start: 0.9446 (t0) cc_final: 0.8844 (m-30) REVERT: C 5006 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8806 (pm20) REVERT: C 5013 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8779 (mpp) REVERT: C 5035 GLN cc_start: 0.9463 (mt0) cc_final: 0.9203 (mp10) REVERT: D 31 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.8908 (pm20) REVERT: D 343 GLU cc_start: 0.8227 (mp0) cc_final: 0.7957 (mp0) REVERT: D 345 LEU cc_start: 0.9563 (mp) cc_final: 0.9305 (mt) REVERT: D 403 MET cc_start: 0.8707 (mtp) cc_final: 0.8256 (mpp) REVERT: D 483 MET cc_start: 0.8645 (mmt) cc_final: 0.8253 (mmm) REVERT: D 960 MET cc_start: 0.0345 (mmm) cc_final: -0.2235 (ptp) REVERT: D 1170 MET cc_start: 0.7741 (tpp) cc_final: 0.7266 (tpp) REVERT: D 1186 ASP cc_start: 0.9489 (OUTLIER) cc_final: 0.9125 (p0) REVERT: D 1494 MET cc_start: 0.7977 (mmm) cc_final: 0.7748 (mmp) REVERT: D 1601 MET cc_start: 0.9004 (tpp) cc_final: 0.8670 (tpp) REVERT: D 1731 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9330 (mt) REVERT: D 1981 MET cc_start: 0.8446 (mmp) cc_final: 0.8042 (mmp) REVERT: D 2170 MET cc_start: 0.8350 (tpp) cc_final: 0.7864 (tpp) REVERT: D 2198 MET cc_start: 0.9202 (mmp) cc_final: 0.8563 (mpp) REVERT: D 2423 MET cc_start: 0.9110 (ptp) cc_final: 0.8810 (ptp) REVERT: D 2582 MET cc_start: 0.9446 (ptt) cc_final: 0.9142 (ttm) REVERT: D 2618 MET cc_start: 0.9214 (mpp) cc_final: 0.8746 (mpp) REVERT: D 2932 MET cc_start: 0.7896 (ptm) cc_final: 0.7043 (ppp) REVERT: D 3437 MET cc_start: 0.8832 (mtt) cc_final: 0.8578 (mtm) REVERT: D 3467 MET cc_start: 0.9279 (ptt) cc_final: 0.8845 (ppp) REVERT: D 3517 MET cc_start: 0.9311 (tpt) cc_final: 0.8676 (tpp) REVERT: D 3652 MET cc_start: 0.9181 (mmm) cc_final: 0.8936 (mpp) REVERT: D 3673 MET cc_start: 0.9454 (mmm) cc_final: 0.9192 (mmm) REVERT: D 4000 MET cc_start: 0.9044 (mmm) cc_final: 0.8641 (mmm) REVERT: D 4014 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.8907 (ptpp) REVERT: D 4015 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.8910 (mm-30) REVERT: D 4047 MET cc_start: 0.9324 (tmm) cc_final: 0.9047 (tmm) REVERT: D 4732 PHE cc_start: 0.8983 (m-80) cc_final: 0.8447 (m-80) REVERT: D 4798 MET cc_start: 0.9282 (mmm) cc_final: 0.9025 (mmm) REVERT: D 4818 MET cc_start: 0.8003 (ttt) cc_final: 0.7558 (ttm) REVERT: D 4879 MET cc_start: 0.9162 (tpt) cc_final: 0.8873 (tpp) REVERT: D 4952 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8852 (tm-30) REVERT: D 4953 ASP cc_start: 0.9444 (t0) cc_final: 0.8847 (m-30) REVERT: D 5006 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8782 (pm20) REVERT: D 5013 MET cc_start: 0.8982 (mtm) cc_final: 0.8500 (mtm) REVERT: D 5035 GLN cc_start: 0.9463 (mt0) cc_final: 0.9202 (mp10) REVERT: E 29 MET cc_start: 0.7660 (mpp) cc_final: 0.7443 (mpp) REVERT: E 47 LYS cc_start: 0.9299 (mttt) cc_final: 0.9014 (mttp) REVERT: E 66 MET cc_start: 0.9071 (ptm) cc_final: 0.8212 (ttp) REVERT: F 47 LYS cc_start: 0.9299 (mttt) cc_final: 0.9015 (mttp) REVERT: F 66 MET cc_start: 0.9074 (ptm) cc_final: 0.8217 (ttp) REVERT: G 47 LYS cc_start: 0.9301 (mttt) cc_final: 0.9017 (mttp) REVERT: G 66 MET cc_start: 0.9075 (ptm) cc_final: 0.8213 (ttp) REVERT: H 47 LYS cc_start: 0.9300 (mttt) cc_final: 0.9015 (mttp) REVERT: H 66 MET cc_start: 0.9076 (ptm) cc_final: 0.8214 (ttp) outliers start: 98 outliers final: 70 residues processed: 787 average time/residue: 1.1834 time to fit residues: 1696.2278 Evaluate side-chains 802 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 705 time to evaluate : 12.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2296 GLU Chi-restraints excluded: chain A residue 2966 TRP Chi-restraints excluded: chain A residue 3440 GLU Chi-restraints excluded: chain A residue 4014 LYS Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4097 MET Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4748 LEU Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4866 SER Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4948 GLU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5013 MET Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2296 GLU Chi-restraints excluded: chain B residue 3440 GLU Chi-restraints excluded: chain B residue 3836 MET Chi-restraints excluded: chain B residue 4014 LYS Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4097 MET Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4585 SER Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4748 LEU Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4822 THR Chi-restraints excluded: chain B residue 4829 SER Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain B residue 5013 MET Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1186 ASP Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2296 GLU Chi-restraints excluded: chain C residue 3440 GLU Chi-restraints excluded: chain C residue 3836 MET Chi-restraints excluded: chain C residue 4014 LYS Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4097 MET Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4585 SER Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4748 LEU Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4822 THR Chi-restraints excluded: chain C residue 4829 SER Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain C residue 5013 MET Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1186 ASP Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2296 GLU Chi-restraints excluded: chain D residue 3440 GLU Chi-restraints excluded: chain D residue 3836 MET Chi-restraints excluded: chain D residue 4014 LYS Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4097 MET Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4748 LEU Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 5006 GLN Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 869 optimal weight: 4.9990 chunk 1126 optimal weight: 50.0000 chunk 1510 optimal weight: 4.9990 chunk 434 optimal weight: 10.0000 chunk 1307 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 394 optimal weight: 20.0000 chunk 1420 optimal weight: 7.9990 chunk 594 optimal weight: 1.9990 chunk 1458 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.048195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.032024 restraints weight = 2876901.838| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 8.64 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 146216 Z= 0.201 Angle : 0.605 16.174 198048 Z= 0.296 Chirality : 0.040 0.229 21768 Planarity : 0.004 0.057 25764 Dihedral : 4.195 56.120 19600 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.76 % Allowed : 10.94 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.34 % 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: 1.10 (0.07), residues: 17840 helix: 1.86 (0.06), residues: 8940 sheet: -0.57 (0.12), residues: 1836 loop : -0.33 (0.08), residues: 7064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1143 HIS 0.007 0.001 HIS B3771 PHE 0.028 0.001 PHE A2973 TYR 0.027 0.001 TYR A5009 ARG 0.004 0.000 ARG A 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34365.19 seconds wall clock time: 603 minutes 21.35 seconds (36201.35 seconds total)