Starting phenix.real_space_refine on Wed May 6 19:29:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qvx_53414/05_2026/9qvx_53414.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qvx_53414/05_2026/9qvx_53414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qvx_53414/05_2026/9qvx_53414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qvx_53414/05_2026/9qvx_53414.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qvx_53414/05_2026/9qvx_53414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qvx_53414/05_2026/9qvx_53414.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.013 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 29022 2.51 5 N 8019 2.21 5 O 8067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 258 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45388 Number of models: 1 Model: "" Number of chains: 30 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: {'ARG:plan': 1, 'ASP:plan': 6, 'GLU:plan': 12, 'GLN:plan1': 1, 'PHE:plan': 1, 'TRP: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: {'ARG:plan': 2, 'GLU:plan': 13, 'ASN:plan1': 5, 'ASP:plan': 5, 'GLN:plan1': 1} 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: {'GLU:plan': 18, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLN:plan1': 1} 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: {'ASP:plan': 10, 'GLU:plan': 15, 'ARG:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 2} 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: {'ASP:plan': 8, 'GLU:plan': 13, 'GLN:plan1': 2} 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: {'ASN:plan1': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 9, 'ASP:plan': 10} 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, 'ASP:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1} 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: {'ASP:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 4, 'GLN:plan1': 1} 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, 'ASP:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 2} 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, 'ASP:plan': 7, 'GLU:plan': 5} 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, 'ASP:plan': 4, 'ARG:plan': 2} 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, 'ASP:plan': 8, 'ASN:plan1': 1} 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, 'ASN:plan1': 2, 'GLU:plan': 9, 'ASP:plan': 4, 'TRP:plan': 1} 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: {'ARG:plan': 1, 'ASP:plan': 6, 'GLU:plan': 12, 'GLN:plan1': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "P" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1670 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 13, 'ASN:plan1': 5, 'ASP:plan': 5, 'GLN:plan1': 1} 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: {'GLU:plan': 18, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLN:plan1': 1} 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: {'ASP:plan': 10, 'GLU:plan': 15, 'ARG:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 2} 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: {'ASP:plan': 8, 'GLU:plan': 13, 'GLN:plan1': 2} 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: {'ASN:plan1': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 9, 'ASP:plan': 10} 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, 'ASP:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1} 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: {'ASP:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 4, 'GLN:plan1': 1} 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, 'ASP:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 2} 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, 'ASP:plan': 7, 'GLU:plan': 5} 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, 'ASP:plan': 4, 'ARG:plan': 2} 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, 'ASP:plan': 8, 'ASN:plan1': 1} 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, 'ASN:plan1': 2, 'GLU:plan': 9, 'ASP:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "c" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "d" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 11.57, per 1000 atoms: 0.25 Number of scatterers: 45388 At special positions: 0 Unit cell: (184.21, 150.41, 131.82, 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 8067 8.00 N 8019 7.00 C 29022 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: 4.13 Conformation dependent library (CDL) restraints added in 1.8 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: 11432 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 75 sheets defined 39.3% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.635A pdb=" N ALA A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 83 through 106 Processing helix chain 'A' and resid 110 through 128 removed outlier: 4.215A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.749A 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 193 through 207 removed outlier: 3.920A pdb=" N VAL A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.908A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 30 removed outlier: 3.551A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 101 removed outlier: 3.704A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.716A pdb=" N THR B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.884A pdb=" N SER B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 231 removed outlier: 4.135A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.910A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 removed outlier: 3.800A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 4.113A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 200 removed outlier: 3.861A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 247 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 76 through 99 removed outlier: 3.657A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 Processing helix chain 'D' and resid 164 through 176 Processing helix chain 'D' and resid 183 through 199 removed outlier: 3.588A pdb=" N VAL D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 232 removed outlier: 3.570A pdb=" N TYR D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 33 removed outlier: 3.508A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 84 through 104 removed outlier: 4.394A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.895A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 185 removed outlier: 6.898A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.535A pdb=" N GLU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 31 removed outlier: 3.710A pdb=" N GLU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 99 Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.853A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix removed outlier: 3.518A pdb=" N ARG F 122 " --> pdb=" O ILE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 175 removed outlier: 4.335A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 182 removed outlier: 3.788A pdb=" N PHE F 179 " --> pdb=" O MET F 176 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N MET F 180 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.714A pdb=" N VAL F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'G' and resid 6 through 10 removed outlier: 3.710A pdb=" N LEU G 9 " --> pdb=" O GLY G 6 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER G 10 " --> pdb=" O TYR G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 10' Processing helix chain 'G' and resid 20 through 32 removed outlier: 3.786A pdb=" N LYS G 28 " --> pdb=" O GLU G 24 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 103 Processing helix chain 'G' and resid 107 through 122 removed outlier: 3.881A pdb=" N TYR G 122 " --> pdb=" O TYR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 177 removed outlier: 4.602A pdb=" N GLU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 184 removed outlier: 3.593A pdb=" N GLU G 183 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET G 184 " --> pdb=" O MET G 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 180 through 184' Processing helix chain 'G' and resid 185 through 201 removed outlier: 4.538A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 228 through 244 removed outlier: 3.548A pdb=" N LYS G 244 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.651A pdb=" N TYR H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.870A pdb=" N SER H 133 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR H 134 " --> pdb=" O GLY H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 143 Processing helix chain 'H' and resid 148 through 167 Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.917A pdb=" N ILE H 194 " --> pdb=" O GLY H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.948A pdb=" N ALA I 136 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE I 138 " --> pdb=" O ALA I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 166 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: 4.374A pdb=" N LYS J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 removed outlier: 3.600A pdb=" N TYR J 146 " --> pdb=" O ALA J 142 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY J 147 " --> pdb=" O GLU J 143 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU J 150 " --> pdb=" O TYR J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 175 removed outlier: 3.506A pdb=" N ASN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 72 removed outlier: 3.588A pdb=" N GLN K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 93 removed outlier: 3.501A pdb=" N ASN K 87 " --> pdb=" O PHE K 83 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 144 removed outlier: 5.120A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 removed outlier: 3.737A pdb=" N LEU K 167 " --> pdb=" O CYS K 163 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN K 168 " --> pdb=" O LEU K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 89 removed outlier: 3.901A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 4.292A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 Processing helix chain 'L' and resid 191 through 200 removed outlier: 3.588A pdb=" N LYS L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 80 removed outlier: 3.506A pdb=" N LYS M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.658A pdb=" N ARG M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 154 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 167 through 186 removed outlier: 3.596A pdb=" N ILE M 180 " --> pdb=" O LYS M 176 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG M 185 " --> pdb=" O SER M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 78 removed outlier: 3.500A pdb=" N PHE N 60 " --> pdb=" O ASP N 56 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN N 69 " --> pdb=" O GLN N 65 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 removed outlier: 3.682A pdb=" N LYS N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 180 Processing helix chain 'O' and resid 22 through 33 removed outlier: 3.875A pdb=" N TYR O 27 " --> pdb=" O TYR O 23 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE O 29 " --> pdb=" O VAL O 25 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 36 No H-bonds generated for 'chain 'O' and resid 34 through 36' Processing helix chain 'O' and resid 83 through 106 Processing helix chain 'O' and resid 110 through 128 removed outlier: 4.092A pdb=" N LYS O 116 " --> pdb=" O ASP O 112 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG O 117 " --> pdb=" O MET O 113 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE O 118 " --> pdb=" O LEU O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 181 removed outlier: 3.776A pdb=" N LYS O 181 " --> pdb=" O SER O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 207 removed outlier: 4.033A pdb=" N VAL O 205 " --> pdb=" O CYS O 201 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU O 206 " --> pdb=" O LEU O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 213 No H-bonds generated for 'chain 'O' and resid 211 through 213' Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.874A pdb=" N ALA O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS O 238 " --> pdb=" O GLU O 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 30 removed outlier: 3.524A pdb=" N ALA P 26 " --> pdb=" O GLU P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 101 removed outlier: 3.664A pdb=" N VAL P 84 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 120 Processing helix chain 'P' and resid 165 through 177 removed outlier: 3.733A pdb=" N THR P 171 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS P 175 " --> pdb=" O THR P 171 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG P 176 " --> pdb=" O PHE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 197 removed outlier: 3.558A pdb=" N HIS P 188 " --> pdb=" O GLU P 184 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER P 197 " --> pdb=" O THR P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 231 removed outlier: 4.164A pdb=" N ALA P 231 " --> pdb=" O ASP P 227 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 30 removed outlier: 3.700A pdb=" N GLU Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 102 removed outlier: 3.989A pdb=" N VAL Q 85 " --> pdb=" O SER Q 81 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 124 removed outlier: 3.845A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 179 removed outlier: 4.498A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP Q 178 " --> pdb=" O MET Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 200 removed outlier: 3.558A pdb=" N LYS Q 199 " --> pdb=" O LYS Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 247 Processing helix chain 'R' and resid 17 through 28 Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.506A pdb=" N ILE R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 121 Processing helix chain 'R' and resid 164 through 175 Processing helix chain 'R' and resid 183 through 199 removed outlier: 3.629A pdb=" N VAL R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 232 removed outlier: 3.552A pdb=" N TYR R 228 " --> pdb=" O GLU R 224 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.563A 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 83 through 104 removed outlier: 4.421A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 119 removed outlier: 3.836A pdb=" N LEU S 119 " --> pdb=" O ALA S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 173 through 185 removed outlier: 6.954A pdb=" N SER S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 206 Processing helix chain 'S' and resid 230 through 241 removed outlier: 3.548A pdb=" N GLU S 235 " --> pdb=" O LYS S 231 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLU S 236 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL S 237 " --> pdb=" O GLU S 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 31 removed outlier: 3.733A pdb=" N GLU T 23 " --> pdb=" O ILE T 19 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 99 removed outlier: 3.527A pdb=" N PHE T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 122 removed outlier: 3.829A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Proline residue: T 119 - end of helix removed outlier: 3.568A pdb=" N ARG T 122 " --> pdb=" O ILE T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 175 removed outlier: 4.303A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 182 removed outlier: 3.677A pdb=" N PHE T 179 " --> pdb=" O MET T 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N MET T 180 " --> pdb=" O SER T 177 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU T 181 " --> pdb=" O GLU T 178 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 197 removed outlier: 3.560A pdb=" N VAL T 188 " --> pdb=" O LEU T 184 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS T 189 " --> pdb=" O ASN T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 234 Processing helix chain 'U' and resid 6 through 10 removed outlier: 4.276A pdb=" N SER U 10 " --> pdb=" O TYR U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 32 removed outlier: 3.629A pdb=" N LYS U 28 " --> pdb=" O GLU U 24 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 103 Processing helix chain 'U' and resid 107 through 122 removed outlier: 3.848A pdb=" N TYR U 122 " --> pdb=" O TYR U 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 177 removed outlier: 4.535A pdb=" N GLU U 175 " --> pdb=" O ALA U 171 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 201 removed outlier: 4.672A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU U 192 " --> pdb=" O ASP U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 219 through 221 No H-bonds generated for 'chain 'U' and resid 219 through 221' Processing helix chain 'U' and resid 228 through 244 removed outlier: 3.558A pdb=" N LYS U 244 " --> pdb=" O LYS U 240 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.697A pdb=" N TYR V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 131 through 134 removed outlier: 3.574A pdb=" N TYR V 134 " --> pdb=" O GLY V 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 131 through 134' Processing helix chain 'V' and resid 135 through 143 Processing helix chain 'V' and resid 148 through 167 Processing helix chain 'V' and resid 190 through 194 removed outlier: 3.917A pdb=" N ILE V 194 " --> pdb=" O GLY V 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.924A pdb=" N ALA W 136 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE W 138 " --> pdb=" O ALA W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 166 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: 4.423A pdb=" N LYS X 97 " --> pdb=" O LEU X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 153 removed outlier: 3.604A pdb=" N TYR X 146 " --> pdb=" O ALA X 142 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY X 147 " --> pdb=" O GLU X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 176 removed outlier: 3.659A pdb=" N ASN X 172 " --> pdb=" O GLN X 168 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG X 176 " --> pdb=" O ASN X 172 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 72 removed outlier: 3.552A pdb=" N GLN Y 55 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 93 removed outlier: 4.408A pdb=" N ARG Y 93 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 144 removed outlier: 5.036A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 171 removed outlier: 3.737A pdb=" N LEU Y 167 " --> pdb=" O CYS Y 163 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 89 removed outlier: 3.816A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 4.242A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 Processing helix chain 'Z' and resid 191 through 200 removed outlier: 3.594A pdb=" N LYS Z 198 " --> pdb=" O ASP Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 80 removed outlier: 3.585A pdb=" N LYS a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 99 removed outlier: 3.606A pdb=" N ARG a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 154 Proline residue: a 147 - end of helix Processing helix chain 'a' and resid 167 through 186 removed outlier: 3.600A pdb=" N ILE a 180 " --> pdb=" O LYS a 176 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG a 185 " --> pdb=" O SER a 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 56 through 78 removed outlier: 3.552A pdb=" N PHE b 60 " --> pdb=" O ASP b 56 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN b 69 " --> pdb=" O GLN b 65 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU b 77 " --> pdb=" O ASP b 73 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 102 Processing helix chain 'b' and resid 141 through 146 Processing helix chain 'b' and resid 146 through 157 removed outlier: 3.601A pdb=" N LYS b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.312A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 53 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 52 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 219 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 228 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.903A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 81 " --> pdb=" O CYS A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 163 removed outlier: 3.796A pdb=" N GLY A 162 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.601A pdb=" N ILE C 37 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 44 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE C 213 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 72 through 78 removed outlier: 3.781A pdb=" N LEU C 134 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C 138 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AA9, 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: 4.147A pdb=" N VAL D 210 " --> pdb=" O LYS D 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 62 through 64 removed outlier: 3.684A pdb=" N MET D 71 " --> pdb=" O CYS D 63 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D 135 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AB3, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.224A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.591A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.418A pdb=" N HIS F 65 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ILE F 72 " --> pdb=" O HIS F 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AB7, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.589A pdb=" N GLU G 225 " --> pdb=" O TRP G 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 66 through 70 removed outlier: 6.549A pdb=" N VAL G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY G 138 " --> pdb=" O GLY G 74 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE G 135 " --> pdb=" O ILE G 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 125 through 128 removed outlier: 3.993A pdb=" N ALA H 177 " --> pdb=" O LEU H 14 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.437A pdb=" N THR H 22 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE H 26 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 34 through 35 removed outlier: 4.196A pdb=" N ILE H 99 " --> pdb=" O CYS H 44 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER H 46 " --> pdb=" O GLY H 97 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY H 97 " --> pdb=" O SER H 46 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL H 121 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 126 through 128 removed outlier: 3.502A pdb=" N LEU I 175 " --> pdb=" O LEU I 186 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.627A pdb=" N ALA I 20 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL I 25 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 35 through 38 removed outlier: 6.457A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 35 through 38 removed outlier: 6.457A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU I 98 " --> pdb=" O ILE I 113 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 213 through 218 removed outlier: 3.807A pdb=" N THR I 213 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ALA J 9 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 41 through 45 removed outlier: 3.614A pdb=" N ILE J 50 " --> pdb=" O PHE J 42 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU J 48 " --> pdb=" O MET J 44 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 129 through 133 removed outlier: 3.553A pdb=" N LEU K 4 " --> pdb=" O HIS K 132 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR K 3 " --> pdb=" O ASP K 18 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL K 15 " --> pdb=" O ARG K 181 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG K 181 " --> pdb=" O VAL K 15 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP K 184 " --> pdb=" O GLY K 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 129 through 133 removed outlier: 3.553A pdb=" N LEU K 4 " --> pdb=" O HIS K 132 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR K 3 " --> pdb=" O ASP K 18 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL K 15 " --> pdb=" O ARG K 181 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG K 181 " --> pdb=" O VAL K 15 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 35 through 37 removed outlier: 3.740A pdb=" N MET K 118 " --> pdb=" O LEU K 102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 125 through 129 removed outlier: 7.222A pdb=" N LEU L 176 " --> pdb=" O VAL L 187 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 20 through 22 removed outlier: 5.979A pdb=" N ALA L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 34 through 38 removed outlier: 5.148A pdb=" N GLU L 36 " --> pdb=" O GLY L 43 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY L 43 " --> pdb=" O GLU L 36 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL L 114 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY L 103 " --> pdb=" O GLY L 110 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 135 through 137 Processing sheet with id=AD7, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.967A pdb=" N LEU M 29 " --> pdb=" O HIS M 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 43 through 44 removed outlier: 4.027A pdb=" N ASN M 108 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 136 through 138 removed outlier: 3.632A pdb=" N THR N 193 " --> pdb=" O GLY N 196 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 136 through 138 Processing sheet with id=AE2, first strand: chain 'N' and resid 42 through 43 removed outlier: 3.709A pdb=" N MET N 110 " --> pdb=" O VAL N 125 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 165 through 169 removed outlier: 6.192A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN O 53 " --> pdb=" O THR O 38 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR O 52 " --> pdb=" O GLU O 216 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL O 219 " --> pdb=" O ARG O 228 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG O 228 " --> pdb=" O VAL O 219 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 69 through 73 removed outlier: 6.898A pdb=" N ILE O 76 " --> pdb=" O ILE O 72 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR O 81 " --> pdb=" O CYS O 137 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 162 through 163 removed outlier: 3.879A pdb=" N GLY O 162 " --> pdb=" O ASP P 57 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 159 through 162 Processing sheet with id=AE7, first strand: chain 'P' and resid 65 through 66 Processing sheet with id=AE8, first strand: chain 'Q' and resid 161 through 164 removed outlier: 3.646A pdb=" N ILE Q 37 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU Q 44 " --> pdb=" O ILE Q 37 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE Q 213 " --> pdb=" O LEU Q 228 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 72 through 75 removed outlier: 3.645A pdb=" N LEU Q 134 " --> pdb=" O SER Q 150 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY Q 138 " --> pdb=" O GLN Q 146 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN Q 146 " --> pdb=" O GLY Q 138 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU Q 147 " --> pdb=" O TRP Q 159 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 10 through 11 removed outlier: 3.539A pdb=" N HIS R 15 " --> pdb=" O SER R 11 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 158 through 161 removed outlier: 3.636A pdb=" N VAL R 41 " --> pdb=" O MET R 211 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL R 210 " --> pdb=" O LYS R 218 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 62 through 64 removed outlier: 3.593A pdb=" N MET R 71 " --> pdb=" O CYS R 63 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY R 135 " --> pdb=" O ARG R 143 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 167 through 170 removed outlier: 3.584A pdb=" N GLY S 45 " --> pdb=" O THR S 42 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.657A pdb=" N ILE S 67 " --> pdb=" O MET S 78 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N MET S 78 " --> pdb=" O ILE S 67 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU S 69 " --> pdb=" O CYS S 76 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N CYS S 76 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA S 140 " --> pdb=" O SER S 79 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU S 153 " --> pdb=" O CYS S 165 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN S 164 " --> pdb=" O ALA T 58 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 158 through 161 removed outlier: 3.539A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 63 through 67 removed outlier: 6.452A pdb=" N HIS T 65 " --> pdb=" O ILE T 72 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE T 72 " --> pdb=" O HIS T 65 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 132 through 133 Processing sheet with id=AF9, first strand: chain 'U' and resid 162 through 165 removed outlier: 3.550A pdb=" N GLU U 225 " --> pdb=" O TRP U 215 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 66 through 70 removed outlier: 6.490A pdb=" N VAL U 73 " --> pdb=" O VAL U 69 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY U 138 " --> pdb=" O GLY U 74 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE U 135 " --> pdb=" O ILE U 151 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 125 through 129 removed outlier: 6.425A pdb=" N THR V 2 " --> pdb=" O ASP V 17 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA V 177 " --> pdb=" O LEU V 14 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.433A pdb=" N THR V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE V 26 " --> pdb=" O THR V 22 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'V' and resid 34 through 35 removed outlier: 4.218A pdb=" N ILE V 99 " --> pdb=" O CYS V 44 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER V 46 " --> pdb=" O GLY V 97 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL V 121 " --> pdb=" O SER V 113 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 126 through 128 removed outlier: 7.244A pdb=" N ILE W 173 " --> pdb=" O PRO W 188 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.683A pdb=" N ALA W 20 " --> pdb=" O ALA W 27 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL W 25 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 35 through 38 removed outlier: 6.472A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 35 through 38 removed outlier: 6.472A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP W 120 " --> pdb=" O SER W 112 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 213 through 218 removed outlier: 3.756A pdb=" N THR W 213 " --> pdb=" O THR X 198 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA X 9 " --> pdb=" O ASP X 24 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'X' and resid 41 through 45 removed outlier: 3.592A pdb=" N ILE X 50 " --> pdb=" O PHE X 42 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU X 48 " --> pdb=" O MET X 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY X 110 " --> pdb=" O PHE X 119 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 129 through 132 removed outlier: 3.514A pdb=" N LEU Y 4 " --> pdb=" O HIS Y 132 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Y 15 " --> pdb=" O ARG Y 181 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP Y 184 " --> pdb=" O GLY Y 187 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 35 through 37 removed outlier: 3.739A pdb=" N MET Y 118 " --> pdb=" O LEU Y 102 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 125 through 129 removed outlier: 7.239A pdb=" N LEU Z 176 " --> pdb=" O VAL Z 187 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 20 through 22 removed outlier: 5.997A pdb=" N ALA Z 22 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE Z 26 " --> pdb=" O ALA Z 22 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Z' and resid 34 through 38 removed outlier: 5.118A pdb=" N GLU Z 36 " --> pdb=" O GLY Z 43 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY Z 43 " --> pdb=" O GLU Z 36 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL Z 114 " --> pdb=" O THR Z 99 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY Z 103 " --> pdb=" O GLY Z 110 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 135 through 137 Processing sheet with id=AH8, first strand: chain 'a' and resid 29 through 31 removed outlier: 6.972A pdb=" N LEU a 29 " --> pdb=" O HIS a 36 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'a' and resid 43 through 44 removed outlier: 4.006A pdb=" N ASN a 108 " --> pdb=" O PHE a 124 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL a 121 " --> pdb=" O ASP a 133 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'b' and resid 136 through 138 removed outlier: 3.530A pdb=" N GLY b 19 " --> pdb=" O PHE b 16 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR b 193 " --> pdb=" O GLY b 196 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'b' and resid 136 through 138 removed outlier: 3.530A pdb=" N GLY b 19 " --> pdb=" O PHE b 16 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'b' and resid 42 through 43 2573 hydrogen bonds defined for protein. 7338 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: 11.16 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11895 1.33 - 1.45: 8974 1.45 - 1.58: 24897 1.58 - 1.70: 0 1.70 - 1.82: 462 Bond restraints: 46228 Sorted by residual: bond pdb=" N SER F 54 " pdb=" CA SER F 54 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.16e-02 7.43e+03 6.60e+00 bond pdb=" N HIS F 59 " pdb=" CA HIS F 59 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.48e+00 bond pdb=" C LYS C 127 " pdb=" N ARG C 128 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.47e-02 4.63e+03 6.45e+00 bond pdb=" N GLU F 55 " pdb=" CA GLU F 55 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.35e+00 bond pdb=" C LYS Q 127 " pdb=" N ARG Q 128 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.47e-02 4.63e+03 4.74e+00 ... (remaining 46223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 62009 2.76 - 5.52: 663 5.52 - 8.29: 65 8.29 - 11.05: 25 11.05 - 13.81: 5 Bond angle restraints: 62767 Sorted by residual: angle pdb=" N ILE B 54 " pdb=" CA ILE B 54 " pdb=" C ILE B 54 " ideal model delta sigma weight residual 113.47 108.24 5.23 1.01e+00 9.80e-01 2.68e+01 angle pdb=" CA GLN T 90 " pdb=" CB GLN T 90 " pdb=" CG GLN T 90 " ideal model delta sigma weight residual 114.10 123.70 -9.60 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CB MET G 117 " pdb=" CG MET G 117 " pdb=" SD MET G 117 " ideal model delta sigma weight residual 112.70 126.51 -13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" CB MET U 117 " pdb=" CG MET U 117 " pdb=" SD MET U 117 " ideal model delta sigma weight residual 112.70 126.01 -13.31 3.00e+00 1.11e-01 1.97e+01 angle pdb=" CB LYS Z 91 " pdb=" CG LYS Z 91 " pdb=" CD LYS Z 91 " ideal model delta sigma weight residual 111.30 121.39 -10.09 2.30e+00 1.89e-01 1.93e+01 ... (remaining 62762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 24576 17.89 - 35.78: 2212 35.78 - 53.66: 545 53.66 - 71.55: 70 71.55 - 89.44: 42 Dihedral angle restraints: 27445 sinusoidal: 9541 harmonic: 17904 Sorted by residual: dihedral pdb=" CA ALA T 58 " pdb=" C ALA T 58 " pdb=" N HIS T 59 " pdb=" CA HIS T 59 " ideal model delta harmonic sigma weight residual -180.00 -148.30 -31.70 0 5.00e+00 4.00e-02 4.02e+01 dihedral pdb=" CA ILE B 104 " pdb=" C ILE B 104 " pdb=" N PRO B 105 " pdb=" CA PRO B 105 " ideal model delta harmonic sigma weight residual 180.00 151.46 28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA LYS F 50 " pdb=" C LYS F 50 " pdb=" N ARG F 51 " pdb=" CA ARG F 51 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 27442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 5071 0.042 - 0.084: 1639 0.084 - 0.127: 578 0.127 - 0.169: 61 0.169 - 0.211: 6 Chirality restraints: 7355 Sorted by residual: chirality pdb=" CG LEU A 140 " pdb=" CB LEU A 140 " pdb=" CD1 LEU A 140 " pdb=" CD2 LEU A 140 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB ILE G 106 " pdb=" CA ILE G 106 " pdb=" CG1 ILE G 106 " pdb=" CG2 ILE G 106 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CG LEU C 114 " pdb=" CB LEU C 114 " pdb=" CD1 LEU C 114 " pdb=" CD2 LEU C 114 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 7352 not shown) Planarity restraints: 7980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE X 42 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.75e+00 pdb=" N PRO X 43 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO X 43 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO X 43 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL Y 13 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" C VAL Y 13 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL Y 13 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU Y 14 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP T 94 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" CG ASP T 94 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP T 94 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP T 94 " -0.015 2.00e-02 2.50e+03 ... (remaining 7977 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 775 2.65 - 3.22: 43805 3.22 - 3.78: 73645 3.78 - 4.34: 96812 4.34 - 4.90: 160058 Nonbonded interactions: 375095 Sorted by model distance: nonbonded pdb=" OD1 ASP Y 52 " pdb=" OH TYR Z 88 " model vdw 2.093 3.040 nonbonded pdb=" OE1 GLN J 32 " pdb=" OH TYR Z 134 " model vdw 2.095 3.040 nonbonded pdb=" NH2 ARG R 109 " pdb=" OD1 ASN Z 70 " model vdw 2.110 3.120 nonbonded pdb=" NH2 ARG D 109 " pdb=" OD1 ASN L 70 " model vdw 2.113 3.120 nonbonded pdb=" OD1 ASP K 52 " pdb=" OH TYR L 88 " model vdw 2.136 3.040 ... (remaining 375090 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' and (resid 3 through 51 or (resid 52 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 231)) } 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' } ncs_group { reference = chain 'c' selection = chain 'd' } 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 44.280 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 : 0.004 0.060 46228 Z= 0.207 Angle : 0.771 13.812 62767 Z= 0.427 Chirality : 0.046 0.211 7355 Planarity : 0.004 0.074 7980 Dihedral : 15.037 89.438 16013 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.84 % Rotamer: Outliers : 3.89 % Allowed : 24.26 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.10), residues: 6142 helix: 0.80 (0.11), residues: 2232 sheet: -0.31 (0.13), residues: 1440 loop : -0.59 (0.12), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 173 TYR 0.037 0.002 TYR L 143 PHE 0.035 0.002 PHE V 125 TRP 0.035 0.003 TRP N 107 HIS 0.008 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00427 (46228) covalent geometry : angle 0.77118 (62767) hydrogen bonds : bond 0.20445 ( 2528) hydrogen bonds : angle 7.89635 ( 7338) *********************** 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 1105 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 939 time to evaluate : 1.674 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 13 ILE cc_start: 0.9062 (pt) cc_final: 0.8474 (mm) REVERT: A 102 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.7941 (tptp) REVERT: B 56 TYR cc_start: 0.5837 (OUTLIER) cc_final: 0.4812 (t80) REVERT: B 85 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8281 (tp) REVERT: B 108 GLN cc_start: 0.8754 (mm110) cc_final: 0.8519 (mm110) REVERT: B 138 TRP cc_start: 0.7115 (t60) cc_final: 0.6900 (t60) REVERT: C 167 ASN cc_start: 0.7829 (t0) cc_final: 0.7312 (p0) REVERT: C 174 MET cc_start: 0.7910 (tpp) cc_final: 0.7362 (tpp) REVERT: C 209 GLU cc_start: 0.7695 (mp0) cc_final: 0.7465 (mp0) REVERT: D 4 ASP cc_start: 0.6588 (t70) cc_final: 0.6210 (t0) REVERT: D 23 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7642 (tm-30) REVERT: D 55 ASP cc_start: 0.5980 (t70) cc_final: 0.5394 (m-30) REVERT: D 211 MET cc_start: 0.0565 (mtm) cc_final: 0.0334 (mtm) REVERT: E 114 GLN cc_start: 0.8814 (tp40) cc_final: 0.8473 (tp40) REVERT: E 125 GLU cc_start: 0.6517 (pp20) cc_final: 0.5940 (pp20) REVERT: E 214 ASN cc_start: 0.8525 (p0) cc_final: 0.8270 (p0) REVERT: E 216 GLU cc_start: 0.7420 (tp30) cc_final: 0.7130 (tp30) REVERT: F 62 LYS cc_start: 0.7430 (mmtm) cc_final: 0.7178 (mmmt) REVERT: F 90 GLN cc_start: 0.8185 (tp40) cc_final: 0.7259 (tp-100) REVERT: F 94 ASP cc_start: 0.8355 (m-30) cc_final: 0.7561 (m-30) REVERT: F 180 MET cc_start: 0.7105 (ppp) cc_final: 0.6646 (pmm) REVERT: G 8 ASP cc_start: 0.7493 (m-30) cc_final: 0.7117 (m-30) REVERT: H 25 TYR cc_start: 0.8977 (t80) cc_final: 0.8601 (t80) REVERT: H 120 MET cc_start: 0.8172 (tmm) cc_final: 0.7860 (tmm) REVERT: H 181 GLU cc_start: 0.7973 (pm20) cc_final: 0.7568 (pm20) REVERT: I 40 ASN cc_start: 0.7987 (p0) cc_final: 0.7667 (p0) REVERT: I 146 MET cc_start: 0.7718 (mtm) cc_final: 0.7343 (mtp) REVERT: J 130 MET cc_start: 0.7251 (mpp) cc_final: 0.7009 (mmt) REVERT: J 164 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7322 (pt0) REVERT: J 188 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8624 (mt) REVERT: K 60 ILE cc_start: 0.9246 (mm) cc_final: 0.8914 (mm) REVERT: K 62 LYS cc_start: 0.9145 (tptp) cc_final: 0.8585 (tptm) REVERT: K 102 LEU cc_start: 0.9155 (mp) cc_final: 0.8908 (mp) REVERT: K 163 CYS cc_start: 0.8683 (m) cc_final: 0.8051 (t) REVERT: L 97 MET cc_start: 0.4020 (mmm) cc_final: 0.3761 (mmm) REVERT: L 184 TRP cc_start: 0.7501 (p-90) cc_final: 0.6614 (p-90) REVERT: M 105 TYR cc_start: 0.7436 (t80) cc_final: 0.7115 (t80) REVERT: M 108 ASN cc_start: 0.8903 (m-40) cc_final: 0.8654 (m-40) REVERT: M 146 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7767 (tp40) REVERT: O 13 ILE cc_start: 0.8834 (pt) cc_final: 0.8548 (mm) REVERT: O 62 ASP cc_start: 0.7923 (t0) cc_final: 0.7474 (t0) REVERT: O 102 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8030 (tptp) REVERT: O 103 TYR cc_start: 0.8541 (t80) cc_final: 0.8300 (t80) REVERT: O 125 TYR cc_start: 0.8887 (m-80) cc_final: 0.8601 (m-80) REVERT: O 132 ARG cc_start: 0.8424 (ptt-90) cc_final: 0.7859 (ptt-90) REVERT: O 150 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7380 (mm110) REVERT: O 160 TYR cc_start: 0.6779 (p90) cc_final: 0.6460 (p90) REVERT: P 56 TYR cc_start: 0.5500 (OUTLIER) cc_final: 0.4371 (t80) REVERT: P 78 MET cc_start: 0.7239 (mmm) cc_final: 0.6896 (mmm) REVERT: P 102 GLU cc_start: 0.8718 (tp30) cc_final: 0.8165 (tt0) REVERT: Q 72 MET cc_start: 0.7486 (tpp) cc_final: 0.7208 (tpp) REVERT: Q 111 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8410 (t) REVERT: Q 121 TYR cc_start: 0.8169 (m-80) cc_final: 0.7715 (m-80) REVERT: Q 136 TYR cc_start: 0.7763 (m-80) cc_final: 0.6892 (m-10) REVERT: Q 174 MET cc_start: 0.8185 (tmm) cc_final: 0.7891 (tmm) REVERT: Q 209 GLU cc_start: 0.7782 (mp0) cc_final: 0.7208 (mp0) REVERT: R 4 ASP cc_start: 0.6574 (t0) cc_final: 0.5998 (t0) REVERT: R 23 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7578 (tm-30) REVERT: S 114 GLN cc_start: 0.8792 (tp40) cc_final: 0.8455 (tp40) REVERT: S 216 GLU cc_start: 0.7412 (tp30) cc_final: 0.7092 (tp30) REVERT: T 7 ASP cc_start: 0.7942 (p0) cc_final: 0.7435 (p0) REVERT: T 117 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8100 (tm-30) REVERT: U 236 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7152 (mm-30) REVERT: V 25 TYR cc_start: 0.8991 (t80) cc_final: 0.8631 (t80) REVERT: V 95 MET cc_start: 0.5858 (mmt) cc_final: 0.5200 (mmt) REVERT: V 116 MET cc_start: 0.7267 (tpt) cc_final: 0.6244 (mtt) REVERT: V 120 MET cc_start: 0.8220 (tmm) cc_final: 0.7972 (tmm) REVERT: W 14 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8825 (tp) REVERT: W 30 ASN cc_start: 0.6574 (t0) cc_final: 0.6118 (t0) REVERT: W 40 ASN cc_start: 0.7636 (p0) cc_final: 0.7222 (p0) REVERT: W 146 MET cc_start: 0.7774 (mtm) cc_final: 0.7360 (mtp) REVERT: W 148 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6949 (tm-30) REVERT: X 138 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7600 (t) REVERT: X 175 ASP cc_start: 0.7252 (p0) cc_final: 0.6779 (m-30) REVERT: X 188 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8568 (mt) REVERT: Y 38 MET cc_start: 0.8128 (mmm) cc_final: 0.7672 (mmp) REVERT: Y 62 LYS cc_start: 0.9130 (tptp) cc_final: 0.8554 (tptm) REVERT: Y 70 ARG cc_start: 0.8795 (ptp-110) cc_final: 0.8148 (ptp-110) REVERT: Y 163 CYS cc_start: 0.8584 (m) cc_final: 0.7890 (m) REVERT: Z 184 TRP cc_start: 0.7642 (p-90) cc_final: 0.6537 (p-90) REVERT: a 60 ASP cc_start: 0.9069 (m-30) cc_final: 0.8642 (m-30) REVERT: b 65 GLN cc_start: 0.7342 (tt0) cc_final: 0.7080 (tt0) outliers start: 166 outliers final: 129 residues processed: 1038 average time/residue: 0.2429 time to fit residues: 431.6467 Evaluate side-chains 1031 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 891 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 221 ASN Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 188 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 102 LYS Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 56 TYR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain S residue 82 ILE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain T residue 23 GLU Chi-restraints excluded: chain T residue 68 ASN Chi-restraints excluded: chain T residue 69 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 92 CYS Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 156 CYS Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 41 CYS Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 165 ILE Chi-restraints excluded: chain U residue 221 ASN Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 138 SER Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 188 ILE Chi-restraints excluded: chain X residue 203 MET Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 150 THR Chi-restraints excluded: chain Y residue 175 LEU Chi-restraints excluded: chain Y residue 188 ILE Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 63 CYS Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 97 MET Chi-restraints excluded: chain Z residue 101 ILE Chi-restraints excluded: chain Z residue 179 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 26 ASP Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 67 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 9.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 9.9990 chunk 597 optimal weight: 20.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN J 168 GLN ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 HIS Q 84 ASN ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 168 GLN X 172 ASN Y 27 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 62 GLN Z 175 ASN ** b 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.094511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.081337 restraints weight = 132502.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.083950 restraints weight = 68772.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085711 restraints weight = 42745.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.086920 restraints weight = 29909.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.087748 restraints weight = 22814.743| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 46228 Z= 0.209 Angle : 0.675 13.261 62767 Z= 0.357 Chirality : 0.046 0.213 7355 Planarity : 0.005 0.056 7980 Dihedral : 6.872 70.241 7030 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.16 % Favored : 96.83 % Rotamer: Outliers : 4.92 % Allowed : 21.66 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.10), residues: 6142 helix: 0.89 (0.11), residues: 2262 sheet: -0.40 (0.13), residues: 1498 loop : -0.69 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 11 TYR 0.029 0.002 TYR C 97 PHE 0.024 0.002 PHE M 124 TRP 0.027 0.002 TRP N 107 HIS 0.008 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00460 (46228) covalent geometry : angle 0.67510 (62767) hydrogen bonds : bond 0.04634 ( 2528) hydrogen bonds : angle 5.89920 ( 7338) *********************** 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 1136 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 926 time to evaluate : 1.766 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: A 13 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 43 ARG cc_start: 0.7513 (ptt90) cc_final: 0.5949 (ptm160) REVERT: A 54 LYS cc_start: 0.6165 (mtpp) cc_final: 0.5867 (mtpp) REVERT: A 62 ASP cc_start: 0.8015 (t0) cc_final: 0.7279 (t0) REVERT: A 132 ARG cc_start: 0.8556 (ptt-90) cc_final: 0.8089 (ptt-90) REVERT: A 150 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7356 (mm110) REVERT: A 227 PHE cc_start: 0.7940 (t80) cc_final: 0.7734 (t80) REVERT: B 56 TYR cc_start: 0.6176 (OUTLIER) cc_final: 0.5121 (t80) REVERT: B 85 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8564 (tp) REVERT: B 219 ARG cc_start: 0.8726 (ptp90) cc_final: 0.8488 (ptp-110) REVERT: C 19 TYR cc_start: 0.6940 (m-80) cc_final: 0.6401 (m-80) REVERT: C 80 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8478 (p) REVERT: C 97 TYR cc_start: 0.8394 (t80) cc_final: 0.8180 (t80) REVERT: C 174 MET cc_start: 0.8044 (tpp) cc_final: 0.7514 (tpp) REVERT: C 187 LYS cc_start: 0.8995 (pptt) cc_final: 0.8614 (mmmm) REVERT: D 4 ASP cc_start: 0.6817 (t70) cc_final: 0.6478 (t0) REVERT: D 23 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 54 GLN cc_start: 0.8701 (mm110) cc_final: 0.7726 (pm20) REVERT: D 69 VAL cc_start: 0.9166 (t) cc_final: 0.8919 (p) REVERT: D 190 LEU cc_start: 0.7380 (tp) cc_final: 0.7072 (mt) REVERT: E 104 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8811 (t0) REVERT: E 114 GLN cc_start: 0.8831 (tp40) cc_final: 0.8515 (tp40) REVERT: F 69 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.8059 (p90) REVERT: F 90 GLN cc_start: 0.8340 (tp40) cc_final: 0.7351 (tp-100) REVERT: F 94 ASP cc_start: 0.8564 (m-30) cc_final: 0.7575 (m-30) REVERT: F 117 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8236 (tm-30) REVERT: F 179 PHE cc_start: 0.8355 (m-80) cc_final: 0.8114 (m-80) REVERT: F 180 MET cc_start: 0.7277 (ppp) cc_final: 0.7072 (pmm) REVERT: G 109 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8028 (tptm) REVERT: H 120 MET cc_start: 0.8254 (tmm) cc_final: 0.8011 (tmm) REVERT: H 181 GLU cc_start: 0.7905 (pm20) cc_final: 0.7601 (pm20) REVERT: I 40 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7799 (p0) REVERT: I 146 MET cc_start: 0.7850 (mtm) cc_final: 0.7458 (mtp) REVERT: I 163 ILE cc_start: 0.9103 (mm) cc_final: 0.8868 (mt) REVERT: J 138 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8407 (t) REVERT: J 164 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7592 (pt0) REVERT: K 4 LEU cc_start: 0.9150 (mt) cc_final: 0.8819 (mp) REVERT: K 47 VAL cc_start: 0.7553 (t) cc_final: 0.7266 (p) REVERT: K 62 LYS cc_start: 0.9215 (tptp) cc_final: 0.8606 (tptm) REVERT: K 102 LEU cc_start: 0.9282 (mp) cc_final: 0.9056 (mp) REVERT: K 104 LEU cc_start: 0.9228 (tp) cc_final: 0.8964 (tt) REVERT: K 150 THR cc_start: 0.8798 (p) cc_final: 0.8582 (t) REVERT: K 163 CYS cc_start: 0.8630 (m) cc_final: 0.8193 (m) REVERT: L 184 TRP cc_start: 0.7568 (p-90) cc_final: 0.6592 (p-90) REVERT: M 79 ASN cc_start: 0.9025 (t0) cc_final: 0.8771 (t0) REVERT: M 146 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: N 65 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8000 (tm-30) REVERT: O 13 ILE cc_start: 0.8989 (pt) cc_final: 0.8669 (mm) REVERT: O 43 ARG cc_start: 0.7381 (ptt90) cc_final: 0.6138 (ptm-80) REVERT: O 62 ASP cc_start: 0.8118 (t0) cc_final: 0.7655 (t0) REVERT: P 56 TYR cc_start: 0.6348 (OUTLIER) cc_final: 0.5461 (t80) REVERT: P 83 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7521 (ttm110) REVERT: P 102 GLU cc_start: 0.8795 (tp30) cc_final: 0.8361 (tt0) REVERT: Q 80 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8472 (p) REVERT: Q 90 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9411 (tp) REVERT: Q 136 TYR cc_start: 0.7778 (m-80) cc_final: 0.7495 (m-80) REVERT: Q 137 ILE cc_start: 0.9264 (pt) cc_final: 0.9040 (pp) REVERT: Q 209 GLU cc_start: 0.8074 (mp0) cc_final: 0.7689 (mp0) REVERT: R 23 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7548 (tm-30) REVERT: R 115 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7718 (mtpt) REVERT: S 114 GLN cc_start: 0.8792 (tp40) cc_final: 0.8537 (tp40) REVERT: S 156 MET cc_start: 0.7750 (mmm) cc_final: 0.7488 (mmm) REVERT: S 216 GLU cc_start: 0.7379 (tp30) cc_final: 0.6968 (tp30) REVERT: T 7 ASP cc_start: 0.8022 (p0) cc_final: 0.7717 (p0) REVERT: T 29 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8486 (t) REVERT: T 117 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8086 (tm-30) REVERT: V 95 MET cc_start: 0.6279 (mmt) cc_final: 0.5539 (mmt) REVERT: V 116 MET cc_start: 0.7456 (tpt) cc_final: 0.5867 (ttm) REVERT: V 120 MET cc_start: 0.8347 (tmm) cc_final: 0.8092 (tmm) REVERT: V 181 GLU cc_start: 0.7862 (pm20) cc_final: 0.7567 (pm20) REVERT: W 30 ASN cc_start: 0.6653 (t0) cc_final: 0.6068 (t0) REVERT: W 146 MET cc_start: 0.7881 (mtm) cc_final: 0.7450 (mtp) REVERT: W 163 ILE cc_start: 0.9028 (mm) cc_final: 0.8818 (mt) REVERT: X 73 TYR cc_start: 0.8661 (t80) cc_final: 0.8457 (t80) REVERT: X 175 ASP cc_start: 0.7524 (p0) cc_final: 0.7005 (m-30) REVERT: X 203 MET cc_start: 0.6833 (mmt) cc_final: 0.5996 (mmt) REVERT: Y 60 ILE cc_start: 0.9268 (mm) cc_final: 0.9053 (mm) REVERT: Y 62 LYS cc_start: 0.9124 (tptp) cc_final: 0.8605 (tptm) REVERT: Y 150 THR cc_start: 0.8716 (p) cc_final: 0.8513 (t) REVERT: Y 159 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8760 (tp) REVERT: Y 163 CYS cc_start: 0.8986 (m) cc_final: 0.8329 (m) REVERT: Y 165 GLU cc_start: 0.8224 (pp20) cc_final: 0.7643 (pp20) REVERT: Y 166 GLU cc_start: 0.8560 (tp30) cc_final: 0.7913 (mm-30) REVERT: Z 45 MET cc_start: 0.4820 (tpt) cc_final: 0.4594 (tpt) REVERT: Z 184 TRP cc_start: 0.7656 (p-90) cc_final: 0.6555 (p-90) REVERT: a 60 ASP cc_start: 0.9148 (m-30) cc_final: 0.8778 (m-30) REVERT: a 130 TYR cc_start: 0.8321 (t80) cc_final: 0.8094 (t80) outliers start: 210 outliers final: 142 residues processed: 1061 average time/residue: 0.2502 time to fit residues: 451.8793 Evaluate side-chains 1008 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 850 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 35 MET 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 12 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 179 PHE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain O residue 25 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 102 LYS Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 56 TYR Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 82 ILE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 238 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 23 GLU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 188 VAL Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 116 HIS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 89 MET Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 139 THR Chi-restraints excluded: chain Y residue 144 ASP Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 101 ILE Chi-restraints excluded: chain Z residue 179 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 26 ASP Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 173 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 52 optimal weight: 8.9990 chunk 79 optimal weight: 30.0000 chunk 593 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 343 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 404 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 401 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN F 20 HIS ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 GLN M 157 ASN N 89 HIS N 188 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN S 104 ASN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 172 ASN Y 27 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 146 GLN ** b 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 188 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.092250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.079339 restraints weight = 133236.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.081889 restraints weight = 68842.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083598 restraints weight = 42739.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.084775 restraints weight = 30022.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.085582 restraints weight = 22941.341| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 46228 Z= 0.224 Angle : 0.665 11.574 62767 Z= 0.350 Chirality : 0.045 0.295 7355 Planarity : 0.005 0.048 7980 Dihedral : 6.319 80.967 6915 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.35 % Allowed : 21.07 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.10), residues: 6142 helix: 0.92 (0.11), residues: 2280 sheet: -0.52 (0.13), residues: 1508 loop : -0.73 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 21 TYR 0.024 0.002 TYR D 228 PHE 0.019 0.002 PHE a 124 TRP 0.027 0.002 TRP N 107 HIS 0.011 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00492 (46228) covalent geometry : angle 0.66453 (62767) hydrogen bonds : bond 0.04109 ( 2528) hydrogen bonds : angle 5.55041 ( 7338) *********************** 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 1168 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 897 time to evaluate : 1.845 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: A 13 ILE cc_start: 0.9046 (pt) cc_final: 0.8729 (mm) REVERT: A 34 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8162 (mm110) REVERT: A 43 ARG cc_start: 0.7584 (ptt90) cc_final: 0.6057 (ptm160) REVERT: A 54 LYS cc_start: 0.6248 (mtpp) cc_final: 0.5938 (mtpp) REVERT: A 62 ASP cc_start: 0.8111 (t0) cc_final: 0.7382 (t0) REVERT: A 102 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8366 (tptp) REVERT: A 123 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8404 (tm-30) REVERT: A 132 ARG cc_start: 0.8336 (ptt-90) cc_final: 0.7951 (ptt-90) REVERT: A 150 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7309 (mm110) REVERT: B 56 TYR cc_start: 0.6107 (OUTLIER) cc_final: 0.5275 (t80) REVERT: B 176 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6912 (mtm-85) REVERT: B 219 ARG cc_start: 0.8735 (ptp90) cc_final: 0.8527 (ptp-110) REVERT: C 19 TYR cc_start: 0.6954 (m-80) cc_final: 0.6444 (m-80) REVERT: C 35 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8580 (pp) REVERT: C 97 TYR cc_start: 0.8329 (t80) cc_final: 0.8028 (t80) REVERT: C 174 MET cc_start: 0.7964 (tpp) cc_final: 0.7543 (tpp) REVERT: C 187 LYS cc_start: 0.8998 (pptt) cc_final: 0.8604 (mmmm) REVERT: D 4 ASP cc_start: 0.7203 (t70) cc_final: 0.6519 (t0) REVERT: D 7 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8880 (tp) REVERT: D 23 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7554 (tm-30) REVERT: D 54 GLN cc_start: 0.8796 (mm110) cc_final: 0.7924 (pm20) REVERT: D 69 VAL cc_start: 0.9044 (t) cc_final: 0.8790 (p) REVERT: E 114 GLN cc_start: 0.8781 (tp40) cc_final: 0.8515 (tp40) REVERT: E 156 MET cc_start: 0.7647 (mmm) cc_final: 0.7437 (mmm) REVERT: F 90 GLN cc_start: 0.8392 (tp40) cc_final: 0.7423 (tp-100) REVERT: F 94 ASP cc_start: 0.8546 (m-30) cc_final: 0.7498 (m-30) REVERT: F 117 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8208 (tm-30) REVERT: F 166 GLN cc_start: 0.8981 (mp10) cc_final: 0.8609 (tp-100) REVERT: F 180 MET cc_start: 0.7262 (ppp) cc_final: 0.7058 (pmm) REVERT: H 116 MET cc_start: 0.8200 (mmm) cc_final: 0.7629 (tpt) REVERT: H 120 MET cc_start: 0.8397 (tmm) cc_final: 0.7908 (tmm) REVERT: H 181 GLU cc_start: 0.7884 (pm20) cc_final: 0.7644 (pm20) REVERT: I 30 ASN cc_start: 0.6797 (t0) cc_final: 0.6177 (t0) REVERT: I 40 ASN cc_start: 0.8296 (p0) cc_final: 0.8019 (p0) REVERT: I 146 MET cc_start: 0.7910 (mtm) cc_final: 0.7529 (mtp) REVERT: J 112 ASP cc_start: 0.6565 (t0) cc_final: 0.6179 (t0) REVERT: J 115 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.8005 (p) REVERT: J 138 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8746 (t) REVERT: K 62 LYS cc_start: 0.9192 (tptp) cc_final: 0.8550 (tptm) REVERT: K 132 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8456 (m-70) REVERT: K 160 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9225 (tt) REVERT: K 163 CYS cc_start: 0.8973 (m) cc_final: 0.8342 (m) REVERT: L 45 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.5587 (tpt) REVERT: L 184 TRP cc_start: 0.7749 (p-90) cc_final: 0.6697 (p-90) REVERT: M 146 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: N 65 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8187 (tm-30) REVERT: N 70 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8130 (ptp) REVERT: O 43 ARG cc_start: 0.7500 (ptt90) cc_final: 0.5943 (ptm160) REVERT: O 62 ASP cc_start: 0.8182 (t0) cc_final: 0.7608 (t0) REVERT: O 102 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8491 (tptp) REVERT: O 110 PRO cc_start: 0.8214 (Cg_exo) cc_final: 0.7656 (Cg_endo) REVERT: O 113 MET cc_start: 0.8083 (pmm) cc_final: 0.7818 (pmm) REVERT: O 123 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8397 (tm-30) REVERT: O 132 ARG cc_start: 0.8410 (ptt-90) cc_final: 0.7908 (ptt-90) REVERT: O 150 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7059 (mm110) REVERT: P 37 ILE cc_start: 0.9463 (mt) cc_final: 0.9148 (mm) REVERT: P 56 TYR cc_start: 0.6336 (OUTLIER) cc_final: 0.5360 (t80) REVERT: P 83 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7522 (ttm110) REVERT: P 224 GLU cc_start: 0.8230 (tp30) cc_final: 0.7861 (tp30) REVERT: Q 25 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7187 (ptp) REVERT: Q 209 GLU cc_start: 0.8065 (mp0) cc_final: 0.7691 (mp0) REVERT: Q 216 LEU cc_start: 0.8779 (tp) cc_final: 0.8385 (tp) REVERT: R 23 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7515 (tm-30) REVERT: S 114 GLN cc_start: 0.8830 (tp40) cc_final: 0.8529 (tp40) REVERT: S 156 MET cc_start: 0.7874 (mmm) cc_final: 0.7627 (mmm) REVERT: S 216 GLU cc_start: 0.7526 (tp30) cc_final: 0.7032 (tp30) REVERT: T 117 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8049 (tm-30) REVERT: U 24 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: V 25 TYR cc_start: 0.9023 (t80) cc_final: 0.8791 (t80) REVERT: V 116 MET cc_start: 0.7821 (tpt) cc_final: 0.6538 (ttm) REVERT: V 125 PHE cc_start: 0.8296 (p90) cc_final: 0.8006 (p90) REVERT: V 181 GLU cc_start: 0.7818 (pm20) cc_final: 0.7610 (pm20) REVERT: W 30 ASN cc_start: 0.6787 (t0) cc_final: 0.6119 (t0) REVERT: W 135 MET cc_start: 0.8734 (tpp) cc_final: 0.8527 (tpp) REVERT: W 146 MET cc_start: 0.7931 (mtm) cc_final: 0.7557 (mtp) REVERT: X 39 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: X 138 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8735 (t) REVERT: X 175 ASP cc_start: 0.7551 (p0) cc_final: 0.7124 (m-30) REVERT: Y 62 LYS cc_start: 0.9123 (tptp) cc_final: 0.8610 (tptm) REVERT: Y 132 HIS cc_start: 0.8994 (OUTLIER) cc_final: 0.8328 (m-70) REVERT: Y 159 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8769 (tp) REVERT: Y 163 CYS cc_start: 0.9099 (m) cc_final: 0.8515 (m) REVERT: Y 166 GLU cc_start: 0.8659 (tp30) cc_final: 0.8435 (tp30) REVERT: Z 134 TYR cc_start: 0.8446 (m-80) cc_final: 0.8183 (m-80) REVERT: Z 184 TRP cc_start: 0.7840 (p-90) cc_final: 0.6704 (p-90) REVERT: a 60 ASP cc_start: 0.9148 (m-30) cc_final: 0.8766 (m-30) REVERT: a 146 GLN cc_start: 0.8561 (tp40) cc_final: 0.8288 (tp40) REVERT: b 65 GLN cc_start: 0.7662 (tt0) cc_final: 0.7352 (tm-30) REVERT: b 70 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8229 (ptp) REVERT: b 108 ASN cc_start: 0.8337 (t0) cc_final: 0.8069 (t0) REVERT: b 164 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7680 (mp0) outliers start: 271 outliers final: 181 residues processed: 1078 average time/residue: 0.2550 time to fit residues: 466.0608 Evaluate side-chains 1022 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 819 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 132 HIS Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 179 PHE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 70 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 102 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 56 TYR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 120 TYR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 176 ARG Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 59 MET Chi-restraints excluded: chain S residue 82 ILE Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 238 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 69 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 13 MET Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 GLN Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 89 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 138 SER Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 139 THR Chi-restraints excluded: chain Y residue 144 ASP Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 188 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 101 ILE Chi-restraints excluded: chain Z residue 179 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 26 ASP Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 173 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 518 optimal weight: 7.9990 chunk 439 optimal weight: 6.9990 chunk 359 optimal weight: 9.9990 chunk 415 optimal weight: 6.9990 chunk 388 optimal weight: 8.9990 chunk 341 optimal weight: 8.9990 chunk 227 optimal weight: 20.0000 chunk 582 optimal weight: 5.9990 chunk 521 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 68 HIS A 92 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 104 ASN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 ASN M 108 ASN M 157 ASN N 188 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 88 ASN ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 198 ASN ** Q 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 120 HIS ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 172 ASN Y 27 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 HIS b 188 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.091703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.078804 restraints weight = 133726.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.081331 restraints weight = 69889.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.083048 restraints weight = 43676.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.084217 restraints weight = 30705.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.085027 restraints weight = 23524.220| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 46228 Z= 0.194 Angle : 0.641 11.881 62767 Z= 0.336 Chirality : 0.045 0.329 7355 Planarity : 0.004 0.051 7980 Dihedral : 6.133 89.311 6903 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 6.60 % Allowed : 21.61 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.11), residues: 6142 helix: 1.03 (0.11), residues: 2276 sheet: -0.48 (0.13), residues: 1496 loop : -0.74 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 151 TYR 0.025 0.002 TYR O 23 PHE 0.024 0.002 PHE Z 54 TRP 0.022 0.002 TRP N 107 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00431 (46228) covalent geometry : angle 0.64083 (62767) hydrogen bonds : bond 0.03726 ( 2528) hydrogen bonds : angle 5.34594 ( 7338) *********************** 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 1185 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 282 poor density : 903 time to evaluate : 1.596 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: A 11 ARG cc_start: 0.7152 (mpt-90) cc_final: 0.6951 (mpt-90) REVERT: A 13 ILE cc_start: 0.8983 (pt) cc_final: 0.8724 (mm) REVERT: A 34 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8099 (mm110) REVERT: A 43 ARG cc_start: 0.7514 (ptt90) cc_final: 0.5871 (ptm160) REVERT: A 54 LYS cc_start: 0.6244 (mtpp) cc_final: 0.5942 (mtpp) REVERT: A 62 ASP cc_start: 0.8135 (t0) cc_final: 0.7572 (t70) REVERT: A 102 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8632 (tptp) REVERT: A 123 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8440 (tm-30) REVERT: A 150 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7241 (mm110) REVERT: B 56 TYR cc_start: 0.6039 (OUTLIER) cc_final: 0.5287 (t80) REVERT: B 219 ARG cc_start: 0.8700 (ptp90) cc_final: 0.8283 (ptp-110) REVERT: B 224 GLU cc_start: 0.8174 (tp30) cc_final: 0.7879 (tp30) REVERT: C 19 TYR cc_start: 0.6812 (m-80) cc_final: 0.6224 (m-80) REVERT: C 35 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8574 (pp) REVERT: C 97 TYR cc_start: 0.8704 (t80) cc_final: 0.8269 (t80) REVERT: C 174 MET cc_start: 0.7901 (tpp) cc_final: 0.7507 (tpp) REVERT: C 187 LYS cc_start: 0.8983 (pptt) cc_final: 0.8620 (mmmm) REVERT: D 4 ASP cc_start: 0.7279 (t0) cc_final: 0.6514 (t0) REVERT: D 23 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7454 (tm-30) REVERT: D 54 GLN cc_start: 0.8810 (mm110) cc_final: 0.7963 (pm20) REVERT: D 69 VAL cc_start: 0.9067 (t) cc_final: 0.8600 (p) REVERT: D 71 MET cc_start: 0.6903 (ppp) cc_final: 0.6275 (ppp) REVERT: E 114 GLN cc_start: 0.8782 (tp40) cc_final: 0.8557 (tp40) REVERT: E 156 MET cc_start: 0.8154 (mmm) cc_final: 0.7737 (mmm) REVERT: F 90 GLN cc_start: 0.8408 (tp40) cc_final: 0.7364 (tp-100) REVERT: F 94 ASP cc_start: 0.8508 (m-30) cc_final: 0.7434 (m-30) REVERT: F 117 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8170 (tm-30) REVERT: G 75 MET cc_start: 0.8138 (tpp) cc_final: 0.7759 (tpp) REVERT: G 109 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8145 (tptm) REVERT: H 53 GLN cc_start: 0.8062 (mt0) cc_final: 0.7516 (mt0) REVERT: H 86 MET cc_start: 0.7777 (ptm) cc_final: 0.7453 (ptm) REVERT: H 116 MET cc_start: 0.8131 (mmm) cc_final: 0.7516 (tpt) REVERT: H 181 GLU cc_start: 0.7718 (pm20) cc_final: 0.7434 (pm20) REVERT: I 30 ASN cc_start: 0.6858 (t0) cc_final: 0.6221 (t0) REVERT: I 146 MET cc_start: 0.7913 (mtm) cc_final: 0.7570 (mtp) REVERT: J 102 TYR cc_start: 0.8423 (m-10) cc_final: 0.8195 (m-80) REVERT: J 138 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8727 (t) REVERT: J 175 ASP cc_start: 0.7981 (p0) cc_final: 0.7491 (m-30) REVERT: K 62 LYS cc_start: 0.9233 (tptp) cc_final: 0.8591 (tptm) REVERT: K 132 HIS cc_start: 0.8917 (OUTLIER) cc_final: 0.8478 (m-70) REVERT: K 160 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9243 (tt) REVERT: K 163 CYS cc_start: 0.8934 (m) cc_final: 0.8287 (m) REVERT: L 45 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.5441 (tpt) REVERT: L 184 TRP cc_start: 0.7792 (p-90) cc_final: 0.6777 (p-90) REVERT: N 65 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8017 (tm-30) REVERT: N 70 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7940 (ptp) REVERT: O 13 ILE cc_start: 0.9026 (pt) cc_final: 0.8756 (mm) REVERT: O 34 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7140 (mm110) REVERT: O 43 ARG cc_start: 0.7623 (ptt90) cc_final: 0.6050 (ptm160) REVERT: O 62 ASP cc_start: 0.8120 (t0) cc_final: 0.7442 (t0) REVERT: O 102 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8589 (tptp) REVERT: O 110 PRO cc_start: 0.8176 (Cg_exo) cc_final: 0.7571 (Cg_endo) REVERT: O 123 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8420 (tm-30) REVERT: P 37 ILE cc_start: 0.9431 (mt) cc_final: 0.9122 (mm) REVERT: P 78 MET cc_start: 0.7761 (mmm) cc_final: 0.7534 (mmm) REVERT: P 83 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7442 (ttm110) REVERT: Q 25 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7367 (ptp) REVERT: Q 209 GLU cc_start: 0.7678 (mp0) cc_final: 0.7418 (mp0) REVERT: R 23 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7452 (tm-30) REVERT: S 114 GLN cc_start: 0.8869 (tp40) cc_final: 0.8571 (tp40) REVERT: S 156 MET cc_start: 0.8042 (mmm) cc_final: 0.7732 (tpp) REVERT: S 216 GLU cc_start: 0.7597 (tp30) cc_final: 0.7080 (tp30) REVERT: T 74 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8192 (pt) REVERT: T 117 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8077 (tm-30) REVERT: U 24 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: U 75 MET cc_start: 0.8140 (tpp) cc_final: 0.7761 (tpp) REVERT: V 17 ASP cc_start: 0.7494 (m-30) cc_final: 0.7293 (m-30) REVERT: V 86 MET cc_start: 0.7740 (ptm) cc_final: 0.7447 (ptm) REVERT: V 116 MET cc_start: 0.7649 (tpt) cc_final: 0.6581 (mtt) REVERT: V 125 PHE cc_start: 0.8151 (p90) cc_final: 0.7921 (p90) REVERT: V 152 CYS cc_start: 0.8778 (m) cc_final: 0.8110 (p) REVERT: V 181 GLU cc_start: 0.7726 (pm20) cc_final: 0.7452 (pm20) REVERT: W 30 ASN cc_start: 0.6787 (t0) cc_final: 0.6189 (t0) REVERT: W 146 MET cc_start: 0.7923 (mtm) cc_final: 0.7605 (mtp) REVERT: W 163 ILE cc_start: 0.9244 (mt) cc_final: 0.8986 (tt) REVERT: X 39 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: X 138 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8823 (t) REVERT: X 175 ASP cc_start: 0.7500 (p0) cc_final: 0.7107 (m-30) REVERT: X 203 MET cc_start: 0.7051 (mmt) cc_final: 0.6586 (mmt) REVERT: Y 62 LYS cc_start: 0.9182 (tptp) cc_final: 0.8605 (tptm) REVERT: Y 132 HIS cc_start: 0.8983 (OUTLIER) cc_final: 0.8385 (m-70) REVERT: Y 159 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8857 (tp) REVERT: Y 163 CYS cc_start: 0.9103 (m) cc_final: 0.8610 (m) REVERT: Y 166 GLU cc_start: 0.8641 (tp30) cc_final: 0.8420 (tp30) REVERT: Z 86 MET cc_start: 0.8639 (ppp) cc_final: 0.8051 (ppp) REVERT: Z 134 TYR cc_start: 0.8417 (m-80) cc_final: 0.8127 (m-80) REVERT: Z 184 TRP cc_start: 0.7762 (p-90) cc_final: 0.6670 (p-90) REVERT: a 60 ASP cc_start: 0.9191 (m-30) cc_final: 0.8789 (m-30) REVERT: a 74 MET cc_start: 0.9065 (tpp) cc_final: 0.8709 (tpp) REVERT: a 100 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.6346 (ptp90) REVERT: b 12 LEU cc_start: 0.9224 (mt) cc_final: 0.9013 (mm) REVERT: b 65 GLN cc_start: 0.7660 (tt0) cc_final: 0.7365 (tm-30) REVERT: b 70 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8286 (ptp) REVERT: b 164 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7717 (mp0) REVERT: b 172 CYS cc_start: 0.8973 (m) cc_final: 0.8476 (p) outliers start: 282 outliers final: 205 residues processed: 1092 average time/residue: 0.2432 time to fit residues: 452.0849 Evaluate side-chains 1042 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 817 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 221 ASN Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 132 HIS Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 179 PHE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 70 MET Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 188 GLN Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 102 LYS Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 56 TYR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 120 TYR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 82 ILE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 238 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 23 GLU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 68 ASN Chi-restraints excluded: chain T residue 69 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 222 THR Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 221 ASN Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 100 LEU Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 13 MET Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 GLN Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 138 SER Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 139 THR Chi-restraints excluded: chain Y residue 144 ASP Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Y residue 188 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 101 ILE Chi-restraints excluded: chain Z residue 179 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 26 ASP Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 173 MET Chi-restraints excluded: chain b residue 188 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 549 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 427 optimal weight: 20.0000 chunk 323 optimal weight: 40.0000 chunk 368 optimal weight: 10.0000 chunk 526 optimal weight: 5.9990 chunk 551 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 547 optimal weight: 6.9990 chunk 533 optimal weight: 5.9990 chunk 432 optimal weight: 9.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 68 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN S 104 ASN S 204 GLN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 166 GLN U 170 GLN V 106 GLN ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 172 ASN Y 27 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 175 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.090302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.077639 restraints weight = 133437.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.080134 restraints weight = 69801.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.081817 restraints weight = 43470.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.082966 restraints weight = 30505.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.083730 restraints weight = 23315.391| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 46228 Z= 0.235 Angle : 0.672 11.195 62767 Z= 0.352 Chirality : 0.046 0.304 7355 Planarity : 0.004 0.050 7980 Dihedral : 6.114 85.999 6892 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 6.84 % Allowed : 22.83 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.11), residues: 6142 helix: 0.96 (0.11), residues: 2276 sheet: -0.50 (0.13), residues: 1492 loop : -0.79 (0.13), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 70 TYR 0.023 0.002 TYR V 25 PHE 0.019 0.002 PHE Z 54 TRP 0.020 0.002 TRP N 107 HIS 0.009 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00517 (46228) covalent geometry : angle 0.67193 (62767) hydrogen bonds : bond 0.03808 ( 2528) hydrogen bonds : angle 5.34775 ( 7338) *********************** 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 1158 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 292 poor density : 866 time to evaluate : 1.777 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: A 13 ILE cc_start: 0.8989 (pt) cc_final: 0.8726 (mm) REVERT: A 43 ARG cc_start: 0.7604 (ptt90) cc_final: 0.5883 (ptm160) REVERT: A 54 LYS cc_start: 0.6224 (mtpp) cc_final: 0.5924 (mtpp) REVERT: A 62 ASP cc_start: 0.8167 (t0) cc_final: 0.7643 (t70) REVERT: A 110 PRO cc_start: 0.8434 (Cg_exo) cc_final: 0.8163 (Cg_endo) REVERT: A 112 ASP cc_start: 0.8742 (p0) cc_final: 0.8474 (p0) REVERT: A 150 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7009 (mm110) REVERT: A 216 GLU cc_start: 0.6210 (pp20) cc_final: 0.6008 (pp20) REVERT: B 37 ILE cc_start: 0.9456 (mt) cc_final: 0.9232 (mm) REVERT: B 56 TYR cc_start: 0.6001 (OUTLIER) cc_final: 0.5200 (t80) REVERT: B 219 ARG cc_start: 0.8724 (ptp90) cc_final: 0.8282 (ptp-110) REVERT: B 224 GLU cc_start: 0.8267 (tp30) cc_final: 0.7929 (tp30) REVERT: C 174 MET cc_start: 0.7646 (tpp) cc_final: 0.7359 (tpp) REVERT: C 187 LYS cc_start: 0.9027 (pptt) cc_final: 0.8729 (mmmm) REVERT: D 4 ASP cc_start: 0.7287 (t0) cc_final: 0.6506 (t0) REVERT: D 7 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8858 (tp) REVERT: D 23 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7421 (tm-30) REVERT: D 69 VAL cc_start: 0.8868 (t) cc_final: 0.8642 (p) REVERT: D 71 MET cc_start: 0.6911 (ppp) cc_final: 0.6340 (ppp) REVERT: E 114 GLN cc_start: 0.8809 (tp40) cc_final: 0.8557 (tp40) REVERT: E 156 MET cc_start: 0.8191 (mmm) cc_final: 0.7745 (mmm) REVERT: F 90 GLN cc_start: 0.8620 (tp40) cc_final: 0.7561 (tp-100) REVERT: F 94 ASP cc_start: 0.8493 (m-30) cc_final: 0.7486 (m-30) REVERT: F 117 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8208 (tm-30) REVERT: G 21 PHE cc_start: 0.7992 (m-80) cc_final: 0.7631 (m-80) REVERT: G 109 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8163 (tptm) REVERT: H 86 MET cc_start: 0.7728 (ptm) cc_final: 0.7458 (ptm) REVERT: H 120 MET cc_start: 0.8419 (tmm) cc_final: 0.7857 (tmm) REVERT: H 152 CYS cc_start: 0.8666 (m) cc_final: 0.8120 (p) REVERT: H 181 GLU cc_start: 0.7790 (pm20) cc_final: 0.7478 (pm20) REVERT: I 30 ASN cc_start: 0.6986 (t0) cc_final: 0.6376 (t0) REVERT: I 114 TYR cc_start: 0.6866 (m-80) cc_final: 0.6612 (m-80) REVERT: I 143 ARG cc_start: 0.8250 (mpp80) cc_final: 0.7921 (mtm110) REVERT: I 146 MET cc_start: 0.7942 (mtm) cc_final: 0.7665 (mtp) REVERT: J 172 ASN cc_start: 0.9143 (m-40) cc_final: 0.8812 (m-40) REVERT: K 62 LYS cc_start: 0.9190 (tptp) cc_final: 0.8629 (tptm) REVERT: K 132 HIS cc_start: 0.8924 (OUTLIER) cc_final: 0.8539 (m-70) REVERT: K 160 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9179 (tt) REVERT: K 163 CYS cc_start: 0.8966 (m) cc_final: 0.8392 (m) REVERT: L 45 MET cc_start: 0.6037 (OUTLIER) cc_final: 0.5570 (tpt) REVERT: L 184 TRP cc_start: 0.7827 (p-90) cc_final: 0.6784 (p-90) REVERT: M 145 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9073 (tp) REVERT: N 50 MET cc_start: 0.8283 (ptm) cc_final: 0.8030 (ptm) REVERT: N 65 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7922 (tm-30) REVERT: N 70 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7808 (ptp) REVERT: N 200 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6909 (tt0) REVERT: O 13 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8726 (mm) REVERT: O 34 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7196 (mm110) REVERT: O 43 ARG cc_start: 0.7604 (ptt90) cc_final: 0.5862 (ptm160) REVERT: O 62 ASP cc_start: 0.7929 (t0) cc_final: 0.7299 (t0) REVERT: O 110 PRO cc_start: 0.8321 (Cg_exo) cc_final: 0.7765 (Cg_endo) REVERT: O 112 ASP cc_start: 0.8818 (p0) cc_final: 0.8455 (p0) REVERT: O 123 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8461 (tm-30) REVERT: O 132 ARG cc_start: 0.8480 (ptt-90) cc_final: 0.8144 (ptt-90) REVERT: P 37 ILE cc_start: 0.9431 (mt) cc_final: 0.9133 (mm) REVERT: P 78 MET cc_start: 0.7903 (mmm) cc_final: 0.7693 (mmm) REVERT: P 83 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7466 (ttm110) REVERT: P 224 GLU cc_start: 0.8162 (tp30) cc_final: 0.7887 (tp30) REVERT: Q 19 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6694 (m-10) REVERT: Q 35 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8582 (pp) REVERT: Q 209 GLU cc_start: 0.7635 (mp0) cc_final: 0.7397 (mp0) REVERT: R 23 GLN cc_start: 0.7723 (tm-30) cc_final: 0.7457 (tm-30) REVERT: S 114 GLN cc_start: 0.8895 (tp40) cc_final: 0.8599 (tp40) REVERT: S 156 MET cc_start: 0.8059 (mmm) cc_final: 0.7720 (tpp) REVERT: S 216 GLU cc_start: 0.7352 (tp30) cc_final: 0.6497 (tp30) REVERT: T 117 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8018 (tm-30) REVERT: U 14 PHE cc_start: 0.8766 (m-80) cc_final: 0.8554 (m-80) REVERT: V 86 MET cc_start: 0.7702 (ptm) cc_final: 0.7411 (ptm) REVERT: V 116 MET cc_start: 0.7617 (tpt) cc_final: 0.6772 (mtt) REVERT: V 152 CYS cc_start: 0.8509 (m) cc_final: 0.7881 (p) REVERT: V 181 GLU cc_start: 0.7785 (pm20) cc_final: 0.7503 (pm20) REVERT: W 30 ASN cc_start: 0.6896 (t0) cc_final: 0.6323 (t0) REVERT: W 110 LEU cc_start: 0.9521 (tp) cc_final: 0.9296 (tp) REVERT: W 143 ARG cc_start: 0.8286 (mpp80) cc_final: 0.8038 (mtm110) REVERT: W 146 MET cc_start: 0.7936 (mtm) cc_final: 0.7624 (mtp) REVERT: X 39 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: X 138 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8913 (t) REVERT: X 175 ASP cc_start: 0.7456 (p0) cc_final: 0.7035 (m-30) REVERT: Y 62 LYS cc_start: 0.9135 (tptp) cc_final: 0.8615 (tptm) REVERT: Y 132 HIS cc_start: 0.8987 (OUTLIER) cc_final: 0.8442 (m-70) REVERT: Y 159 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8868 (tp) REVERT: Y 163 CYS cc_start: 0.8913 (m) cc_final: 0.8400 (m) REVERT: Z 134 TYR cc_start: 0.8415 (m-80) cc_final: 0.8121 (m-80) REVERT: Z 184 TRP cc_start: 0.7842 (p-90) cc_final: 0.6742 (p-90) REVERT: a 46 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8808 (pp) REVERT: a 60 ASP cc_start: 0.9253 (m-30) cc_final: 0.8883 (m-30) REVERT: a 100 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6400 (ptp90) REVERT: a 130 TYR cc_start: 0.8528 (t80) cc_final: 0.8318 (t80) REVERT: a 145 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9024 (tp) REVERT: b 65 GLN cc_start: 0.7721 (tt0) cc_final: 0.7301 (tm-30) REVERT: b 70 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8331 (ptp) REVERT: b 108 ASN cc_start: 0.8424 (t0) cc_final: 0.7421 (t0) REVERT: b 164 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7710 (mp0) REVERT: b 172 CYS cc_start: 0.8941 (m) cc_final: 0.8556 (p) outliers start: 292 outliers final: 227 residues processed: 1062 average time/residue: 0.2446 time to fit residues: 442.8046 Evaluate side-chains 1051 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 803 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 221 ASN Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 132 HIS Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 144 ASP Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 182 ILE Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 179 PHE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 70 MET Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 102 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 228 ARG Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 56 TYR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 120 TYR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 176 ARG Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 19 TYR Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 82 ILE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 238 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 68 ASN Chi-restraints excluded: chain T residue 69 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 222 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 221 ASN Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 13 MET Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 GLN Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 138 SER Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 139 THR Chi-restraints excluded: chain Y residue 144 ASP Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Y residue 188 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 101 ILE Chi-restraints excluded: chain Z residue 179 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 26 ASP Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 22 ILE Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 173 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 167 optimal weight: 6.9990 chunk 509 optimal weight: 3.9990 chunk 528 optimal weight: 20.0000 chunk 372 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 590 optimal weight: 5.9990 chunk 526 optimal weight: 9.9990 chunk 547 optimal weight: 2.9990 chunk 537 optimal weight: 10.0000 chunk 461 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 68 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS O 193 GLN ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 92 GLN S 104 ASN S 204 GLN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 166 GLN ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 172 ASN Y 27 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 175 ASN a 79 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.078711 restraints weight = 133128.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.081273 restraints weight = 68621.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.083010 restraints weight = 42492.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.084182 restraints weight = 29636.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.085022 restraints weight = 22598.054| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 46228 Z= 0.150 Angle : 0.631 12.897 62767 Z= 0.327 Chirality : 0.045 0.370 7355 Planarity : 0.004 0.051 7980 Dihedral : 5.869 88.016 6891 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 6.18 % Allowed : 23.95 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.11), residues: 6142 helix: 1.13 (0.11), residues: 2276 sheet: -0.48 (0.13), residues: 1506 loop : -0.70 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 70 TYR 0.023 0.001 TYR J 95 PHE 0.033 0.001 PHE L 54 TRP 0.016 0.002 TRP N 107 HIS 0.004 0.001 HIS S 99 Details of bonding type rmsd covalent geometry : bond 0.00336 (46228) covalent geometry : angle 0.63139 (62767) hydrogen bonds : bond 0.03498 ( 2528) hydrogen bonds : angle 5.16970 ( 7338) *********************** 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 1160 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 896 time to evaluate : 1.770 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 13 ILE cc_start: 0.8961 (pt) cc_final: 0.8688 (mm) REVERT: A 43 ARG cc_start: 0.7578 (ptt90) cc_final: 0.5867 (ptm160) REVERT: A 54 LYS cc_start: 0.6216 (mtpp) cc_final: 0.5903 (mtpp) REVERT: A 62 ASP cc_start: 0.8191 (t0) cc_final: 0.7417 (t70) REVERT: A 110 PRO cc_start: 0.8312 (Cg_exo) cc_final: 0.8041 (Cg_endo) REVERT: A 112 ASP cc_start: 0.8682 (p0) cc_final: 0.7808 (t0) REVERT: A 150 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7041 (mm110) REVERT: B 37 ILE cc_start: 0.9430 (mt) cc_final: 0.9140 (mm) REVERT: B 56 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.5211 (t80) REVERT: B 219 ARG cc_start: 0.8700 (ptp90) cc_final: 0.8266 (ptp-110) REVERT: C 35 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8592 (pp) REVERT: C 38 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7326 (tt) REVERT: C 114 LEU cc_start: 0.9288 (tp) cc_final: 0.8950 (mp) REVERT: C 187 LYS cc_start: 0.8991 (pptt) cc_final: 0.8719 (mmmm) REVERT: D 4 ASP cc_start: 0.7254 (t0) cc_final: 0.6461 (t0) REVERT: D 69 VAL cc_start: 0.8889 (t) cc_final: 0.8624 (p) REVERT: D 71 MET cc_start: 0.7193 (ppp) cc_final: 0.6656 (ppp) REVERT: E 98 ASN cc_start: 0.8744 (m-40) cc_final: 0.8502 (m-40) REVERT: E 114 GLN cc_start: 0.8836 (tp40) cc_final: 0.8477 (tp40) REVERT: E 156 MET cc_start: 0.8107 (mmm) cc_final: 0.7632 (mmm) REVERT: F 90 GLN cc_start: 0.8548 (tp40) cc_final: 0.7568 (tp-100) REVERT: F 94 ASP cc_start: 0.8294 (m-30) cc_final: 0.7355 (m-30) REVERT: F 117 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8186 (tm-30) REVERT: G 21 PHE cc_start: 0.7810 (m-80) cc_final: 0.7474 (m-80) REVERT: G 75 MET cc_start: 0.8112 (tpp) cc_final: 0.7704 (tpp) REVERT: G 109 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8145 (tptm) REVERT: H 25 TYR cc_start: 0.8506 (t80) cc_final: 0.8266 (t80) REVERT: H 120 MET cc_start: 0.8522 (tmm) cc_final: 0.8274 (tmm) REVERT: H 144 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7087 (mpp80) REVERT: H 152 CYS cc_start: 0.8692 (m) cc_final: 0.8055 (p) REVERT: H 181 GLU cc_start: 0.7845 (pm20) cc_final: 0.7528 (pm20) REVERT: I 30 ASN cc_start: 0.7064 (t0) cc_final: 0.6435 (t0) REVERT: I 143 ARG cc_start: 0.8242 (mpp80) cc_final: 0.7936 (mtm110) REVERT: J 98 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7214 (ttt90) REVERT: J 148 MET cc_start: 0.8919 (mmm) cc_final: 0.8707 (mmm) REVERT: J 172 ASN cc_start: 0.9125 (m-40) cc_final: 0.8895 (m-40) REVERT: J 175 ASP cc_start: 0.8002 (p0) cc_final: 0.7609 (m-30) REVERT: K 62 LYS cc_start: 0.9176 (tptp) cc_final: 0.8597 (tptm) REVERT: K 107 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7582 (t80) REVERT: K 132 HIS cc_start: 0.8909 (OUTLIER) cc_final: 0.8512 (m-70) REVERT: K 160 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9095 (tt) REVERT: K 163 CYS cc_start: 0.8978 (m) cc_final: 0.8294 (m) REVERT: L 45 MET cc_start: 0.5825 (OUTLIER) cc_final: 0.5410 (tpt) REVERT: L 184 TRP cc_start: 0.7801 (p-90) cc_final: 0.6749 (p-90) REVERT: M 46 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8816 (pp) REVERT: M 172 MET cc_start: 0.8169 (mtp) cc_final: 0.7940 (mtp) REVERT: N 50 MET cc_start: 0.8255 (ptm) cc_final: 0.8030 (ptm) REVERT: N 65 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7886 (tm-30) REVERT: N 119 GLU cc_start: 0.8770 (pt0) cc_final: 0.8545 (pm20) REVERT: N 168 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8633 (tt) REVERT: O 13 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8721 (mm) REVERT: O 34 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7198 (mm110) REVERT: O 43 ARG cc_start: 0.7573 (ptt90) cc_final: 0.5821 (ptm160) REVERT: O 62 ASP cc_start: 0.8128 (t0) cc_final: 0.7492 (t0) REVERT: O 102 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8344 (tptp) REVERT: O 110 PRO cc_start: 0.8229 (Cg_exo) cc_final: 0.7802 (Cg_endo) REVERT: O 112 ASP cc_start: 0.8755 (p0) cc_final: 0.8266 (p0) REVERT: O 113 MET cc_start: 0.8235 (pmm) cc_final: 0.7905 (pmm) REVERT: O 123 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8588 (tm-30) REVERT: O 132 ARG cc_start: 0.8424 (ptt-90) cc_final: 0.8055 (ptt-90) REVERT: P 37 ILE cc_start: 0.9424 (mt) cc_final: 0.9129 (mm) REVERT: P 78 MET cc_start: 0.7823 (mmm) cc_final: 0.7578 (mmm) REVERT: P 83 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8283 (tpp-160) REVERT: P 102 GLU cc_start: 0.8941 (tp30) cc_final: 0.8253 (tt0) REVERT: Q 35 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8523 (pp) REVERT: Q 38 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7632 (tt) REVERT: Q 114 LEU cc_start: 0.9315 (tp) cc_final: 0.8930 (mp) REVERT: Q 147 LEU cc_start: 0.8734 (mt) cc_final: 0.8317 (mt) REVERT: Q 209 GLU cc_start: 0.7585 (mp0) cc_final: 0.7337 (mp0) REVERT: R 23 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7459 (tm-30) REVERT: R 71 MET cc_start: 0.6905 (ppp) cc_final: 0.6363 (ppp) REVERT: R 89 VAL cc_start: 0.9281 (t) cc_final: 0.9046 (t) REVERT: S 156 MET cc_start: 0.7980 (mmm) cc_final: 0.7625 (tpp) REVERT: S 216 GLU cc_start: 0.7298 (tp30) cc_final: 0.6482 (tp30) REVERT: T 117 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8005 (tm-30) REVERT: T 179 PHE cc_start: 0.8203 (m-10) cc_final: 0.7892 (m-10) REVERT: T 180 MET cc_start: 0.6939 (ppp) cc_final: 0.6689 (pmm) REVERT: U 14 PHE cc_start: 0.8787 (m-80) cc_final: 0.8564 (m-80) REVERT: U 24 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: U 75 MET cc_start: 0.8107 (tpp) cc_final: 0.7697 (tpp) REVERT: U 85 ARG cc_start: 0.9016 (mtm-85) cc_final: 0.8774 (mtt90) REVERT: V 86 MET cc_start: 0.7765 (ptm) cc_final: 0.7545 (ptm) REVERT: V 89 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7698 (ttp80) REVERT: V 116 MET cc_start: 0.7455 (tpt) cc_final: 0.6566 (mtt) REVERT: V 120 MET cc_start: 0.8305 (tmm) cc_final: 0.7852 (tmm) REVERT: V 152 CYS cc_start: 0.8636 (m) cc_final: 0.8019 (p) REVERT: V 181 GLU cc_start: 0.7850 (pm20) cc_final: 0.7558 (pm20) REVERT: W 30 ASN cc_start: 0.7010 (t0) cc_final: 0.6380 (t0) REVERT: W 146 MET cc_start: 0.7990 (mtm) cc_final: 0.7775 (mtp) REVERT: X 39 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: X 138 SER cc_start: 0.9014 (OUTLIER) cc_final: 0.8789 (t) REVERT: X 175 ASP cc_start: 0.7416 (p0) cc_final: 0.6939 (m-30) REVERT: Y 62 LYS cc_start: 0.9116 (tptp) cc_final: 0.8576 (tptm) REVERT: Y 132 HIS cc_start: 0.8966 (OUTLIER) cc_final: 0.8325 (m-70) REVERT: Y 159 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8880 (tp) REVERT: Y 163 CYS cc_start: 0.9117 (m) cc_final: 0.8647 (m) REVERT: Z 127 SER cc_start: 0.9020 (t) cc_final: 0.8704 (p) REVERT: Z 134 TYR cc_start: 0.8366 (m-80) cc_final: 0.8088 (m-80) REVERT: Z 184 TRP cc_start: 0.7774 (p-90) cc_final: 0.6686 (p-90) REVERT: a 46 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8543 (pp) REVERT: a 60 ASP cc_start: 0.9225 (m-30) cc_final: 0.8829 (m-30) REVERT: a 100 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6283 (ptp90) REVERT: a 130 TYR cc_start: 0.8423 (t80) cc_final: 0.8135 (t80) REVERT: a 145 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8999 (tp) REVERT: b 43 MET cc_start: 0.9056 (tpp) cc_final: 0.8836 (tpt) REVERT: b 65 GLN cc_start: 0.7767 (tt0) cc_final: 0.7325 (tm-30) REVERT: b 69 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8554 (tp40) REVERT: b 108 ASN cc_start: 0.7557 (t0) cc_final: 0.7282 (t0) REVERT: b 164 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7756 (mp0) REVERT: b 172 CYS cc_start: 0.8926 (m) cc_final: 0.8537 (p) outliers start: 264 outliers final: 186 residues processed: 1083 average time/residue: 0.2662 time to fit residues: 486.3202 Evaluate side-chains 1037 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 826 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 144 ARG Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 98 ARG Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 107 TYR Chi-restraints excluded: chain K residue 132 HIS Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 144 ASP Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 182 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 179 PHE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 102 LYS Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 228 ARG Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 56 TYR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 120 TYR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 176 ARG Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain S residue 82 ILE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 23 GLU Chi-restraints excluded: chain T residue 69 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 222 THR Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 100 LEU Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 13 MET Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 GLN Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 138 SER Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 66 LEU Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 139 THR Chi-restraints excluded: chain Y residue 144 ASP Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 101 ILE Chi-restraints excluded: chain Z residue 179 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 173 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 485 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 chunk 561 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 438 optimal weight: 30.0000 chunk 310 optimal weight: 30.0000 chunk 158 optimal weight: 6.9990 chunk 351 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 68 HIS A 238 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 ASN M 108 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN R 92 GLN S 104 ASN S 204 GLN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 77 HIS ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 157 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.090085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.077586 restraints weight = 134623.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.080061 restraints weight = 69831.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.081712 restraints weight = 43477.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.082845 restraints weight = 30579.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.083632 restraints weight = 23414.455| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 46228 Z= 0.196 Angle : 0.659 12.004 62767 Z= 0.342 Chirality : 0.045 0.263 7355 Planarity : 0.004 0.052 7980 Dihedral : 5.861 87.797 6883 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 6.56 % Allowed : 24.21 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.11), residues: 6142 helix: 1.07 (0.11), residues: 2286 sheet: -0.46 (0.13), residues: 1494 loop : -0.76 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 70 TYR 0.022 0.002 TYR W 8 PHE 0.023 0.002 PHE I 36 TRP 0.020 0.002 TRP N 107 HIS 0.005 0.001 HIS S 99 Details of bonding type rmsd covalent geometry : bond 0.00434 (46228) covalent geometry : angle 0.65865 (62767) hydrogen bonds : bond 0.03535 ( 2528) hydrogen bonds : angle 5.15793 ( 7338) *********************** 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 1148 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 868 time to evaluate : 1.186 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 43 ARG cc_start: 0.7595 (ptt90) cc_final: 0.5858 (ptm160) REVERT: A 54 LYS cc_start: 0.5983 (mtpp) cc_final: 0.5697 (mtpp) REVERT: A 62 ASP cc_start: 0.8083 (t0) cc_final: 0.7706 (t0) REVERT: A 80 MET cc_start: 0.7930 (mmm) cc_final: 0.7643 (mmm) REVERT: A 112 ASP cc_start: 0.8465 (p0) cc_final: 0.7895 (t0) REVERT: A 123 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8538 (tm-30) REVERT: A 150 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7003 (mm110) REVERT: B 37 ILE cc_start: 0.9411 (mt) cc_final: 0.9206 (mm) REVERT: B 56 TYR cc_start: 0.5979 (OUTLIER) cc_final: 0.5143 (t80) REVERT: B 219 ARG cc_start: 0.8673 (ptp90) cc_final: 0.8261 (ptp-110) REVERT: B 224 GLU cc_start: 0.8266 (tp30) cc_final: 0.7971 (tp30) REVERT: C 35 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8623 (pp) REVERT: C 38 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7380 (tt) REVERT: C 187 LYS cc_start: 0.9024 (pptt) cc_final: 0.8756 (mmmm) REVERT: D 4 ASP cc_start: 0.7289 (t0) cc_final: 0.6534 (t0) REVERT: D 54 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: D 71 MET cc_start: 0.7244 (ppp) cc_final: 0.6735 (ppp) REVERT: E 156 MET cc_start: 0.8254 (mmm) cc_final: 0.7760 (mmm) REVERT: F 90 GLN cc_start: 0.8639 (tp40) cc_final: 0.7567 (tp-100) REVERT: F 94 ASP cc_start: 0.8271 (m-30) cc_final: 0.7499 (m-30) REVERT: F 115 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8930 (tttm) REVERT: F 117 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8179 (tm-30) REVERT: G 21 PHE cc_start: 0.7842 (m-80) cc_final: 0.7499 (m-80) REVERT: G 75 MET cc_start: 0.8157 (tpp) cc_final: 0.7767 (tpp) REVERT: G 109 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8131 (tptm) REVERT: H 25 TYR cc_start: 0.8595 (t80) cc_final: 0.8353 (t80) REVERT: H 86 MET cc_start: 0.8022 (ptm) cc_final: 0.7788 (ptm) REVERT: H 144 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6982 (mpp80) REVERT: H 152 CYS cc_start: 0.8762 (m) cc_final: 0.8085 (p) REVERT: H 181 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: H 196 LYS cc_start: 0.6833 (mptt) cc_final: 0.6238 (mmtm) REVERT: I 30 ASN cc_start: 0.7085 (t0) cc_final: 0.6450 (t0) REVERT: I 80 ASN cc_start: 0.9449 (p0) cc_final: 0.9207 (p0) REVERT: J 148 MET cc_start: 0.8787 (mmm) cc_final: 0.8528 (mmm) REVERT: J 161 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7682 (t-90) REVERT: J 164 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7720 (mm-30) REVERT: J 172 ASN cc_start: 0.9073 (m-40) cc_final: 0.8862 (m-40) REVERT: J 175 ASP cc_start: 0.7852 (p0) cc_final: 0.7651 (m-30) REVERT: K 62 LYS cc_start: 0.9134 (tptp) cc_final: 0.8588 (tptm) REVERT: K 107 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7472 (t80) REVERT: K 132 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.8528 (m-70) REVERT: K 160 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9153 (tt) REVERT: K 163 CYS cc_start: 0.8963 (m) cc_final: 0.8378 (m) REVERT: L 54 PHE cc_start: 0.7359 (m-80) cc_final: 0.7136 (m-80) REVERT: L 97 MET cc_start: 0.6361 (mmm) cc_final: 0.6147 (mmm) REVERT: L 184 TRP cc_start: 0.7815 (p-90) cc_final: 0.6790 (p-90) REVERT: M 46 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8786 (pp) REVERT: M 172 MET cc_start: 0.8148 (mtp) cc_final: 0.7913 (mtp) REVERT: M 179 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7540 (t80) REVERT: N 65 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7785 (tm-30) REVERT: N 168 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8585 (tt) REVERT: N 200 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6837 (tt0) REVERT: O 13 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8708 (mm) REVERT: O 34 GLN cc_start: 0.8092 (mm-40) cc_final: 0.6676 (mm110) REVERT: O 43 ARG cc_start: 0.7579 (ptt90) cc_final: 0.5823 (ptm160) REVERT: O 62 ASP cc_start: 0.8110 (t0) cc_final: 0.7580 (t0) REVERT: O 110 PRO cc_start: 0.8203 (Cg_exo) cc_final: 0.7696 (Cg_endo) REVERT: O 112 ASP cc_start: 0.8714 (p0) cc_final: 0.8335 (p0) REVERT: O 113 MET cc_start: 0.8195 (pmm) cc_final: 0.7889 (pmm) REVERT: O 123 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8542 (tm-30) REVERT: P 37 ILE cc_start: 0.9399 (mt) cc_final: 0.9114 (mm) REVERT: P 78 MET cc_start: 0.7838 (mmm) cc_final: 0.7570 (mmm) REVERT: P 224 GLU cc_start: 0.8297 (tp30) cc_final: 0.8034 (tp30) REVERT: Q 19 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6487 (m-10) REVERT: Q 35 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8559 (pp) REVERT: Q 38 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7752 (tt) REVERT: Q 136 TYR cc_start: 0.7763 (m-80) cc_final: 0.7475 (m-80) REVERT: Q 174 MET cc_start: 0.8315 (tmm) cc_final: 0.8059 (tmm) REVERT: R 23 GLN cc_start: 0.7480 (tm-30) cc_final: 0.7234 (tm-30) REVERT: R 55 ASP cc_start: 0.6854 (m-30) cc_final: 0.6357 (p0) REVERT: R 71 MET cc_start: 0.6931 (ppp) cc_final: 0.6301 (ppp) REVERT: R 116 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8122 (tp40) REVERT: S 68 VAL cc_start: 0.8987 (m) cc_final: 0.8757 (p) REVERT: S 156 MET cc_start: 0.7922 (mmm) cc_final: 0.7464 (tpp) REVERT: T 117 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8019 (tm-30) REVERT: T 180 MET cc_start: 0.7074 (ppp) cc_final: 0.6671 (pmm) REVERT: U 24 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: U 59 GLU cc_start: 0.6750 (tp30) cc_final: 0.6281 (tm-30) REVERT: U 75 MET cc_start: 0.8143 (tpp) cc_final: 0.7749 (tpp) REVERT: V 4 MET cc_start: 0.8210 (ttt) cc_final: 0.7899 (ttt) REVERT: V 17 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7085 (p0) REVERT: V 25 TYR cc_start: 0.8499 (t80) cc_final: 0.8156 (t80) REVERT: V 89 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7415 (ttp80) REVERT: V 116 MET cc_start: 0.7470 (tpt) cc_final: 0.6703 (mtt) REVERT: V 144 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7222 (mpp80) REVERT: V 147 MET cc_start: 0.4968 (mtp) cc_final: 0.4398 (mtp) REVERT: V 152 CYS cc_start: 0.8529 (m) cc_final: 0.7978 (p) REVERT: V 181 GLU cc_start: 0.7758 (pm20) cc_final: 0.7468 (pm20) REVERT: W 8 TYR cc_start: 0.8105 (p90) cc_final: 0.7905 (p90) REVERT: W 30 ASN cc_start: 0.7047 (t0) cc_final: 0.6458 (t0) REVERT: W 135 MET cc_start: 0.8698 (tpp) cc_final: 0.8461 (tpp) REVERT: W 146 MET cc_start: 0.8234 (mtm) cc_final: 0.7859 (mtp) REVERT: X 39 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: X 117 LYS cc_start: 0.8456 (tptt) cc_final: 0.8110 (tppt) REVERT: X 138 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8880 (t) REVERT: X 175 ASP cc_start: 0.7365 (p0) cc_final: 0.6936 (m-30) REVERT: Y 38 MET cc_start: 0.8662 (mmp) cc_final: 0.8449 (mmm) REVERT: Y 62 LYS cc_start: 0.9106 (tptp) cc_final: 0.8563 (tptm) REVERT: Y 70 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8354 (ptp-110) REVERT: Y 132 HIS cc_start: 0.8854 (OUTLIER) cc_final: 0.8349 (m-70) REVERT: Y 159 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8866 (tp) REVERT: Y 160 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9064 (tt) REVERT: Y 163 CYS cc_start: 0.8907 (m) cc_final: 0.8426 (m) REVERT: Z 86 MET cc_start: 0.8515 (ppp) cc_final: 0.8016 (ppp) REVERT: Z 184 TRP cc_start: 0.7932 (p-90) cc_final: 0.6733 (p-90) REVERT: a 46 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8625 (pp) REVERT: a 60 ASP cc_start: 0.9245 (m-30) cc_final: 0.8874 (m-30) REVERT: a 100 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6336 (ptp90) REVERT: a 145 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8929 (tp) REVERT: a 149 LEU cc_start: 0.9103 (mm) cc_final: 0.8877 (mm) REVERT: b 65 GLN cc_start: 0.7800 (tt0) cc_final: 0.7184 (tm-30) REVERT: b 108 ASN cc_start: 0.7408 (t0) cc_final: 0.7079 (t0) REVERT: b 164 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7713 (mp0) REVERT: b 172 CYS cc_start: 0.8992 (m) cc_final: 0.8562 (p) outliers start: 280 outliers final: 214 residues processed: 1059 average time/residue: 0.2419 time to fit residues: 432.9683 Evaluate side-chains 1062 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 817 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 144 ARG Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 107 TYR Chi-restraints excluded: chain K residue 132 HIS Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 144 ASP Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 182 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 79 ASN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 179 PHE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 102 LYS Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 228 ARG Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 56 TYR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 120 TYR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 176 ARG Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 19 TYR Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 82 ILE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 68 ASN Chi-restraints excluded: chain T residue 69 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 222 THR Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain V residue 17 ASP Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 13 MET Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 GLN Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 89 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 138 SER Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 85 ARG Chi-restraints excluded: chain Y residue 118 MET Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 139 THR Chi-restraints excluded: chain Y residue 144 ASP Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 160 LEU Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 101 ILE Chi-restraints excluded: chain Z residue 179 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 173 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 548 optimal weight: 6.9990 chunk 482 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 305 optimal weight: 30.0000 chunk 517 optimal weight: 6.9990 chunk 413 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 337 optimal weight: 2.9990 chunk 49 optimal weight: 40.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 68 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS O 238 HIS ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN S 104 ASN S 204 GLN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.090509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.077981 restraints weight = 134476.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.080465 restraints weight = 69950.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.082139 restraints weight = 43508.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.083265 restraints weight = 30458.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.084068 restraints weight = 23346.755| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 46228 Z= 0.171 Angle : 0.659 11.827 62767 Z= 0.342 Chirality : 0.045 0.389 7355 Planarity : 0.004 0.052 7980 Dihedral : 5.727 88.219 6874 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 6.39 % Allowed : 24.54 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.11), residues: 6142 helix: 1.14 (0.11), residues: 2272 sheet: -0.48 (0.13), residues: 1520 loop : -0.72 (0.13), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 132 TYR 0.020 0.002 TYR W 8 PHE 0.020 0.001 PHE Z 54 TRP 0.019 0.002 TRP N 107 HIS 0.005 0.001 HIS S 99 Details of bonding type rmsd covalent geometry : bond 0.00385 (46228) covalent geometry : angle 0.65873 (62767) hydrogen bonds : bond 0.03444 ( 2528) hydrogen bonds : angle 5.11672 ( 7338) *********************** 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 1138 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 273 poor density : 865 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7570 (ptt90) cc_final: 0.5844 (ptm160) REVERT: A 54 LYS cc_start: 0.5921 (mtpp) cc_final: 0.5688 (mtpp) REVERT: A 62 ASP cc_start: 0.8078 (t0) cc_final: 0.7699 (t0) REVERT: A 112 ASP cc_start: 0.8348 (p0) cc_final: 0.7597 (t0) REVERT: A 123 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 150 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7124 (mm110) REVERT: B 37 ILE cc_start: 0.9406 (mt) cc_final: 0.9203 (mm) REVERT: B 49 LYS cc_start: 0.6384 (tptt) cc_final: 0.6110 (tttp) REVERT: B 56 TYR cc_start: 0.5922 (OUTLIER) cc_final: 0.5049 (t80) REVERT: B 219 ARG cc_start: 0.8655 (ptp90) cc_final: 0.8244 (ptp-110) REVERT: B 224 GLU cc_start: 0.8348 (tp30) cc_final: 0.8020 (tp30) REVERT: C 35 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8606 (pp) REVERT: C 38 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7388 (tt) REVERT: C 114 LEU cc_start: 0.9306 (tp) cc_final: 0.8946 (mp) REVERT: C 187 LYS cc_start: 0.9043 (pptt) cc_final: 0.8787 (mmmm) REVERT: D 4 ASP cc_start: 0.7323 (t0) cc_final: 0.6547 (t0) REVERT: D 54 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: D 71 MET cc_start: 0.7194 (ppp) cc_final: 0.6744 (ppp) REVERT: E 156 MET cc_start: 0.8344 (mmm) cc_final: 0.7849 (mmm) REVERT: F 90 GLN cc_start: 0.8586 (tp40) cc_final: 0.7436 (tp-100) REVERT: F 94 ASP cc_start: 0.8260 (m-30) cc_final: 0.7448 (m-30) REVERT: F 115 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8915 (tttm) REVERT: F 117 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8161 (tm-30) REVERT: G 21 PHE cc_start: 0.7800 (m-80) cc_final: 0.7480 (m-80) REVERT: G 75 MET cc_start: 0.8135 (tpp) cc_final: 0.7752 (tpp) REVERT: G 109 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8136 (tptm) REVERT: H 86 MET cc_start: 0.7961 (ptm) cc_final: 0.7752 (ptm) REVERT: H 116 MET cc_start: 0.7925 (mmm) cc_final: 0.7693 (mmm) REVERT: H 120 MET cc_start: 0.8130 (tmm) cc_final: 0.7873 (tmm) REVERT: H 144 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6991 (mpp80) REVERT: H 152 CYS cc_start: 0.8725 (m) cc_final: 0.8060 (p) REVERT: H 181 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: H 196 LYS cc_start: 0.6823 (mptt) cc_final: 0.6272 (mmtm) REVERT: I 10 ASP cc_start: 0.7692 (p0) cc_final: 0.7007 (p0) REVERT: I 30 ASN cc_start: 0.7122 (t0) cc_final: 0.6496 (t0) REVERT: I 114 TYR cc_start: 0.6887 (m-80) cc_final: 0.6635 (m-80) REVERT: J 148 MET cc_start: 0.8768 (mmm) cc_final: 0.8498 (mmm) REVERT: J 161 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7645 (t-90) REVERT: J 164 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7694 (mm-30) REVERT: K 62 LYS cc_start: 0.9122 (tptp) cc_final: 0.8580 (tptm) REVERT: K 107 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7372 (t80) REVERT: K 132 HIS cc_start: 0.8904 (OUTLIER) cc_final: 0.8517 (m-70) REVERT: K 160 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9130 (tt) REVERT: K 163 CYS cc_start: 0.8967 (m) cc_final: 0.8310 (m) REVERT: L 184 TRP cc_start: 0.7923 (p-90) cc_final: 0.6790 (p-90) REVERT: M 46 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8689 (pp) REVERT: M 172 MET cc_start: 0.8135 (mtp) cc_final: 0.7903 (mtp) REVERT: M 179 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7476 (t80) REVERT: N 65 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7831 (tm-30) REVERT: N 127 MET cc_start: 0.8875 (ttp) cc_final: 0.8524 (ttt) REVERT: N 168 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8589 (tt) REVERT: N 200 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6814 (tt0) REVERT: O 13 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8702 (mm) REVERT: O 34 GLN cc_start: 0.8098 (mm-40) cc_final: 0.6682 (mm110) REVERT: O 43 ARG cc_start: 0.7556 (ptt90) cc_final: 0.5803 (ptm160) REVERT: O 62 ASP cc_start: 0.8081 (t0) cc_final: 0.7559 (t0) REVERT: O 110 PRO cc_start: 0.8184 (Cg_exo) cc_final: 0.7479 (Cg_endo) REVERT: O 112 ASP cc_start: 0.8684 (p0) cc_final: 0.8175 (p0) REVERT: O 113 MET cc_start: 0.8142 (pmm) cc_final: 0.7811 (pmm) REVERT: O 123 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8547 (tm-30) REVERT: P 37 ILE cc_start: 0.9389 (mt) cc_final: 0.9107 (mm) REVERT: P 78 MET cc_start: 0.7718 (mmm) cc_final: 0.7457 (mmm) REVERT: P 224 GLU cc_start: 0.8222 (tp30) cc_final: 0.7914 (tp30) REVERT: Q 19 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6363 (m-10) REVERT: Q 35 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8886 (pp) REVERT: Q 38 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7675 (tt) REVERT: Q 114 LEU cc_start: 0.9340 (tp) cc_final: 0.8984 (mp) REVERT: Q 136 TYR cc_start: 0.7744 (m-80) cc_final: 0.7469 (m-80) REVERT: Q 137 ILE cc_start: 0.9205 (pt) cc_final: 0.8914 (pp) REVERT: Q 147 LEU cc_start: 0.8639 (mt) cc_final: 0.8330 (mt) REVERT: Q 174 MET cc_start: 0.8344 (tmm) cc_final: 0.8108 (tmm) REVERT: Q 209 GLU cc_start: 0.6965 (mp0) cc_final: 0.6572 (mp0) REVERT: R 7 ILE cc_start: 0.9259 (mt) cc_final: 0.8850 (mm) REVERT: R 55 ASP cc_start: 0.6917 (m-30) cc_final: 0.6461 (p0) REVERT: R 116 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8139 (tp40) REVERT: S 68 VAL cc_start: 0.8959 (m) cc_final: 0.8736 (p) REVERT: S 156 MET cc_start: 0.7889 (mmm) cc_final: 0.7424 (tpp) REVERT: S 216 GLU cc_start: 0.7379 (tp30) cc_final: 0.6531 (tp30) REVERT: T 117 GLN cc_start: 0.8727 (tm-30) cc_final: 0.7889 (tm-30) REVERT: T 121 GLN cc_start: 0.7959 (tt0) cc_final: 0.7747 (tt0) REVERT: T 179 PHE cc_start: 0.8068 (m-10) cc_final: 0.7866 (m-10) REVERT: T 180 MET cc_start: 0.7012 (ppp) cc_final: 0.6669 (pmm) REVERT: U 24 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: U 59 GLU cc_start: 0.7273 (tp30) cc_final: 0.6900 (tm-30) REVERT: U 75 MET cc_start: 0.8129 (tpp) cc_final: 0.7744 (tpp) REVERT: U 125 TYR cc_start: 0.8728 (m-80) cc_final: 0.8240 (m-10) REVERT: V 4 MET cc_start: 0.7837 (ttt) cc_final: 0.7413 (ttt) REVERT: V 17 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7211 (p0) REVERT: V 25 TYR cc_start: 0.8558 (t80) cc_final: 0.8251 (t80) REVERT: V 144 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7216 (mpp80) REVERT: V 147 MET cc_start: 0.4991 (mtp) cc_final: 0.4231 (mtp) REVERT: V 152 CYS cc_start: 0.8536 (m) cc_final: 0.7974 (p) REVERT: V 181 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: W 30 ASN cc_start: 0.7226 (t0) cc_final: 0.6680 (t0) REVERT: W 135 MET cc_start: 0.8672 (tpp) cc_final: 0.8402 (tpp) REVERT: W 146 MET cc_start: 0.8099 (mtm) cc_final: 0.7821 (mtp) REVERT: X 39 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: X 117 LYS cc_start: 0.8460 (tptt) cc_final: 0.8107 (tppt) REVERT: X 138 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8863 (t) REVERT: X 175 ASP cc_start: 0.7344 (p0) cc_final: 0.6906 (m-30) REVERT: Y 62 LYS cc_start: 0.9095 (tptp) cc_final: 0.8635 (tptm) REVERT: Y 70 ARG cc_start: 0.8774 (ttm110) cc_final: 0.8376 (ptp-110) REVERT: Y 132 HIS cc_start: 0.8852 (OUTLIER) cc_final: 0.8331 (m-70) REVERT: Y 159 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8859 (tp) REVERT: Y 160 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9052 (tt) REVERT: Y 163 CYS cc_start: 0.8906 (m) cc_final: 0.8429 (m) REVERT: Z 45 MET cc_start: 0.6137 (tpt) cc_final: 0.4875 (tpt) REVERT: Z 184 TRP cc_start: 0.7937 (p-90) cc_final: 0.6746 (p-90) REVERT: a 46 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8568 (pp) REVERT: a 60 ASP cc_start: 0.9234 (m-30) cc_final: 0.8853 (m-30) REVERT: a 100 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6339 (ptp90) REVERT: a 130 TYR cc_start: 0.8136 (t80) cc_final: 0.7795 (t80) REVERT: a 145 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8903 (tp) REVERT: a 149 LEU cc_start: 0.9091 (mm) cc_final: 0.8873 (mm) REVERT: a 179 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7527 (t80) REVERT: b 65 GLN cc_start: 0.7770 (tt0) cc_final: 0.7234 (tm-30) REVERT: b 108 ASN cc_start: 0.7381 (t0) cc_final: 0.7001 (t0) REVERT: b 164 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7796 (mp0) REVERT: b 172 CYS cc_start: 0.9028 (m) cc_final: 0.8504 (p) outliers start: 273 outliers final: 205 residues processed: 1047 average time/residue: 0.2292 time to fit residues: 406.3757 Evaluate side-chains 1067 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 829 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 144 ARG Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 107 TYR Chi-restraints excluded: chain K residue 132 HIS Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 144 ASP Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 182 ILE Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 179 PHE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 102 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 228 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 56 TYR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 120 TYR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 176 ARG Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 19 TYR Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain S residue 82 ILE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 23 GLU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 68 ASN Chi-restraints excluded: chain T residue 69 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 222 THR Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain V residue 17 ASP Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain V residue 181 GLU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 13 MET Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 GLN Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 89 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 138 SER Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 85 ARG Chi-restraints excluded: chain Y residue 118 MET Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 139 THR Chi-restraints excluded: chain Y residue 144 ASP Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 160 LEU Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 101 ILE Chi-restraints excluded: chain Z residue 179 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain a residue 156 LYS Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 173 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 591 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 379 optimal weight: 30.0000 chunk 69 optimal weight: 6.9990 chunk 285 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 371 optimal weight: 20.0000 chunk 411 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 68 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN S 104 ASN S 204 GLN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 166 GLN ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 175 ASN ** a 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 157 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.077181 restraints weight = 134528.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.079600 restraints weight = 69874.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.081249 restraints weight = 43523.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082394 restraints weight = 30579.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.083162 restraints weight = 23300.978| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 46228 Z= 0.201 Angle : 0.680 11.746 62767 Z= 0.353 Chirality : 0.045 0.335 7355 Planarity : 0.004 0.053 7980 Dihedral : 5.763 88.328 6870 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 6.23 % Allowed : 24.89 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.11), residues: 6142 helix: 1.10 (0.11), residues: 2280 sheet: -0.45 (0.13), residues: 1506 loop : -0.80 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 132 TYR 0.041 0.002 TYR H 25 PHE 0.024 0.002 PHE I 36 TRP 0.021 0.002 TRP N 107 HIS 0.009 0.001 HIS S 99 Details of bonding type rmsd covalent geometry : bond 0.00449 (46228) covalent geometry : angle 0.68018 (62767) hydrogen bonds : bond 0.03547 ( 2528) hydrogen bonds : angle 5.12533 ( 7338) *********************** 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 1115 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 266 poor density : 849 time to evaluate : 1.079 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: A 13 ILE cc_start: 0.8845 (pt) cc_final: 0.8452 (mm) REVERT: A 24 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: A 43 ARG cc_start: 0.7587 (ptt90) cc_final: 0.5851 (ptm160) REVERT: A 54 LYS cc_start: 0.5977 (mtpp) cc_final: 0.5728 (mtpp) REVERT: A 62 ASP cc_start: 0.8094 (t0) cc_final: 0.7726 (t0) REVERT: A 112 ASP cc_start: 0.8231 (p0) cc_final: 0.7646 (t0) REVERT: A 123 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8557 (tm-30) REVERT: A 150 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7150 (mm110) REVERT: B 37 ILE cc_start: 0.9420 (mt) cc_final: 0.9211 (mm) REVERT: B 49 LYS cc_start: 0.6711 (tptt) cc_final: 0.6479 (tttp) REVERT: B 56 TYR cc_start: 0.5847 (OUTLIER) cc_final: 0.4867 (t80) REVERT: B 219 ARG cc_start: 0.8674 (ptp90) cc_final: 0.8245 (ptp-110) REVERT: B 224 GLU cc_start: 0.8368 (tp30) cc_final: 0.8027 (tp30) REVERT: C 35 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8617 (pp) REVERT: C 38 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7467 (tt) REVERT: C 114 LEU cc_start: 0.9277 (tp) cc_final: 0.8878 (mp) REVERT: C 187 LYS cc_start: 0.9067 (pptt) cc_final: 0.8782 (mmmm) REVERT: D 4 ASP cc_start: 0.7335 (t0) cc_final: 0.6636 (t0) REVERT: D 54 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: D 71 MET cc_start: 0.7671 (ppp) cc_final: 0.7247 (ppp) REVERT: E 104 ASN cc_start: 0.9085 (t0) cc_final: 0.8795 (t0) REVERT: E 156 MET cc_start: 0.8392 (mmm) cc_final: 0.7881 (mmm) REVERT: F 90 GLN cc_start: 0.8606 (tp40) cc_final: 0.7461 (tp-100) REVERT: F 94 ASP cc_start: 0.8255 (m-30) cc_final: 0.7514 (m-30) REVERT: F 117 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8165 (tm-30) REVERT: G 21 PHE cc_start: 0.7858 (m-80) cc_final: 0.7533 (m-80) REVERT: G 75 MET cc_start: 0.8134 (tpp) cc_final: 0.7736 (tpp) REVERT: G 109 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8133 (tptm) REVERT: H 86 MET cc_start: 0.7953 (ptm) cc_final: 0.7730 (ptm) REVERT: H 89 ARG cc_start: 0.8063 (ttm170) cc_final: 0.7418 (ttp80) REVERT: H 116 MET cc_start: 0.7989 (mmm) cc_final: 0.6872 (mtt) REVERT: H 144 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6965 (mpp80) REVERT: H 152 CYS cc_start: 0.8813 (m) cc_final: 0.8023 (p) REVERT: H 181 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: H 196 LYS cc_start: 0.6817 (mptt) cc_final: 0.6231 (mmtm) REVERT: I 8 TYR cc_start: 0.8082 (p90) cc_final: 0.7774 (p90) REVERT: I 30 ASN cc_start: 0.7236 (t0) cc_final: 0.6664 (t0) REVERT: I 114 TYR cc_start: 0.6989 (m-80) cc_final: 0.6708 (m-80) REVERT: I 132 LEU cc_start: 0.8498 (tp) cc_final: 0.8287 (tp) REVERT: J 148 MET cc_start: 0.8765 (mmm) cc_final: 0.8479 (mmm) REVERT: J 164 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7608 (mm-30) REVERT: K 62 LYS cc_start: 0.9105 (tptp) cc_final: 0.8582 (tptm) REVERT: K 70 ARG cc_start: 0.9026 (ptp-110) cc_final: 0.8823 (ptp-170) REVERT: K 107 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7470 (t80) REVERT: K 132 HIS cc_start: 0.8909 (OUTLIER) cc_final: 0.8538 (m-70) REVERT: K 160 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9184 (tt) REVERT: K 163 CYS cc_start: 0.8965 (m) cc_final: 0.8394 (m) REVERT: L 45 MET cc_start: 0.4458 (OUTLIER) cc_final: 0.2956 (mmm) REVERT: L 97 MET cc_start: 0.4815 (mmm) cc_final: 0.4593 (mmm) REVERT: L 119 ASN cc_start: 0.7616 (m-40) cc_final: 0.6515 (p0) REVERT: L 184 TRP cc_start: 0.7971 (p-90) cc_final: 0.6804 (p-90) REVERT: M 46 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8700 (pp) REVERT: M 172 MET cc_start: 0.8152 (mtp) cc_final: 0.7916 (mtp) REVERT: M 179 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7482 (t80) REVERT: N 65 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7792 (tm-30) REVERT: N 127 MET cc_start: 0.8873 (ttp) cc_final: 0.8515 (ttt) REVERT: N 168 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8599 (tt) REVERT: N 200 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6818 (tt0) REVERT: O 13 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8674 (mm) REVERT: O 26 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7803 (mm-30) REVERT: O 34 GLN cc_start: 0.8105 (mm-40) cc_final: 0.6719 (mm110) REVERT: O 43 ARG cc_start: 0.7511 (ptt90) cc_final: 0.5819 (ptm160) REVERT: O 62 ASP cc_start: 0.8045 (t0) cc_final: 0.7677 (t70) REVERT: O 110 PRO cc_start: 0.8158 (Cg_exo) cc_final: 0.7706 (Cg_endo) REVERT: O 112 ASP cc_start: 0.8658 (p0) cc_final: 0.8250 (p0) REVERT: O 113 MET cc_start: 0.8141 (pmm) cc_final: 0.7885 (pmm) REVERT: O 123 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8560 (tm-30) REVERT: O 132 ARG cc_start: 0.8653 (ptt-90) cc_final: 0.8292 (ptt-90) REVERT: P 37 ILE cc_start: 0.9431 (mt) cc_final: 0.9220 (mm) REVERT: P 78 MET cc_start: 0.7742 (mmm) cc_final: 0.7490 (mmm) REVERT: P 102 GLU cc_start: 0.8942 (tp30) cc_final: 0.8185 (tt0) REVERT: P 224 GLU cc_start: 0.8236 (tp30) cc_final: 0.7927 (tp30) REVERT: Q 19 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.5990 (m-10) REVERT: Q 35 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8921 (pp) REVERT: Q 38 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7741 (tt) REVERT: Q 114 LEU cc_start: 0.9336 (tp) cc_final: 0.8990 (mp) REVERT: Q 147 LEU cc_start: 0.8651 (mt) cc_final: 0.8370 (mt) REVERT: Q 174 MET cc_start: 0.8313 (tmm) cc_final: 0.8065 (tmm) REVERT: Q 209 GLU cc_start: 0.7061 (mp0) cc_final: 0.6685 (mp0) REVERT: R 7 ILE cc_start: 0.9280 (mt) cc_final: 0.8866 (mm) REVERT: R 55 ASP cc_start: 0.6657 (m-30) cc_final: 0.6401 (p0) REVERT: R 71 MET cc_start: 0.6865 (ppp) cc_final: 0.6055 (ppp) REVERT: S 68 VAL cc_start: 0.8949 (m) cc_final: 0.8723 (p) REVERT: S 156 MET cc_start: 0.7937 (mmm) cc_final: 0.7443 (tpp) REVERT: T 117 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8317 (tm-30) REVERT: T 121 GLN cc_start: 0.7958 (tt0) cc_final: 0.7603 (tt0) REVERT: T 180 MET cc_start: 0.7028 (ppp) cc_final: 0.6700 (pmm) REVERT: U 24 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: U 59 GLU cc_start: 0.6909 (tp30) cc_final: 0.6550 (tm-30) REVERT: U 125 TYR cc_start: 0.8728 (m-80) cc_final: 0.8283 (m-10) REVERT: V 4 MET cc_start: 0.7765 (ttt) cc_final: 0.7387 (ttt) REVERT: V 17 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7479 (p0) REVERT: V 25 TYR cc_start: 0.8562 (t80) cc_final: 0.8223 (t80) REVERT: V 69 GLU cc_start: 0.7340 (pm20) cc_final: 0.7114 (pm20) REVERT: V 84 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8598 (ttmm) REVERT: V 86 MET cc_start: 0.8682 (ptm) cc_final: 0.8163 (ptm) REVERT: V 89 ARG cc_start: 0.7994 (ttm170) cc_final: 0.7513 (ttp80) REVERT: V 116 MET cc_start: 0.7524 (tpt) cc_final: 0.6270 (mtt) REVERT: V 144 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7225 (mpp80) REVERT: V 147 MET cc_start: 0.5069 (mtp) cc_final: 0.4325 (mtp) REVERT: V 152 CYS cc_start: 0.8557 (m) cc_final: 0.7979 (p) REVERT: V 181 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: W 30 ASN cc_start: 0.7186 (t0) cc_final: 0.6608 (t0) REVERT: W 135 MET cc_start: 0.8661 (tpp) cc_final: 0.8404 (tpp) REVERT: W 146 MET cc_start: 0.8099 (mtm) cc_final: 0.7819 (mtp) REVERT: X 39 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: X 117 LYS cc_start: 0.8475 (tptt) cc_final: 0.8119 (tppt) REVERT: X 175 ASP cc_start: 0.7284 (p0) cc_final: 0.6887 (m-30) REVERT: Y 62 LYS cc_start: 0.9090 (tptp) cc_final: 0.8566 (tptm) REVERT: Y 70 ARG cc_start: 0.8803 (ttm110) cc_final: 0.8389 (ptp-110) REVERT: Y 132 HIS cc_start: 0.8866 (OUTLIER) cc_final: 0.8345 (m-70) REVERT: Y 159 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8860 (tp) REVERT: Y 160 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9068 (tt) REVERT: Y 163 CYS cc_start: 0.8923 (m) cc_final: 0.8450 (m) REVERT: Z 86 MET cc_start: 0.8441 (ppp) cc_final: 0.7971 (ppp) REVERT: Z 184 TRP cc_start: 0.7976 (p-90) cc_final: 0.6760 (p-90) REVERT: a 46 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8565 (pp) REVERT: a 60 ASP cc_start: 0.9128 (m-30) cc_final: 0.8769 (m-30) REVERT: a 100 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6306 (ptp90) REVERT: a 108 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8593 (m-40) REVERT: a 130 TYR cc_start: 0.8258 (t80) cc_final: 0.7949 (t80) REVERT: a 145 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8958 (tp) REVERT: a 149 LEU cc_start: 0.9133 (mm) cc_final: 0.8888 (mm) REVERT: a 179 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7527 (t80) REVERT: b 43 MET cc_start: 0.8667 (tpt) cc_final: 0.8374 (tpt) REVERT: b 65 GLN cc_start: 0.7844 (tt0) cc_final: 0.7317 (tm-30) REVERT: b 108 ASN cc_start: 0.7348 (t0) cc_final: 0.6896 (t0) REVERT: b 164 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7794 (mp0) REVERT: b 172 CYS cc_start: 0.9047 (m) cc_final: 0.8553 (p) outliers start: 266 outliers final: 215 residues processed: 1031 average time/residue: 0.2111 time to fit residues: 367.3745 Evaluate side-chains 1062 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 814 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 ASN Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 144 ARG Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 107 TYR Chi-restraints excluded: chain K residue 132 HIS Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 144 ASP Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 182 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 179 PHE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 102 LYS Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 228 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 56 TYR Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 120 TYR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 176 ARG Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 19 TYR Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 160 LYS Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 82 ILE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 23 GLU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 68 ASN Chi-restraints excluded: chain T residue 69 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 222 THR Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain V residue 17 ASP Chi-restraints excluded: chain V residue 43 CYS Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain V residue 181 GLU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 13 MET Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 GLN Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 89 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 188 ILE Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 118 MET Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 139 THR Chi-restraints excluded: chain Y residue 144 ASP Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 160 LEU Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 101 ILE Chi-restraints excluded: chain Z residue 179 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 70 MET Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 173 MET Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 124 optimal weight: 9.9990 chunk 540 optimal weight: 7.9990 chunk 504 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 480 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 chunk 557 optimal weight: 30.0000 chunk 67 optimal weight: 6.9990 chunk 350 optimal weight: 20.0000 chunk 307 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 68 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 ASN M 108 ASN N 188 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS O 92 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 166 GLN ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 175 ASN ** a 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 188 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.089073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076675 restraints weight = 135838.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.079117 restraints weight = 70522.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.080747 restraints weight = 43890.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.081877 restraints weight = 30855.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.082650 restraints weight = 23572.096| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 46228 Z= 0.219 Angle : 0.704 12.082 62767 Z= 0.365 Chirality : 0.046 0.278 7355 Planarity : 0.004 0.052 7980 Dihedral : 5.841 88.334 6870 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.02 % Allowed : 25.22 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.11), residues: 6142 helix: 1.07 (0.11), residues: 2270 sheet: -0.46 (0.13), residues: 1496 loop : -0.82 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 132 TYR 0.046 0.002 TYR H 25 PHE 0.021 0.002 PHE M 124 TRP 0.023 0.002 TRP b 107 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00489 (46228) covalent geometry : angle 0.70425 (62767) hydrogen bonds : bond 0.03616 ( 2528) hydrogen bonds : angle 5.16104 ( 7338) ********************** 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 1081 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 824 time to evaluate : 1.240 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: A 13 ILE cc_start: 0.8812 (pt) cc_final: 0.8427 (mm) REVERT: A 24 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: A 43 ARG cc_start: 0.7651 (ptt90) cc_final: 0.6076 (ptm160) REVERT: A 54 LYS cc_start: 0.5975 (mtpp) cc_final: 0.5734 (mtpp) REVERT: A 62 ASP cc_start: 0.8152 (t0) cc_final: 0.7641 (t70) REVERT: A 112 ASP cc_start: 0.8199 (p0) cc_final: 0.7623 (t0) REVERT: A 123 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8528 (tm-30) REVERT: A 150 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7099 (mm110) REVERT: A 174 GLU cc_start: 0.7379 (mp0) cc_final: 0.7160 (mp0) REVERT: B 37 ILE cc_start: 0.9380 (mt) cc_final: 0.9111 (mm) REVERT: B 49 LYS cc_start: 0.6750 (tptt) cc_final: 0.6535 (tttp) REVERT: B 56 TYR cc_start: 0.5828 (OUTLIER) cc_final: 0.4800 (t80) REVERT: B 162 MET cc_start: 0.6534 (mmm) cc_final: 0.5913 (ptp) REVERT: B 219 ARG cc_start: 0.8681 (ptp90) cc_final: 0.8258 (ptp-110) REVERT: C 35 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8638 (pp) REVERT: C 38 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7619 (tt) REVERT: C 114 LEU cc_start: 0.9283 (tp) cc_final: 0.8880 (mp) REVERT: C 187 LYS cc_start: 0.9064 (pptt) cc_final: 0.8778 (mmmm) REVERT: D 4 ASP cc_start: 0.7308 (t0) cc_final: 0.6560 (t0) REVERT: D 54 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7666 (mp10) REVERT: D 71 MET cc_start: 0.7764 (ppp) cc_final: 0.7317 (ppp) REVERT: E 156 MET cc_start: 0.8384 (mmm) cc_final: 0.7890 (mmm) REVERT: F 90 GLN cc_start: 0.8611 (tp40) cc_final: 0.7466 (tp-100) REVERT: F 94 ASP cc_start: 0.8434 (m-30) cc_final: 0.7583 (m-30) REVERT: F 117 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8131 (tm-30) REVERT: G 21 PHE cc_start: 0.7917 (m-80) cc_final: 0.7595 (m-80) REVERT: G 109 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8162 (tptm) REVERT: H 86 MET cc_start: 0.7945 (ptm) cc_final: 0.7715 (ptm) REVERT: H 89 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7708 (ttp-110) REVERT: H 116 MET cc_start: 0.8042 (mmm) cc_final: 0.6980 (mtt) REVERT: H 144 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6966 (mpp80) REVERT: H 152 CYS cc_start: 0.8814 (m) cc_final: 0.8036 (p) REVERT: H 196 LYS cc_start: 0.6806 (mptt) cc_final: 0.6199 (mmtm) REVERT: I 8 TYR cc_start: 0.8025 (p90) cc_final: 0.7726 (p90) REVERT: I 30 ASN cc_start: 0.7287 (t0) cc_final: 0.6730 (t0) REVERT: I 114 TYR cc_start: 0.7136 (m-80) cc_final: 0.6802 (m-80) REVERT: J 148 MET cc_start: 0.8752 (mmm) cc_final: 0.8498 (mmm) REVERT: J 164 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7608 (mm-30) REVERT: K 62 LYS cc_start: 0.9107 (tptp) cc_final: 0.8591 (tptm) REVERT: K 107 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7459 (t80) REVERT: K 132 HIS cc_start: 0.8914 (OUTLIER) cc_final: 0.8536 (m-70) REVERT: K 163 CYS cc_start: 0.8966 (m) cc_final: 0.8409 (m) REVERT: L 97 MET cc_start: 0.4864 (mmm) cc_final: 0.4654 (mmm) REVERT: L 119 ASN cc_start: 0.7599 (m-40) cc_final: 0.6334 (p0) REVERT: L 184 TRP cc_start: 0.8019 (p-90) cc_final: 0.6835 (p-90) REVERT: M 46 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8723 (pp) REVERT: M 179 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7469 (t80) REVERT: N 65 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7812 (tm-30) REVERT: N 168 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8614 (tt) REVERT: N 188 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8044 (mt0) REVERT: N 200 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6795 (tt0) REVERT: O 13 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8662 (mm) REVERT: O 26 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7570 (mm-30) REVERT: O 34 GLN cc_start: 0.8115 (mm-40) cc_final: 0.6751 (mm110) REVERT: O 43 ARG cc_start: 0.7650 (ptt90) cc_final: 0.6079 (ptm160) REVERT: O 62 ASP cc_start: 0.8100 (t0) cc_final: 0.7708 (t70) REVERT: O 110 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.7758 (Cg_endo) REVERT: O 112 ASP cc_start: 0.8757 (p0) cc_final: 0.8253 (p0) REVERT: O 113 MET cc_start: 0.8139 (pmm) cc_final: 0.7823 (pmm) REVERT: O 123 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8570 (tm-30) REVERT: O 132 ARG cc_start: 0.8391 (ptt-90) cc_final: 0.8134 (ptt-90) REVERT: P 37 ILE cc_start: 0.9385 (mt) cc_final: 0.9117 (mm) REVERT: P 78 MET cc_start: 0.7784 (mmm) cc_final: 0.7536 (mmm) REVERT: P 224 GLU cc_start: 0.8250 (tp30) cc_final: 0.7932 (tp30) REVERT: Q 19 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.5852 (m-10) REVERT: Q 35 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8640 (pp) REVERT: Q 38 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7791 (tt) REVERT: Q 114 LEU cc_start: 0.9234 (tp) cc_final: 0.8839 (mp) REVERT: Q 147 LEU cc_start: 0.8672 (mt) cc_final: 0.8404 (mt) REVERT: Q 174 MET cc_start: 0.8313 (tmm) cc_final: 0.8058 (tmm) REVERT: Q 209 GLU cc_start: 0.6713 (mp0) cc_final: 0.6370 (mp0) REVERT: R 116 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8143 (tp40) REVERT: S 68 VAL cc_start: 0.8942 (m) cc_final: 0.8705 (p) REVERT: S 78 MET cc_start: 0.7018 (ppp) cc_final: 0.6446 (ppp) REVERT: T 117 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8340 (tm-30) REVERT: T 121 GLN cc_start: 0.8264 (tt0) cc_final: 0.7750 (tt0) REVERT: T 180 MET cc_start: 0.6964 (ppp) cc_final: 0.6634 (pmm) REVERT: U 24 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: U 59 GLU cc_start: 0.6829 (tp30) cc_final: 0.6534 (tm-30) REVERT: U 125 TYR cc_start: 0.8769 (m-80) cc_final: 0.8314 (m-10) REVERT: V 4 MET cc_start: 0.7798 (ttt) cc_final: 0.7365 (ttt) REVERT: V 17 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7584 (p0) REVERT: V 84 LYS cc_start: 0.9086 (ttpt) cc_final: 0.8613 (ttmm) REVERT: V 86 MET cc_start: 0.8709 (ptm) cc_final: 0.8171 (ptm) REVERT: V 89 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7545 (ttp80) REVERT: V 144 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7244 (mpp80) REVERT: V 147 MET cc_start: 0.5120 (mtp) cc_final: 0.4436 (mtp) REVERT: V 152 CYS cc_start: 0.8608 (m) cc_final: 0.7955 (p) REVERT: V 181 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: W 10 ASP cc_start: 0.7676 (p0) cc_final: 0.7211 (p0) REVERT: W 30 ASN cc_start: 0.7235 (t0) cc_final: 0.6684 (t0) REVERT: W 146 MET cc_start: 0.8108 (mtm) cc_final: 0.7796 (mtp) REVERT: X 39 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: X 117 LYS cc_start: 0.8362 (tptt) cc_final: 0.8001 (tppt) REVERT: X 175 ASP cc_start: 0.7249 (p0) cc_final: 0.6910 (m-30) REVERT: Y 38 MET cc_start: 0.8310 (mmm) cc_final: 0.8026 (mmp) REVERT: Y 62 LYS cc_start: 0.9075 (tptp) cc_final: 0.8569 (tptm) REVERT: Y 132 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.8356 (m-70) REVERT: Y 159 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8864 (tp) REVERT: Y 160 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9093 (tt) REVERT: Y 163 CYS cc_start: 0.8892 (m) cc_final: 0.8402 (m) REVERT: Z 86 MET cc_start: 0.8373 (ppp) cc_final: 0.7952 (ppp) REVERT: Z 184 TRP cc_start: 0.8027 (p-90) cc_final: 0.6778 (p-90) REVERT: a 46 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8543 (pp) REVERT: a 60 ASP cc_start: 0.9126 (m-30) cc_final: 0.8791 (m-30) REVERT: a 97 TYR cc_start: 0.7037 (t80) cc_final: 0.6411 (t80) REVERT: a 100 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.5818 (ptp90) REVERT: a 108 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8653 (m-40) REVERT: a 130 TYR cc_start: 0.8252 (t80) cc_final: 0.8014 (t80) REVERT: a 179 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7521 (t80) REVERT: b 43 MET cc_start: 0.8712 (tpt) cc_final: 0.8258 (tpt) REVERT: b 65 GLN cc_start: 0.7841 (tt0) cc_final: 0.7357 (tm-30) REVERT: b 108 ASN cc_start: 0.7181 (t0) cc_final: 0.6740 (t0) REVERT: b 164 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7783 (mp0) REVERT: b 172 CYS cc_start: 0.9060 (m) cc_final: 0.8540 (p) REVERT: b 188 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: b 200 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6825 (tp30) outliers start: 257 outliers final: 209 residues processed: 998 average time/residue: 0.1926 time to fit residues: 324.9683 Evaluate side-chains 1043 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 802 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 144 ARG Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 107 TYR Chi-restraints excluded: chain K residue 132 HIS Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 144 ASP Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 182 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 79 ASN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 146 GLN Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 179 PHE Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 188 GLN Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 102 LYS Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 219 VAL Chi-restraints excluded: chain O residue 228 ARG Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 120 TYR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 176 ARG Chi-restraints excluded: chain P residue 189 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 19 TYR Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 160 LYS Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain S residue 21 LEU Chi-restraints excluded: chain S residue 82 ILE Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 68 ASN Chi-restraints excluded: chain T residue 69 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 222 THR Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain V residue 17 ASP Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain V residue 181 GLU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain W residue 217 THR Chi-restraints excluded: chain X residue 13 MET Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 39 GLN Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 89 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 188 ILE Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 118 MET Chi-restraints excluded: chain Y residue 132 HIS Chi-restraints excluded: chain Y residue 139 THR Chi-restraints excluded: chain Y residue 144 ASP Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 160 LEU Chi-restraints excluded: chain Y residue 167 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 101 ILE Chi-restraints excluded: chain Z residue 179 VAL Chi-restraints excluded: chain Z residue 187 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 91 MET Chi-restraints excluded: chain a residue 100 ARG Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 173 MET Chi-restraints excluded: chain b residue 188 GLN Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 200 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 555 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 chunk 341 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 390 optimal weight: 5.9990 chunk 269 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 349 optimal weight: 30.0000 chunk 587 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 68 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 ASN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 108 GLN ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** T 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 166 GLN ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 175 ASN a 79 ASN ** a 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 188 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.090626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.078060 restraints weight = 134881.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.080572 restraints weight = 69854.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.082247 restraints weight = 43434.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.083401 restraints weight = 30461.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084202 restraints weight = 23341.803| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 46228 Z= 0.165 Angle : 0.690 13.950 62767 Z= 0.354 Chirality : 0.045 0.275 7355 Planarity : 0.004 0.053 7980 Dihedral : 5.707 88.598 6868 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.64 % Allowed : 25.83 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.11), residues: 6142 helix: 1.16 (0.11), residues: 2272 sheet: -0.42 (0.13), residues: 1484 loop : -0.80 (0.13), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 132 TYR 0.044 0.002 TYR H 25 PHE 0.024 0.002 PHE W 36 TRP 0.021 0.002 TRP b 107 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00377 (46228) covalent geometry : angle 0.69045 (62767) hydrogen bonds : bond 0.03466 ( 2528) hydrogen bonds : angle 5.08714 ( 7338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8152.32 seconds wall clock time: 141 minutes 27.38 seconds (8487.38 seconds total)