Starting phenix.real_space_refine on Wed Oct 9 12:13:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azk_15767/10_2024/8azk_15767.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azk_15767/10_2024/8azk_15767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azk_15767/10_2024/8azk_15767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azk_15767/10_2024/8azk_15767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azk_15767/10_2024/8azk_15767.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azk_15767/10_2024/8azk_15767.cif" } resolution = 3.1 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= -0.000 sd= 0.026 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: 4 Type Number sf(0) Gaussians S 291 5.16 5 C 29764 2.51 5 N 8072 2.21 5 O 8838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 46965 Number of models: 1 Model: "" Number of chains: 28 Chain: "J" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1588 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1587 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1783 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 8, 'TRANS': 228} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1727 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 217} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1887 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 247} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "D" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1774 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 6, 'TRANS': 234} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "E" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1732 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "F" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1795 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 226} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 49 Chain: "G" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1844 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 235} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1485 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1617 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "K" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1565 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 189} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1538 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 204} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "N" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1617 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "O" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1817 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "P" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1720 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 217} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Q" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1819 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 72 Chain: "R" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1765 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 6, 'TRANS': 235} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "S" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1735 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 223} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "T" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1749 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "U" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1819 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 235} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "V" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1456 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 192} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 23 Chain: "W" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "Y" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1553 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "Z" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1540 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "1" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "2" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1625 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 21.96, per 1000 atoms: 0.47 Number of scatterers: 46965 At special positions: 0 Unit cell: (145.34, 147.06, 183.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 291 16.00 O 8838 8.00 N 8072 7.00 C 29764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.05 Conformation dependent library (CDL) restraints added in 4.8 seconds 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11462 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 80 sheets defined 37.3% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'J' and resid 3 through 7 removed outlier: 4.013A pdb=" N ASN J 7 " --> pdb=" O MET J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 78 removed outlier: 3.844A pdb=" N LEU J 73 " --> pdb=" O PHE J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 98 removed outlier: 4.161A pdb=" N LYS J 98 " --> pdb=" O LEU J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 removed outlier: 3.849A pdb=" N MET J 146 " --> pdb=" O CYS J 142 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU J 151 " --> pdb=" O TYR J 147 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU J 153 " --> pdb=" O MET J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 176 Processing helix chain 'X' and resid 3 through 7 removed outlier: 4.199A pdb=" N ASN X 7 " --> pdb=" O MET X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 78 Processing helix chain 'X' and resid 83 through 97 Processing helix chain 'X' and resid 143 through 151 removed outlier: 4.073A pdb=" N GLY X 148 " --> pdb=" O GLU X 144 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N MET X 149 " --> pdb=" O GLN X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 159 through 176 removed outlier: 3.808A pdb=" N GLN X 169 " --> pdb=" O GLU X 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 30 removed outlier: 3.784A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 34 removed outlier: 3.725A pdb=" N GLN A 34 " --> pdb=" O ALA A 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 83 through 106 removed outlier: 3.594A pdb=" N SER A 87 " --> pdb=" O MET A 83 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 removed outlier: 3.615A pdb=" N LEU A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 removed outlier: 3.825A pdb=" N PHE A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 4.052A pdb=" N VAL A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 removed outlier: 3.931A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 242 " --> pdb=" O HIS A 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.888A pdb=" N GLU B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 101 removed outlier: 3.793A pdb=" N ARG B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.615A pdb=" N LEU B 109 " --> pdb=" O PRO B 105 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.709A pdb=" N ALA B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.545A pdb=" N ALA B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 29 Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.648A pdb=" N ALA C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 removed outlier: 4.002A pdb=" N LEU C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 175 removed outlier: 3.686A pdb=" N ALA C 171 " --> pdb=" O ASN C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 178 No H-bonds generated for 'chain 'C' and resid 176 through 178' Processing helix chain 'C' and resid 185 through 201 removed outlier: 3.900A pdb=" N ALA C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 254 Processing helix chain 'D' and resid 16 through 27 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 76 through 98 removed outlier: 3.596A pdb=" N ALA D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG D 95 " --> pdb=" O CYS D 91 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.654A pdb=" N ILE D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 removed outlier: 3.955A pdb=" N VAL D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 184 through 199 removed outlier: 3.728A pdb=" N ILE D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 242 removed outlier: 4.066A pdb=" N ILE D 225 " --> pdb=" O ASN D 221 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU D 226 " --> pdb=" O PRO D 222 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU D 233 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU D 235 " --> pdb=" O GLU D 231 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 32 removed outlier: 3.703A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 31 " --> pdb=" O ASP E 27 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 87 through 104 removed outlier: 3.937A pdb=" N LYS E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 3.798A pdb=" N VAL E 112 " --> pdb=" O THR E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 190 through 206 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.545A pdb=" N GLU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 232 through 237' Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.624A pdb=" N GLU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA F 28 " --> pdb=" O TYR F 24 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 99 Processing helix chain 'F' and resid 105 through 118 removed outlier: 3.985A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 121 No H-bonds generated for 'chain 'F' and resid 119 through 121' Processing helix chain 'F' and resid 165 through 175 Processing helix chain 'F' and resid 183 through 196 Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'G' and resid 20 through 28 removed outlier: 3.825A pdb=" N GLU G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 33 Processing helix chain 'G' and resid 80 through 102 removed outlier: 3.570A pdb=" N ALA G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.997A pdb=" N LEU G 111 " --> pdb=" O PRO G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 178 removed outlier: 3.700A pdb=" N LYS G 178 " --> pdb=" O THR G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 200 Processing helix chain 'G' and resid 228 through 243 removed outlier: 4.109A pdb=" N GLU G 234 " --> pdb=" O ASP G 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 removed outlier: 3.707A pdb=" N THR H 52 " --> pdb=" O SER H 48 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU H 70 " --> pdb=" O HIS H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 89 removed outlier: 3.904A pdb=" N ALA H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 136 removed outlier: 3.589A pdb=" N SER H 132 " --> pdb=" O GLY H 129 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER H 133 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR H 134 " --> pdb=" O GLY H 131 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR H 136 " --> pdb=" O SER H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 143 removed outlier: 3.605A pdb=" N ALA H 141 " --> pdb=" O GLY H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 167 removed outlier: 3.517A pdb=" N GLU H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'I' and resid 50 through 71 removed outlier: 3.607A pdb=" N THR I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 89 removed outlier: 4.302A pdb=" N ALA I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.866A pdb=" N ALA I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 164 removed outlier: 3.996A pdb=" N ASN I 153 " --> pdb=" O GLU I 149 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY I 162 " --> pdb=" O ALA I 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 72 Processing helix chain 'K' and resid 76 through 93 removed outlier: 3.929A pdb=" N ARG K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 135 No H-bonds generated for 'chain 'K' and resid 133 through 135' Processing helix chain 'K' and resid 136 through 147 removed outlier: 4.759A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 166 removed outlier: 3.569A pdb=" N VAL K 157 " --> pdb=" O ARG K 153 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 171 Processing helix chain 'L' and resid 48 through 71 removed outlier: 4.166A pdb=" N GLU L 56 " --> pdb=" O CYS L 52 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU L 59 " --> pdb=" O TRP L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 88 removed outlier: 3.720A pdb=" N ALA L 79 " --> pdb=" O SER L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'L' and resid 132 through 140 removed outlier: 3.735A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 165 Processing helix chain 'L' and resid 192 through 199 removed outlier: 4.851A pdb=" N GLU L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 80 removed outlier: 3.911A pdb=" N THR M 63 " --> pdb=" O GLY M 59 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR M 65 " --> pdb=" O CYS M 61 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS M 66 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.547A pdb=" N ILE M 88 " --> pdb=" O THR M 84 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 155 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 167 through 183 removed outlier: 3.676A pdb=" N ALA M 171 " --> pdb=" O SER M 167 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA M 183 " --> pdb=" O PHE M 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 78 removed outlier: 4.587A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 101 Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 155 Processing helix chain 'N' and resid 161 through 180 Processing helix chain 'N' and resid 209 through 214 Processing helix chain 'O' and resid 22 through 29 removed outlier: 3.656A pdb=" N GLU O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 36 removed outlier: 4.281A pdb=" N GLY O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY O 36 " --> pdb=" O ILE O 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 31 through 36' Processing helix chain 'O' and resid 85 through 106 removed outlier: 3.954A pdb=" N SER O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 125 removed outlier: 3.637A pdb=" N LEU O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 180 Processing helix chain 'O' and resid 191 through 207 removed outlier: 3.963A pdb=" N VAL O 195 " --> pdb=" O PHE O 191 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU O 196 " --> pdb=" O GLU O 192 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 243 Processing helix chain 'P' and resid 18 through 26 removed outlier: 3.923A pdb=" N GLU P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 101 removed outlier: 3.545A pdb=" N GLN P 94 " --> pdb=" O ARG P 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 120 removed outlier: 3.750A pdb=" N LEU P 109 " --> pdb=" O PRO P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 175 removed outlier: 3.648A pdb=" N LYS P 175 " --> pdb=" O THR P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 196 removed outlier: 3.979A pdb=" N HIS P 188 " --> pdb=" O GLU P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 230 Processing helix chain 'Q' and resid 18 through 29 removed outlier: 4.008A pdb=" N GLU Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY Q 29 " --> pdb=" O MET Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 102 removed outlier: 4.369A pdb=" N VAL Q 85 " --> pdb=" O SER Q 81 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN Q 88 " --> pdb=" O ASN Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 116 removed outlier: 3.592A pdb=" N LEU Q 110 " --> pdb=" O PRO Q 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU Q 114 " --> pdb=" O LEU Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 124 Processing helix chain 'Q' and resid 167 through 176 removed outlier: 3.656A pdb=" N ALA Q 171 " --> pdb=" O ASN Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 201 removed outlier: 4.018A pdb=" N LEU Q 190 " --> pdb=" O LEU Q 186 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA Q 191 " --> pdb=" O LYS Q 187 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN Q 198 " --> pdb=" O ILE Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 246 Processing helix chain 'R' and resid 16 through 26 removed outlier: 3.876A pdb=" N GLU R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA R 25 " --> pdb=" O TYR R 21 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 98 removed outlier: 3.534A pdb=" N ALA R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 118 removed outlier: 3.718A pdb=" N TYR R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 173 Processing helix chain 'R' and resid 183 through 199 removed outlier: 3.616A pdb=" N ILE R 188 " --> pdb=" O ASP R 184 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS R 189 " --> pdb=" O ASP R 185 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL R 191 " --> pdb=" O THR R 187 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 243 Processing helix chain 'S' and resid 21 through 28 removed outlier: 3.791A pdb=" N GLU S 25 " --> pdb=" O LEU S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 34 Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 81 through 104 removed outlier: 3.771A pdb=" N ALA S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS S 86 " --> pdb=" O ILE S 82 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP S 90 " --> pdb=" O LYS S 86 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 176 through 184 Processing helix chain 'S' and resid 190 through 206 removed outlier: 3.554A pdb=" N ALA S 194 " --> pdb=" O THR S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 231 through 239 removed outlier: 3.959A pdb=" N GLU S 235 " --> pdb=" O LYS S 231 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU S 236 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL S 237 " --> pdb=" O GLU S 233 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE S 238 " --> pdb=" O LEU S 234 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS S 239 " --> pdb=" O GLU S 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 231 through 239' Processing helix chain 'T' and resid 19 through 27 removed outlier: 3.630A pdb=" N GLU T 23 " --> pdb=" O ILE T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 99 removed outlier: 3.666A pdb=" N ARG T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU T 83 " --> pdb=" O ALA T 79 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU T 84 " --> pdb=" O ASP T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 118 removed outlier: 4.187A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 122 removed outlier: 4.150A pdb=" N ARG T 122 " --> pdb=" O PRO T 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 119 through 122' Processing helix chain 'T' and resid 165 through 175 Processing helix chain 'T' and resid 176 through 179 removed outlier: 3.696A pdb=" N PHE T 179 " --> pdb=" O MET T 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 176 through 179' Processing helix chain 'T' and resid 183 through 196 Processing helix chain 'T' and resid 229 through 233 Processing helix chain 'U' and resid 20 through 31 removed outlier: 3.852A pdb=" N LYS U 28 " --> pdb=" O GLU U 24 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA U 29 " --> pdb=" O TYR U 25 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU U 31 " --> pdb=" O MET U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 102 removed outlier: 3.547A pdb=" N ALA U 84 " --> pdb=" O LEU U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 121 removed outlier: 3.866A pdb=" N LEU U 111 " --> pdb=" O PRO U 107 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA U 121 " --> pdb=" O MET U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 177 removed outlier: 3.647A pdb=" N ALA U 172 " --> pdb=" O ALA U 168 " (cutoff:3.500A) Processing helix chain 'U' and resid 180 through 184 Processing helix chain 'U' and resid 189 through 201 removed outlier: 3.502A pdb=" N HIS U 201 " --> pdb=" O ILE U 197 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 243 Processing helix chain 'V' and resid 48 through 67 Processing helix chain 'V' and resid 75 through 90 removed outlier: 4.170A pdb=" N ALA V 79 " --> pdb=" O LEU V 75 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 131 through 134 removed outlier: 3.942A pdb=" N TYR V 134 " --> pdb=" O GLY V 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 131 through 134' Processing helix chain 'V' and resid 135 through 143 Processing helix chain 'V' and resid 148 through 167 removed outlier: 3.988A pdb=" N ARG V 166 " --> pdb=" O LEU V 162 " (cutoff:3.500A) Processing helix chain 'V' and resid 190 through 194 removed outlier: 3.563A pdb=" N GLN V 193 " --> pdb=" O LEU V 190 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 71 removed outlier: 3.668A pdb=" N THR W 55 " --> pdb=" O ASP W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 88 removed outlier: 3.674A pdb=" N ALA W 79 " --> pdb=" O ARG W 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 141 removed outlier: 3.753A pdb=" N ALA W 134 " --> pdb=" O GLY W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 164 Processing helix chain 'Y' and resid 51 through 72 removed outlier: 3.993A pdb=" N GLN Y 55 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 93 removed outlier: 3.893A pdb=" N ASN Y 82 " --> pdb=" O THR Y 78 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG Y 93 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 147 removed outlier: 4.760A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU Y 143 " --> pdb=" O THR Y 139 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 171 removed outlier: 3.607A pdb=" N ALA Y 156 " --> pdb=" O SER Y 152 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 71 removed outlier: 4.280A pdb=" N GLU Z 56 " --> pdb=" O CYS Z 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 88 removed outlier: 3.589A pdb=" N VAL Z 87 " --> pdb=" O LEU Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 89 through 91 No H-bonds generated for 'chain 'Z' and resid 89 through 91' Processing helix chain 'Z' and resid 131 through 141 removed outlier: 3.928A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 removed outlier: 3.648A pdb=" N ALA Z 152 " --> pdb=" O GLU Z 148 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR Z 153 " --> pdb=" O VAL Z 149 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP Z 154 " --> pdb=" O GLU Z 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG Z 166 " --> pdb=" O GLN Z 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 192 through 197 removed outlier: 4.164A pdb=" N GLU Z 197 " --> pdb=" O ALA Z 193 " (cutoff:3.500A) Processing helix chain '1' and resid 57 through 80 removed outlier: 3.831A pdb=" N LYS 1 73 " --> pdb=" O GLU 1 69 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET 1 74 " --> pdb=" O ALA 1 70 " (cutoff:3.500A) Processing helix chain '1' and resid 84 through 99 removed outlier: 3.605A pdb=" N ILE 1 88 " --> pdb=" O THR 1 84 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR 1 94 " --> pdb=" O ALA 1 90 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG 1 99 " --> pdb=" O ILE 1 95 " (cutoff:3.500A) Processing helix chain '1' and resid 141 through 153 Proline residue: 1 147 - end of helix removed outlier: 3.557A pdb=" N ASP 1 150 " --> pdb=" O GLN 1 146 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN 1 151 " --> pdb=" O PRO 1 147 " (cutoff:3.500A) Processing helix chain '1' and resid 167 through 182 removed outlier: 3.730A pdb=" N ALA 1 171 " --> pdb=" O SER 1 167 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 75 removed outlier: 3.689A pdb=" N PHE 2 60 " --> pdb=" O ASP 2 56 " (cutoff:3.500A) Processing helix chain '2' and resid 84 through 102 Processing helix chain '2' and resid 141 through 146 removed outlier: 3.640A pdb=" N LEU 2 145 " --> pdb=" O TYR 2 141 " (cutoff:3.500A) Processing helix chain '2' and resid 146 through 157 removed outlier: 3.988A pdb=" N LYS 2 156 " --> pdb=" O GLU 2 152 " (cutoff:3.500A) Processing helix chain '2' and resid 161 through 173 removed outlier: 3.615A pdb=" N LEU 2 168 " --> pdb=" O GLU 2 164 " (cutoff:3.500A) Processing helix chain '2' and resid 174 through 180 Processing helix chain '2' and resid 209 through 214 removed outlier: 3.752A pdb=" N HIS 2 213 " --> pdb=" O ASP 2 210 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET 2 214 " --> pdb=" O ILE 2 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 136 through 140 removed outlier: 6.129A pdb=" N ALA J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR J 199 " --> pdb=" O THR I 213 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR I 213 " --> pdb=" O THR J 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 28 through 29 removed outlier: 7.161A pdb=" N PHE J 28 " --> pdb=" O VAL J 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 42 through 44 Processing sheet with id=AA4, first strand: chain 'X' and resid 136 through 140 removed outlier: 6.023A pdb=" N ALA X 10 " --> pdb=" O ASP X 25 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP X 25 " --> pdb=" O ALA X 10 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA X 21 " --> pdb=" O MET X 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL X 20 " --> pdb=" O ILE X 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 28 through 29 removed outlier: 7.150A pdb=" N PHE X 28 " --> pdb=" O VAL X 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 42 through 44 removed outlier: 3.787A pdb=" N SER X 123 " --> pdb=" O MET X 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.832A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN A 53 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.332A pdb=" N LEU A 69 " --> pdb=" O MET A 80 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N MET A 80 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LYS A 71 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N CYS A 78 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 73 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL A 151 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 163 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 153 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS A 161 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.611A pdb=" N ILE B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 72 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 69 removed outlier: 3.779A pdb=" N LEU C 68 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 157 " --> pdb=" O GLN C 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 160 through 161 removed outlier: 3.571A pdb=" N VAL D 41 " --> pdb=" O MET D 211 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 43 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 209 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 63 through 66 removed outlier: 3.589A pdb=" N MET D 71 " --> pdb=" O CYS D 63 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 134 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 148 removed outlier: 6.646A pdb=" N GLN D 146 " --> pdb=" O TYR D 153 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR D 153 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP D 148 " --> pdb=" O GLY D 151 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY D 151 " --> pdb=" O ASP D 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 167 through 170 removed outlier: 3.623A pdb=" N GLY E 45 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR E 219 " --> pdb=" O HIS E 227 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS E 227 " --> pdb=" O THR E 219 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.813A pdb=" N ILE E 67 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N MET E 78 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY E 144 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY E 145 " --> pdb=" O GLN E 152 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.722A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLY F 216 " --> pdb=" O GLU F 220 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU F 220 " --> pdb=" O GLY F 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.547A pdb=" N ILE F 63 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N HIS F 65 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE F 72 " --> pdb=" O HIS F 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'G' and resid 50 through 52 Processing sheet with id=AC4, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.586A pdb=" N PHE G 67 " --> pdb=" O MET G 75 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL G 69 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 125 through 128 removed outlier: 3.635A pdb=" N GLY H 11 " --> pdb=" O PHE H 8 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.866A pdb=" N ASN H 28 " --> pdb=" O THR H 20 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 41 through 44 removed outlier: 3.782A pdb=" N ALA H 101 " --> pdb=" O PHE H 42 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 124 through 127 removed outlier: 3.640A pdb=" N MET I 127 " --> pdb=" O ILE I 3 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY I 11 " --> pdb=" O TYR I 8 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AD1, first strand: chain 'I' and resid 34 through 38 removed outlier: 5.095A pdb=" N PHE I 36 " --> pdb=" O CYS I 43 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N CYS I 43 " --> pdb=" O PHE I 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 112 through 113 Processing sheet with id=AD3, first strand: chain 'K' and resid 129 through 131 removed outlier: 3.575A pdb=" N ILE K 182 " --> pdb=" O HIS K 189 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP K 184 " --> pdb=" O GLY K 187 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.603A pdb=" N ALA K 21 " --> pdb=" O MET K 28 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL K 26 " --> pdb=" O SER K 23 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'K' and resid 116 through 117 removed outlier: 3.896A pdb=" N TYR K 117 " --> pdb=" O ALA K 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.814A pdb=" N VAL L 12 " --> pdb=" O VAL L 179 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL L 14 " --> pdb=" O TYR L 177 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA L 16 " --> pdb=" O ASN L 175 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN L 175 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL L 174 " --> pdb=" O SER L 189 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER L 189 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU L 176 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY L 183 " --> pdb=" O ARG L 180 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.554A pdb=" N ALA L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 98 through 105 Processing sheet with id=AE1, first strand: chain 'M' and resid 135 through 136 Processing sheet with id=AE2, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.305A pdb=" N GLU M 31 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE M 35 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 43 through 45 removed outlier: 4.140A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 6 through 7 removed outlier: 6.781A pdb=" N GLY N 28 " --> pdb=" O ARG N 35 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG N 35 " --> pdb=" O GLY N 28 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 136 through 138 removed outlier: 3.505A pdb=" N LEU N 137 " --> pdb=" O GLY N 13 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY N 13 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL N 20 " --> pdb=" O VAL N 192 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE N 187 " --> pdb=" O PRO N 202 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR N 189 " --> pdb=" O GLU N 200 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 42 through 46 removed outlier: 3.983A pdb=" N LEU N 51 " --> pdb=" O MET N 43 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE N 112 " --> pdb=" O GLY N 123 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR N 132 " --> pdb=" O TYR N 124 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 165 through 169 Processing sheet with id=AE8, first strand: chain 'O' and resid 69 through 73 removed outlier: 5.938A pdb=" N LYS O 71 " --> pdb=" O CYS O 78 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N CYS O 78 " --> pdb=" O LYS O 71 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR O 73 " --> pdb=" O ILE O 76 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 138 through 143 removed outlier: 3.583A pdb=" N MET O 138 " --> pdb=" O CYS O 154 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS O 153 " --> pdb=" O CYS O 161 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS O 161 " --> pdb=" O LYS O 153 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 160 through 162 removed outlier: 3.532A pdb=" N THR P 160 " --> pdb=" O GLY P 36 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY P 36 " --> pdb=" O THR P 160 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET P 162 " --> pdb=" O SER P 34 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU P 208 " --> pdb=" O THR P 47 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN P 213 " --> pdb=" O GLY P 216 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY P 216 " --> pdb=" O ASN P 213 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 134 through 139 Processing sheet with id=AF3, first strand: chain 'Q' and resid 161 through 164 removed outlier: 3.567A pdb=" N LYS Q 222 " --> pdb=" O GLU Q 219 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 72 through 74 Processing sheet with id=AF5, first strand: chain 'R' and resid 160 through 161 removed outlier: 3.644A pdb=" N LEU R 43 " --> pdb=" O ALA R 209 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 62 through 64 removed outlier: 3.923A pdb=" N VAL R 134 " --> pdb=" O CYS R 70 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 167 through 170 removed outlier: 4.183A pdb=" N GLY S 45 " --> pdb=" O THR S 42 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 67 through 71 removed outlier: 3.532A pdb=" N CYS S 76 " --> pdb=" O VAL S 68 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE S 70 " --> pdb=" O ILE S 74 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY S 144 " --> pdb=" O GLY S 75 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU S 141 " --> pdb=" O MET S 156 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET S 156 " --> pdb=" O LEU S 141 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE S 154 " --> pdb=" O PHE S 143 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 35 through 38 Processing sheet with id=AG1, first strand: chain 'T' and resid 43 through 46 removed outlier: 3.669A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY T 216 " --> pdb=" O GLU T 220 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU T 220 " --> pdb=" O GLY T 216 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 63 through 67 removed outlier: 6.135A pdb=" N ILE T 63 " --> pdb=" O ILE T 74 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE T 74 " --> pdb=" O ILE T 63 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HIS T 65 " --> pdb=" O ILE T 72 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE T 72 " --> pdb=" O HIS T 65 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 162 through 163 Processing sheet with id=AG4, first strand: chain 'U' and resid 162 through 163 Processing sheet with id=AG5, first strand: chain 'U' and resid 66 through 70 removed outlier: 6.432A pdb=" N VAL U 73 " --> pdb=" O VAL U 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY U 138 " --> pdb=" O GLY U 74 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA U 76 " --> pdb=" O MET U 136 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR U 158 " --> pdb=" O MET U 150 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'V' and resid 125 through 129 Processing sheet with id=AG7, first strand: chain 'V' and resid 20 through 21 Processing sheet with id=AG8, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.658A pdb=" N ILE V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE V 99 " --> pdb=" O CYS V 44 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 124 through 128 removed outlier: 6.721A pdb=" N THR W 2 " --> pdb=" O ASP W 17 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY W 11 " --> pdb=" O TYR W 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA W 16 " --> pdb=" O ASP W 174 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W' and resid 20 through 21 removed outlier: 6.696A pdb=" N ALA W 20 " --> pdb=" O ALA W 27 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.682A pdb=" N ILE W 34 " --> pdb=" O GLY W 45 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY W 45 " --> pdb=" O ILE W 34 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE W 36 " --> pdb=" O CYS W 43 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS W 43 " --> pdb=" O PHE W 36 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 129 through 131 Processing sheet with id=AH4, first strand: chain 'Y' and resid 129 through 131 Processing sheet with id=AH5, first strand: chain 'Y' and resid 21 through 22 removed outlier: 3.739A pdb=" N ALA Y 21 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS Y 29 " --> pdb=" O ALA Y 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'Y' and resid 35 through 39 removed outlier: 3.639A pdb=" N MET Y 38 " --> pdb=" O ILE Y 42 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE Y 42 " --> pdb=" O MET Y 38 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 106 through 107 Processing sheet with id=AH8, first strand: chain 'Y' and resid 116 through 117 removed outlier: 3.896A pdb=" N TYR Y 117 " --> pdb=" O ALA Y 125 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Z' and resid 125 through 129 removed outlier: 3.719A pdb=" N VAL Z 12 " --> pdb=" O VAL Z 179 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU Z 176 " --> pdb=" O SER Z 188 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER Z 188 " --> pdb=" O LEU Z 176 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N HIS Z 178 " --> pdb=" O ARG Z 186 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ARG Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Z' and resid 20 through 22 removed outlier: 7.270A pdb=" N ALA Z 20 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR Z 25 " --> pdb=" O ALA Z 22 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Z' and resid 98 through 105 Processing sheet with id=AI3, first strand: chain '1' and resid 135 through 136 removed outlier: 3.587A pdb=" N LYS 1 136 " --> pdb=" O ALA 1 14 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain '1' and resid 29 through 31 removed outlier: 6.763A pdb=" N LEU 1 29 " --> pdb=" O HIS 1 36 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER 1 34 " --> pdb=" O GLU 1 31 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain '1' and resid 43 through 47 removed outlier: 6.908A pdb=" N THR 1 50 " --> pdb=" O LEU 1 46 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL 1 121 " --> pdb=" O ASP 1 133 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER 1 123 " --> pdb=" O GLN 1 131 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN 1 131 " --> pdb=" O SER 1 123 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain '2' and resid 12 through 15 removed outlier: 3.956A pdb=" N ALA 2 23 " --> pdb=" O LEU 2 12 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain '2' and resid 42 through 46 removed outlier: 6.506A pdb=" N THR 2 49 " --> pdb=" O VAL 2 45 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain '2' and resid 113 through 115 2148 hydrogen bonds defined for protein. 6075 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: 17.61 Time building geometry restraints manager: 10.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8870 1.33 - 1.45: 11690 1.45 - 1.57: 26795 1.57 - 1.69: 0 1.69 - 1.81: 472 Bond restraints: 47827 Sorted by residual: bond pdb=" CA ALA V 96 " pdb=" C ALA V 96 " ideal model delta sigma weight residual 1.528 1.488 0.039 8.80e-03 1.29e+04 2.01e+01 bond pdb=" CA MET V 95 " pdb=" C MET V 95 " ideal model delta sigma weight residual 1.524 1.472 0.051 1.29e-02 6.01e+03 1.56e+01 bond pdb=" N ILE V 98 " pdb=" CA ILE V 98 " ideal model delta sigma weight residual 1.458 1.412 0.046 1.19e-02 7.06e+03 1.49e+01 bond pdb=" CA CYS R 63 " pdb=" C CYS R 63 " ideal model delta sigma weight residual 1.522 1.483 0.038 1.24e-02 6.50e+03 9.59e+00 bond pdb=" CA ALA R 64 " pdb=" C ALA R 64 " ideal model delta sigma weight residual 1.521 1.486 0.035 1.19e-02 7.06e+03 8.62e+00 ... (remaining 47822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 64179 2.17 - 4.34: 619 4.34 - 6.51: 25 6.51 - 8.68: 1 8.68 - 10.85: 2 Bond angle restraints: 64826 Sorted by residual: angle pdb=" C ALA B 39 " pdb=" N ALA B 40 " pdb=" CA ALA B 40 " ideal model delta sigma weight residual 120.28 131.13 -10.85 1.34e+00 5.57e-01 6.55e+01 angle pdb=" C LYS D 47 " pdb=" N LYS D 48 " pdb=" CA LYS D 48 " ideal model delta sigma weight residual 120.72 131.13 -10.41 1.67e+00 3.59e-01 3.89e+01 angle pdb=" N MET V 95 " pdb=" CA MET V 95 " pdb=" C MET V 95 " ideal model delta sigma weight residual 111.36 105.51 5.85 1.09e+00 8.42e-01 2.88e+01 angle pdb=" C ALA V 96 " pdb=" CA ALA V 96 " pdb=" CB ALA V 96 " ideal model delta sigma weight residual 116.63 110.52 6.11 1.16e+00 7.43e-01 2.77e+01 angle pdb=" CA ALA V 96 " pdb=" C ALA V 96 " pdb=" N GLY V 97 " ideal model delta sigma weight residual 119.63 115.82 3.81 8.10e-01 1.52e+00 2.21e+01 ... (remaining 64821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 25608 17.91 - 35.81: 2288 35.81 - 53.72: 556 53.72 - 71.62: 103 71.62 - 89.53: 30 Dihedral angle restraints: 28585 sinusoidal: 10634 harmonic: 17951 Sorted by residual: dihedral pdb=" CA LEU B 55 " pdb=" C LEU B 55 " pdb=" N TYR B 56 " pdb=" CA TYR B 56 " ideal model delta harmonic sigma weight residual 180.00 150.15 29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA GLY V 97 " pdb=" C GLY V 97 " pdb=" N ILE V 98 " pdb=" CA ILE V 98 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA PHE C 60 " pdb=" C PHE C 60 " pdb=" N PHE C 61 " pdb=" CA PHE C 61 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 28582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 6625 0.068 - 0.136: 779 0.136 - 0.204: 16 0.204 - 0.272: 0 0.272 - 0.340: 1 Chirality restraints: 7421 Sorted by residual: chirality pdb=" CA LYS D 48 " pdb=" N LYS D 48 " pdb=" C LYS D 48 " pdb=" CB LYS D 48 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA LYS R 61 " pdb=" N LYS R 61 " pdb=" C LYS R 61 " pdb=" CB LYS R 61 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CB VAL J 60 " pdb=" CA VAL J 60 " pdb=" CG1 VAL J 60 " pdb=" CG2 VAL J 60 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.34e-01 ... (remaining 7418 not shown) Planarity restraints: 8344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP Q 151 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO Q 152 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO Q 152 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO Q 152 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 114 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO H 115 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 115 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 115 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN 2 147 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO 2 148 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO 2 148 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO 2 148 " 0.022 5.00e-02 4.00e+02 ... (remaining 8341 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 420 2.58 - 3.16: 38844 3.16 - 3.74: 64622 3.74 - 4.32: 90908 4.32 - 4.90: 162624 Nonbonded interactions: 357418 Sorted by model distance: nonbonded pdb=" OG SER C 13 " pdb=" O ARG C 17 " model vdw 1.998 3.040 nonbonded pdb=" OD2 ASP G 152 " pdb=" OG SER G 154 " model vdw 2.006 3.040 nonbonded pdb=" OE1 GLN J 169 " pdb=" OG1 THR I 209 " model vdw 2.008 3.040 nonbonded pdb=" OE1 GLN H 110 " pdb=" OH TYR H 112 " model vdw 2.014 3.040 nonbonded pdb=" OG1 THR S 108 " pdb=" OG SER S 111 " model vdw 2.026 3.040 ... (remaining 357413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and (resid 3 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 172 or (resid 17 \ 3 and (name N or name CA or name C or name O or name CB or name CG or name CD )) \ or resid 174 through 199 or (resid 200 and (name N or name CA or name C or name \ O or name CB )) or resid 201 through 213)) selection = (chain 'M' and (resid 3 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 132 or (resid 133 and (name N or na \ me CA or name C or name O or name CB )) or resid 134 through 203 or (resid 204 a \ nd (name N or name CA or name C or name O or name CB )) or resid 205 through 212 \ or (resid 213 and (name N or name CA or name C or name O or name CB or name CG \ or name OD1 or name OD2)))) } ncs_group { reference = (chain '2' and (resid 3 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB )) or resid 76 through 116 or (resid 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 or (resid 119 and (name N o \ r name CA or name C or name O or name CB )) or resid 120 through 154 or (resid 1 \ 55 through 156 and (name N or name CA or name C or name O or name CB )) or resid \ 157 through 158 or (resid 159 and (name N or name CA or name C or name O or nam \ e CB )) or resid 160 through 163 or (resid 164 through 165 and (name N or name C \ A or name C or name O or name CB )) or resid 166 through 193 or (resid 194 throu \ gh 195 and (name N or name CA or name C or name O or name CB )) or resid 196 thr \ ough 199 or (resid 200 and (name N or name CA or name C or name O or name CB )) \ or resid 201 through 214)) selection = (chain 'N' and (resid 3 through 72 or (resid 73 through 75 and (name N or name C \ A or name C or name O or name CB )) or resid 76 through 169 or (resid 170 and (n \ ame N or name CA or name C or name O or name CB )) or resid 171 through 194 or ( \ resid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 \ through 197 or (resid 198 and (name N or name CA or name C or name O or name CB \ )) or resid 199 through 209 or (resid 210 and (name N or name CA or name C or na \ me O or name CB )) or resid 211 through 214)) } ncs_group { reference = (chain 'A' and (resid 7 through 107 or (resid 108 and (name N or name CA or name \ C or name O or name CB )) or resid 109 through 203 or (resid 204 and (name N or \ name CA or name C or name O or name CB )) or resid 205 through 210 or (resid 21 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 212 or (resi \ d 213 and (name N or name CA or name C or name O or name CB )) or resid 214 thro \ ugh 230 or (resid 231 through 233 and (name N or name CA or name C or name O or \ name CB )) or resid 234 through 235 or (resid 236 through 237 and (name N or nam \ e CA or name C or name O or name CB )) or resid 238 through 239 or (resid 240 th \ rough 241 and (name N or name CA or name C or name O or name CB )) or resid 242 \ through 243)) selection = (chain 'O' and (resid 7 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 54 or (resid 55 and (nam \ e N or name CA or name C or name O or name CB )) or resid 56 through 145 or (res \ id 146 and (name N or name CA or name C or name O or name CB )) or resid 147 thr \ ough 173 or (resid 174 and (name N or name CA or name C or name O or name CB )) \ or resid 175 through 180 or (resid 181 and (name N or name CA or name C or name \ O or name CB )) or resid 182 through 183 or (resid 184 and (name N or name CA or \ name C or name O or name CB )) or resid 185 through 207 or (resid 208 and (name \ N or name CA or name C or name O or name CB )) or resid 209 through 222 or (res \ id 223 and (name N or name CA or name C or name O or name CB )) or resid 224 thr \ ough 231 or (resid 232 through 233 and (name N or name CA or name C or name O or \ name CB )) or resid 234 through 243)) } ncs_group { reference = (chain 'B' and (resid 4 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 52 or (resid 53 through 54 and (nam \ e N or name CA or name C or name O or name CB )) or resid 55 through 57 or (resi \ d 58 through 59 and (name N or name CA or name C or name O or name CB )) or resi \ d 60 through 68 or (resid 69 and (name N or name CA or name C or name O or name \ CB )) or resid 70 through 177 or (resid 178 through 180 and (name N or name CA o \ r name C or name O or name CB )) or resid 181 through 194 or (resid 195 and (nam \ e N or name CA or name C or name O or name CB )) or resid 196 through 224 or (re \ sid 225 through 227 and (name N or name CA or name C or name O or name CB )) or \ resid 228 through 231)) selection = (chain 'P' and (resid 4 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 138 or (resid 139 through 140 and ( \ name N or name CA or name C or name O or name CB )) or resid 141 or (resid 142 a \ nd (name N or name CA or name C or name O or name CB )) or resid 143 through 175 \ or (resid 176 and (name N or name CA or name C or name O or name CB )) or resid \ 177 through 203 or (resid 204 and (name N or name CA or name C or name O or nam \ e CB )) or resid 205 through 231)) } ncs_group { reference = (chain 'C' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 47 or (resid 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )) or resid 55 through 56 or (re \ sid 57 through 58 and (name N or name CA or name C or name O or name CB )) or re \ sid 59 through 62 or (resid 63 and (name N or name CA or name C or name O or nam \ e CB )) or resid 64 through 88 or (resid 89 and (name N or name CA or name C or \ name O or name CB )) or resid 90 through 173 or (resid 174 and (name N or name C \ A or name C or name O or name CB )) or resid 175 through 179 or (resid 180 throu \ gh 181 and (name N or name CA or name C or name O or name CB )) or resid 182 or \ (resid 183 and (name N or name CA or name C or name O or name CB )) or resid 184 \ through 198 or (resid 199 and (name N or name CA or name C or name O or name CB \ )) or resid 200 through 208 or (resid 209 through 210 and (name N or name CA or \ name C or name O or name CB )) or resid 211 through 218 or (resid 219 through 2 \ 20 and (name N or name CA or name C or name O or name CB )) or resid 221 through \ 233 or (resid 234 through 235 and (name N or name CA or name C or name O or nam \ e CB )) or resid 236 through 242 or (resid 243 through 247 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'Q' and (resid 2 through 66 or (resid 67 and (name N or name CA or name C \ or name O or name CB )) or resid 68 through 176 or (resid 177 through 178 and ( \ name N or name CA or name C or name O or name CB )) or resid 179 through 204 or \ (resid 205 and (name N or name CA or name C or name O or name CB )) or resid 206 \ through 209 or (resid 210 and (name N or name CA or name C or name O or name CB \ )) or resid 211 through 237 or (resid 238 and (name N or name CA or name C or n \ ame O or name CB )) or resid 239 through 240 or (resid 241 through 247 and (name \ N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'D' and (resid 2 through 38 or (resid 39 and (name N or name CA or name C \ or name O or name CB )) or resid 40 through 59 or (resid 60 and (name N or name \ CA or name C or name O or name CB )) or resid 61 through 158 or (resid 159 thro \ ugh 160 and (name N or name CA or name C or name O or name CB )) or resid 161 th \ rough 172 or (resid 173 through 174 and (name N or name CA or name C or name O o \ r name CB )) or resid 175 through 177 or (resid 178 through 180 and (name N or n \ ame CA or name C or name O or name CB )) or resid 181 through 195 or (resid 196 \ and (name N or name CA or name C or name O or name CB )) or resid 197 or (resid \ 198 through 201 and (name N or name CA or name C or name O or name CB )) or resi \ d 202 through 203 or (resid 204 and (name N or name CA or name C or name O or na \ me CB )) or resid 205 through 212 or (resid 213 and (name N or name CA or name C \ or name O or name CB )) or resid 214 through 220 or (resid 221 and (name N or n \ ame CA or name C or name O or name CB )) or resid 222 through 224 or (resid 225 \ through 227 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 8 through 242)) selection = (chain 'R' and (resid 2 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 49 or (resid 50 through 52 and (nam \ e N or name CA or name C or name O or name CB )) or resid 53 through 57 or (resi \ d 58 through 60 and (name N or name CA or name C or name O or name CB )) or resi \ d 61 through 98 or (resid 99 and (name N or name CA or name C or name O or name \ CB )) or resid 100 through 104 or (resid 105 and (name N or name CA or name C or \ name O or name CB )) or resid 106 through 137 or (resid 138 through 139 and (na \ me N or name CA or name C or name O or name CB )) or resid 140 through 165 or (r \ esid 166 and (name N or name CA or name C or name O or name CB )) or resid 167 t \ hrough 169 or (resid 170 and (name N or name CA or name C or name O or name CB ) \ ) or resid 171 through 181 or (resid 182 through 183 and (name N or name CA or n \ ame C or name O or name CB )) or resid 184 through 242)) } ncs_group { reference = (chain 'E' and (resid 9 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 83 or (resid 84 through 85 and (nam \ e N or name CA or name C or name O or name CB )) or resid 86 through 109 or (res \ id 110 and (name N or name CA or name C or name O or name CB )) or resid 111 thr \ ough 186 or (resid 187 and (name N or name CA or name C or name O or name CB )) \ or resid 188 or (resid 189 and (name N or name CA or name C or name O or name CB \ )) or resid 190 through 231 or (resid 232 and (name N or name CA or name C or n \ ame O or name CB )) or resid 233 through 240)) selection = (chain 'S' and (resid 9 through 124 or (resid 125 and (name N or name CA or name \ C or name O or name CB )) or resid 126 through 191 or (resid 192 and (name N or \ name CA or name C or name O or name CB )) or resid 193 through 206 or (resid 20 \ 7 through 209 and (name N or name CA or name C or name O or name CB )) or resid \ 210 or (resid 211 through 212 and (name N or name CA or name C or name O or name \ CB )) or resid 213 through 223 or (resid 224 and (name N or name CA or name C o \ r name O or name CB )) or resid 225 through 238 or (resid 239 through 240 and (n \ ame N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'F' and (resid 5 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 52 or (resid 53 and (name N or name \ CA or name C or name O or name CB )) or (resid 57 through 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 93 or (resid 94 and ( \ name N or name CA or name C or name O or name CB )) or resid 95 through 172 or ( \ resid 173 through 174 and (name N or name CA or name C or name O or name CB )) o \ r resid 175 through 188 or (resid 189 and (name N or name CA or name C or name O \ or name CB )) or resid 190 through 207 or (resid 208 and (name N or name CA or \ name C or name O or name CB )) or resid 209 through 225 or (resid 226 through 22 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 228 through \ 233 or (resid 234 and (name N or name CA or name C or name O or name CB )) or re \ sid 235 through 238)) selection = (chain 'T' and (resid 5 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 60 or (resid 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 67 or (resid 68 and (n \ ame N or name CA or name C or name O or name CB )) or resid 69 through 137 or (r \ esid 138 through 140 and (name N or name CA or name C or name O or name CB )) or \ resid 141 through 173 or (resid 174 and (name N or name CA or name C or name O \ or name CB )) or resid 175 through 195 or (resid 196 and (name N or name CA or n \ ame C or name O or name CB )) or resid 197 through 202 or (resid 203 through 204 \ and (name N or name CA or name C or name O or name CB )) or resid 205 through 2 \ 38)) } ncs_group { reference = (chain 'G' and (resid 4 through 41 or (resid 42 and (name N or name CA or name C \ or name O or name CB )) or resid 43 through 55 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 141 or (resid 142 and \ (name N or name CA or name C or name O or name CB )) or resid 143 or (resid 144 \ and (name N or name CA or name C or name O or name CB )) or resid 145 through 18 \ 1 or (resid 182 and (name N or name CA or name C or name O or name CB )) or resi \ d 183 through 187 or (resid 188 and (name N or name CA or name C or name O or na \ me CB )) or resid 189 through 203 or (resid 204 through 205 and (name N or name \ CA or name C or name O or name CB )) or resid 206 through 218 or (resid 219 and \ (name N or name CA or name C or name O or name CB )) or resid 220 through 228 or \ (resid 229 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 0 through 236 or (resid 237 and (name N or name CA or name C or name O or name C \ B )) or resid 238 through 240 or (resid 241 and (name N or name CA or name C or \ name O or name CB )) or resid 242 or (resid 243 through 244 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'U' and (resid 4 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB )) or resid 110 through 169 or (resid 170 through 172 an \ d (name N or name CA or name C or name O or name CB )) or resid 173 through 178 \ or (resid 179 and (name N or name CA or name C or name O or name CB )) or resid \ 180 through 191 or (resid 192 and (name N or name CA or name C or name O or name \ CB )) or resid 193 through 244)) } ncs_group { reference = (chain 'H' and (resid 1 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 56 or (resid 57 through 58 and (nam \ e N or name CA or name C or name O or name CB )) or resid 59 through 92 or (resi \ d 93 through 96 and (name N or name CA or name C or name O or name CB )) or resi \ d 97 through 103 or (resid 104 and (name N or name CA or name C or name O or nam \ e CB )) or resid 105 through 115 or (resid 116 and (name N or name CA or name C \ or name O or name CB )) or resid 117 through 149 or (resid 150 and (name N or na \ me CA or name C or name O or name CB )) or resid 151 through 198 or (resid 199 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'V' and (resid 1 through 70 or (resid 71 through 72 and (name N or name C \ A or name C or name O or name CB )) or resid 73 through 88 or (resid 89 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name NE ) \ ) or resid 90 through 144 or (resid 145 and (name N or name CA or name C or name \ O or name CB )) or resid 146 through 199)) } ncs_group { reference = (chain 'I' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 90 or (resid 91 and (name N or name C \ A or name C or name O or name CB )) or resid 92 through 142 or (resid 143 and (n \ ame N or name CA or name C or name O or name CB )) or resid 144 through 179 or ( \ resid 180 through 181 and (name N or name CA or name C or name O or name CB )) o \ r resid 182 through 192 or (resid 193 and (name N or name CA or name C or name O \ or name CB )) or resid 194 through 220)) selection = (chain 'W' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 180 or (resid 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 through 193 or (resid 194 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 195 \ through 200 or (resid 201 and (name N or name CA or name C or name O or name CB \ or name CG or name CD )) or resid 202 through 205 or (resid 206 and (name N or n \ ame CA or name C or name O or name CB )) or resid 207 through 220)) } ncs_group { reference = (chain 'J' and (resid 2 through 114 or (resid 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 205)) selection = (chain 'X' and (resid 2 through 133 or (resid 134 and (name N or name CA or name \ C or name O or name CB )) or resid 135 through 205)) } ncs_group { reference = (chain 'K' and (resid 1 through 22 or (resid 23 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 through 61 or (resid 62 and (nam \ e N or name CA or name C or name O or name CB )) or resid 63 through 189 or (res \ id 190 and (name N or name CA or name C or name O or name CB )) or resid 191 thr \ ough 197)) selection = (chain 'Y' and (resid 1 through 57 or (resid 58 and (name N or name CA or name C \ or name O or name CB )) or resid 59 through 197)) } ncs_group { reference = (chain 'L' and (resid 1 through 145 or (resid 146 and (name N or name CA or name \ C or name O or name CB )) or resid 147 through 200)) selection = (chain 'Z' and (resid 1 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 181 or (resid 182 and (name N or \ name CA or name C or name O or name CB )) or resid 183 through 200)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.490 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 85.470 Find NCS groups from input model: 3.390 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 47827 Z= 0.399 Angle : 0.593 10.847 64826 Z= 0.344 Chirality : 0.043 0.340 7421 Planarity : 0.003 0.042 8344 Dihedral : 14.858 89.527 17123 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 1.46 % Allowed : 16.02 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -3.78 (0.09), residues: 6164 helix: -1.24 (0.10), residues: 2033 sheet: -2.21 (0.13), residues: 1353 loop : -3.69 (0.09), residues: 2778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 101 HIS 0.006 0.001 HIS 2 89 PHE 0.020 0.001 PHE X 69 TYR 0.017 0.001 TYR Y 120 ARG 0.006 0.000 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12328 Ramachandran restraints generated. 6164 Oldfield, 0 Emsley, 6164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1063 time to evaluate : 4.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 56 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8368 (mp) REVERT: E 121 LEU cc_start: 0.8024 (mt) cc_final: 0.7667 (pt) REVERT: F 179 PHE cc_start: 0.7396 (m-80) cc_final: 0.7175 (m-10) REVERT: G 94 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: K 62 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8249 (tttt) REVERT: M 132 ARG cc_start: 0.7750 (ttt180) cc_final: 0.7510 (ttm-80) REVERT: N 147 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: O 144 ASP cc_start: 0.7479 (t70) cc_final: 0.7275 (t70) REVERT: R 132 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8109 (mp) REVERT: R 157 LYS cc_start: 0.8368 (mttp) cc_final: 0.8138 (mtpt) REVERT: T 62 LYS cc_start: 0.7958 (tppt) cc_final: 0.7637 (mtpp) REVERT: T 100 ASP cc_start: 0.8129 (t0) cc_final: 0.7851 (t0) REVERT: T 159 MET cc_start: 0.7722 (tpp) cc_final: 0.7337 (tpt) REVERT: W 182 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7434 (ttmt) REVERT: W 215 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7915 (ttpt) REVERT: Z 64 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7298 (tpt-90) REVERT: Z 186 ARG cc_start: 0.7750 (ttt-90) cc_final: 0.7514 (ttt-90) REVERT: Z 190 ASP cc_start: 0.7458 (m-30) cc_final: 0.7219 (m-30) REVERT: 1 177 ASP cc_start: 0.8187 (t0) cc_final: 0.7876 (t0) REVERT: 2 166 ARG cc_start: 0.7590 (ttm170) cc_final: 0.7329 (tpp80) outliers start: 70 outliers final: 37 residues processed: 1125 average time/residue: 0.4908 time to fit residues: 880.2197 Evaluate side-chains 772 residues out of total 5170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 730 time to evaluate : 4.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain N residue 147 GLN Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain S residue 27 ASP Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 215 TRP Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Z residue 64 ARG Chi-restraints excluded: chain Z residue 182 ASP Chi-restraints excluded: chain 1 residue 140 SER Chi-restraints excluded: chain 1 residue 198 VAL Chi-restraints excluded: chain 2 residue 139 THR Chi-restraints excluded: chain 2 residue 191 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 517 optimal weight: 0.9980 chunk 464 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 313 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 480 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 292 optimal weight: 0.9980 chunk 357 optimal weight: 0.8980 chunk 556 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 18 ASN J 162 HIS X 65 GLN A 24 GLN C 88 ASN C 95 GLN D 120 GLN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN G 101 ASN G 221 ASN K 168 GLN L 29 GLN M 58 HIS M 157 ASN N 208 ASN O 24 GLN P 108 GLN P 139 ASN P 206 ASN Q 20 GLN Q 102 GLN Q 123 GLN R 23 GLN R 92 GLN S 13 ASN S 23 GLN S 97 GLN S 99 HIS S 155 HIS S 211 ASN T 43 HIS T 65 HIS T 90 GLN T 190 HIS W 80 ASN Y 71 ASN Y 168 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1947 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: