Starting phenix.real_space_refine on Thu Dec 26 10:30:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v5m_31727/12_2024/7v5m_31727.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v5m_31727/12_2024/7v5m_31727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v5m_31727/12_2024/7v5m_31727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v5m_31727/12_2024/7v5m_31727.map" model { file = "/net/cci-nas-00/data/ceres_data/7v5m_31727/12_2024/7v5m_31727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v5m_31727/12_2024/7v5m_31727.cif" } resolution = 3.88 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= 0.003 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 280 5.16 5 C 28992 2.51 5 N 8010 2.21 5 O 8058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 45340 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1734 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1786 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "D" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1633 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1659 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "F" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1704 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1760 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 77 Chain: "H" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1465 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "I" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1576 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "J" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1534 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "K" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1506 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1500 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1583 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 55 Chain: "N" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1568 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "O" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1734 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "P" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "Q" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1786 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "R" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1633 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "S" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1659 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "T" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1704 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "U" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1760 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 77 Chain: "V" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1465 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "W" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1576 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "X" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1534 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "Y" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1506 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "Z" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1500 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "a" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1583 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 55 Chain: "b" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1568 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 25.04, per 1000 atoms: 0.55 Number of scatterers: 45340 At special positions: 0 Unit cell: (192.428, 156.842, 131.8, 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 280 16.00 O 8058 8.00 N 8010 7.00 C 28992 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: 11.00 Conformation dependent library (CDL) restraints added in 6.3 seconds 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11416 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 70 sheets defined 38.8% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.66 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 removed outlier: 3.863A pdb=" N ASP A 10 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG A 11 " --> pdb=" O GLY A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.869A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 36 Processing helix chain 'A' and resid 83 through 106 removed outlier: 3.848A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.712A pdb=" N CYS A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.506A pdb=" N SER A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 189 removed outlier: 4.346A pdb=" N TRP A 189 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 207 removed outlier: 3.740A pdb=" N THR A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 removed outlier: 3.580A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 30 removed outlier: 3.798A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 27 " --> pdb=" O TYR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 101 removed outlier: 3.532A pdb=" N ARG B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.526A pdb=" N ARG B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.517A pdb=" N THR B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 4.046A pdb=" N HIS B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 removed outlier: 3.961A pdb=" N ILE B 207 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 removed outlier: 3.592A pdb=" N ASP B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.649A pdb=" N GLU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.878A pdb=" N ASN C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 removed outlier: 3.550A pdb=" N VAL C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 176 Processing helix chain 'C' and resid 185 through 200 removed outlier: 4.055A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 247 removed outlier: 3.698A pdb=" N LEU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 removed outlier: 3.633A pdb=" N VAL D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 99 removed outlier: 3.673A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.800A pdb=" N THR D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.663A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 removed outlier: 3.738A pdb=" N VAL D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 232 removed outlier: 3.765A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.576A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.584A 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 85 through 104 Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 173 through 185 removed outlier: 6.819A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E 184 " --> pdb=" O SER E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 removed outlier: 3.532A pdb=" N LEU E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.725A pdb=" N GLU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 29 removed outlier: 3.503A pdb=" N GLU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 99 removed outlier: 3.700A pdb=" N PHE F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.816A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix removed outlier: 3.504A pdb=" N ARG F 122 " --> pdb=" O ILE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 176 Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.701A pdb=" N VAL F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'G' and resid 6 through 10 removed outlier: 4.305A pdb=" N SER G 10 " --> pdb=" O TYR G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 32 removed outlier: 3.529A pdb=" N LYS G 28 " --> pdb=" O GLU G 24 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA G 29 " --> pdb=" O TYR G 25 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU G 31 " --> pdb=" O MET G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 103 removed outlier: 3.641A pdb=" N SER G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE G 98 " --> pdb=" O GLU G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.573A pdb=" N ASP G 113 " --> pdb=" O LYS G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 removed outlier: 4.174A pdb=" N ALA G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS G 173 " --> pdb=" O ARG G 169 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS G 178 " --> pdb=" O THR G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 3.993A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 244 removed outlier: 3.566A pdb=" N SER G 242 " --> pdb=" O TYR G 238 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS G 244 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 removed outlier: 3.564A pdb=" N ALA H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.574A pdb=" N ALA H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU H 82 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 134 removed outlier: 3.527A pdb=" N TYR H 134 " --> pdb=" O GLY H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 142 removed outlier: 3.519A pdb=" N ALA H 141 " --> pdb=" O GLY H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 167 removed outlier: 3.509A pdb=" N GLN H 154 " --> pdb=" O GLU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.879A pdb=" N ILE H 194 " --> pdb=" O GLY H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 71 removed outlier: 3.697A pdb=" N LEU I 58 " --> pdb=" O MET I 54 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 90 Processing helix chain 'I' and resid 130 through 142 removed outlier: 4.043A pdb=" N ALA I 136 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE I 138 " --> pdb=" O ALA I 134 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 164 removed outlier: 3.531A pdb=" N GLY I 162 " --> pdb=" O ALA I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 5 Processing helix chain 'J' and resid 55 through 78 Processing helix chain 'J' and resid 82 through 97 removed outlier: 3.846A pdb=" N SER J 88 " --> pdb=" O TYR J 84 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 removed outlier: 3.591A pdb=" N TYR J 146 " --> pdb=" O ALA J 142 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY J 147 " --> pdb=" O GLU J 143 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET J 148 " --> pdb=" O GLN J 144 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU J 150 " --> pdb=" O TYR J 146 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU J 152 " --> pdb=" O MET J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 175 removed outlier: 3.555A pdb=" N GLU J 164 " --> pdb=" O ASP J 160 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 72 removed outlier: 3.743A pdb=" N GLN K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU K 58 " --> pdb=" O VAL K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 90 removed outlier: 3.852A pdb=" N ASN K 87 " --> pdb=" O PHE K 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU K 88 " --> pdb=" O THR K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 143 removed outlier: 4.628A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 170 removed outlier: 3.538A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU K 167 " --> pdb=" O CYS K 163 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN K 168 " --> pdb=" O LEU K 164 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS K 169 " --> pdb=" O GLU K 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 71 removed outlier: 3.600A pdb=" N GLU L 56 " --> pdb=" O CYS L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 88 removed outlier: 3.508A pdb=" N VAL L 87 " --> pdb=" O LEU L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 4.250A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG L 141 " --> pdb=" O GLY L 137 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY L 142 " --> pdb=" O VAL L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 removed outlier: 3.623A pdb=" N ASP L 154 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU L 155 " --> pdb=" O GLN L 151 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE L 160 " --> pdb=" O ALA L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 199 removed outlier: 4.219A pdb=" N GLU L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 80 removed outlier: 3.787A pdb=" N LYS M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET M 74 " --> pdb=" O ALA M 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.553A pdb=" N THR M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 153 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 167 through 186 removed outlier: 3.521A pdb=" N MET M 172 " --> pdb=" O LEU M 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE M 180 " --> pdb=" O LYS M 176 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER M 181 " --> pdb=" O ASP M 177 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG M 185 " --> pdb=" O SER M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 78 removed outlier: 3.538A pdb=" N GLN N 69 " --> pdb=" O GLN N 65 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET N 70 " --> pdb=" O VAL N 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL N 71 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE N 72 " --> pdb=" O GLY N 68 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 removed outlier: 3.504A pdb=" N ARG N 99 " --> pdb=" O ALA N 95 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG N 100 " --> pdb=" O MET N 96 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS N 102 " --> pdb=" O SER N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 removed outlier: 3.926A pdb=" N LYS N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 180 removed outlier: 3.570A pdb=" N ARG N 179 " --> pdb=" O VAL N 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 12 removed outlier: 3.864A pdb=" N ASP O 10 " --> pdb=" O ALA O 7 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG O 11 " --> pdb=" O GLY O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 31 removed outlier: 3.869A pdb=" N LYS O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 36 Processing helix chain 'O' and resid 83 through 106 removed outlier: 3.847A pdb=" N SER O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 128 removed outlier: 3.712A pdb=" N CYS O 115 " --> pdb=" O VAL O 111 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS O 116 " --> pdb=" O ASP O 112 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG O 117 " --> pdb=" O MET O 113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE O 118 " --> pdb=" O LEU O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 181 removed outlier: 3.507A pdb=" N SER O 177 " --> pdb=" O THR O 173 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS O 181 " --> pdb=" O SER O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 184 No H-bonds generated for 'chain 'O' and resid 182 through 184' Processing helix chain 'O' and resid 185 through 189 Processing helix chain 'O' and resid 193 through 207 removed outlier: 3.740A pdb=" N THR O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL O 205 " --> pdb=" O CYS O 201 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU O 206 " --> pdb=" O LEU O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 241 removed outlier: 3.579A pdb=" N ALA O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS O 238 " --> pdb=" O GLU O 234 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA O 241 " --> pdb=" O ALA O 237 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 30 removed outlier: 3.798A pdb=" N ALA P 26 " --> pdb=" O GLU P 22 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA P 27 " --> pdb=" O TYR P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 101 removed outlier: 3.532A pdb=" N ARG P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL P 84 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU P 85 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 120 removed outlier: 3.526A pdb=" N ARG P 112 " --> pdb=" O GLN P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 177 removed outlier: 3.517A pdb=" N THR P 171 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE P 172 " --> pdb=" O ASN P 168 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU P 174 " --> pdb=" O LYS P 170 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS P 175 " --> pdb=" O THR P 171 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG P 176 " --> pdb=" O PHE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 197 removed outlier: 4.046A pdb=" N HIS P 188 " --> pdb=" O GLU P 184 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR P 189 " --> pdb=" O ASP P 185 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU P 194 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER P 197 " --> pdb=" O THR P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 207 removed outlier: 3.961A pdb=" N ILE P 207 " --> pdb=" O GLU P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 230 removed outlier: 3.592A pdb=" N ASP P 227 " --> pdb=" O THR P 223 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR P 228 " --> pdb=" O GLU P 224 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA P 230 " --> pdb=" O LYS P 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 30 removed outlier: 3.648A pdb=" N GLU Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 102 removed outlier: 3.879A pdb=" N ASN Q 84 " --> pdb=" O THR Q 80 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL Q 85 " --> pdb=" O SER Q 81 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 124 removed outlier: 3.551A pdb=" N VAL Q 111 " --> pdb=" O CYS Q 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 176 Processing helix chain 'Q' and resid 185 through 200 removed outlier: 4.055A pdb=" N LYS Q 199 " --> pdb=" O LYS Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 247 removed outlier: 3.698A pdb=" N LEU Q 236 " --> pdb=" O GLU Q 232 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA Q 245 " --> pdb=" O GLU Q 241 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS Q 246 " --> pdb=" O GLU Q 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 27 removed outlier: 3.633A pdb=" N VAL R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.674A pdb=" N ILE R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 121 removed outlier: 3.799A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 176 removed outlier: 3.663A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 199 removed outlier: 3.738A pdb=" N VAL R 191 " --> pdb=" O THR R 187 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 232 removed outlier: 3.763A pdb=" N LYS R 227 " --> pdb=" O GLU R 223 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR R 228 " --> pdb=" O GLU R 224 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.575A pdb=" N GLU S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS S 32 " --> pdb=" O ILE S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 85 through 104 Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 173 through 185 removed outlier: 6.818A pdb=" N SER S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER S 180 " --> pdb=" O GLY S 176 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU S 183 " --> pdb=" O SER S 179 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL S 184 " --> pdb=" O SER S 180 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 206 removed outlier: 3.531A pdb=" N LEU S 199 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE S 201 " --> pdb=" O SER S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 230 through 241 removed outlier: 3.725A pdb=" N GLU S 235 " --> pdb=" O LYS S 231 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU S 236 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL S 237 " --> pdb=" O GLU S 233 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP S 240 " --> pdb=" O GLU S 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 29 removed outlier: 3.504A pdb=" N GLU T 23 " --> pdb=" O ILE T 19 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 99 removed outlier: 3.700A pdb=" N PHE T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 122 removed outlier: 3.817A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Proline residue: T 119 - end of helix removed outlier: 3.503A pdb=" N ARG T 122 " --> pdb=" O ILE T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 176 Processing helix chain 'T' and resid 178 through 182 Processing helix chain 'T' and resid 183 through 197 removed outlier: 3.702A pdb=" N VAL T 188 " --> pdb=" O LEU T 184 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS T 189 " --> pdb=" O ASN T 185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS T 190 " --> pdb=" O GLU T 186 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY T 191 " --> pdb=" O LEU T 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU T 197 " --> pdb=" O ARG T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 234 Processing helix chain 'U' and resid 6 through 10 removed outlier: 4.306A pdb=" N SER U 10 " --> pdb=" O TYR U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 32 removed outlier: 3.530A pdb=" N LYS U 28 " --> pdb=" O GLU U 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA U 29 " --> pdb=" O TYR U 25 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU U 31 " --> pdb=" O MET U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 103 removed outlier: 3.641A pdb=" N SER U 86 " --> pdb=" O ALA U 82 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE U 98 " --> pdb=" O GLU U 94 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 121 removed outlier: 3.573A pdb=" N ASP U 113 " --> pdb=" O LYS U 109 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 178 removed outlier: 4.174A pdb=" N ALA U 172 " --> pdb=" O ALA U 168 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS U 173 " --> pdb=" O ARG U 169 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU U 175 " --> pdb=" O ALA U 171 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS U 178 " --> pdb=" O THR U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 201 removed outlier: 3.992A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU U 192 " --> pdb=" O ASP U 188 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS U 195 " --> pdb=" O LYS U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 244 removed outlier: 3.567A pdb=" N SER U 242 " --> pdb=" O TYR U 238 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS U 244 " --> pdb=" O LYS U 240 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 71 removed outlier: 3.565A pdb=" N ALA V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU V 69 " --> pdb=" O PHE V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.573A pdb=" N ALA V 79 " --> pdb=" O LEU V 75 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU V 82 " --> pdb=" O THR V 78 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG V 89 " --> pdb=" O GLU V 85 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 134 removed outlier: 3.528A pdb=" N TYR V 134 " --> pdb=" O GLY V 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 142 removed outlier: 3.519A pdb=" N ALA V 141 " --> pdb=" O GLY V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 167 removed outlier: 3.510A pdb=" N GLN V 154 " --> pdb=" O GLU V 150 " (cutoff:3.500A) Processing helix chain 'V' and resid 190 through 194 removed outlier: 3.878A pdb=" N ILE V 194 " --> pdb=" O GLY V 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 71 removed outlier: 3.697A pdb=" N LEU W 58 " --> pdb=" O MET W 54 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER W 69 " --> pdb=" O LEU W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 90 Processing helix chain 'W' and resid 130 through 142 removed outlier: 4.042A pdb=" N ALA W 136 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE W 138 " --> pdb=" O ALA W 134 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 164 removed outlier: 3.531A pdb=" N GLY W 162 " --> pdb=" O ALA W 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 1 through 5 Processing helix chain 'X' and resid 55 through 78 Processing helix chain 'X' and resid 82 through 97 removed outlier: 3.846A pdb=" N SER X 88 " --> pdb=" O TYR X 84 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS X 97 " --> pdb=" O LEU X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 153 removed outlier: 3.590A pdb=" N TYR X 146 " --> pdb=" O ALA X 142 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY X 147 " --> pdb=" O GLU X 143 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET X 148 " --> pdb=" O GLN X 144 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU X 150 " --> pdb=" O TYR X 146 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER X 151 " --> pdb=" O GLY X 147 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU X 152 " --> pdb=" O MET X 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 175 removed outlier: 3.555A pdb=" N GLU X 164 " --> pdb=" O ASP X 160 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN X 172 " --> pdb=" O GLN X 168 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA X 173 " --> pdb=" O ALA X 169 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 72 removed outlier: 3.743A pdb=" N GLN Y 55 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU Y 58 " --> pdb=" O VAL Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 90 removed outlier: 3.851A pdb=" N ASN Y 87 " --> pdb=" O PHE Y 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU Y 88 " --> pdb=" O THR Y 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 143 removed outlier: 4.628A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 170 removed outlier: 3.538A pdb=" N GLU Y 166 " --> pdb=" O LYS Y 162 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU Y 167 " --> pdb=" O CYS Y 163 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN Y 168 " --> pdb=" O LEU Y 164 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS Y 169 " --> pdb=" O GLU Y 165 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 71 removed outlier: 3.600A pdb=" N GLU Z 56 " --> pdb=" O CYS Z 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 88 removed outlier: 3.508A pdb=" N VAL Z 87 " --> pdb=" O LEU Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 4.250A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG Z 141 " --> pdb=" O GLY Z 137 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY Z 142 " --> pdb=" O VAL Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 removed outlier: 3.623A pdb=" N ASP Z 154 " --> pdb=" O GLU Z 150 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU Z 155 " --> pdb=" O GLN Z 151 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE Z 160 " --> pdb=" O ALA Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 191 through 199 removed outlier: 4.218A pdb=" N GLU Z 197 " --> pdb=" O ALA Z 193 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS Z 198 " --> pdb=" O ASP Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 80 removed outlier: 3.788A pdb=" N LYS a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET a 74 " --> pdb=" O ALA a 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR a 75 " --> pdb=" O ARG a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 99 removed outlier: 3.553A pdb=" N THR a 94 " --> pdb=" O ALA a 90 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 153 Proline residue: a 147 - end of helix Processing helix chain 'a' and resid 167 through 186 removed outlier: 3.521A pdb=" N MET a 172 " --> pdb=" O LEU a 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE a 179 " --> pdb=" O VAL a 175 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE a 180 " --> pdb=" O LYS a 176 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER a 181 " --> pdb=" O ASP a 177 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG a 185 " --> pdb=" O SER a 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 78 removed outlier: 3.538A pdb=" N GLN b 69 " --> pdb=" O GLN b 65 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET b 70 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE b 72 " --> pdb=" O GLY b 68 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU b 77 " --> pdb=" O ASP b 73 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 102 removed outlier: 3.503A pdb=" N ARG b 99 " --> pdb=" O ALA b 95 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG b 100 " --> pdb=" O MET b 96 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS b 102 " --> pdb=" O SER b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 146 Processing helix chain 'b' and resid 146 through 157 removed outlier: 3.925A pdb=" N LYS b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 180 removed outlier: 3.570A pdb=" N ARG b 179 " --> pdb=" O VAL b 175 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 5.784A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 52 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 216 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 217 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 removed outlier: 4.590A pdb=" N VAL A 151 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.563A pdb=" N GLY B 36 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.559A pdb=" N GLU B 65 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 132 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.556A pdb=" N ILE C 37 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 44 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.739A pdb=" N SER C 75 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 138 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY C 158 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.580A pdb=" N HIS D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.656A pdb=" N VAL D 41 " --> pdb=" O MET D 211 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL D 210 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS D 218 " --> pdb=" O VAL D 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AB1, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 69 removed outlier: 4.333A pdb=" N LEU E 153 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN E 164 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.933A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 70 through 76 Processing sheet with id=AB5, first strand: chain 'F' and resid 70 through 76 Processing sheet with id=AB6, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.606A pdb=" N TRP G 215 " --> pdb=" O GLU G 225 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU G 225 " --> pdb=" O TRP G 215 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY G 217 " --> pdb=" O ARG G 223 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG G 223 " --> pdb=" O GLY G 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 66 through 68 removed outlier: 3.528A pdb=" N PHE G 135 " --> pdb=" O ILE G 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 125 through 128 removed outlier: 3.663A pdb=" N GLY H 11 " --> pdb=" O PHE H 8 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA H 177 " --> pdb=" O LEU H 14 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.189A pdb=" N THR H 22 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE H 26 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 41 through 47 removed outlier: 3.586A pdb=" N ALA H 101 " --> pdb=" O PHE H 42 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE H 99 " --> pdb=" O CYS H 44 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL H 121 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 124 through 127 removed outlier: 3.744A pdb=" N VAL I 125 " --> pdb=" O GLY I 5 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE I 173 " --> pdb=" O PRO I 188 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU I 175 " --> pdb=" O LEU I 186 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.021A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 35 through 36 removed outlier: 3.532A pdb=" N CYS I 43 " --> pdb=" O HIS I 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 213 through 218 removed outlier: 3.522A pdb=" N THR I 213 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA J 9 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 41 through 45 removed outlier: 3.666A pdb=" N ILE J 50 " --> pdb=" O PHE J 42 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU J 48 " --> pdb=" O MET J 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 129 through 132 removed outlier: 3.615A pdb=" N LEU K 4 " --> pdb=" O HIS K 132 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL K 15 " --> pdb=" O ARG K 181 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG K 181 " --> pdb=" O VAL K 15 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 35 through 37 removed outlier: 3.660A pdb=" N LEU K 104 " --> pdb=" O TYR K 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.547A pdb=" N ALA L 5 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL L 12 " --> pdb=" O VAL L 179 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU L 176 " --> pdb=" O VAL L 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 22 removed outlier: 7.405A pdb=" N ALA L 20 " --> pdb=" O ALA L 27 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 34 through 38 removed outlier: 3.566A pdb=" N ILE L 37 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR L 44 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY L 103 " --> pdb=" O GLY L 110 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.793A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 29 through 31 removed outlier: 7.052A pdb=" N LEU M 29 " --> pdb=" O HIS M 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 43 through 45 removed outlier: 3.583A pdb=" N ILE M 109 " --> pdb=" O GLY M 53 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN M 108 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 7 through 8 removed outlier: 3.506A pdb=" N GLY N 55 " --> pdb=" O GLY N 8 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 7 through 8 removed outlier: 3.506A pdb=" N GLY N 55 " --> pdb=" O GLY N 8 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR N 132 " --> pdb=" O TYR N 124 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 14 through 16 removed outlier: 3.640A pdb=" N GLY N 19 " --> pdb=" O PHE N 16 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.783A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR O 52 " --> pdb=" O GLU O 216 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU O 216 " --> pdb=" O THR O 52 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL O 217 " --> pdb=" O LEU O 230 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 69 through 71 removed outlier: 4.589A pdb=" N VAL O 151 " --> pdb=" O PHE O 163 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 159 through 162 removed outlier: 3.563A pdb=" N GLY P 36 " --> pdb=" O THR P 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 65 through 68 removed outlier: 3.560A pdb=" N GLU P 65 " --> pdb=" O LEU P 73 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE P 71 " --> pdb=" O ILE P 67 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER P 132 " --> pdb=" O SER P 76 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 161 through 164 removed outlier: 3.556A pdb=" N ILE Q 37 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU Q 44 " --> pdb=" O ILE Q 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 72 through 75 removed outlier: 3.739A pdb=" N SER Q 75 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY Q 138 " --> pdb=" O GLN Q 146 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU Q 147 " --> pdb=" O TRP Q 159 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY Q 158 " --> pdb=" O ASP R 55 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 10 through 11 removed outlier: 3.579A pdb=" N HIS R 15 " --> pdb=" O SER R 11 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 158 through 161 removed outlier: 3.655A pdb=" N VAL R 41 " --> pdb=" O MET R 211 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL R 210 " --> pdb=" O LYS R 218 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS R 218 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 62 through 64 Processing sheet with id=AE9, first strand: chain 'S' and resid 167 through 170 Processing sheet with id=AF1, first strand: chain 'S' and resid 67 through 69 removed outlier: 4.333A pdb=" N LEU S 153 " --> pdb=" O CYS S 165 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN S 164 " --> pdb=" O ALA T 58 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 158 through 161 removed outlier: 3.932A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 70 through 76 Processing sheet with id=AF4, first strand: chain 'T' and resid 70 through 76 Processing sheet with id=AF5, first strand: chain 'U' and resid 162 through 165 removed outlier: 3.605A pdb=" N TRP U 215 " --> pdb=" O GLU U 225 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU U 225 " --> pdb=" O TRP U 215 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY U 217 " --> pdb=" O ARG U 223 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG U 223 " --> pdb=" O GLY U 217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 66 through 68 removed outlier: 3.528A pdb=" N PHE U 135 " --> pdb=" O ILE U 151 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 125 through 128 removed outlier: 3.663A pdb=" N GLY V 11 " --> pdb=" O PHE V 8 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA V 177 " --> pdb=" O LEU V 14 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.189A pdb=" N THR V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE V 26 " --> pdb=" O THR V 22 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 41 through 47 removed outlier: 3.586A pdb=" N ALA V 101 " --> pdb=" O PHE V 42 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE V 99 " --> pdb=" O CYS V 44 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL V 121 " --> pdb=" O SER V 113 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 124 through 127 removed outlier: 3.744A pdb=" N VAL W 125 " --> pdb=" O GLY W 5 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE W 173 " --> pdb=" O PRO W 188 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU W 175 " --> pdb=" O LEU W 186 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.022A pdb=" N GLU W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL W 26 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 35 through 36 removed outlier: 3.531A pdb=" N CYS W 43 " --> pdb=" O HIS W 35 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 213 through 218 removed outlier: 3.521A pdb=" N THR W 213 " --> pdb=" O THR X 198 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA X 9 " --> pdb=" O ASP X 24 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 41 through 45 removed outlier: 3.666A pdb=" N ILE X 50 " --> pdb=" O PHE X 42 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU X 48 " --> pdb=" O MET X 44 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 129 through 132 removed outlier: 3.617A pdb=" N LEU Y 4 " --> pdb=" O HIS Y 132 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL Y 15 " --> pdb=" O ARG Y 181 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG Y 181 " --> pdb=" O VAL Y 15 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 35 through 37 removed outlier: 3.659A pdb=" N LEU Y 104 " --> pdb=" O TYR Y 116 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 125 through 129 removed outlier: 3.547A pdb=" N ALA Z 5 " --> pdb=" O PHE Z 126 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL Z 12 " --> pdb=" O VAL Z 179 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU Z 176 " --> pdb=" O VAL Z 187 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 20 through 22 removed outlier: 7.405A pdb=" N ALA Z 20 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.567A pdb=" N ILE Z 37 " --> pdb=" O LEU Z 41 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR Z 44 " --> pdb=" O MET Z 100 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY Z 103 " --> pdb=" O GLY Z 110 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'a' and resid 135 through 139 removed outlier: 5.794A pdb=" N THR a 11 " --> pdb=" O ASP a 26 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 29 through 31 removed outlier: 7.052A pdb=" N LEU a 29 " --> pdb=" O HIS a 36 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 43 through 45 removed outlier: 3.583A pdb=" N ILE a 109 " --> pdb=" O GLY a 53 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN a 108 " --> pdb=" O PHE a 124 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL a 121 " --> pdb=" O ASP a 133 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 7 through 8 removed outlier: 3.506A pdb=" N GLY b 55 " --> pdb=" O GLY b 8 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 7 through 8 removed outlier: 3.506A pdb=" N GLY b 55 " --> pdb=" O GLY b 8 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR b 132 " --> pdb=" O TYR b 124 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 14 through 16 removed outlier: 3.641A pdb=" N GLY b 19 " --> pdb=" O PHE b 16 " (cutoff:3.500A) 2343 hydrogen bonds defined for protein. 6630 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: 20.15 Time building geometry restraints manager: 12.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14838 1.34 - 1.46: 9965 1.46 - 1.58: 20917 1.58 - 1.69: 0 1.69 - 1.81: 462 Bond restraints: 46182 Sorted by residual: bond pdb=" C ARG W 187 " pdb=" O ARG W 187 " ideal model delta sigma weight residual 1.244 1.230 0.013 9.10e-03 1.21e+04 2.17e+00 bond pdb=" C ARG I 187 " pdb=" O ARG I 187 " ideal model delta sigma weight residual 1.244 1.231 0.013 9.10e-03 1.21e+04 1.94e+00 bond pdb=" C ASN L 38 " pdb=" N PRO L 39 " ideal model delta sigma weight residual 1.334 1.352 -0.018 1.51e-02 4.39e+03 1.38e+00 bond pdb=" CA PHE A 187 " pdb=" C PHE A 187 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.50e-02 4.44e+03 1.26e+00 bond pdb=" N ARG D 213 " pdb=" CA ARG D 213 " ideal model delta sigma weight residual 1.468 1.454 0.014 1.24e-02 6.50e+03 1.25e+00 ... (remaining 46177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 61011 1.60 - 3.20: 1532 3.20 - 4.80: 145 4.80 - 6.40: 18 6.40 - 8.00: 2 Bond angle restraints: 62708 Sorted by residual: angle pdb=" CA ARG W 187 " pdb=" C ARG W 187 " pdb=" N PRO W 188 " ideal model delta sigma weight residual 120.58 116.55 4.03 7.40e-01 1.83e+00 2.96e+01 angle pdb=" CA ARG I 187 " pdb=" C ARG I 187 " pdb=" N PRO I 188 " ideal model delta sigma weight residual 120.58 116.64 3.94 7.40e-01 1.83e+00 2.84e+01 angle pdb=" C GLN X 30 " pdb=" N ALA X 31 " pdb=" CA ALA X 31 " ideal model delta sigma weight residual 122.95 117.29 5.66 1.44e+00 4.82e-01 1.54e+01 angle pdb=" C GLN J 30 " pdb=" N ALA J 31 " pdb=" CA ALA J 31 " ideal model delta sigma weight residual 122.95 117.35 5.60 1.44e+00 4.82e-01 1.51e+01 angle pdb=" O ARG W 187 " pdb=" C ARG W 187 " pdb=" N PRO W 188 " ideal model delta sigma weight residual 120.27 122.87 -2.60 6.90e-01 2.10e+00 1.42e+01 ... (remaining 62703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 26860 16.05 - 32.09: 404 32.09 - 48.14: 118 48.14 - 64.19: 12 64.19 - 80.23: 22 Dihedral angle restraints: 27416 sinusoidal: 9534 harmonic: 17882 Sorted by residual: dihedral pdb=" CA GLN F 60 " pdb=" C GLN F 60 " pdb=" N LYS F 61 " pdb=" CA LYS F 61 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLN T 60 " pdb=" C GLN T 60 " pdb=" N LYS T 61 " pdb=" CA LYS T 61 " ideal model delta harmonic sigma weight residual 180.00 151.78 28.22 0 5.00e+00 4.00e-02 3.19e+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 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 27413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 6602 0.070 - 0.139: 727 0.139 - 0.209: 14 0.209 - 0.279: 2 0.279 - 0.348: 1 Chirality restraints: 7346 Sorted by residual: chirality pdb=" CA PHE A 187 " pdb=" N PHE A 187 " pdb=" C PHE A 187 " pdb=" CB PHE A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA SER R 216 " pdb=" N SER R 216 " pdb=" C SER R 216 " pdb=" CB SER R 216 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA SER D 216 " pdb=" N SER D 216 " pdb=" C SER D 216 " pdb=" CB SER D 216 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 7343 not shown) Planarity restraints: 7974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL O 183 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C VAL O 183 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL O 183 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS O 184 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER I 38 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO I 39 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO I 39 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 39 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER W 38 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO W 39 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO W 39 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO W 39 " -0.027 5.00e-02 4.00e+02 ... (remaining 7971 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1211 2.70 - 3.25: 43944 3.25 - 3.80: 71841 3.80 - 4.35: 94907 4.35 - 4.90: 160145 Nonbonded interactions: 372048 Sorted by model distance: nonbonded pdb=" O LYS M 49 " pdb=" OG1 THR M 50 " model vdw 2.155 3.040 nonbonded pdb=" O LYS a 49 " pdb=" OG1 THR a 50 " model vdw 2.156 3.040 nonbonded pdb=" O GLY D 140 " pdb=" NH2 ARG D 213 " model vdw 2.215 3.120 nonbonded pdb=" O GLY R 140 " pdb=" NH2 ARG R 213 " model vdw 2.222 3.120 nonbonded pdb=" O GLN R 116 " pdb=" OG1 THR R 119 " model vdw 2.227 3.040 ... (remaining 372043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.740 Check model and map are aligned: 0.310 Set scattering table: 0.430 Process input model: 100.300 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 46182 Z= 0.133 Angle : 0.613 7.999 62708 Z= 0.400 Chirality : 0.043 0.348 7346 Planarity : 0.004 0.049 7974 Dihedral : 7.670 80.232 16000 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.09), residues: 6142 helix: -3.32 (0.07), residues: 2082 sheet: -0.95 (0.12), residues: 1468 loop : -0.96 (0.10), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 215 HIS 0.007 0.001 HIS B 87 PHE 0.020 0.001 PHE F 145 TYR 0.018 0.001 TYR X 146 ARG 0.003 0.000 ARG R 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1951 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1951 time to evaluate : 5.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.6607 (m-10) cc_final: 0.6229 (m-10) REVERT: A 175 SER cc_start: 0.8243 (p) cc_final: 0.7854 (p) REVERT: A 235 ILE cc_start: 0.8467 (mt) cc_final: 0.8095 (tt) REVERT: B 71 ILE cc_start: 0.8561 (mt) cc_final: 0.8343 (mt) REVERT: B 99 VAL cc_start: 0.7852 (t) cc_final: 0.7184 (t) REVERT: B 160 THR cc_start: 0.7034 (t) cc_final: 0.6796 (m) REVERT: D 21 TYR cc_start: 0.7675 (m-10) cc_final: 0.7340 (m-80) REVERT: D 68 ASN cc_start: 0.7508 (p0) cc_final: 0.7146 (p0) REVERT: D 110 TYR cc_start: 0.6159 (t80) cc_final: 0.5767 (t80) REVERT: E 76 CYS cc_start: 0.7089 (t) cc_final: 0.6337 (t) REVERT: E 101 PHE cc_start: 0.7252 (t80) cc_final: 0.6929 (t80) REVERT: E 107 MET cc_start: 0.7396 (ttt) cc_final: 0.7162 (ttt) REVERT: E 137 PHE cc_start: 0.8166 (m-80) cc_final: 0.7577 (m-10) REVERT: E 143 PHE cc_start: 0.7279 (m-80) cc_final: 0.6866 (m-80) REVERT: G 110 HIS cc_start: 0.7056 (t-170) cc_final: 0.6780 (t70) REVERT: I 209 THR cc_start: 0.6525 (m) cc_final: 0.6186 (t) REVERT: J 196 THR cc_start: 0.8479 (m) cc_final: 0.8213 (p) REVERT: O 78 CYS cc_start: 0.8039 (t) cc_final: 0.7561 (t) REVERT: O 163 PHE cc_start: 0.4977 (m-80) cc_final: 0.4685 (m-80) REVERT: P 228 TYR cc_start: 0.5873 (m-80) cc_final: 0.5450 (m-80) REVERT: Q 30 HIS cc_start: 0.6255 (m-70) cc_final: 0.6017 (m-70) REVERT: R 10 PHE cc_start: 0.4951 (m-80) cc_final: 0.4727 (m-80) REVERT: V 65 PHE cc_start: 0.7426 (t80) cc_final: 0.6829 (t80) REVERT: V 104 ASP cc_start: 0.4741 (p0) cc_final: 0.4246 (p0) REVERT: X 192 ASP cc_start: 0.6235 (p0) cc_final: 0.6006 (p0) REVERT: Y 11 ASP cc_start: 0.5266 (p0) cc_final: 0.4867 (p0) REVERT: Y 62 LYS cc_start: 0.8304 (ttpp) cc_final: 0.7965 (tttp) REVERT: Z 65 ILE cc_start: 0.7823 (mt) cc_final: 0.6705 (mt) REVERT: Z 85 ASN cc_start: 0.7116 (m-40) cc_final: 0.6471 (m-40) REVERT: Z 90 TYR cc_start: 0.5833 (m-80) cc_final: 0.5523 (m-80) REVERT: a 12 ILE cc_start: 0.7551 (pt) cc_final: 0.7144 (pt) REVERT: a 50 THR cc_start: 0.7231 (m) cc_final: 0.6997 (t) REVERT: a 168 LEU cc_start: 0.7669 (tp) cc_final: 0.7400 (tp) REVERT: b 59 ASP cc_start: 0.5519 (m-30) cc_final: 0.5296 (m-30) outliers start: 0 outliers final: 0 residues processed: 1951 average time/residue: 0.6705 time to fit residues: 2083.1912 Evaluate side-chains 1081 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1081 time to evaluate : 5.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 515 optimal weight: 0.9990 chunk 462 optimal weight: 0.9990 chunk 256 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 311 optimal weight: 0.0670 chunk 247 optimal weight: 10.0000 chunk 478 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 355 optimal weight: 7.9990 chunk 553 optimal weight: 4.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 127 GLN A 193 GLN B 94 GLN C 40 ASN C 167 ASN C 198 ASN C 240 HIS D 54 GLN D 92 GLN E 98 ASN E 114 GLN E 178 GLN F 43 HIS F 86 ASN F 121 GLN F 175 HIS G 180 GLN H 38 HIS ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS J 80 GLN ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN M 108 ASN N 38 ASN N 81 HIS O 24 GLN O 75 ASN O 90 GLN O 128 ASN ** O 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN Q 109 GLN Q 198 ASN R 54 GLN R 146 GLN S 98 ASN S 152 GLN S 164 GLN T 43 HIS T 65 HIS T 90 GLN T 121 GLN U 101 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 66 HIS ** W 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 GLN X 156 ASN Z 175 ASN a 8 ASN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 131 GLN a 157 ASN ** a 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 61 GLN b 108 ASN b 147 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 46182 Z= 0.225 Angle : 0.700 9.982 62708 Z= 0.365 Chirality : 0.046 0.194 7346 Planarity : 0.005 0.060 7974 Dihedral : 4.588 27.909 6788 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.24 % Rotamer: Outliers : 3.35 % Allowed : 15.37 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.09), residues: 6142 helix: -0.91 (0.10), residues: 2166 sheet: -0.44 (0.12), residues: 1418 loop : -0.68 (0.11), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 55 HIS 0.007 0.001 HIS S 99 PHE 0.024 0.002 PHE L 54 TYR 0.031 0.002 TYR Q 136 ARG 0.011 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1356 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1213 time to evaluate : 5.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8108 (ttpt) REVERT: A 235 ILE cc_start: 0.8629 (mt) cc_final: 0.8253 (tt) REVERT: B 99 VAL cc_start: 0.8090 (t) cc_final: 0.7828 (t) REVERT: B 112 ARG cc_start: 0.7815 (mtt90) cc_final: 0.7570 (mmt90) REVERT: D 21 TYR cc_start: 0.7767 (m-10) cc_final: 0.7533 (m-80) REVERT: D 68 ASN cc_start: 0.7337 (p0) cc_final: 0.7136 (p0) REVERT: E 152 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7220 (mm110) REVERT: G 111 LEU cc_start: 0.9009 (tt) cc_final: 0.8725 (tt) REVERT: H 65 PHE cc_start: 0.7760 (t80) cc_final: 0.6799 (t80) REVERT: I 24 MET cc_start: 0.7570 (ppp) cc_final: 0.6906 (ppp) REVERT: J 3 MET cc_start: 0.7283 (mmm) cc_final: 0.6685 (mmm) REVERT: J 4 SER cc_start: 0.8816 (p) cc_final: 0.8602 (t) REVERT: K 13 VAL cc_start: 0.7345 (OUTLIER) cc_final: 0.7051 (t) REVERT: K 63 ASN cc_start: 0.7618 (m110) cc_final: 0.7376 (m110) REVERT: K 160 LEU cc_start: 0.8727 (tt) cc_final: 0.8376 (tt) REVERT: K 177 THR cc_start: 0.7781 (p) cc_final: 0.7399 (p) REVERT: M 75 TYR cc_start: 0.7933 (t80) cc_final: 0.7672 (t80) REVERT: M 83 MET cc_start: 0.8354 (tpp) cc_final: 0.8030 (tpp) REVERT: N 76 LEU cc_start: 0.7689 (mt) cc_final: 0.7393 (mt) REVERT: O 78 CYS cc_start: 0.7384 (t) cc_final: 0.7037 (t) REVERT: P 102 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6636 (tm-30) REVERT: P 104 ILE cc_start: 0.7595 (tp) cc_final: 0.7389 (tp) REVERT: P 160 THR cc_start: 0.7486 (t) cc_final: 0.6912 (t) REVERT: Q 88 ASN cc_start: 0.7369 (t0) cc_final: 0.7154 (t0) REVERT: R 54 GLN cc_start: 0.6858 (mm110) cc_final: 0.6372 (mp10) REVERT: R 66 ASP cc_start: 0.7379 (t70) cc_final: 0.5233 (t70) REVERT: R 71 MET cc_start: 0.7580 (ppp) cc_final: 0.7039 (ptm) REVERT: R 84 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8278 (mt) REVERT: T 153 TYR cc_start: 0.7632 (p90) cc_final: 0.7343 (p90) REVERT: U 147 GLN cc_start: 0.7173 (mp10) cc_final: 0.6881 (mp10) REVERT: V 65 PHE cc_start: 0.7345 (t80) cc_final: 0.6853 (t80) REVERT: X 166 ILE cc_start: 0.7159 (tt) cc_final: 0.6844 (tt) REVERT: X 192 ASP cc_start: 0.6504 (p0) cc_final: 0.6281 (p0) REVERT: Y 28 MET cc_start: 0.5448 (mmm) cc_final: 0.5230 (mmm) REVERT: Y 69 MET cc_start: 0.7600 (mmm) cc_final: 0.7396 (mmm) REVERT: Y 87 ASN cc_start: 0.7023 (p0) cc_final: 0.6453 (p0) REVERT: Z 54 PHE cc_start: 0.7510 (t80) cc_final: 0.7166 (t80) REVERT: b 50 MET cc_start: 0.7419 (tmm) cc_final: 0.7132 (tmm) REVERT: b 56 ASP cc_start: 0.6752 (t0) cc_final: 0.6225 (t0) REVERT: b 76 LEU cc_start: 0.7528 (mt) cc_final: 0.7049 (mt) REVERT: b 127 MET cc_start: 0.6731 (ptp) cc_final: 0.6490 (ptm) REVERT: b 173 MET cc_start: 0.6894 (tpp) cc_final: 0.6680 (mmt) outliers start: 143 outliers final: 71 residues processed: 1291 average time/residue: 0.6054 time to fit residues: 1283.0050 Evaluate side-chains 1064 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 990 time to evaluate : 5.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 134 TYR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain K residue 12 TYR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 193 GLN Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 78 MET Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 166 TYR Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 213 ILE Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain V residue 91 ARG Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain X residue 146 TYR Chi-restraints excluded: chain X residue 163 PHE Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 54 CYS Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain b residue 108 ASN Chi-restraints excluded: chain b residue 147 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 307 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 461 optimal weight: 0.0170 chunk 377 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 554 optimal weight: 0.9980 chunk 599 optimal weight: 9.9990 chunk 494 optimal weight: 10.0000 chunk 550 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 445 optimal weight: 5.9990 overall best weight: 4.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN D 54 GLN D 85 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 118 ASN E 178 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS J 60 GLN ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS M 8 ASN M 79 ASN M 108 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 238 HIS P 108 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 HIS ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 72 HIS ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 110 HIS Y 189 HIS a 79 ASN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 131 GLN ** a 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 HIS b 147 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 46182 Z= 0.348 Angle : 0.746 11.389 62708 Z= 0.390 Chirality : 0.047 0.240 7346 Planarity : 0.005 0.053 7974 Dihedral : 4.848 26.783 6788 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer: Outliers : 4.19 % Allowed : 16.92 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.10), residues: 6142 helix: 0.03 (0.11), residues: 2202 sheet: -0.36 (0.12), residues: 1516 loop : -0.46 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 157 HIS 0.013 0.002 HIS S 155 PHE 0.040 0.002 PHE A 191 TYR 0.026 0.002 TYR C 136 ARG 0.013 0.001 ARG Z 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 1041 time to evaluate : 6.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.8704 (mt) cc_final: 0.8464 (tt) REVERT: C 98 LEU cc_start: 0.8425 (mp) cc_final: 0.8039 (tt) REVERT: C 194 ILE cc_start: 0.8860 (pt) cc_final: 0.8604 (pt) REVERT: D 66 ASP cc_start: 0.8629 (t0) cc_final: 0.8333 (t70) REVERT: D 67 ASP cc_start: 0.7983 (p0) cc_final: 0.7683 (p0) REVERT: D 157 LYS cc_start: 0.8354 (mttt) cc_final: 0.7854 (mtmm) REVERT: E 152 GLN cc_start: 0.8495 (mm-40) cc_final: 0.7789 (mp10) REVERT: E 156 MET cc_start: 0.7650 (mmm) cc_final: 0.7403 (mmm) REVERT: E 216 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6724 (tt0) REVERT: F 228 ASP cc_start: 0.7567 (m-30) cc_final: 0.7351 (t0) REVERT: H 65 PHE cc_start: 0.7851 (t80) cc_final: 0.7190 (t80) REVERT: H 133 SER cc_start: 0.7492 (p) cc_final: 0.7181 (t) REVERT: I 82 MET cc_start: 0.7099 (mtt) cc_final: 0.6880 (mtt) REVERT: J 71 ASN cc_start: 0.7953 (m-40) cc_final: 0.7585 (m-40) REVERT: J 82 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8000 (mtpp) REVERT: J 97 LYS cc_start: 0.8098 (ptpp) cc_final: 0.7866 (ptpp) REVERT: J 105 GLU cc_start: 0.8017 (mp0) cc_final: 0.7814 (mp0) REVERT: K 38 MET cc_start: 0.7735 (mmm) cc_final: 0.7109 (tpp) REVERT: K 44 LEU cc_start: 0.8684 (mt) cc_final: 0.8406 (mt) REVERT: K 63 ASN cc_start: 0.7700 (m110) cc_final: 0.7394 (m110) REVERT: K 160 LEU cc_start: 0.9068 (tt) cc_final: 0.8850 (tt) REVERT: L 90 TYR cc_start: 0.7276 (m-80) cc_final: 0.6953 (m-80) REVERT: M 83 MET cc_start: 0.8935 (tpp) cc_final: 0.8219 (tpp) REVERT: N 38 ASN cc_start: 0.7144 (t0) cc_final: 0.6931 (t0) REVERT: N 76 LEU cc_start: 0.8190 (mt) cc_final: 0.7893 (mt) REVERT: O 12 HIS cc_start: 0.7065 (m-70) cc_final: 0.6707 (m-70) REVERT: O 114 LEU cc_start: 0.8836 (tp) cc_final: 0.8464 (tp) REVERT: P 28 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8653 (p) REVERT: Q 68 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7662 (mt) REVERT: R 90 GLU cc_start: 0.7958 (tp30) cc_final: 0.7511 (tp30) REVERT: R 106 TYR cc_start: 0.7136 (t80) cc_final: 0.6696 (t80) REVERT: R 146 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7399 (tm-30) REVERT: S 89 ILE cc_start: 0.8732 (pt) cc_final: 0.8292 (mt) REVERT: S 149 LYS cc_start: 0.7939 (tttt) cc_final: 0.7540 (pttp) REVERT: S 237 VAL cc_start: 0.8658 (m) cc_final: 0.8446 (m) REVERT: T 153 TYR cc_start: 0.8068 (p90) cc_final: 0.7840 (p90) REVERT: V 48 SER cc_start: 0.7670 (OUTLIER) cc_final: 0.6907 (p) REVERT: V 65 PHE cc_start: 0.7475 (t80) cc_final: 0.7228 (t80) REVERT: V 120 MET cc_start: 0.7324 (ttp) cc_final: 0.7092 (ttp) REVERT: V 133 SER cc_start: 0.7678 (p) cc_final: 0.7465 (t) REVERT: V 135 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8320 (tp) REVERT: V 147 MET cc_start: 0.6316 (mmp) cc_final: 0.5411 (mtp) REVERT: V 167 ASP cc_start: 0.6721 (t70) cc_final: 0.6359 (t0) REVERT: V 197 PHE cc_start: 0.7491 (m-80) cc_final: 0.7101 (m-80) REVERT: W 86 MET cc_start: 0.7735 (ttp) cc_final: 0.7463 (ttp) REVERT: W 94 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8392 (pt) REVERT: X 175 ASP cc_start: 0.7183 (p0) cc_final: 0.6973 (p0) REVERT: X 192 ASP cc_start: 0.6741 (p0) cc_final: 0.6435 (p0) REVERT: Y 11 ASP cc_start: 0.5831 (p0) cc_final: 0.5627 (p0) REVERT: Y 13 VAL cc_start: 0.7540 (t) cc_final: 0.7305 (t) REVERT: Y 29 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8308 (tptp) REVERT: Y 87 ASN cc_start: 0.7433 (p0) cc_final: 0.6843 (p0) REVERT: Z 45 MET cc_start: 0.6577 (mmm) cc_final: 0.6062 (ttm) REVERT: Z 100 MET cc_start: 0.8104 (mpp) cc_final: 0.7551 (mpp) REVERT: Z 139 MET cc_start: 0.6716 (tmm) cc_final: 0.6427 (tmm) REVERT: b 56 ASP cc_start: 0.7298 (t0) cc_final: 0.6978 (t0) REVERT: b 96 MET cc_start: 0.7187 (tpp) cc_final: 0.6984 (tpp) REVERT: b 108 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.8013 (t0) outliers start: 179 outliers final: 96 residues processed: 1150 average time/residue: 0.6117 time to fit residues: 1160.2471 Evaluate side-chains 968 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 863 time to evaluate : 5.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 99 PHE Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 160 TYR Chi-restraints excluded: chain O residue 161 CYS Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain T residue 233 LEU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 126 ILE Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 157 VAL Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 108 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 548 optimal weight: 0.9990 chunk 417 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 264 optimal weight: 2.9990 chunk 372 optimal weight: 6.9990 chunk 556 optimal weight: 4.9990 chunk 589 optimal weight: 0.0770 chunk 290 optimal weight: 5.9990 chunk 527 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 70 HIS D 54 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN H 53 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 HIS O 100 ASN ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 120 GLN S 23 GLN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 164 GLN S 221 GLN ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 66 HIS ** Z 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN ** a 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 159 GLN ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 46182 Z= 0.209 Angle : 0.652 10.730 62708 Z= 0.336 Chirality : 0.045 0.252 7346 Planarity : 0.004 0.071 7974 Dihedral : 4.604 25.705 6788 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.28 % Allowed : 18.60 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.10), residues: 6142 helix: 0.46 (0.11), residues: 2208 sheet: -0.25 (0.13), residues: 1486 loop : -0.38 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 157 HIS 0.007 0.001 HIS E 99 PHE 0.020 0.002 PHE K 83 TYR 0.026 0.001 TYR C 136 ARG 0.009 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 957 time to evaluate : 5.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.8713 (mt) cc_final: 0.8383 (tt) REVERT: C 98 LEU cc_start: 0.8375 (mp) cc_final: 0.7943 (tt) REVERT: D 66 ASP cc_start: 0.8598 (t0) cc_final: 0.8003 (t70) REVERT: D 67 ASP cc_start: 0.7856 (p0) cc_final: 0.7435 (p0) REVERT: D 190 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8250 (tp) REVERT: E 156 MET cc_start: 0.7549 (mmm) cc_final: 0.7307 (mmm) REVERT: E 228 MET cc_start: 0.7765 (tpt) cc_final: 0.7562 (tpt) REVERT: G 158 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6481 (m-10) REVERT: H 4 MET cc_start: 0.8220 (tmm) cc_final: 0.7799 (tmm) REVERT: H 133 SER cc_start: 0.7459 (p) cc_final: 0.7248 (t) REVERT: J 105 GLU cc_start: 0.8037 (mp0) cc_final: 0.7771 (mp0) REVERT: J 203 MET cc_start: 0.7917 (mmm) cc_final: 0.7507 (mmp) REVERT: K 18 ASP cc_start: 0.8410 (t0) cc_final: 0.8009 (t70) REVERT: K 160 LEU cc_start: 0.8915 (tt) cc_final: 0.8712 (tt) REVERT: M 83 MET cc_start: 0.8615 (tpp) cc_final: 0.8093 (tpp) REVERT: Q 68 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7615 (mt) REVERT: R 90 GLU cc_start: 0.7916 (tp30) cc_final: 0.7459 (tp30) REVERT: R 106 TYR cc_start: 0.7122 (t80) cc_final: 0.6744 (t80) REVERT: R 146 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7714 (tm-30) REVERT: S 89 ILE cc_start: 0.8750 (pt) cc_final: 0.8280 (mt) REVERT: S 149 LYS cc_start: 0.7914 (tttt) cc_final: 0.7596 (tmmt) REVERT: U 136 MET cc_start: 0.6700 (mtp) cc_final: 0.6346 (mtt) REVERT: V 48 SER cc_start: 0.7440 (OUTLIER) cc_final: 0.7146 (p) REVERT: V 65 PHE cc_start: 0.7420 (t80) cc_final: 0.7158 (t80) REVERT: V 133 SER cc_start: 0.7703 (p) cc_final: 0.7448 (t) REVERT: V 135 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8209 (tp) REVERT: V 139 VAL cc_start: 0.8482 (t) cc_final: 0.8267 (p) REVERT: V 147 MET cc_start: 0.6195 (mmp) cc_final: 0.5938 (mtp) REVERT: W 14 LEU cc_start: 0.8164 (mt) cc_final: 0.7945 (mt) REVERT: W 19 ARG cc_start: 0.7197 (ttm170) cc_final: 0.6789 (ttm170) REVERT: X 97 LYS cc_start: 0.7684 (ptpp) cc_final: 0.6721 (ptpp) REVERT: X 102 TYR cc_start: 0.8039 (m-10) cc_final: 0.7768 (m-10) REVERT: X 157 MET cc_start: 0.6635 (mmm) cc_final: 0.5983 (mpp) REVERT: Y 11 ASP cc_start: 0.5677 (p0) cc_final: 0.5452 (p0) REVERT: Y 13 VAL cc_start: 0.7634 (t) cc_final: 0.7362 (t) REVERT: Y 29 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8012 (tptm) REVERT: Y 69 MET cc_start: 0.7825 (mmm) cc_final: 0.7454 (mmm) REVERT: Z 45 MET cc_start: 0.6489 (mmm) cc_final: 0.5773 (ttt) REVERT: Z 139 MET cc_start: 0.6877 (tmm) cc_final: 0.6609 (tmm) REVERT: a 188 TYR cc_start: 0.7671 (m-80) cc_final: 0.7292 (m-80) REVERT: b 168 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7715 (mm) outliers start: 140 outliers final: 76 residues processed: 1045 average time/residue: 0.6016 time to fit residues: 1031.9799 Evaluate side-chains 925 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 842 time to evaluate : 5.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain X residue 60 GLN Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 491 optimal weight: 8.9990 chunk 334 optimal weight: 30.0000 chunk 8 optimal weight: 0.9990 chunk 439 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 503 optimal weight: 10.0000 chunk 407 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 301 optimal weight: 6.9990 chunk 529 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 101 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS H 62 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 ASN N 108 ASN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 GLN O 100 ASN ** O 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 GLN P 111 GLN ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 23 GLN ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN ** a 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 108 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.7134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 46182 Z= 0.261 Angle : 0.663 10.943 62708 Z= 0.343 Chirality : 0.045 0.202 7346 Planarity : 0.005 0.058 7974 Dihedral : 4.600 25.385 6788 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.89 % Allowed : 18.79 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.10), residues: 6142 helix: 0.65 (0.11), residues: 2222 sheet: -0.13 (0.13), residues: 1448 loop : -0.38 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 156 HIS 0.007 0.001 HIS S 99 PHE 0.026 0.002 PHE A 163 TYR 0.027 0.002 TYR C 136 ARG 0.010 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 892 time to evaluate : 5.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.8857 (mt) cc_final: 0.8545 (tt) REVERT: B 109 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8925 (tp) REVERT: B 111 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: C 98 LEU cc_start: 0.8398 (mp) cc_final: 0.8100 (tt) REVERT: D 67 ASP cc_start: 0.7868 (p0) cc_final: 0.7592 (p0) REVERT: D 190 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8363 (tp) REVERT: E 228 MET cc_start: 0.7915 (tpt) cc_final: 0.7698 (tpt) REVERT: G 118 TYR cc_start: 0.7389 (t80) cc_final: 0.6855 (t80) REVERT: G 150 MET cc_start: 0.7868 (tmm) cc_final: 0.7665 (tmm) REVERT: G 158 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.6504 (m-10) REVERT: I 126 THR cc_start: 0.8561 (p) cc_final: 0.8310 (p) REVERT: K 18 ASP cc_start: 0.8395 (t0) cc_final: 0.7969 (t70) REVERT: M 83 MET cc_start: 0.8408 (tpp) cc_final: 0.8079 (ttm) REVERT: P 28 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8653 (p) REVERT: P 134 LEU cc_start: 0.8559 (mt) cc_final: 0.8170 (mt) REVERT: R 18 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8610 (mm-40) REVERT: R 90 GLU cc_start: 0.7931 (tp30) cc_final: 0.7327 (tp30) REVERT: R 106 TYR cc_start: 0.7429 (t80) cc_final: 0.7009 (t80) REVERT: R 146 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7864 (tm-30) REVERT: R 190 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8300 (tp) REVERT: S 89 ILE cc_start: 0.8772 (pt) cc_final: 0.8408 (mt) REVERT: U 13 THR cc_start: 0.7976 (p) cc_final: 0.7730 (p) REVERT: U 117 MET cc_start: 0.6471 (mmt) cc_final: 0.6247 (mmm) REVERT: V 48 SER cc_start: 0.7495 (OUTLIER) cc_final: 0.7259 (p) REVERT: V 133 SER cc_start: 0.8112 (p) cc_final: 0.7899 (t) REVERT: W 94 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8490 (pt) REVERT: W 127 MET cc_start: 0.7331 (ptt) cc_final: 0.7129 (ptt) REVERT: X 97 LYS cc_start: 0.8003 (ptpp) cc_final: 0.7362 (ptpp) REVERT: Y 11 ASP cc_start: 0.6011 (p0) cc_final: 0.5712 (p0) REVERT: Y 29 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8230 (tptm) REVERT: Y 118 MET cc_start: 0.7393 (ttp) cc_final: 0.7133 (ttm) REVERT: Z 32 LYS cc_start: 0.8552 (mmpt) cc_final: 0.8341 (mmpt) REVERT: Z 45 MET cc_start: 0.7156 (mmm) cc_final: 0.6913 (ttm) REVERT: a 168 LEU cc_start: 0.8359 (tp) cc_final: 0.8107 (tp) REVERT: b 168 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7804 (mm) outliers start: 166 outliers final: 92 residues processed: 1000 average time/residue: 0.6207 time to fit residues: 1024.1665 Evaluate side-chains 909 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 806 time to evaluate : 5.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain T residue 233 LEU Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 60 GLN Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 143 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 108 ASN Chi-restraints excluded: chain b residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 198 optimal weight: 10.0000 chunk 530 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 346 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 590 optimal weight: 3.9990 chunk 489 optimal weight: 6.9990 chunk 273 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 309 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN N 162 GLN ** O 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN P 111 GLN ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN X 32 GLN X 71 ASN Y 55 GLN Y 63 ASN Z 175 ASN a 8 ASN b 108 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.7519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 46182 Z= 0.222 Angle : 0.662 14.180 62708 Z= 0.338 Chirality : 0.044 0.251 7346 Planarity : 0.004 0.058 7974 Dihedral : 4.539 24.807 6788 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.26 % Allowed : 19.94 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.11), residues: 6142 helix: 0.77 (0.11), residues: 2224 sheet: -0.05 (0.13), residues: 1438 loop : -0.34 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 55 HIS 0.006 0.001 HIS S 99 PHE 0.021 0.001 PHE A 191 TYR 0.029 0.001 TYR Q 136 ARG 0.015 0.001 ARG O 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 875 time to evaluate : 5.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.8867 (mt) cc_final: 0.8550 (tt) REVERT: B 109 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8890 (tp) REVERT: C 98 LEU cc_start: 0.8477 (mp) cc_final: 0.8111 (tt) REVERT: D 61 LYS cc_start: 0.8418 (mmmm) cc_final: 0.7991 (mmmt) REVERT: D 66 ASP cc_start: 0.8520 (t70) cc_final: 0.8077 (t70) REVERT: D 190 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8573 (tp) REVERT: D 192 ILE cc_start: 0.9200 (pt) cc_final: 0.8987 (mt) REVERT: E 228 MET cc_start: 0.7865 (tpt) cc_final: 0.7636 (tpt) REVERT: G 158 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6571 (m-10) REVERT: I 126 THR cc_start: 0.8806 (p) cc_final: 0.8539 (p) REVERT: J 162 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8533 (tt) REVERT: N 162 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.6158 (tm-30) REVERT: O 88 ARG cc_start: 0.7534 (mmm160) cc_final: 0.7329 (mmm160) REVERT: O 93 ARG cc_start: 0.7707 (tpt90) cc_final: 0.7500 (tpt170) REVERT: P 134 LEU cc_start: 0.8522 (mt) cc_final: 0.8179 (mt) REVERT: R 90 GLU cc_start: 0.7946 (tp30) cc_final: 0.7643 (tp30) REVERT: R 106 TYR cc_start: 0.7476 (t80) cc_final: 0.7184 (t80) REVERT: R 146 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7958 (tm-30) REVERT: R 190 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8387 (tp) REVERT: S 89 ILE cc_start: 0.8835 (pt) cc_final: 0.8500 (mt) REVERT: T 130 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8893 (p) REVERT: U 13 THR cc_start: 0.8039 (p) cc_final: 0.7825 (p) REVERT: V 48 SER cc_start: 0.7500 (OUTLIER) cc_final: 0.7254 (p) REVERT: V 92 GLU cc_start: 0.6493 (pm20) cc_final: 0.5466 (pm20) REVERT: V 133 SER cc_start: 0.8171 (p) cc_final: 0.7930 (t) REVERT: X 49 TYR cc_start: 0.7958 (m-80) cc_final: 0.7664 (m-80) REVERT: X 58 ASP cc_start: 0.7050 (m-30) cc_final: 0.6756 (m-30) REVERT: X 97 LYS cc_start: 0.7703 (ptpp) cc_final: 0.6970 (ptpp) REVERT: X 102 TYR cc_start: 0.8379 (m-10) cc_final: 0.8014 (m-10) REVERT: Y 11 ASP cc_start: 0.6115 (p0) cc_final: 0.5834 (p0) REVERT: Y 29 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8260 (tptm) REVERT: Z 45 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6974 (mtt) REVERT: b 76 LEU cc_start: 0.8496 (mt) cc_final: 0.8151 (mt) outliers start: 139 outliers final: 86 residues processed: 961 average time/residue: 0.5963 time to fit residues: 946.1514 Evaluate side-chains 900 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 804 time to evaluate : 5.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 96 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 162 GLN Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 233 LEU Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 147 MET Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 143 LEU Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Z residue 45 MET Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 108 ASN Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 569 optimal weight: 5.9990 chunk 66 optimal weight: 0.0770 chunk 336 optimal weight: 0.0170 chunk 431 optimal weight: 7.9990 chunk 333 optimal weight: 6.9990 chunk 496 optimal weight: 6.9990 chunk 329 optimal weight: 10.0000 chunk 587 optimal weight: 10.0000 chunk 367 optimal weight: 20.0000 chunk 358 optimal weight: 6.9990 chunk 271 optimal weight: 9.9990 overall best weight: 4.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN B 94 GLN C 230 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 72 HIS H 62 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN K 168 GLN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 23 GLN ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 32 GLN X 60 GLN Y 82 ASN Z 175 ASN a 8 ASN ** a 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 108 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.8025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 46182 Z= 0.281 Angle : 0.696 11.475 62708 Z= 0.358 Chirality : 0.045 0.303 7346 Planarity : 0.005 0.060 7974 Dihedral : 4.620 25.071 6788 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.58 % Allowed : 21.20 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.11), residues: 6142 helix: 0.73 (0.11), residues: 2224 sheet: -0.14 (0.13), residues: 1456 loop : -0.34 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 55 HIS 0.008 0.001 HIS E 99 PHE 0.022 0.002 PHE A 191 TYR 0.037 0.002 TYR I 90 ARG 0.015 0.001 ARG I 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 842 time to evaluate : 5.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.8944 (mt) cc_final: 0.8654 (tt) REVERT: B 95 GLN cc_start: 0.7638 (pt0) cc_final: 0.7405 (pt0) REVERT: B 111 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7103 (mp10) REVERT: B 191 ILE cc_start: 0.8676 (pt) cc_final: 0.8305 (mt) REVERT: C 98 LEU cc_start: 0.8581 (mp) cc_final: 0.8167 (tt) REVERT: D 66 ASP cc_start: 0.8605 (t70) cc_final: 0.8353 (t0) REVERT: E 107 MET cc_start: 0.8494 (mmm) cc_final: 0.7889 (tpt) REVERT: E 182 GLN cc_start: 0.7430 (pp30) cc_final: 0.6749 (pp30) REVERT: E 228 MET cc_start: 0.7861 (tpt) cc_final: 0.7647 (tpt) REVERT: G 59 GLU cc_start: 0.5549 (mt-10) cc_final: 0.5251 (mt-10) REVERT: G 158 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.6537 (m-10) REVERT: H 147 MET cc_start: 0.6990 (mmp) cc_final: 0.4993 (mtt) REVERT: I 89 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7904 (tmm-80) REVERT: I 174 ASP cc_start: 0.7578 (t0) cc_final: 0.7347 (t0) REVERT: J 11 MET cc_start: 0.8917 (tmm) cc_final: 0.8711 (tmm) REVERT: J 57 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8160 (t) REVERT: J 162 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8614 (tt) REVERT: M 83 MET cc_start: 0.8530 (ttm) cc_final: 0.8255 (mtp) REVERT: M 166 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7216 (mp) REVERT: P 134 LEU cc_start: 0.8454 (mt) cc_final: 0.8076 (mt) REVERT: Q 72 MET cc_start: 0.6656 (ptm) cc_final: 0.6361 (ptm) REVERT: R 106 TYR cc_start: 0.7574 (t80) cc_final: 0.7356 (t80) REVERT: R 146 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7999 (tm-30) REVERT: R 190 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8527 (tp) REVERT: T 130 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.8948 (p) REVERT: U 13 THR cc_start: 0.8142 (p) cc_final: 0.7933 (p) REVERT: V 95 MET cc_start: 0.6798 (tmm) cc_final: 0.6526 (tmm) REVERT: W 1 THR cc_start: 0.7539 (m) cc_final: 0.7252 (p) REVERT: X 11 MET cc_start: 0.8202 (tmm) cc_final: 0.7948 (ptm) REVERT: X 97 LYS cc_start: 0.8130 (ptpp) cc_final: 0.7220 (ptpp) REVERT: X 102 TYR cc_start: 0.8429 (m-10) cc_final: 0.7991 (m-10) REVERT: X 117 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7799 (tppt) REVERT: X 146 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.6326 (m-10) REVERT: Y 11 ASP cc_start: 0.6451 (p0) cc_final: 0.6246 (p0) REVERT: Y 29 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8421 (tptm) REVERT: Y 37 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7643 (tttp) REVERT: Y 111 GLU cc_start: 0.7384 (pp20) cc_final: 0.7152 (pp20) REVERT: b 76 LEU cc_start: 0.8665 (mt) cc_final: 0.8300 (mt) outliers start: 153 outliers final: 96 residues processed: 943 average time/residue: 0.5934 time to fit residues: 920.2074 Evaluate side-chains 878 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 773 time to evaluate : 5.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 96 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 161 CYS Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 224 ASN Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain T residue 233 LEU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 147 MET Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain X residue 146 TYR Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 96 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 363 optimal weight: 0.9990 chunk 234 optimal weight: 20.0000 chunk 351 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 400 optimal weight: 6.9990 chunk 290 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 462 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN N 162 GLN O 172 GLN P 111 GLN Q 119 GLN S 23 GLN ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 57 GLN W 85 GLN a 8 ASN a 131 GLN ** a 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.8409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 46182 Z= 0.271 Angle : 0.711 12.128 62708 Z= 0.365 Chirality : 0.046 0.292 7346 Planarity : 0.005 0.067 7974 Dihedral : 4.652 26.858 6788 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.26 % Allowed : 21.72 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.11), residues: 6142 helix: 0.69 (0.11), residues: 2234 sheet: -0.16 (0.13), residues: 1454 loop : -0.35 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 103 HIS 0.007 0.001 HIS E 99 PHE 0.020 0.002 PHE A 191 TYR 0.038 0.002 TYR D 110 ARG 0.015 0.001 ARG O 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 825 time to evaluate : 5.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6444 (OUTLIER) cc_final: 0.6233 (ptm) REVERT: A 235 ILE cc_start: 0.8941 (mt) cc_final: 0.8702 (tt) REVERT: B 111 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: B 162 MET cc_start: 0.8030 (ptt) cc_final: 0.7525 (ptt) REVERT: B 191 ILE cc_start: 0.8717 (pt) cc_final: 0.8412 (mt) REVERT: C 98 LEU cc_start: 0.8584 (mp) cc_final: 0.8193 (tt) REVERT: E 107 MET cc_start: 0.8493 (mmm) cc_final: 0.8203 (mmm) REVERT: E 182 GLN cc_start: 0.7448 (pp30) cc_final: 0.6939 (pp30) REVERT: E 228 MET cc_start: 0.7819 (tpt) cc_final: 0.7540 (tpt) REVERT: G 158 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6620 (m-10) REVERT: I 174 ASP cc_start: 0.7626 (t0) cc_final: 0.7377 (t0) REVERT: J 57 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8147 (t) REVERT: J 162 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8632 (tt) REVERT: M 83 MET cc_start: 0.8634 (ttm) cc_final: 0.8428 (mtp) REVERT: M 166 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7252 (mp) REVERT: P 134 LEU cc_start: 0.8451 (mt) cc_final: 0.8081 (mt) REVERT: R 146 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8093 (tm-30) REVERT: S 89 ILE cc_start: 0.8824 (pt) cc_final: 0.8488 (mt) REVERT: T 130 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9029 (p) REVERT: V 92 GLU cc_start: 0.6773 (pm20) cc_final: 0.6486 (pm20) REVERT: X 73 TYR cc_start: 0.7817 (t80) cc_final: 0.7224 (t80) REVERT: X 97 LYS cc_start: 0.8116 (ptpp) cc_final: 0.7412 (ptpp) REVERT: X 182 MET cc_start: 0.8041 (mmp) cc_final: 0.7816 (mmp) REVERT: Y 29 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8584 (tptm) REVERT: Y 38 MET cc_start: 0.7200 (mmt) cc_final: 0.6831 (tpp) REVERT: Y 55 GLN cc_start: 0.7263 (mt0) cc_final: 0.6819 (mt0) REVERT: Y 111 GLU cc_start: 0.7306 (pp20) cc_final: 0.6955 (pp20) REVERT: Z 88 TYR cc_start: 0.7809 (t80) cc_final: 0.7192 (t80) REVERT: Z 139 MET cc_start: 0.7593 (tmm) cc_final: 0.7389 (tmm) REVERT: b 76 LEU cc_start: 0.8747 (mt) cc_final: 0.8494 (mt) outliers start: 139 outliers final: 92 residues processed: 913 average time/residue: 0.5967 time to fit residues: 903.4783 Evaluate side-chains 862 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 762 time to evaluate : 5.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 172 GLN Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain T residue 233 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 147 MET Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 156 LYS Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 534 optimal weight: 10.0000 chunk 563 optimal weight: 3.9990 chunk 513 optimal weight: 1.9990 chunk 547 optimal weight: 7.9990 chunk 329 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 430 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 495 optimal weight: 4.9990 chunk 518 optimal weight: 10.0000 chunk 545 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN C 30 HIS ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 172 GLN ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN P 188 HIS S 23 GLN ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 HIS ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 57 GLN W 85 GLN X 32 GLN ** X 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN ** a 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.8642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 46182 Z= 0.276 Angle : 0.726 12.464 62708 Z= 0.372 Chirality : 0.046 0.344 7346 Planarity : 0.005 0.093 7974 Dihedral : 4.703 25.313 6788 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.86 % Allowed : 22.70 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.11), residues: 6142 helix: 0.70 (0.11), residues: 2222 sheet: -0.10 (0.13), residues: 1404 loop : -0.39 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 103 HIS 0.016 0.001 HIS C 30 PHE 0.020 0.002 PHE S 22 TYR 0.029 0.002 TYR C 136 ARG 0.012 0.001 ARG R 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 799 time to evaluate : 5.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6482 (ppp) cc_final: 0.6214 (ptm) REVERT: B 111 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: B 162 MET cc_start: 0.8032 (ptt) cc_final: 0.7615 (ptt) REVERT: B 191 ILE cc_start: 0.8819 (pt) cc_final: 0.8444 (mt) REVERT: C 98 LEU cc_start: 0.8595 (mp) cc_final: 0.8208 (tt) REVERT: E 182 GLN cc_start: 0.7223 (pp30) cc_final: 0.6733 (pp30) REVERT: E 228 MET cc_start: 0.7831 (tpt) cc_final: 0.7556 (tpt) REVERT: G 158 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.6629 (m-10) REVERT: H 4 MET cc_start: 0.7916 (tpp) cc_final: 0.7241 (tpp) REVERT: H 147 MET cc_start: 0.7065 (mmp) cc_final: 0.5512 (mtt) REVERT: I 174 ASP cc_start: 0.7721 (t0) cc_final: 0.7489 (t0) REVERT: J 57 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8030 (t) REVERT: J 146 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6666 (t80) REVERT: M 83 MET cc_start: 0.8659 (ttm) cc_final: 0.8174 (mtm) REVERT: M 166 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7317 (mp) REVERT: O 120 ASP cc_start: 0.7372 (p0) cc_final: 0.7153 (p0) REVERT: P 134 LEU cc_start: 0.8453 (mt) cc_final: 0.8112 (mt) REVERT: R 146 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8186 (tm-30) REVERT: S 89 ILE cc_start: 0.8821 (pt) cc_final: 0.8496 (mt) REVERT: T 130 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8980 (p) REVERT: X 102 TYR cc_start: 0.8483 (m-10) cc_final: 0.8008 (m-10) REVERT: Y 29 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8610 (tptm) REVERT: Y 111 GLU cc_start: 0.7299 (pp20) cc_final: 0.6944 (pp20) REVERT: Z 139 MET cc_start: 0.7503 (tmm) cc_final: 0.7269 (tmm) REVERT: a 169 ASP cc_start: 0.6942 (p0) cc_final: 0.6714 (p0) REVERT: b 76 LEU cc_start: 0.8789 (mt) cc_final: 0.8573 (mt) outliers start: 122 outliers final: 92 residues processed: 879 average time/residue: 0.6103 time to fit residues: 886.7013 Evaluate side-chains 856 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 757 time to evaluate : 6.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 161 CYS Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 204 GLN Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain T residue 233 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 184 VAL Chi-restraints excluded: chain W residue 57 GLN Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 96 MET Chi-restraints excluded: chain b residue 188 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 359 optimal weight: 0.8980 chunk 579 optimal weight: 20.0000 chunk 353 optimal weight: 5.9990 chunk 274 optimal weight: 6.9990 chunk 402 optimal weight: 3.9990 chunk 607 optimal weight: 6.9990 chunk 559 optimal weight: 6.9990 chunk 483 optimal weight: 0.3980 chunk 50 optimal weight: 6.9990 chunk 373 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS D 154 HIS H 123 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 172 GLN ** O 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN R 120 GLN S 23 GLN ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN X 92 ASN ** X 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 10 HIS ** a 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.8840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 46182 Z= 0.273 Angle : 0.748 14.008 62708 Z= 0.383 Chirality : 0.046 0.348 7346 Planarity : 0.005 0.086 7974 Dihedral : 4.744 25.453 6788 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.74 % Allowed : 23.15 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.11), residues: 6142 helix: 0.67 (0.11), residues: 2228 sheet: -0.05 (0.13), residues: 1384 loop : -0.43 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 103 HIS 0.010 0.001 HIS E 99 PHE 0.027 0.002 PHE E 143 TYR 0.053 0.002 TYR a 75 ARG 0.011 0.001 ARG I 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 794 time to evaluate : 6.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6399 (ppp) cc_final: 0.6158 (ptm) REVERT: B 111 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: B 162 MET cc_start: 0.8045 (ptt) cc_final: 0.7734 (ptt) REVERT: B 191 ILE cc_start: 0.8792 (pt) cc_final: 0.8467 (mt) REVERT: C 98 LEU cc_start: 0.8591 (mp) cc_final: 0.8186 (tt) REVERT: E 182 GLN cc_start: 0.7189 (pp30) cc_final: 0.6762 (pp30) REVERT: E 228 MET cc_start: 0.7844 (tpt) cc_final: 0.7564 (tpt) REVERT: G 158 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6680 (m-10) REVERT: H 4 MET cc_start: 0.7867 (tpp) cc_final: 0.7187 (tpp) REVERT: H 57 ASP cc_start: 0.7407 (p0) cc_final: 0.6966 (t0) REVERT: H 147 MET cc_start: 0.7141 (mmp) cc_final: 0.5691 (mtt) REVERT: I 174 ASP cc_start: 0.7756 (t0) cc_final: 0.7539 (t70) REVERT: J 33 MET cc_start: 0.8206 (tmm) cc_final: 0.7920 (tmm) REVERT: J 57 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7951 (t) REVERT: J 146 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6451 (t80) REVERT: M 75 TYR cc_start: 0.8547 (t80) cc_final: 0.8058 (t80) REVERT: M 83 MET cc_start: 0.8673 (ttm) cc_final: 0.7820 (mtm) REVERT: M 166 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7342 (mp) REVERT: O 120 ASP cc_start: 0.7354 (p0) cc_final: 0.7151 (p0) REVERT: P 134 LEU cc_start: 0.8404 (mt) cc_final: 0.8016 (mt) REVERT: R 146 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8226 (tm-30) REVERT: S 78 MET cc_start: 0.7805 (mpp) cc_final: 0.7599 (mpp) REVERT: S 89 ILE cc_start: 0.8804 (pt) cc_final: 0.8470 (mt) REVERT: T 130 VAL cc_start: 0.9277 (OUTLIER) cc_final: 0.9054 (p) REVERT: W 85 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: W 94 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8646 (pt) REVERT: X 97 LYS cc_start: 0.8064 (ptpp) cc_final: 0.7325 (ptpp) REVERT: X 102 TYR cc_start: 0.8424 (m-10) cc_final: 0.8024 (m-10) REVERT: X 157 MET cc_start: 0.8030 (mmt) cc_final: 0.7760 (mmt) REVERT: Y 29 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8327 (tptm) REVERT: Y 111 GLU cc_start: 0.7267 (pp20) cc_final: 0.6837 (pp20) REVERT: Z 139 MET cc_start: 0.7533 (tmm) cc_final: 0.7295 (tmm) REVERT: a 83 MET cc_start: 0.8571 (tpp) cc_final: 0.8032 (mmm) outliers start: 117 outliers final: 87 residues processed: 873 average time/residue: 0.6111 time to fit residues: 883.0271 Evaluate side-chains 858 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 762 time to evaluate : 5.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 158 TYR Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 193 LYS Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 70 MET Chi-restraints excluded: chain N residue 162 GLN Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 161 CYS Chi-restraints excluded: chain O residue 166 THR Chi-restraints excluded: chain O residue 172 GLN Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 PHE Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain S residue 204 GLN Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain T residue 233 LEU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 182 LYS Chi-restraints excluded: chain W residue 219 LEU Chi-restraints excluded: chain X residue 146 TYR Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 29 LYS Chi-restraints excluded: chain Y residue 37 LYS Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 172 ILE Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 86 MET Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain b residue 70 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 384 optimal weight: 10.0000 chunk 515 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 446 optimal weight: 8.9990 chunk 71 optimal weight: 0.0010 chunk 134 optimal weight: 9.9990 chunk 484 optimal weight: 6.9990 chunk 202 optimal weight: 30.0000 chunk 497 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 HIS ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN S 23 GLN ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.060566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.051662 restraints weight = 164738.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.053595 restraints weight = 79082.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.054902 restraints weight = 46405.093| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.8835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.288 46182 Z= 0.370 Angle : 0.858 59.200 62708 Z= 0.470 Chirality : 0.047 0.684 7346 Planarity : 0.006 0.240 7974 Dihedral : 4.735 25.449 6788 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.58 % Allowed : 23.50 % Favored : 73.92 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.11), residues: 6142 helix: 0.66 (0.11), residues: 2228 sheet: -0.04 (0.13), residues: 1384 loop : -0.45 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP V 103 HIS 0.036 0.001 HIS C 30 PHE 0.029 0.002 PHE P 198 TYR 0.084 0.002 TYR Z 88 ARG 0.018 0.001 ARG W 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14804.36 seconds wall clock time: 271 minutes 28.62 seconds (16288.62 seconds total)