Starting phenix.real_space_refine on Sat Mar 7 14:10:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pg9_13389/03_2026/7pg9_13389.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pg9_13389/03_2026/7pg9_13389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pg9_13389/03_2026/7pg9_13389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pg9_13389/03_2026/7pg9_13389.map" model { file = "/net/cci-nas-00/data/ceres_data/7pg9_13389/03_2026/7pg9_13389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pg9_13389/03_2026/7pg9_13389.cif" } resolution = 3.7 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 280 5.16 5 C 28984 2.51 5 N 8007 2.21 5 O 8055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45326 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1729 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 12, 'GLN:plan1': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 85 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: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1725 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 8, 'TRANS': 229} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 12, 'GLN:plan1': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 85 Chain: "P" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'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 Time building chain proxies: 10.54, per 1000 atoms: 0.23 Number of scatterers: 45326 At special positions: 0 Unit cell: (192.428, 158.16, 133.118, 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 8055 8.00 N 8007 7.00 C 28984 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: 3.41 Conformation dependent library (CDL) restraints added in 1.9 seconds 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11412 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 70 sheets defined 39.1% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 removed outlier: 3.852A pdb=" N ASP A 10 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG A 11 " --> pdb=" O GLY A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.899A pdb=" N PHE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.501A pdb=" N GLY A 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 106 removed outlier: 3.756A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.635A pdb=" N CYS A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.604A pdb=" N LYS A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 193 through 207 removed outlier: 3.721A pdb=" N THR A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.518A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 30 removed outlier: 3.651A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 101 removed outlier: 3.546A pdb=" N ARG B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 123 removed outlier: 3.537A pdb=" N GLN B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.597A pdb=" N PHE B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.923A pdb=" N HIS B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 removed outlier: 3.535A pdb=" N LYS B 226 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.704A pdb=" N GLU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.685A pdb=" N ASN C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 removed outlier: 3.503A pdb=" N THR C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 4.172A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 200 removed outlier: 4.047A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 247 removed outlier: 3.718A pdb=" N ALA C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 Processing helix chain 'D' and resid 76 through 99 removed outlier: 3.603A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.535A pdb=" N TYR D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.672A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 removed outlier: 3.523A pdb=" N ILE D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 232 removed outlier: 3.610A pdb=" N GLU D 226 " --> pdb=" O PRO D 222 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.722A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 removed outlier: 3.871A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 173 through 185 removed outlier: 6.653A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 removed outlier: 3.556A pdb=" N LEU E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.600A pdb=" N GLU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 29 removed outlier: 3.740A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 99 removed outlier: 3.748A pdb=" N PHE F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.527A pdb=" N SER F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix removed outlier: 3.547A pdb=" N ARG F 122 " --> pdb=" O ILE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 176 removed outlier: 4.096A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.577A pdb=" N VAL F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'G' and resid 6 through 10 removed outlier: 3.704A pdb=" N LEU G 9 " --> pdb=" O GLY G 6 " (cutoff:3.500A) removed outlier: 4.357A 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 27 Processing helix chain 'G' and resid 27 through 32 removed outlier: 3.528A pdb=" N GLU G 31 " --> pdb=" O MET G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 103 Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.552A pdb=" N ASP G 113 " --> pdb=" O LYS G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 removed outlier: 4.210A pdb=" N ALA G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS G 173 " --> pdb=" O ARG G 169 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS G 178 " --> pdb=" O THR G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 4.025A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 244 Processing helix chain 'H' and resid 48 through 71 removed outlier: 3.871A pdb=" N GLU H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.936A pdb=" N ARG H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 134 removed outlier: 3.700A pdb=" N SER H 133 " --> pdb=" O SER H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 142 Processing helix chain 'H' and resid 148 through 167 removed outlier: 3.676A pdb=" N GLN H 154 " --> pdb=" O GLU H 150 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.791A pdb=" N ILE H 194 " --> pdb=" O GLY H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 71 removed outlier: 3.761A pdb=" N LEU I 58 " --> pdb=" O MET I 54 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 90 Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.950A pdb=" N ALA I 136 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 164 removed outlier: 3.522A pdb=" N GLY I 162 " --> pdb=" O ALA I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 5 Processing helix chain 'J' and resid 55 through 78 removed outlier: 3.552A pdb=" N LEU J 72 " --> pdb=" O PHE J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 97 removed outlier: 3.649A pdb=" N SER J 88 " --> pdb=" O TYR J 84 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 removed outlier: 4.262A pdb=" N GLY J 147 " --> pdb=" O GLU J 143 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET J 148 " --> pdb=" O GLN J 144 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU J 152 " --> pdb=" O MET J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 175 removed outlier: 3.505A pdb=" N GLU J 164 " --> pdb=" O ASP J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 72 removed outlier: 3.626A pdb=" N GLN K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU K 58 " --> pdb=" O VAL K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 90 removed outlier: 3.769A pdb=" N ASN K 87 " --> pdb=" O PHE K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 147 removed outlier: 4.651A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 170 removed outlier: 3.526A pdb=" N GLN K 168 " --> pdb=" O LEU K 164 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS K 169 " --> pdb=" O GLU K 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 71 removed outlier: 3.600A pdb=" N GLN L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 89 removed outlier: 3.981A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 3.555A pdb=" N ALA L 135 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY L 142 " --> pdb=" O VAL L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 removed outlier: 3.642A pdb=" N ASP L 154 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE L 160 " --> pdb=" O ALA L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 199 removed outlier: 4.240A pdb=" N GLU L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 80 removed outlier: 3.832A pdb=" N LYS M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.539A pdb=" N SER M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 153 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 167 through 186 removed outlier: 3.512A pdb=" N MET M 172 " --> pdb=" O LEU M 168 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE M 180 " --> pdb=" O LYS M 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER M 181 " --> pdb=" O ASP M 177 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG M 185 " --> pdb=" O SER M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 78 removed outlier: 3.543A pdb=" N ILE N 72 " --> pdb=" O GLY N 68 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 removed outlier: 3.753A pdb=" N ARG N 100 " --> pdb=" O MET N 96 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS N 102 " --> pdb=" O SER N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 removed outlier: 3.829A 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 31 removed outlier: 3.543A pdb=" N TYR O 27 " --> pdb=" O TYR O 23 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE O 29 " --> pdb=" O VAL O 25 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 36 removed outlier: 3.501A pdb=" N GLY O 35 " --> pdb=" O ILE O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 106 removed outlier: 3.755A pdb=" N SER O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 128 removed outlier: 3.634A pdb=" N CYS O 115 " --> pdb=" O VAL O 111 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS O 116 " --> pdb=" O ASP O 112 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG O 117 " --> pdb=" O MET O 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE O 118 " --> pdb=" O LEU O 114 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL O 124 " --> pdb=" O ASP O 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR O 126 " --> pdb=" O SER O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 181 removed outlier: 3.604A pdb=" N LYS O 181 " --> pdb=" O SER O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 184 No H-bonds generated for 'chain 'O' and resid 182 through 184' Processing helix chain 'O' and resid 185 through 189 Processing helix chain 'O' and resid 193 through 207 removed outlier: 3.721A pdb=" N THR O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL O 205 " --> pdb=" O CYS O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.518A pdb=" N ALA O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS O 238 " --> pdb=" O GLU O 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 30 removed outlier: 3.651A pdb=" N ALA P 26 " --> pdb=" O GLU P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 101 removed outlier: 3.547A pdb=" N ARG P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL P 84 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU P 85 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 123 removed outlier: 3.535A pdb=" N GLN P 111 " --> pdb=" O ALA P 107 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR P 120 " --> pdb=" O VAL P 116 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR P 121 " --> pdb=" O MET P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 177 removed outlier: 3.597A pdb=" N PHE P 172 " --> pdb=" O ASN P 168 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU P 174 " --> pdb=" O LYS P 170 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS P 175 " --> pdb=" O THR P 171 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG P 176 " --> pdb=" O PHE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 197 removed outlier: 3.924A pdb=" N HIS P 188 " --> pdb=" O GLU P 184 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR P 189 " --> pdb=" O ASP P 185 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER P 197 " --> pdb=" O THR P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 229 removed outlier: 3.535A pdb=" N LYS P 226 " --> pdb=" O PRO P 222 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR P 228 " --> pdb=" O GLU P 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 30 removed outlier: 3.705A pdb=" N GLU Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 102 removed outlier: 3.686A pdb=" N ASN Q 84 " --> pdb=" O THR Q 80 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL Q 85 " --> pdb=" O SER Q 81 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 124 removed outlier: 3.503A pdb=" N THR Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 179 removed outlier: 4.172A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR Q 179 " --> pdb=" O LEU Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 200 removed outlier: 4.047A pdb=" N LYS Q 199 " --> pdb=" O LYS Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 247 removed outlier: 3.718A pdb=" N ALA Q 245 " --> pdb=" O GLU Q 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 27 Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.604A pdb=" N ILE R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 121 removed outlier: 3.536A pdb=" N TYR R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 176 removed outlier: 3.672A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 199 removed outlier: 3.524A pdb=" N ILE R 188 " --> pdb=" O ASP R 184 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL R 191 " --> pdb=" O THR R 187 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 232 removed outlier: 3.610A pdb=" N GLU R 226 " --> pdb=" O PRO R 222 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS R 227 " --> pdb=" O GLU R 223 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR R 228 " --> pdb=" O GLU R 224 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 32 removed outlier: 3.721A pdb=" N GLU S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 3.658A 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 81 through 104 removed outlier: 3.871A pdb=" N ALA S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS S 86 " --> pdb=" O ILE S 82 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 173 through 185 removed outlier: 6.653A pdb=" N SER S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER S 180 " --> pdb=" O GLY S 176 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU S 183 " --> pdb=" O SER S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 206 removed outlier: 3.556A pdb=" N LEU S 199 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE S 201 " --> pdb=" O SER S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 230 through 241 removed outlier: 3.600A pdb=" N GLU S 235 " --> pdb=" O LYS S 231 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU S 236 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL S 237 " --> pdb=" O GLU S 233 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP S 240 " --> pdb=" O GLU S 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 29 removed outlier: 3.739A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 99 removed outlier: 3.747A pdb=" N PHE T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 122 removed outlier: 3.528A pdb=" N SER T 110 " --> pdb=" O SER T 106 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Proline residue: T 119 - end of helix removed outlier: 3.547A pdb=" N ARG T 122 " --> pdb=" O ILE T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 176 removed outlier: 4.097A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 178 through 182 Processing helix chain 'T' and resid 183 through 197 removed outlier: 3.577A pdb=" N VAL T 188 " --> pdb=" O LEU T 184 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS T 189 " --> pdb=" O ASN T 185 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS T 190 " --> pdb=" O GLU T 186 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY T 191 " --> pdb=" O LEU T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 234 Processing helix chain 'U' and resid 6 through 10 removed outlier: 3.703A pdb=" N LEU U 9 " --> pdb=" O GLY U 6 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER U 10 " --> pdb=" O TYR U 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 6 through 10' Processing helix chain 'U' and resid 20 through 27 Processing helix chain 'U' and resid 27 through 32 removed outlier: 3.529A pdb=" N GLU U 31 " --> pdb=" O MET U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 103 Processing helix chain 'U' and resid 107 through 121 removed outlier: 3.553A pdb=" N ASP U 113 " --> pdb=" O LYS U 109 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 178 removed outlier: 4.209A pdb=" N ALA U 172 " --> pdb=" O ALA U 168 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS U 173 " --> pdb=" O ARG U 169 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU U 175 " --> pdb=" O ALA U 171 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS U 178 " --> pdb=" O THR U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 201 removed outlier: 4.024A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU U 192 " --> pdb=" O ASP U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 244 Processing helix chain 'V' and resid 48 through 71 removed outlier: 3.870A pdb=" N GLU V 69 " --> pdb=" O PHE V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.936A pdb=" N ARG V 89 " --> pdb=" O GLU V 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 134 removed outlier: 3.700A pdb=" N SER V 133 " --> pdb=" O SER V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 135 through 142 Processing helix chain 'V' and resid 148 through 167 removed outlier: 3.677A pdb=" N GLN V 154 " --> pdb=" O GLU V 150 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU V 165 " --> pdb=" O ALA V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 190 through 194 removed outlier: 3.791A pdb=" N ILE V 194 " --> pdb=" O GLY V 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 71 removed outlier: 3.761A pdb=" N LEU W 58 " --> pdb=" O MET W 54 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 90 Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.949A pdb=" N ALA W 136 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 164 removed outlier: 3.522A pdb=" N GLY W 162 " --> pdb=" O ALA W 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 1 through 5 Processing helix chain 'X' and resid 55 through 78 removed outlier: 3.553A pdb=" N LEU X 72 " --> pdb=" O PHE X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 97 removed outlier: 3.649A pdb=" N SER X 88 " --> pdb=" O TYR X 84 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS X 97 " --> pdb=" O LEU X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 153 removed outlier: 4.261A pdb=" N GLY X 147 " --> pdb=" O GLU X 143 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET X 148 " --> pdb=" O GLN X 144 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER X 151 " --> pdb=" O GLY X 147 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU X 152 " --> pdb=" O MET X 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 175 removed outlier: 3.506A pdb=" N GLU X 164 " --> pdb=" O ASP X 160 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 72 removed outlier: 3.627A pdb=" N GLN Y 55 " --> pdb=" O GLY Y 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU Y 58 " --> pdb=" O VAL Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 90 removed outlier: 3.769A pdb=" N ASN Y 87 " --> pdb=" O PHE Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 147 removed outlier: 4.651A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 170 removed outlier: 3.527A pdb=" N GLN Y 168 " --> pdb=" O LEU Y 164 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS Y 169 " --> pdb=" O GLU Y 165 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 71 removed outlier: 3.600A pdb=" N GLN Z 62 " --> pdb=" O LEU Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 89 removed outlier: 3.981A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 removed outlier: 3.556A pdb=" N ALA Z 135 " --> pdb=" O GLY Z 131 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY Z 142 " --> pdb=" O VAL Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 167 removed outlier: 3.641A pdb=" N ASP Z 154 " --> pdb=" O GLU Z 150 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE Z 160 " --> pdb=" O ALA Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 191 through 199 removed outlier: 4.240A pdb=" N GLU Z 197 " --> pdb=" O ALA Z 193 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS Z 198 " --> pdb=" O ASP Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 80 removed outlier: 3.831A pdb=" N LYS a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 99 removed outlier: 3.538A pdb=" N SER a 93 " --> pdb=" O ALA a 89 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR a 94 " --> pdb=" O ALA a 90 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 153 Proline residue: a 147 - end of helix Processing helix chain 'a' and resid 167 through 186 removed outlier: 3.513A pdb=" N MET a 172 " --> pdb=" O LEU a 168 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE a 180 " --> pdb=" O LYS a 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER a 181 " --> pdb=" O ASP a 177 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG a 185 " --> pdb=" O SER a 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 78 removed outlier: 3.543A pdb=" N ILE b 72 " --> pdb=" O GLY b 68 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU b 77 " --> pdb=" O ASP b 73 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 102 removed outlier: 3.753A pdb=" N ARG b 100 " --> pdb=" O MET b 96 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS b 102 " --> pdb=" O SER b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 146 Processing helix chain 'b' and resid 146 through 157 removed outlier: 3.830A 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: 5.847A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 52 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 216 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 removed outlier: 4.567A pdb=" N VAL A 151 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.575A pdb=" N GLY B 36 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 34 " --> pdb=" O MET B 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN B 213 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.617A pdb=" N ILE B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.538A pdb=" N LEU C 44 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 72 through 77 removed outlier: 3.637A pdb=" N SER C 75 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.592A pdb=" N HIS D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.635A pdb=" N VAL D 41 " --> pdb=" O MET D 211 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL D 210 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS D 218 " --> pdb=" O VAL D 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AB1, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 69 removed outlier: 4.165A pdb=" N LEU E 153 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN E 164 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.854A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB5, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB6, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB7, first strand: chain 'G' and resid 66 through 68 Processing sheet with id=AB8, first strand: chain 'H' and resid 125 through 128 removed outlier: 3.590A pdb=" N GLY H 11 " --> pdb=" O PHE H 8 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA H 177 " --> pdb=" O LEU H 14 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.088A pdb=" N THR H 22 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE H 26 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 41 through 47 removed outlier: 3.535A pdb=" N ALA H 101 " --> pdb=" O PHE H 42 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL H 121 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 124 through 127 removed outlier: 7.622A pdb=" N ILE I 173 " --> pdb=" O PRO I 188 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 20 through 22 removed outlier: 5.770A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.694A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA I 97 " --> pdb=" O ALA I 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 213 through 218 removed outlier: 3.537A pdb=" N THR I 213 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA J 9 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 41 through 45 removed outlier: 6.131A pdb=" N LEU J 48 " --> pdb=" O MET J 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 129 through 132 removed outlier: 3.643A pdb=" N LEU K 4 " --> pdb=" O HIS K 132 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL K 15 " --> pdb=" O ARG K 181 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG K 181 " --> pdb=" O VAL K 15 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 35 through 37 removed outlier: 3.905A pdb=" N MET K 118 " --> pdb=" O LEU K 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.861A pdb=" N SER L 188 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N HIS L 178 " --> pdb=" O ARG L 186 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 22 removed outlier: 7.168A pdb=" N ALA L 20 " --> pdb=" O ALA L 27 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.849A pdb=" N LEU L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR L 44 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY L 103 " --> pdb=" O GLY L 110 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.751A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 29 through 31 removed outlier: 7.048A pdb=" N LEU M 29 " --> pdb=" O HIS M 36 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU M 31 " --> pdb=" O SER M 34 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 43 through 45 removed outlier: 3.831A pdb=" N ASN M 108 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 7 through 8 removed outlier: 3.543A pdb=" N GLY N 55 " --> pdb=" O GLY N 8 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 7 through 8 removed outlier: 3.543A pdb=" N GLY N 55 " --> pdb=" O GLY N 8 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 14 through 16 removed outlier: 3.531A pdb=" N GLY N 19 " --> pdb=" O PHE N 16 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE N 187 " --> pdb=" O PRO N 202 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE N 189 " --> pdb=" O GLU N 200 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.848A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR O 52 " --> pdb=" O GLU O 216 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU O 216 " --> pdb=" O THR O 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 69 through 71 removed outlier: 4.566A pdb=" N VAL O 151 " --> pdb=" O PHE O 163 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 159 through 162 removed outlier: 3.575A pdb=" N GLY P 36 " --> pdb=" O THR P 160 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER P 34 " --> pdb=" O MET P 162 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN P 213 " --> pdb=" O GLY P 216 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 65 through 68 removed outlier: 6.616A pdb=" N ILE P 71 " --> pdb=" O ILE P 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 161 through 164 removed outlier: 3.538A pdb=" N LEU Q 44 " --> pdb=" O ILE Q 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 72 through 77 removed outlier: 3.638A pdb=" N SER Q 75 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 10 through 11 removed outlier: 3.591A pdb=" N HIS R 15 " --> pdb=" O SER R 11 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 158 through 161 removed outlier: 3.635A pdb=" N VAL R 41 " --> pdb=" O MET R 211 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL R 210 " --> pdb=" O LYS R 218 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS R 218 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 62 through 64 Processing sheet with id=AE9, first strand: chain 'S' and resid 167 through 170 Processing sheet with id=AF1, first strand: chain 'S' and resid 67 through 69 removed outlier: 4.165A pdb=" N LEU S 153 " --> pdb=" O CYS S 165 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN S 164 " --> pdb=" O ALA T 58 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 158 through 161 removed outlier: 3.854A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 63 through 65 Processing sheet with id=AF4, first strand: chain 'T' and resid 63 through 65 Processing sheet with id=AF5, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AF6, first strand: chain 'U' and resid 66 through 68 Processing sheet with id=AF7, first strand: chain 'V' and resid 125 through 128 removed outlier: 3.590A pdb=" N GLY V 11 " --> pdb=" O PHE V 8 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA V 177 " --> pdb=" O LEU V 14 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.088A pdb=" N THR V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE V 26 " --> pdb=" O THR V 22 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 41 through 47 removed outlier: 3.535A pdb=" N ALA V 101 " --> pdb=" O PHE V 42 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL V 121 " --> pdb=" O SER V 113 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 124 through 127 removed outlier: 7.617A pdb=" N ILE W 173 " --> pdb=" O PRO W 188 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 20 through 22 removed outlier: 5.770A pdb=" N GLU W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL W 26 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.694A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA W 97 " --> pdb=" O ALA W 46 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 213 through 218 removed outlier: 3.536A pdb=" N THR W 213 " --> pdb=" O THR X 198 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA X 9 " --> pdb=" O ASP X 24 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 41 through 45 removed outlier: 6.132A pdb=" N LEU X 48 " --> pdb=" O MET X 44 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 129 through 132 removed outlier: 3.643A pdb=" N LEU Y 4 " --> pdb=" O HIS Y 132 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL Y 15 " --> pdb=" O ARG Y 181 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG Y 181 " --> pdb=" O VAL Y 15 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 35 through 37 removed outlier: 3.905A pdb=" N MET Y 118 " --> pdb=" O LEU Y 102 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 125 through 129 removed outlier: 3.860A pdb=" N SER Z 188 " --> pdb=" O LEU Z 176 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N HIS Z 178 " --> pdb=" O ARG Z 186 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 20 through 22 removed outlier: 7.168A pdb=" N ALA Z 20 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.849A pdb=" N LEU Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR Z 44 " --> pdb=" O MET Z 100 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY Z 103 " --> pdb=" O GLY Z 110 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'a' and resid 135 through 139 removed outlier: 5.752A pdb=" N THR a 11 " --> pdb=" O ASP a 26 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 29 through 31 removed outlier: 7.047A pdb=" N LEU a 29 " --> pdb=" O HIS a 36 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU a 31 " --> pdb=" O SER a 34 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 43 through 45 removed outlier: 3.830A pdb=" N ASN a 108 " --> pdb=" O PHE a 124 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL a 121 " --> pdb=" O ASP a 133 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 7 through 8 removed outlier: 3.544A pdb=" N GLY b 55 " --> pdb=" O GLY b 8 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR b 49 " --> pdb=" O VAL b 45 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 7 through 8 removed outlier: 3.544A pdb=" N GLY b 55 " --> pdb=" O GLY b 8 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 14 through 16 removed outlier: 3.532A pdb=" N GLY b 19 " --> pdb=" O PHE b 16 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE b 187 " --> pdb=" O PRO b 202 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE b 189 " --> pdb=" O GLU b 200 " (cutoff:3.500A) 2438 hydrogen bonds defined for protein. 6927 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: 10.86 Time building geometry restraints manager: 4.75 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: 12846 1.33 - 1.45: 7337 1.45 - 1.57: 25523 1.57 - 1.69: 0 1.69 - 1.81: 462 Bond restraints: 46168 Sorted by residual: bond pdb=" CA GLN O 24 " pdb=" C GLN O 24 " ideal model delta sigma weight residual 1.523 1.497 0.027 1.30e-02 5.92e+03 4.16e+00 bond pdb=" N GLN O 24 " pdb=" CA GLN O 24 " ideal model delta sigma weight residual 1.459 1.437 0.022 1.21e-02 6.83e+03 3.35e+00 bond pdb=" N GLN D 215 " pdb=" CA GLN D 215 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.05e+00 bond pdb=" C SER B 15 " pdb=" O SER B 15 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.33e-02 5.65e+03 2.84e+00 bond pdb=" C GLN O 24 " pdb=" O GLN O 24 " ideal model delta sigma weight residual 1.237 1.219 0.017 1.17e-02 7.31e+03 2.21e+00 ... (remaining 46163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 61173 1.72 - 3.44: 1367 3.44 - 5.15: 131 5.15 - 6.87: 13 6.87 - 8.59: 5 Bond angle restraints: 62689 Sorted by residual: angle pdb=" N SER D 216 " pdb=" CA SER D 216 " pdb=" C SER D 216 " ideal model delta sigma weight residual 110.33 118.92 -8.59 1.29e+00 6.01e-01 4.43e+01 angle pdb=" N ASP A 10 " pdb=" CA ASP A 10 " pdb=" C ASP A 10 " ideal model delta sigma weight residual 111.28 106.23 5.05 1.09e+00 8.42e-01 2.15e+01 angle pdb=" N HIS O 12 " pdb=" CA HIS O 12 " pdb=" C HIS O 12 " ideal model delta sigma weight residual 111.36 115.86 -4.50 1.09e+00 8.42e-01 1.70e+01 angle pdb=" C GLN J 30 " pdb=" N ALA J 31 " pdb=" CA ALA J 31 " ideal model delta sigma weight residual 122.95 117.04 5.91 1.44e+00 4.82e-01 1.68e+01 angle pdb=" C GLN X 30 " pdb=" N ALA X 31 " pdb=" CA ALA X 31 " ideal model delta sigma weight residual 122.95 117.04 5.91 1.44e+00 4.82e-01 1.68e+01 ... (remaining 62684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 26832 16.05 - 32.09: 421 32.09 - 48.14: 123 48.14 - 64.18: 11 64.18 - 80.23: 22 Dihedral angle restraints: 27409 sinusoidal: 9534 harmonic: 17875 Sorted by residual: dihedral pdb=" CA ASN K 24 " pdb=" C ASN K 24 " pdb=" N ILE K 25 " pdb=" CA ILE K 25 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASN Y 24 " pdb=" C ASN Y 24 " pdb=" N ILE Y 25 " pdb=" CA ILE Y 25 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLN F 60 " pdb=" C GLN F 60 " pdb=" N LYS F 61 " pdb=" CA LYS F 61 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 27406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 6025 0.055 - 0.109: 1149 0.109 - 0.164: 160 0.164 - 0.219: 7 0.219 - 0.273: 3 Chirality restraints: 7344 Sorted by residual: chirality pdb=" CA GLN D 215 " pdb=" N GLN D 215 " pdb=" C GLN D 215 " pdb=" CB GLN D 215 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA SER D 216 " pdb=" N SER D 216 " pdb=" C SER D 216 " pdb=" CB SER D 216 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA SER R 216 " pdb=" N SER R 216 " pdb=" C SER R 216 " pdb=" CB SER R 216 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 7341 not shown) Planarity restraints: 7971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 183 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.15e+00 pdb=" C VAL A 183 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL A 183 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS A 184 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL O 183 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C VAL O 183 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL O 183 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS O 184 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER O 17 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO O 18 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO O 18 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO O 18 " -0.031 5.00e-02 4.00e+02 ... (remaining 7968 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 1010 2.70 - 3.25: 43354 3.25 - 3.80: 69704 3.80 - 4.35: 94561 4.35 - 4.90: 160484 Nonbonded interactions: 369113 Sorted by model distance: nonbonded pdb=" O LYS M 49 " pdb=" OG1 THR M 50 " model vdw 2.144 3.040 nonbonded pdb=" O LYS a 49 " pdb=" OG1 THR a 50 " model vdw 2.144 3.040 nonbonded pdb=" OH TYR a 5 " pdb=" O PRO a 103 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR M 5 " pdb=" O PRO M 103 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR D 31 " pdb=" O ARG D 163 " model vdw 2.233 3.040 ... (remaining 369108 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' and resid 5 through 242) selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.050 Extract box with map and model: 0.590 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 41.820 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.210 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.003 0.038 46168 Z= 0.147 Angle : 0.634 8.590 62689 Z= 0.408 Chirality : 0.044 0.273 7344 Planarity : 0.004 0.059 7971 Dihedral : 7.813 80.226 15997 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.95 % Rotamer: Outliers : 0.02 % Allowed : 0.37 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.89 (0.09), residues: 6139 helix: -3.35 (0.07), residues: 2162 sheet: -0.87 (0.12), residues: 1470 loop : -0.91 (0.11), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 141 TYR 0.018 0.001 TYR V 136 PHE 0.020 0.001 PHE K 171 TRP 0.028 0.002 TRP G 215 HIS 0.007 0.001 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.00259 (46168) covalent geometry : angle 0.63353 (62689) hydrogen bonds : bond 0.28505 ( 2420) hydrogen bonds : angle 9.60123 ( 6927) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1782 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1781 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7132 (m-30) cc_final: 0.6520 (m-30) REVERT: B 70 HIS cc_start: 0.5995 (p-80) cc_final: 0.5719 (p-80) REVERT: B 71 ILE cc_start: 0.9049 (mt) cc_final: 0.8564 (mt) REVERT: B 94 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7438 (mm110) REVERT: C 6 ASP cc_start: 0.7582 (t0) cc_final: 0.7180 (t0) REVERT: D 110 TYR cc_start: 0.7905 (t80) cc_final: 0.7362 (t80) REVERT: E 13 ASN cc_start: 0.8643 (m-40) cc_final: 0.8337 (m-40) REVERT: G 81 LEU cc_start: 0.8248 (tp) cc_final: 0.7828 (tp) REVERT: G 118 TYR cc_start: 0.7407 (t80) cc_final: 0.7181 (t80) REVERT: H 53 GLN cc_start: 0.7977 (mt0) cc_final: 0.7528 (mt0) REVERT: I 209 THR cc_start: 0.7671 (m) cc_final: 0.7336 (t) REVERT: J 4 SER cc_start: 0.8318 (p) cc_final: 0.8065 (t) REVERT: J 192 ASP cc_start: 0.7304 (p0) cc_final: 0.6942 (p0) REVERT: K 62 LYS cc_start: 0.8355 (ttpp) cc_final: 0.8132 (tttm) REVERT: K 63 ASN cc_start: 0.8178 (m110) cc_final: 0.7879 (m-40) REVERT: K 87 ASN cc_start: 0.7739 (p0) cc_final: 0.7265 (p0) REVERT: K 90 ASP cc_start: 0.7162 (p0) cc_final: 0.6891 (p0) REVERT: K 101 ASN cc_start: 0.7281 (m110) cc_final: 0.7078 (m-40) REVERT: K 139 THR cc_start: 0.8482 (p) cc_final: 0.8108 (p) REVERT: L 33 LYS cc_start: 0.8335 (mttt) cc_final: 0.8080 (mttt) REVERT: M 91 MET cc_start: 0.7716 (ttp) cc_final: 0.7375 (ttm) REVERT: O 39 SER cc_start: 0.8419 (m) cc_final: 0.8210 (m) REVERT: P 57 ASP cc_start: 0.6948 (t0) cc_final: 0.6631 (t0) REVERT: Q 107 CYS cc_start: 0.7361 (m) cc_final: 0.6909 (m) REVERT: R 110 TYR cc_start: 0.7834 (t80) cc_final: 0.6910 (t80) REVERT: S 89 ILE cc_start: 0.8541 (pt) cc_final: 0.8211 (mt) REVERT: T 147 THR cc_start: 0.8187 (p) cc_final: 0.7984 (m) REVERT: V 90 TYR cc_start: 0.7476 (m-80) cc_final: 0.7117 (m-80) REVERT: V 99 ILE cc_start: 0.8926 (tt) cc_final: 0.8602 (mt) REVERT: W 53 ASP cc_start: 0.6460 (m-30) cc_final: 0.6189 (m-30) REVERT: X 164 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6613 (mm-30) REVERT: X 180 SER cc_start: 0.8475 (m) cc_final: 0.7746 (m) REVERT: Y 61 GLN cc_start: 0.7678 (tt0) cc_final: 0.6482 (tt0) REVERT: Y 62 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8119 (tttp) REVERT: Y 90 ASP cc_start: 0.7314 (p0) cc_final: 0.7058 (p0) REVERT: Y 108 ASP cc_start: 0.6930 (t0) cc_final: 0.4385 (t0) REVERT: Y 177 THR cc_start: 0.7623 (p) cc_final: 0.7098 (p) REVERT: a 75 TYR cc_start: 0.8328 (t80) cc_final: 0.8016 (t80) outliers start: 1 outliers final: 0 residues processed: 1782 average time/residue: 0.2911 time to fit residues: 819.0369 Evaluate side-chains 1101 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1101 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 0.0170 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 523 optimal weight: 0.8980 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 9.9990 chunk 597 optimal weight: 8.9990 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 193 GLN B 87 HIS B 108 GLN B 111 GLN B 147 GLN C 40 ASN C 109 GLN C 167 ASN D 54 GLN D 154 HIS E 23 GLN E 152 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 HIS F 166 GLN H 7 GLN I 66 HIS I 91 GLN J 60 GLN J 92 ASN K 63 ASN K 101 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 GLN L 62 GLN L 85 ASN M 8 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 146 GLN N 61 GLN N 81 HIS N 89 HIS N 108 ASN N 147 GLN N 185 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 GLN O 128 ASN ** O 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN Q 88 ASN R 54 GLN R 120 GLN S 23 GLN T 43 HIS W 66 HIS X 92 ASN Y 32 HIS Y 63 ASN a 79 ASN a 131 GLN a 146 GLN b 81 HIS b 89 HIS ** b 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.071394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.059016 restraints weight = 140291.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.061483 restraints weight = 63422.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.063148 restraints weight = 36742.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.064229 restraints weight = 24810.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.065038 restraints weight = 18665.425| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 46168 Z= 0.182 Angle : 0.690 9.977 62689 Z= 0.367 Chirality : 0.046 0.243 7344 Planarity : 0.005 0.054 7971 Dihedral : 4.677 27.524 6785 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 2.53 % Allowed : 13.10 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.92 (0.10), residues: 6139 helix: -0.45 (0.10), residues: 2200 sheet: -0.43 (0.12), residues: 1482 loop : -0.64 (0.11), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 89 TYR 0.028 0.002 TYR Q 97 PHE 0.030 0.002 PHE E 162 TRP 0.023 0.002 TRP G 215 HIS 0.012 0.001 HIS E 227 Details of bonding type rmsd covalent geometry : bond 0.00403 (46168) covalent geometry : angle 0.69013 (62689) hydrogen bonds : bond 0.04968 ( 2420) hydrogen bonds : angle 5.61583 ( 6927) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1160 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.9076 (mp) cc_final: 0.8862 (mp) REVERT: A 92 GLN cc_start: 0.9049 (tp40) cc_final: 0.8591 (tp-100) REVERT: A 123 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8778 (tm-30) REVERT: A 150 GLN cc_start: 0.7390 (mm-40) cc_final: 0.7091 (mm-40) REVERT: B 10 THR cc_start: 0.9159 (m) cc_final: 0.8873 (p) REVERT: B 48 GLU cc_start: 0.8464 (tm-30) cc_final: 0.7597 (tm-30) REVERT: B 70 HIS cc_start: 0.7996 (p-80) cc_final: 0.7747 (p-80) REVERT: B 71 ILE cc_start: 0.9187 (mt) cc_final: 0.8909 (mt) REVERT: B 122 GLN cc_start: 0.9053 (tt0) cc_final: 0.8674 (tp40) REVERT: B 147 GLN cc_start: 0.8329 (tt0) cc_final: 0.7542 (tm-30) REVERT: B 155 PHE cc_start: 0.8246 (m-80) cc_final: 0.7863 (m-10) REVERT: B 160 THR cc_start: 0.9139 (t) cc_final: 0.8713 (t) REVERT: B 218 ARG cc_start: 0.9241 (tmm-80) cc_final: 0.8919 (tmm-80) REVERT: C 25 MET cc_start: 0.8784 (mmt) cc_final: 0.8419 (mmp) REVERT: C 26 GLU cc_start: 0.8742 (tp30) cc_final: 0.8399 (tp30) REVERT: C 136 TYR cc_start: 0.8487 (m-80) cc_final: 0.8167 (m-80) REVERT: C 206 LEU cc_start: 0.8861 (mp) cc_final: 0.8560 (mp) REVERT: D 21 TYR cc_start: 0.8971 (m-80) cc_final: 0.8519 (m-80) REVERT: D 66 ASP cc_start: 0.8414 (t0) cc_final: 0.8136 (t0) REVERT: D 110 TYR cc_start: 0.8590 (t80) cc_final: 0.8352 (t80) REVERT: D 116 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8840 (tm-30) REVERT: D 122 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7825 (t0) REVERT: D 146 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7112 (tm-30) REVERT: D 190 LEU cc_start: 0.9346 (tp) cc_final: 0.9145 (tp) REVERT: E 13 ASN cc_start: 0.9265 (m-40) cc_final: 0.9006 (m-40) REVERT: E 29 GLU cc_start: 0.8571 (tp30) cc_final: 0.8019 (tm-30) REVERT: E 152 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7734 (mp10) REVERT: E 225 ASN cc_start: 0.8795 (p0) cc_final: 0.8557 (p0) REVERT: F 117 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8726 (tp40) REVERT: F 176 MET cc_start: 0.8032 (tmm) cc_final: 0.7762 (tmm) REVERT: F 182 CYS cc_start: 0.8117 (m) cc_final: 0.7319 (m) REVERT: G 27 MET cc_start: 0.8221 (ppp) cc_final: 0.7758 (mtt) REVERT: G 70 ASP cc_start: 0.9038 (t70) cc_final: 0.8691 (t70) REVERT: G 105 ASN cc_start: 0.9234 (m-40) cc_final: 0.8930 (m110) REVERT: G 136 MET cc_start: 0.8430 (mtp) cc_final: 0.7810 (mtp) REVERT: G 175 GLU cc_start: 0.9050 (mp0) cc_final: 0.8603 (mp0) REVERT: G 179 LEU cc_start: 0.9031 (tp) cc_final: 0.8812 (tt) REVERT: H 51 ASP cc_start: 0.9008 (m-30) cc_final: 0.8553 (p0) REVERT: H 90 TYR cc_start: 0.8598 (m-10) cc_final: 0.8201 (m-10) REVERT: H 95 MET cc_start: 0.8230 (tmm) cc_final: 0.6648 (tmm) REVERT: H 110 GLN cc_start: 0.8272 (mt0) cc_final: 0.7929 (mt0) REVERT: H 120 MET cc_start: 0.8723 (ttm) cc_final: 0.8461 (ttm) REVERT: I 24 MET cc_start: 0.8578 (ppp) cc_final: 0.8362 (ppp) REVERT: I 53 ASP cc_start: 0.8731 (t0) cc_final: 0.8129 (t0) REVERT: I 57 GLN cc_start: 0.8357 (mt0) cc_final: 0.8030 (mt0) REVERT: I 91 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: I 139 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8632 (mm-30) REVERT: I 174 ASP cc_start: 0.8326 (t0) cc_final: 0.7725 (m-30) REVERT: J 79 ARG cc_start: 0.8895 (ptp90) cc_final: 0.8232 (ttp80) REVERT: J 144 GLN cc_start: 0.9315 (mp10) cc_final: 0.8232 (mp10) REVERT: J 150 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8710 (mm-30) REVERT: J 164 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8245 (mm-30) REVERT: J 177 ASP cc_start: 0.8336 (t0) cc_final: 0.8135 (t0) REVERT: J 192 ASP cc_start: 0.8560 (p0) cc_final: 0.8287 (p0) REVERT: K 8 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7760 (tm-30) REVERT: K 37 LYS cc_start: 0.8659 (ptmm) cc_final: 0.8074 (tttp) REVERT: K 141 SER cc_start: 0.9441 (m) cc_final: 0.9218 (p) REVERT: K 160 LEU cc_start: 0.9422 (tt) cc_final: 0.9217 (tt) REVERT: L 7 LYS cc_start: 0.8895 (ttpp) cc_final: 0.8322 (ttmm) REVERT: L 33 LYS cc_start: 0.8393 (mttt) cc_final: 0.8004 (mttt) REVERT: L 175 ASN cc_start: 0.8711 (m-40) cc_final: 0.8105 (t0) REVERT: M 131 GLN cc_start: 0.7278 (tm-30) cc_final: 0.7052 (tm-30) REVERT: M 157 ASN cc_start: 0.8779 (m110) cc_final: 0.8571 (m-40) REVERT: N 26 MET cc_start: 0.8700 (mtm) cc_final: 0.8323 (mpp) REVERT: N 62 TYR cc_start: 0.9350 (t80) cc_final: 0.9140 (t80) REVERT: N 79 ASP cc_start: 0.8119 (p0) cc_final: 0.7907 (p0) REVERT: N 170 GLU cc_start: 0.8351 (pp20) cc_final: 0.8093 (pp20) REVERT: N 180 ASP cc_start: 0.8975 (t0) cc_final: 0.8691 (t0) REVERT: O 166 THR cc_start: 0.8132 (m) cc_final: 0.7703 (p) REVERT: O 174 GLU cc_start: 0.8834 (mp0) cc_final: 0.8551 (mp0) REVERT: O 216 GLU cc_start: 0.7235 (pt0) cc_final: 0.7005 (pm20) REVERT: P 85 LEU cc_start: 0.9282 (tt) cc_final: 0.8919 (tp) REVERT: P 94 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8784 (mm-40) REVERT: P 122 GLN cc_start: 0.9080 (tt0) cc_final: 0.8621 (tp40) REVERT: P 207 ILE cc_start: 0.9100 (pt) cc_final: 0.8897 (pt) REVERT: Q 26 GLU cc_start: 0.8913 (mp0) cc_final: 0.8669 (mp0) REVERT: Q 66 TYR cc_start: 0.8059 (m-80) cc_final: 0.7745 (m-80) REVERT: Q 136 TYR cc_start: 0.7931 (m-80) cc_final: 0.7653 (m-80) REVERT: Q 198 ASN cc_start: 0.8725 (m-40) cc_final: 0.7886 (m110) REVERT: Q 232 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8782 (mp0) REVERT: R 90 GLU cc_start: 0.9175 (tp30) cc_final: 0.8452 (tt0) REVERT: S 51 GLU cc_start: 0.8001 (tt0) cc_final: 0.7493 (tp30) REVERT: S 89 ILE cc_start: 0.9545 (pt) cc_final: 0.9241 (mt) REVERT: S 107 MET cc_start: 0.9080 (tpp) cc_final: 0.8803 (ttm) REVERT: S 114 GLN cc_start: 0.9099 (tt0) cc_final: 0.8856 (pt0) REVERT: S 156 MET cc_start: 0.8038 (ttm) cc_final: 0.7300 (ttt) REVERT: S 225 ASN cc_start: 0.9159 (p0) cc_final: 0.8937 (p0) REVERT: T 21 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8674 (mm-40) REVERT: T 117 GLN cc_start: 0.9017 (tp40) cc_final: 0.8742 (tp40) REVERT: T 176 MET cc_start: 0.8344 (tmm) cc_final: 0.8035 (tmm) REVERT: U 75 MET cc_start: 0.8470 (ttt) cc_final: 0.8254 (ttt) REVERT: U 135 PHE cc_start: 0.8761 (p90) cc_final: 0.8310 (p90) REVERT: U 184 MET cc_start: 0.7460 (mtp) cc_final: 0.7102 (mtp) REVERT: U 236 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8972 (pt0) REVERT: V 89 ARG cc_start: 0.8724 (mtm110) cc_final: 0.8287 (mtm110) REVERT: V 90 TYR cc_start: 0.8772 (m-10) cc_final: 0.8265 (m-80) REVERT: V 95 MET cc_start: 0.7076 (tmm) cc_final: 0.6606 (tmm) REVERT: V 99 ILE cc_start: 0.9036 (tt) cc_final: 0.8628 (mt) REVERT: V 104 ASP cc_start: 0.8415 (p0) cc_final: 0.7965 (p0) REVERT: W 24 MET cc_start: 0.8164 (ppp) cc_final: 0.7934 (ppp) REVERT: W 57 GLN cc_start: 0.8535 (mt0) cc_final: 0.8226 (mt0) REVERT: W 89 ARG cc_start: 0.8821 (ttp80) cc_final: 0.8564 (ttp80) REVERT: W 139 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8762 (mm-30) REVERT: W 148 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8043 (mm-30) REVERT: X 13 MET cc_start: 0.8367 (ttp) cc_final: 0.8062 (ttp) REVERT: X 117 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8984 (mmmm) REVERT: X 150 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8066 (mt-10) REVERT: X 164 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7814 (tp30) REVERT: X 170 MET cc_start: 0.8908 (mmm) cc_final: 0.8570 (mmm) REVERT: Y 37 LYS cc_start: 0.8731 (tttp) cc_final: 0.8481 (tttp) REVERT: Y 52 ASP cc_start: 0.8709 (m-30) cc_final: 0.8427 (t0) REVERT: Y 55 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8963 (mm-40) REVERT: Y 61 GLN cc_start: 0.9237 (tt0) cc_final: 0.9028 (tt0) REVERT: Z 36 GLU cc_start: 0.8381 (mp0) cc_final: 0.8139 (mp0) REVERT: Z 62 GLN cc_start: 0.9514 (mm-40) cc_final: 0.9257 (mm-40) REVERT: Z 85 ASN cc_start: 0.9026 (m-40) cc_final: 0.8780 (m110) REVERT: Z 97 MET cc_start: 0.8326 (ttp) cc_final: 0.8033 (tmm) REVERT: Z 99 THR cc_start: 0.8091 (t) cc_final: 0.7748 (m) REVERT: Z 102 CYS cc_start: 0.8806 (m) cc_final: 0.8417 (m) REVERT: a 130 TYR cc_start: 0.8246 (t80) cc_final: 0.8034 (t80) REVERT: a 131 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: a 205 GLU cc_start: 0.7213 (tp30) cc_final: 0.6992 (tp30) REVERT: b 56 ASP cc_start: 0.8677 (t0) cc_final: 0.8310 (t0) REVERT: b 76 LEU cc_start: 0.9143 (mt) cc_final: 0.8884 (mt) REVERT: b 104 ASN cc_start: 0.8370 (t0) cc_final: 0.8118 (t0) REVERT: b 173 MET cc_start: 0.8731 (tpt) cc_final: 0.8343 (mmt) REVERT: b 180 ASP cc_start: 0.8449 (t0) cc_final: 0.7950 (t0) outliers start: 108 outliers final: 51 residues processed: 1221 average time/residue: 0.2629 time to fit residues: 527.4808 Evaluate side-chains 1062 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 1007 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 187 LYS Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain T residue 85 CYS Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 131 GLN Chi-restraints excluded: chain a residue 146 GLN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 204 optimal weight: 9.9990 chunk 383 optimal weight: 8.9990 chunk 565 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 518 optimal weight: 5.9990 chunk 431 optimal weight: 7.9990 chunk 389 optimal weight: 8.9990 chunk 313 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN B 111 GLN C 230 GLN D 18 GLN E 118 ASN E 152 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN G 22 GLN G 32 ASN G 110 HIS H 38 HIS H 53 GLN J 17 ASN J 80 GLN J 92 ASN J 156 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN M 8 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 ASN N 188 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 GLN P 51 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN V 53 GLN ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 ASN X 168 GLN ** Y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN a 8 ASN a 79 ASN a 146 GLN b 65 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.065422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.053475 restraints weight = 143779.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.055748 restraints weight = 65117.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.057288 restraints weight = 38075.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.058332 restraints weight = 25997.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.059080 restraints weight = 19533.875| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 46168 Z= 0.236 Angle : 0.665 10.216 62689 Z= 0.352 Chirality : 0.045 0.269 7344 Planarity : 0.005 0.058 7971 Dihedral : 4.670 27.499 6785 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.23 % Favored : 97.75 % Rotamer: Outliers : 3.07 % Allowed : 14.81 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.12 (0.10), residues: 6139 helix: 0.61 (0.11), residues: 2226 sheet: -0.26 (0.13), residues: 1482 loop : -0.45 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 144 TYR 0.021 0.002 TYR Q 136 PHE 0.026 0.002 PHE A 191 TRP 0.028 0.002 TRP G 215 HIS 0.009 0.001 HIS E 227 Details of bonding type rmsd covalent geometry : bond 0.00532 (46168) covalent geometry : angle 0.66488 (62689) hydrogen bonds : bond 0.04166 ( 2420) hydrogen bonds : angle 5.07349 ( 6927) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1052 time to evaluate : 1.426 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 123 GLN cc_start: 0.9468 (tm-30) cc_final: 0.9074 (tm-30) REVERT: A 159 TYR cc_start: 0.8159 (t80) cc_final: 0.7906 (t80) REVERT: B 10 THR cc_start: 0.9019 (m) cc_final: 0.8807 (p) REVERT: B 48 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7670 (tm-30) REVERT: B 70 HIS cc_start: 0.8328 (p-80) cc_final: 0.8106 (p-80) REVERT: B 71 ILE cc_start: 0.9149 (mt) cc_final: 0.8852 (mt) REVERT: B 94 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8937 (mm110) REVERT: B 117 MET cc_start: 0.9189 (ttm) cc_final: 0.8954 (ttm) REVERT: B 122 GLN cc_start: 0.8949 (tt0) cc_final: 0.8541 (tp40) REVERT: B 155 PHE cc_start: 0.8357 (m-80) cc_final: 0.8039 (m-10) REVERT: B 160 THR cc_start: 0.9289 (t) cc_final: 0.8884 (m) REVERT: B 218 ARG cc_start: 0.9320 (tmm-80) cc_final: 0.8956 (tmm-80) REVERT: B 224 GLU cc_start: 0.9207 (mp0) cc_final: 0.8929 (mp0) REVERT: C 25 MET cc_start: 0.8936 (mmt) cc_final: 0.8540 (mmp) REVERT: C 26 GLU cc_start: 0.8676 (tp30) cc_final: 0.8329 (tp30) REVERT: C 184 MET cc_start: 0.6986 (mpp) cc_final: 0.6781 (mmt) REVERT: D 66 ASP cc_start: 0.8829 (t0) cc_final: 0.8614 (t0) REVERT: D 110 TYR cc_start: 0.8627 (t80) cc_final: 0.8382 (t80) REVERT: D 116 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8771 (tm-30) REVERT: D 122 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8023 (t0) REVERT: D 146 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7805 (tm-30) REVERT: D 190 LEU cc_start: 0.9503 (tp) cc_final: 0.9294 (tp) REVERT: E 13 ASN cc_start: 0.9324 (m-40) cc_final: 0.9080 (m-40) REVERT: E 51 GLU cc_start: 0.6839 (tt0) cc_final: 0.6486 (tt0) REVERT: E 216 GLU cc_start: 0.6879 (tt0) cc_final: 0.6676 (tt0) REVERT: E 225 ASN cc_start: 0.8832 (p0) cc_final: 0.8581 (p0) REVERT: F 27 GLU cc_start: 0.9104 (tp30) cc_final: 0.8593 (tm-30) REVERT: F 117 GLN cc_start: 0.9140 (tm-30) cc_final: 0.8784 (tp40) REVERT: F 182 CYS cc_start: 0.8094 (m) cc_final: 0.7314 (m) REVERT: G 47 PHE cc_start: 0.9197 (m-80) cc_final: 0.8880 (m-80) REVERT: G 136 MET cc_start: 0.8557 (mtp) cc_final: 0.8336 (mtp) REVERT: G 175 GLU cc_start: 0.9117 (mp0) cc_final: 0.8535 (mp0) REVERT: G 179 LEU cc_start: 0.9006 (tp) cc_final: 0.8648 (tt) REVERT: H 62 GLN cc_start: 0.9332 (mm-40) cc_final: 0.9056 (mm-40) REVERT: H 90 TYR cc_start: 0.8714 (m-10) cc_final: 0.8404 (m-80) REVERT: H 116 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8118 (mmt) REVERT: H 134 TYR cc_start: 0.9057 (m-80) cc_final: 0.8762 (m-80) REVERT: I 24 MET cc_start: 0.8415 (ppp) cc_final: 0.8028 (ppp) REVERT: I 53 ASP cc_start: 0.8771 (t0) cc_final: 0.8224 (t0) REVERT: I 57 GLN cc_start: 0.8475 (mt0) cc_final: 0.8139 (mt0) REVERT: I 91 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: I 139 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8633 (mm-30) REVERT: J 88 SER cc_start: 0.9423 (m) cc_final: 0.9113 (t) REVERT: J 143 GLU cc_start: 0.8679 (pm20) cc_final: 0.8449 (pm20) REVERT: J 144 GLN cc_start: 0.9465 (mp10) cc_final: 0.8278 (mp10) REVERT: J 164 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8286 (mm-30) REVERT: J 192 ASP cc_start: 0.8601 (p0) cc_final: 0.8366 (p0) REVERT: K 37 LYS cc_start: 0.8896 (ptmm) cc_final: 0.8253 (tttm) REVERT: K 59 TYR cc_start: 0.8972 (t80) cc_final: 0.8503 (t80) REVERT: K 86 ARG cc_start: 0.9313 (tpp-160) cc_final: 0.8808 (tpp80) REVERT: K 163 CYS cc_start: 0.9407 (m) cc_final: 0.9048 (m) REVERT: M 196 CYS cc_start: 0.8595 (m) cc_final: 0.8346 (m) REVERT: N 170 GLU cc_start: 0.8392 (pp20) cc_final: 0.8065 (pp20) REVERT: N 180 ASP cc_start: 0.9102 (t0) cc_final: 0.8808 (t0) REVERT: N 188 GLN cc_start: 0.8243 (mt0) cc_final: 0.7858 (mt0) REVERT: O 19 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8605 (mp0) REVERT: O 150 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: O 159 TYR cc_start: 0.8024 (t80) cc_final: 0.7740 (t80) REVERT: O 174 GLU cc_start: 0.8930 (mp0) cc_final: 0.8671 (mp0) REVERT: O 224 ASN cc_start: 0.8724 (p0) cc_final: 0.8422 (p0) REVERT: P 63 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8289 (mtpt) REVERT: P 78 MET cc_start: 0.8164 (mtp) cc_final: 0.7749 (ptp) REVERT: P 81 ASP cc_start: 0.8616 (m-30) cc_final: 0.7943 (m-30) REVERT: P 122 GLN cc_start: 0.9134 (tt0) cc_final: 0.8585 (tp40) REVERT: P 195 LYS cc_start: 0.9392 (mmmm) cc_final: 0.9166 (mmmm) REVERT: P 207 ILE cc_start: 0.9339 (pt) cc_final: 0.9139 (pt) REVERT: Q 26 GLU cc_start: 0.8860 (mp0) cc_final: 0.8618 (mp0) REVERT: Q 66 TYR cc_start: 0.8134 (m-80) cc_final: 0.7702 (m-80) REVERT: Q 84 ASN cc_start: 0.9380 (m110) cc_final: 0.9137 (m110) REVERT: Q 88 ASN cc_start: 0.8587 (p0) cc_final: 0.8302 (p0) REVERT: R 20 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7954 (tm-30) REVERT: R 23 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8201 (pp30) REVERT: R 66 ASP cc_start: 0.8142 (t0) cc_final: 0.7235 (t0) REVERT: R 90 GLU cc_start: 0.9328 (tp30) cc_final: 0.8811 (tt0) REVERT: R 118 TYR cc_start: 0.8893 (m-10) cc_final: 0.8656 (m-10) REVERT: R 157 LYS cc_start: 0.9287 (mttt) cc_final: 0.9004 (mtmt) REVERT: S 69 GLU cc_start: 0.7994 (tt0) cc_final: 0.7688 (tt0) REVERT: S 89 ILE cc_start: 0.9563 (pt) cc_final: 0.9289 (mt) REVERT: S 192 LYS cc_start: 0.9288 (ptmm) cc_final: 0.9003 (ptmm) REVERT: S 225 ASN cc_start: 0.9199 (p0) cc_final: 0.8926 (p0) REVERT: T 26 MET cc_start: 0.8839 (tpp) cc_final: 0.8467 (tpp) REVERT: T 27 GLU cc_start: 0.9029 (tp30) cc_final: 0.8591 (tm-30) REVERT: T 117 GLN cc_start: 0.9257 (tp40) cc_final: 0.8926 (tp40) REVERT: T 176 MET cc_start: 0.8278 (tmm) cc_final: 0.7901 (tmm) REVERT: U 75 MET cc_start: 0.8504 (ttt) cc_final: 0.8247 (ttt) REVERT: U 135 PHE cc_start: 0.8923 (p90) cc_final: 0.8443 (p90) REVERT: U 179 LEU cc_start: 0.9072 (tt) cc_final: 0.8763 (tt) REVERT: U 184 MET cc_start: 0.7595 (mtp) cc_final: 0.7249 (mtp) REVERT: U 236 GLU cc_start: 0.9332 (mt-10) cc_final: 0.9034 (pt0) REVERT: V 53 GLN cc_start: 0.9233 (mt0) cc_final: 0.8964 (mt0) REVERT: V 90 TYR cc_start: 0.8697 (m-10) cc_final: 0.8358 (m-80) REVERT: V 104 ASP cc_start: 0.8388 (p0) cc_final: 0.8036 (p0) REVERT: V 107 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8122 (tm-30) REVERT: W 89 ARG cc_start: 0.8876 (ttp80) cc_final: 0.8593 (ttp80) REVERT: X 13 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8252 (ttp) REVERT: X 105 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8136 (mp0) REVERT: X 150 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8370 (mt-10) REVERT: X 182 MET cc_start: 0.8599 (mmm) cc_final: 0.8153 (mmm) REVERT: Y 37 LYS cc_start: 0.9020 (tttp) cc_final: 0.8771 (tttp) REVERT: Y 52 ASP cc_start: 0.8616 (m-30) cc_final: 0.8126 (t0) REVERT: Y 108 ASP cc_start: 0.8218 (t0) cc_final: 0.7794 (t0) REVERT: Y 111 GLU cc_start: 0.7809 (mp0) cc_final: 0.7244 (mp0) REVERT: Z 36 GLU cc_start: 0.8341 (mp0) cc_final: 0.8008 (mp0) REVERT: a 127 VAL cc_start: 0.9441 (m) cc_final: 0.9116 (p) REVERT: a 131 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8011 (tm-30) REVERT: a 188 TYR cc_start: 0.9408 (m-80) cc_final: 0.9140 (m-80) REVERT: b 76 LEU cc_start: 0.9251 (mt) cc_final: 0.9023 (mt) REVERT: b 104 ASN cc_start: 0.8369 (t0) cc_final: 0.7958 (t0) REVERT: b 173 MET cc_start: 0.8818 (tpt) cc_final: 0.8421 (mmt) REVERT: b 180 ASP cc_start: 0.8889 (t0) cc_final: 0.8547 (t0) REVERT: b 200 GLU cc_start: 0.7570 (mp0) cc_final: 0.7346 (mp0) outliers start: 131 outliers final: 78 residues processed: 1121 average time/residue: 0.2576 time to fit residues: 475.9104 Evaluate side-chains 1039 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 956 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 186 ARG Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 150 GLN Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 193 THR Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 187 LYS Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 133 MET Chi-restraints excluded: chain S residue 203 LYS Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain X residue 13 MET Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 79 ARG Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Y residue 188 ILE Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 384 optimal weight: 6.9990 chunk 367 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 82 optimal weight: 0.0050 chunk 254 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 119 optimal weight: 0.0040 chunk 241 optimal weight: 3.9990 chunk 434 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 overall best weight: 2.8012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 100 ASN A 193 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 147 GLN C 88 ASN E 118 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN F 86 ASN F 166 GLN G 110 HIS H 154 GLN I 91 GLN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 GLN P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** S 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 180 GLN ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 ASN Y 61 GLN a 8 ASN ** a 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.065236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.053391 restraints weight = 143465.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.055666 restraints weight = 64356.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.057213 restraints weight = 37431.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.058272 restraints weight = 25368.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.059017 restraints weight = 18985.983| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 46168 Z= 0.165 Angle : 0.618 9.767 62689 Z= 0.323 Chirality : 0.044 0.177 7344 Planarity : 0.004 0.060 7971 Dihedral : 4.546 30.585 6785 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.12 % Favored : 97.87 % Rotamer: Outliers : 2.84 % Allowed : 16.26 % Favored : 80.90 % 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: 0.24 (0.10), residues: 6139 helix: 1.07 (0.11), residues: 2231 sheet: -0.10 (0.13), residues: 1462 loop : -0.41 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 9 TYR 0.023 0.001 TYR R 21 PHE 0.023 0.001 PHE T 87 TRP 0.023 0.001 TRP G 215 HIS 0.009 0.001 HIS E 227 Details of bonding type rmsd covalent geometry : bond 0.00372 (46168) covalent geometry : angle 0.61770 (62689) hydrogen bonds : bond 0.03623 ( 2420) hydrogen bonds : angle 4.84337 ( 6927) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 1047 time to evaluate : 1.628 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: A 23 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.6573 (t80) REVERT: A 39 SER cc_start: 0.9434 (m) cc_final: 0.8968 (p) REVERT: A 123 GLN cc_start: 0.9460 (tm-30) cc_final: 0.8877 (tm-30) REVERT: A 224 ASN cc_start: 0.8747 (p0) cc_final: 0.8422 (p0) REVERT: B 10 THR cc_start: 0.9023 (m) cc_final: 0.8810 (p) REVERT: B 48 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 71 ILE cc_start: 0.9070 (mt) cc_final: 0.8842 (mt) REVERT: B 112 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8677 (mtt90) REVERT: B 117 MET cc_start: 0.9120 (ttm) cc_final: 0.8867 (ttm) REVERT: B 147 GLN cc_start: 0.8315 (tt0) cc_final: 0.7816 (tm-30) REVERT: B 155 PHE cc_start: 0.8332 (m-80) cc_final: 0.7831 (m-10) REVERT: B 160 THR cc_start: 0.9301 (t) cc_final: 0.8740 (m) REVERT: B 208 GLU cc_start: 0.8519 (tp30) cc_final: 0.8222 (tp30) REVERT: B 218 ARG cc_start: 0.9286 (tmm-80) cc_final: 0.8877 (tmm-80) REVERT: B 219 ARG cc_start: 0.9541 (ptp90) cc_final: 0.9320 (ttp80) REVERT: B 224 GLU cc_start: 0.9116 (mp0) cc_final: 0.8827 (mp0) REVERT: C 25 MET cc_start: 0.8910 (mmt) cc_final: 0.8564 (mmp) REVERT: C 26 GLU cc_start: 0.8659 (tp30) cc_final: 0.8413 (tp30) REVERT: C 30 HIS cc_start: 0.8566 (m-70) cc_final: 0.7986 (m-70) REVERT: D 55 ASP cc_start: 0.8544 (t0) cc_final: 0.8248 (t0) REVERT: D 66 ASP cc_start: 0.8833 (t0) cc_final: 0.8160 (t0) REVERT: D 90 GLU cc_start: 0.9135 (tp30) cc_final: 0.8648 (tp30) REVERT: D 110 TYR cc_start: 0.8602 (t80) cc_final: 0.8294 (t80) REVERT: D 116 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8794 (tm-30) REVERT: D 120 GLN cc_start: 0.8565 (tt0) cc_final: 0.8185 (tt0) REVERT: D 146 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7929 (tm-30) REVERT: D 190 LEU cc_start: 0.9539 (tp) cc_final: 0.9307 (tp) REVERT: E 29 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8129 (tm-30) REVERT: E 51 GLU cc_start: 0.7284 (tt0) cc_final: 0.6892 (tt0) REVERT: E 59 MET cc_start: 0.8530 (mtp) cc_final: 0.8156 (ptp) REVERT: E 118 ASN cc_start: 0.9090 (m-40) cc_final: 0.8862 (m110) REVERT: E 133 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.6946 (mmm) REVERT: E 189 MET cc_start: 0.8105 (ptp) cc_final: 0.7763 (ptp) REVERT: E 216 GLU cc_start: 0.6812 (tt0) cc_final: 0.6575 (tt0) REVERT: E 225 ASN cc_start: 0.8911 (p0) cc_final: 0.8628 (p0) REVERT: F 26 MET cc_start: 0.8587 (ttm) cc_final: 0.8238 (mmm) REVERT: F 27 GLU cc_start: 0.9115 (tp30) cc_final: 0.8647 (tm-30) REVERT: F 145 PHE cc_start: 0.9016 (m-80) cc_final: 0.8745 (m-80) REVERT: F 182 CYS cc_start: 0.7890 (m) cc_final: 0.7127 (m) REVERT: G 27 MET cc_start: 0.8263 (ppp) cc_final: 0.7869 (mtt) REVERT: G 47 PHE cc_start: 0.9174 (m-80) cc_final: 0.8932 (m-80) REVERT: G 175 GLU cc_start: 0.9156 (mp0) cc_final: 0.8720 (mp0) REVERT: H 51 ASP cc_start: 0.8874 (m-30) cc_final: 0.8613 (p0) REVERT: H 62 GLN cc_start: 0.9333 (mm-40) cc_final: 0.9042 (mm-40) REVERT: H 90 TYR cc_start: 0.8653 (m-10) cc_final: 0.8278 (m-10) REVERT: H 95 MET cc_start: 0.8319 (tmm) cc_final: 0.7481 (tmm) REVERT: H 120 MET cc_start: 0.8692 (ttm) cc_final: 0.8457 (ttm) REVERT: H 165 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8510 (tm-30) REVERT: I 24 MET cc_start: 0.8418 (ppp) cc_final: 0.8207 (ppp) REVERT: I 53 ASP cc_start: 0.8638 (t0) cc_final: 0.8117 (t0) REVERT: I 57 GLN cc_start: 0.8480 (mt0) cc_final: 0.8088 (mt0) REVERT: I 139 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8631 (mm-30) REVERT: I 174 ASP cc_start: 0.8381 (t0) cc_final: 0.8053 (t70) REVERT: J 79 ARG cc_start: 0.8960 (ptp90) cc_final: 0.8623 (ttp80) REVERT: J 88 SER cc_start: 0.9475 (m) cc_final: 0.9145 (t) REVERT: J 108 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8582 (pp) REVERT: J 143 GLU cc_start: 0.8701 (pm20) cc_final: 0.8487 (pm20) REVERT: J 144 GLN cc_start: 0.9463 (mp10) cc_final: 0.8298 (mp10) REVERT: J 192 ASP cc_start: 0.8605 (p0) cc_final: 0.8362 (p0) REVERT: J 203 MET cc_start: 0.8151 (mmm) cc_final: 0.7925 (mmp) REVERT: K 37 LYS cc_start: 0.8941 (ptmm) cc_final: 0.8274 (tttm) REVERT: K 59 TYR cc_start: 0.9003 (t80) cc_final: 0.8500 (t80) REVERT: K 163 CYS cc_start: 0.9343 (m) cc_final: 0.8979 (m) REVERT: L 44 THR cc_start: 0.8266 (p) cc_final: 0.8021 (t) REVERT: L 139 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8296 (ttp) REVERT: M 131 GLN cc_start: 0.7271 (tm-30) cc_final: 0.6996 (tm-30) REVERT: M 196 CYS cc_start: 0.8665 (m) cc_final: 0.8399 (m) REVERT: N 26 MET cc_start: 0.8673 (mtm) cc_final: 0.8447 (mpp) REVERT: N 110 MET cc_start: 0.8457 (mmm) cc_final: 0.8249 (mmm) REVERT: N 170 GLU cc_start: 0.8465 (pp20) cc_final: 0.8141 (pp20) REVERT: N 180 ASP cc_start: 0.9072 (t0) cc_final: 0.8714 (t0) REVERT: O 19 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8576 (mp0) REVERT: O 174 GLU cc_start: 0.8949 (mp0) cc_final: 0.8685 (mp0) REVERT: O 224 ASN cc_start: 0.8760 (p0) cc_final: 0.8407 (p0) REVERT: P 48 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8225 (tm-30) REVERT: P 78 MET cc_start: 0.8111 (mtp) cc_final: 0.7595 (ptm) REVERT: P 81 ASP cc_start: 0.8712 (m-30) cc_final: 0.8014 (m-30) REVERT: P 122 GLN cc_start: 0.9011 (tt0) cc_final: 0.8474 (tp40) REVERT: P 208 GLU cc_start: 0.8392 (tp30) cc_final: 0.7856 (tp30) REVERT: P 219 ARG cc_start: 0.9194 (ptp90) cc_final: 0.8944 (ttp-110) REVERT: P 224 GLU cc_start: 0.9281 (mp0) cc_final: 0.8882 (mp0) REVERT: Q 26 GLU cc_start: 0.8844 (mp0) cc_final: 0.8616 (mp0) REVERT: Q 30 HIS cc_start: 0.8235 (m90) cc_final: 0.7956 (m90) REVERT: Q 66 TYR cc_start: 0.8192 (m-80) cc_final: 0.7833 (m-80) REVERT: Q 84 ASN cc_start: 0.9369 (m110) cc_final: 0.9097 (m110) REVERT: Q 88 ASN cc_start: 0.8656 (p0) cc_final: 0.8334 (p0) REVERT: R 27 LYS cc_start: 0.8868 (mtmm) cc_final: 0.8612 (mtmm) REVERT: R 90 GLU cc_start: 0.9223 (tp30) cc_final: 0.8545 (tt0) REVERT: R 118 TYR cc_start: 0.8869 (m-10) cc_final: 0.8635 (m-10) REVERT: R 157 LYS cc_start: 0.9263 (mttt) cc_final: 0.8975 (mtmt) REVERT: S 89 ILE cc_start: 0.9522 (pt) cc_final: 0.9279 (mt) REVERT: S 143 PHE cc_start: 0.8924 (m-80) cc_final: 0.8481 (m-80) REVERT: S 156 MET cc_start: 0.8021 (ttm) cc_final: 0.6876 (ttt) REVERT: S 189 MET cc_start: 0.8039 (ptp) cc_final: 0.7684 (ptp) REVERT: S 192 LYS cc_start: 0.9271 (ptmm) cc_final: 0.9009 (ptmm) REVERT: S 196 LYS cc_start: 0.9288 (ptpp) cc_final: 0.8786 (pttm) REVERT: S 225 ASN cc_start: 0.9241 (p0) cc_final: 0.8950 (p0) REVERT: T 26 MET cc_start: 0.8835 (tpp) cc_final: 0.8468 (tpp) REVERT: T 27 GLU cc_start: 0.8987 (tp30) cc_final: 0.8677 (tm-30) REVERT: T 86 ASN cc_start: 0.9101 (m110) cc_final: 0.8875 (m110) REVERT: T 117 GLN cc_start: 0.9200 (tp40) cc_final: 0.8968 (tp40) REVERT: T 176 MET cc_start: 0.8294 (tmm) cc_final: 0.7915 (tmm) REVERT: T 189 LYS cc_start: 0.9553 (OUTLIER) cc_final: 0.9206 (mmmt) REVERT: U 75 MET cc_start: 0.8544 (ttt) cc_final: 0.8279 (ttt) REVERT: U 135 PHE cc_start: 0.8951 (p90) cc_final: 0.8508 (p90) REVERT: U 175 GLU cc_start: 0.9259 (mp0) cc_final: 0.9035 (mp0) REVERT: U 179 LEU cc_start: 0.9122 (tt) cc_final: 0.8730 (tt) REVERT: U 184 MET cc_start: 0.7787 (mtp) cc_final: 0.7531 (mtp) REVERT: U 236 GLU cc_start: 0.9370 (mt-10) cc_final: 0.9062 (pt0) REVERT: V 53 GLN cc_start: 0.9223 (mt0) cc_final: 0.9017 (mt0) REVERT: V 90 TYR cc_start: 0.8672 (m-10) cc_final: 0.8327 (m-80) REVERT: V 104 ASP cc_start: 0.8351 (p0) cc_final: 0.7998 (p0) REVERT: V 107 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8150 (tm-30) REVERT: V 116 MET cc_start: 0.8437 (mmt) cc_final: 0.8223 (mmt) REVERT: V 120 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7893 (ttp) REVERT: W 30 ASN cc_start: 0.8834 (t0) cc_final: 0.8623 (t0) REVERT: W 53 ASP cc_start: 0.8759 (m-30) cc_final: 0.8536 (m-30) REVERT: X 3 MET cc_start: 0.8782 (mmm) cc_final: 0.8373 (mmm) REVERT: X 13 MET cc_start: 0.8495 (ttp) cc_final: 0.8220 (ttp) REVERT: X 49 TYR cc_start: 0.9338 (m-80) cc_final: 0.8843 (m-80) REVERT: X 105 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8179 (mp0) REVERT: X 150 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8424 (mt-10) REVERT: Y 52 ASP cc_start: 0.8627 (m-30) cc_final: 0.8111 (t0) REVERT: Y 55 GLN cc_start: 0.9264 (mm-40) cc_final: 0.8939 (mm-40) REVERT: Y 111 GLU cc_start: 0.7919 (mp0) cc_final: 0.7612 (mp0) REVERT: Y 186 ASN cc_start: 0.9503 (m-40) cc_final: 0.9275 (m-40) REVERT: Z 99 THR cc_start: 0.8418 (t) cc_final: 0.8007 (t) REVERT: a 127 VAL cc_start: 0.9433 (m) cc_final: 0.9143 (p) REVERT: a 131 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7107 (tm-30) REVERT: b 56 ASP cc_start: 0.8659 (t0) cc_final: 0.8438 (t0) REVERT: b 76 LEU cc_start: 0.9212 (mt) cc_final: 0.8865 (mt) REVERT: b 79 ASP cc_start: 0.8727 (p0) cc_final: 0.8455 (p0) REVERT: b 104 ASN cc_start: 0.8393 (t0) cc_final: 0.7949 (t0) REVERT: b 147 GLN cc_start: 0.9280 (tp40) cc_final: 0.8930 (mm110) REVERT: b 173 MET cc_start: 0.8887 (tpt) cc_final: 0.8537 (mmt) REVERT: b 180 ASP cc_start: 0.8886 (t0) cc_final: 0.8267 (t0) REVERT: b 200 GLU cc_start: 0.7726 (mp0) cc_final: 0.7424 (mp0) outliers start: 121 outliers final: 78 residues processed: 1106 average time/residue: 0.2622 time to fit residues: 476.5669 Evaluate side-chains 1046 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 961 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 154 GLN Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 51 GLN Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 193 THR Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain S residue 76 CYS Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 198 SER Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 120 MET Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 79 ARG Chi-restraints excluded: chain X residue 105 GLU Chi-restraints excluded: chain Y residue 34 LYS Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 98 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 283 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 282 optimal weight: 7.9990 chunk 170 optimal weight: 0.0980 chunk 563 optimal weight: 9.9990 chunk 580 optimal weight: 6.9990 chunk 69 optimal weight: 0.2980 chunk 502 optimal weight: 6.9990 chunk 461 optimal weight: 8.9990 chunk 601 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 193 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN D 122 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN G 110 HIS I 91 GLN J 71 ASN K 132 HIS M 8 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN O 24 GLN P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN S 204 GLN ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN X 92 ASN a 8 ASN a 146 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.066249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.054536 restraints weight = 141620.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.056825 restraints weight = 63213.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.058370 restraints weight = 36499.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.059393 restraints weight = 24665.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.060138 restraints weight = 18651.715| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 46168 Z= 0.119 Angle : 0.604 11.129 62689 Z= 0.313 Chirality : 0.043 0.178 7344 Planarity : 0.004 0.059 7971 Dihedral : 4.384 29.311 6785 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.25 % Favored : 97.74 % Rotamer: Outliers : 2.62 % Allowed : 17.29 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.45 (0.11), residues: 6139 helix: 1.32 (0.11), residues: 2231 sheet: -0.06 (0.13), residues: 1452 loop : -0.31 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 89 TYR 0.025 0.001 TYR R 21 PHE 0.025 0.001 PHE A 191 TRP 0.018 0.001 TRP G 215 HIS 0.009 0.001 HIS F 69 Details of bonding type rmsd covalent geometry : bond 0.00268 (46168) covalent geometry : angle 0.60450 (62689) hydrogen bonds : bond 0.03265 ( 2420) hydrogen bonds : angle 4.66134 ( 6927) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1039 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7084 (t80) REVERT: A 39 SER cc_start: 0.9452 (m) cc_final: 0.8967 (p) REVERT: A 123 GLN cc_start: 0.9450 (tm-30) cc_final: 0.8884 (tm-30) REVERT: A 224 ASN cc_start: 0.8780 (p0) cc_final: 0.8492 (p0) REVERT: B 48 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 117 MET cc_start: 0.9094 (ttm) cc_final: 0.8832 (ttm) REVERT: B 122 GLN cc_start: 0.8863 (tp40) cc_final: 0.8624 (tp40) REVERT: B 147 GLN cc_start: 0.8167 (tt0) cc_final: 0.7704 (tm-30) REVERT: B 155 PHE cc_start: 0.8361 (m-80) cc_final: 0.7898 (m-10) REVERT: B 208 GLU cc_start: 0.8626 (tp30) cc_final: 0.8014 (tp30) REVERT: B 218 ARG cc_start: 0.9268 (tmm-80) cc_final: 0.8837 (tmm-80) REVERT: C 25 MET cc_start: 0.8928 (mmt) cc_final: 0.8556 (mmp) REVERT: C 26 GLU cc_start: 0.8559 (tp30) cc_final: 0.8298 (tp30) REVERT: C 30 HIS cc_start: 0.8470 (m-70) cc_final: 0.7664 (m-70) REVERT: C 93 ILE cc_start: 0.9611 (mt) cc_final: 0.9396 (mm) REVERT: D 55 ASP cc_start: 0.8482 (t0) cc_final: 0.8275 (t0) REVERT: D 90 GLU cc_start: 0.9064 (tp30) cc_final: 0.8692 (tp30) REVERT: D 110 TYR cc_start: 0.8607 (t80) cc_final: 0.8374 (t80) REVERT: D 116 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8807 (tm-30) REVERT: D 120 GLN cc_start: 0.8475 (tt0) cc_final: 0.8113 (tt0) REVERT: D 146 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7941 (tm-30) REVERT: D 190 LEU cc_start: 0.9572 (tp) cc_final: 0.9369 (tp) REVERT: E 29 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8190 (tm-30) REVERT: E 51 GLU cc_start: 0.7275 (tt0) cc_final: 0.7000 (tt0) REVERT: E 118 ASN cc_start: 0.9084 (m-40) cc_final: 0.8863 (m110) REVERT: E 133 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.6688 (mmm) REVERT: E 192 LYS cc_start: 0.8854 (tptt) cc_final: 0.8571 (tptp) REVERT: E 196 LYS cc_start: 0.9216 (pttm) cc_final: 0.8834 (pttm) REVERT: E 216 GLU cc_start: 0.6864 (tt0) cc_final: 0.6637 (tt0) REVERT: E 225 ASN cc_start: 0.8920 (p0) cc_final: 0.8641 (p0) REVERT: F 26 MET cc_start: 0.8527 (ttm) cc_final: 0.8286 (mmt) REVERT: F 27 GLU cc_start: 0.9083 (tp30) cc_final: 0.8664 (tm-30) REVERT: F 90 GLN cc_start: 0.9278 (tp40) cc_final: 0.9062 (tp40) REVERT: F 145 PHE cc_start: 0.9040 (m-80) cc_final: 0.8732 (m-80) REVERT: F 179 PHE cc_start: 0.9016 (m-80) cc_final: 0.8779 (m-80) REVERT: F 182 CYS cc_start: 0.7793 (m) cc_final: 0.7141 (m) REVERT: G 27 MET cc_start: 0.8337 (ppp) cc_final: 0.8003 (mtt) REVERT: G 150 MET cc_start: 0.8173 (tmm) cc_final: 0.7879 (tmm) REVERT: G 175 GLU cc_start: 0.9156 (mp0) cc_final: 0.8732 (mp0) REVERT: G 225 GLU cc_start: 0.7829 (mp0) cc_final: 0.7608 (mp0) REVERT: H 95 MET cc_start: 0.8073 (tmm) cc_final: 0.7238 (tmm) REVERT: H 120 MET cc_start: 0.8606 (ttm) cc_final: 0.8298 (ttm) REVERT: H 165 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8629 (tm-30) REVERT: H 167 ASP cc_start: 0.8553 (t0) cc_final: 0.8344 (t0) REVERT: I 90 TYR cc_start: 0.8607 (m-10) cc_final: 0.8394 (m-10) REVERT: I 91 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8272 (tm-30) REVERT: I 139 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8688 (mm-30) REVERT: I 174 ASP cc_start: 0.8477 (t0) cc_final: 0.8046 (t70) REVERT: J 144 GLN cc_start: 0.9465 (mp10) cc_final: 0.8234 (mp10) REVERT: J 164 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8176 (mm-30) REVERT: J 177 ASP cc_start: 0.8160 (t0) cc_final: 0.7852 (t0) REVERT: K 37 LYS cc_start: 0.8858 (ptmm) cc_final: 0.8228 (tttm) REVERT: K 59 TYR cc_start: 0.8929 (t80) cc_final: 0.8410 (t80) REVERT: K 65 GLN cc_start: 0.9262 (mm-40) cc_final: 0.9013 (mm-40) REVERT: K 160 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9402 (mp) REVERT: K 163 CYS cc_start: 0.9321 (m) cc_final: 0.8886 (m) REVERT: L 140 ASP cc_start: 0.8692 (m-30) cc_final: 0.8480 (m-30) REVERT: M 131 GLN cc_start: 0.7314 (tm-30) cc_final: 0.7109 (tm-30) REVERT: M 196 CYS cc_start: 0.8750 (m) cc_final: 0.8508 (m) REVERT: N 110 MET cc_start: 0.8426 (mmm) cc_final: 0.8199 (mmm) REVERT: N 170 GLU cc_start: 0.8421 (pp20) cc_final: 0.8103 (pp20) REVERT: N 180 ASP cc_start: 0.9027 (t0) cc_final: 0.8595 (t0) REVERT: O 19 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8583 (mp0) REVERT: O 174 GLU cc_start: 0.9007 (mp0) cc_final: 0.8790 (mp0) REVERT: O 224 ASN cc_start: 0.8695 (p0) cc_final: 0.8469 (p0) REVERT: P 48 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8060 (tm-30) REVERT: P 78 MET cc_start: 0.8088 (mtp) cc_final: 0.7580 (ptm) REVERT: P 81 ASP cc_start: 0.8638 (m-30) cc_final: 0.7975 (m-30) REVERT: P 122 GLN cc_start: 0.8898 (tt0) cc_final: 0.8378 (tp40) REVERT: P 208 GLU cc_start: 0.8243 (tp30) cc_final: 0.7741 (tp30) REVERT: P 219 ARG cc_start: 0.9193 (ptp90) cc_final: 0.8772 (ttp-110) REVERT: P 224 GLU cc_start: 0.9236 (mp0) cc_final: 0.8825 (mp0) REVERT: Q 30 HIS cc_start: 0.8206 (m90) cc_final: 0.7868 (m90) REVERT: Q 66 TYR cc_start: 0.8116 (m-80) cc_final: 0.7703 (m-80) REVERT: Q 84 ASN cc_start: 0.9316 (m110) cc_final: 0.9042 (m110) REVERT: Q 88 ASN cc_start: 0.8673 (p0) cc_final: 0.8347 (p0) REVERT: Q 167 ASN cc_start: 0.8872 (m-40) cc_final: 0.8629 (m-40) REVERT: Q 209 GLU cc_start: 0.8688 (pm20) cc_final: 0.8473 (pm20) REVERT: R 20 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7832 (tm-30) REVERT: R 23 GLN cc_start: 0.8342 (tm-30) cc_final: 0.8096 (pp30) REVERT: R 110 TYR cc_start: 0.8915 (t80) cc_final: 0.8246 (t80) REVERT: R 118 TYR cc_start: 0.8780 (m-10) cc_final: 0.8553 (m-10) REVERT: R 157 LYS cc_start: 0.9246 (mttt) cc_final: 0.8978 (mtmt) REVERT: S 143 PHE cc_start: 0.8974 (m-80) cc_final: 0.8499 (m-80) REVERT: S 156 MET cc_start: 0.7934 (ttm) cc_final: 0.6867 (ttt) REVERT: S 164 GLN cc_start: 0.7423 (tm-30) cc_final: 0.7178 (tm-30) REVERT: S 225 ASN cc_start: 0.9283 (p0) cc_final: 0.8984 (p0) REVERT: T 26 MET cc_start: 0.8835 (tpp) cc_final: 0.8480 (tpp) REVERT: T 86 ASN cc_start: 0.9111 (m110) cc_final: 0.8833 (m110) REVERT: T 176 MET cc_start: 0.8330 (tmm) cc_final: 0.7945 (tmm) REVERT: T 189 LYS cc_start: 0.9599 (OUTLIER) cc_final: 0.9231 (mmmt) REVERT: U 75 MET cc_start: 0.8525 (ttt) cc_final: 0.8272 (ttt) REVERT: U 135 PHE cc_start: 0.8867 (p90) cc_final: 0.8484 (p90) REVERT: U 175 GLU cc_start: 0.9225 (mp0) cc_final: 0.8997 (mp0) REVERT: U 179 LEU cc_start: 0.9138 (tt) cc_final: 0.8759 (tt) REVERT: U 184 MET cc_start: 0.7749 (mtp) cc_final: 0.7494 (mtp) REVERT: U 236 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9049 (pt0) REVERT: V 95 MET cc_start: 0.7202 (tmm) cc_final: 0.6025 (tmm) REVERT: V 104 ASP cc_start: 0.8472 (p0) cc_final: 0.8110 (p0) REVERT: V 107 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8171 (tm-30) REVERT: V 119 MET cc_start: 0.7791 (ttp) cc_final: 0.7336 (ptp) REVERT: V 120 MET cc_start: 0.7814 (ttm) cc_final: 0.7496 (ttp) REVERT: W 127 MET cc_start: 0.8500 (mtm) cc_final: 0.8134 (mtp) REVERT: X 3 MET cc_start: 0.8779 (mmm) cc_final: 0.8382 (mmm) REVERT: X 13 MET cc_start: 0.8472 (ttp) cc_final: 0.8161 (ttp) REVERT: X 105 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: X 145 MET cc_start: 0.8915 (ptp) cc_final: 0.8631 (pmm) REVERT: X 150 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8309 (tt0) REVERT: Y 52 ASP cc_start: 0.8491 (m-30) cc_final: 0.8065 (t0) REVERT: Y 55 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8929 (mm-40) REVERT: Y 140 LEU cc_start: 0.9508 (mt) cc_final: 0.9254 (mm) REVERT: Y 163 CYS cc_start: 0.9317 (m) cc_final: 0.8855 (t) REVERT: Y 186 ASN cc_start: 0.9500 (m-40) cc_final: 0.9267 (m-40) REVERT: a 127 VAL cc_start: 0.9419 (m) cc_final: 0.9171 (p) REVERT: a 131 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7247 (tm-30) REVERT: a 188 TYR cc_start: 0.9380 (m-80) cc_final: 0.9091 (m-80) REVERT: b 56 ASP cc_start: 0.8660 (t0) cc_final: 0.8224 (t0) REVERT: b 76 LEU cc_start: 0.9170 (mt) cc_final: 0.8845 (mt) REVERT: b 79 ASP cc_start: 0.8697 (p0) cc_final: 0.8465 (p0) REVERT: b 104 ASN cc_start: 0.8429 (t0) cc_final: 0.8029 (t0) REVERT: b 173 MET cc_start: 0.8951 (tpt) cc_final: 0.8592 (mmt) REVERT: b 180 ASP cc_start: 0.8895 (t0) cc_final: 0.8254 (t0) REVERT: b 200 GLU cc_start: 0.7726 (mp0) cc_final: 0.7390 (mp0) outliers start: 112 outliers final: 66 residues processed: 1097 average time/residue: 0.2639 time to fit residues: 478.0985 Evaluate side-chains 1053 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 981 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 154 GLN Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain O residue 13 ILE Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain X residue 79 ARG Chi-restraints excluded: chain X residue 105 GLU Chi-restraints excluded: chain Y residue 34 LYS Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 146 GLN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 463 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 579 optimal weight: 9.9990 chunk 598 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 chunk 514 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN F 166 GLN G 32 ASN H 7 GLN ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 GLN J 80 GLN M 8 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN S 204 GLN ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN X 92 ASN Y 63 ASN a 8 ASN a 146 GLN b 65 GLN b 147 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.061709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.050036 restraints weight = 146665.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.052219 restraints weight = 65867.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.053714 restraints weight = 38408.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.054716 restraints weight = 26119.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.055395 restraints weight = 19735.846| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 46168 Z= 0.270 Angle : 0.691 9.857 62689 Z= 0.360 Chirality : 0.045 0.175 7344 Planarity : 0.004 0.058 7971 Dihedral : 4.557 31.780 6785 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.09 % Allowed : 17.90 % Favored : 79.01 % 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: 0.49 (0.11), residues: 6139 helix: 1.37 (0.11), residues: 2236 sheet: -0.18 (0.13), residues: 1530 loop : -0.19 (0.13), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Y 70 TYR 0.031 0.002 TYR R 21 PHE 0.028 0.002 PHE C 124 TRP 0.035 0.002 TRP G 215 HIS 0.008 0.001 HIS F 69 Details of bonding type rmsd covalent geometry : bond 0.00604 (46168) covalent geometry : angle 0.69150 (62689) hydrogen bonds : bond 0.03783 ( 2420) hydrogen bonds : angle 4.80051 ( 6927) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 960 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.6781 (t80) REVERT: A 93 ARG cc_start: 0.9293 (mmm-85) cc_final: 0.9031 (tpp80) REVERT: A 123 GLN cc_start: 0.9515 (tm-30) cc_final: 0.9192 (tm-30) REVERT: A 224 ASN cc_start: 0.8742 (p0) cc_final: 0.8524 (p0) REVERT: B 48 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 50 LYS cc_start: 0.9134 (tppt) cc_final: 0.8791 (tppt) REVERT: B 122 GLN cc_start: 0.8864 (tp40) cc_final: 0.8563 (tp40) REVERT: B 147 GLN cc_start: 0.8426 (tt0) cc_final: 0.7659 (tm-30) REVERT: B 155 PHE cc_start: 0.8591 (m-80) cc_final: 0.8102 (m-10) REVERT: B 170 LYS cc_start: 0.9415 (mmtm) cc_final: 0.9152 (mmtt) REVERT: B 208 GLU cc_start: 0.8351 (tp30) cc_final: 0.7924 (tp30) REVERT: B 218 ARG cc_start: 0.9319 (tmm-80) cc_final: 0.8875 (tmm-80) REVERT: B 219 ARG cc_start: 0.9535 (ttp80) cc_final: 0.9294 (ttm110) REVERT: B 224 GLU cc_start: 0.9339 (mp0) cc_final: 0.9103 (pm20) REVERT: C 25 MET cc_start: 0.8997 (mmt) cc_final: 0.8595 (mmp) REVERT: C 26 GLU cc_start: 0.8617 (tp30) cc_final: 0.8311 (tp30) REVERT: D 110 TYR cc_start: 0.8749 (t80) cc_final: 0.8511 (t80) REVERT: D 120 GLN cc_start: 0.8552 (tt0) cc_final: 0.8308 (tt0) REVERT: D 146 GLN cc_start: 0.8471 (tm-30) cc_final: 0.7967 (tm-30) REVERT: E 51 GLU cc_start: 0.7826 (tt0) cc_final: 0.7411 (pt0) REVERT: E 59 MET cc_start: 0.8568 (ptp) cc_final: 0.8350 (ptp) REVERT: E 60 GLU cc_start: 0.7593 (tp30) cc_final: 0.7240 (tm-30) REVERT: E 118 ASN cc_start: 0.9098 (m-40) cc_final: 0.8814 (m110) REVERT: E 133 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.6805 (mmm) REVERT: E 216 GLU cc_start: 0.6819 (tt0) cc_final: 0.6516 (tt0) REVERT: E 225 ASN cc_start: 0.9027 (p0) cc_final: 0.8734 (p0) REVERT: F 26 MET cc_start: 0.8680 (ttm) cc_final: 0.8351 (mmm) REVERT: F 27 GLU cc_start: 0.9075 (tp30) cc_final: 0.8803 (tm-30) REVERT: F 90 GLN cc_start: 0.9329 (tp40) cc_final: 0.9089 (tp40) REVERT: F 182 CYS cc_start: 0.7817 (m) cc_final: 0.7105 (m) REVERT: G 27 MET cc_start: 0.8406 (ppp) cc_final: 0.8098 (mtt) REVERT: G 70 ASP cc_start: 0.9146 (t70) cc_final: 0.8892 (t70) REVERT: G 75 MET cc_start: 0.8320 (ttt) cc_final: 0.8089 (ttt) REVERT: G 83 ASP cc_start: 0.8966 (m-30) cc_final: 0.8752 (m-30) REVERT: G 150 MET cc_start: 0.8224 (tmm) cc_final: 0.7894 (tmm) REVERT: G 175 GLU cc_start: 0.9156 (mp0) cc_final: 0.8931 (mm-30) REVERT: G 180 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8576 (pp30) REVERT: G 225 GLU cc_start: 0.7847 (mp0) cc_final: 0.7355 (mp0) REVERT: H 51 ASP cc_start: 0.8885 (m-30) cc_final: 0.8596 (p0) REVERT: H 90 TYR cc_start: 0.8765 (m-10) cc_final: 0.8372 (m-10) REVERT: H 95 MET cc_start: 0.8181 (tmm) cc_final: 0.6395 (tmm) REVERT: H 116 MET cc_start: 0.8126 (mmm) cc_final: 0.7875 (mmt) REVERT: H 120 MET cc_start: 0.8807 (ttm) cc_final: 0.8387 (ttm) REVERT: H 134 TYR cc_start: 0.9267 (m-80) cc_final: 0.9055 (m-80) REVERT: H 165 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8612 (tm-30) REVERT: H 167 ASP cc_start: 0.8643 (t0) cc_final: 0.8373 (t0) REVERT: I 53 ASP cc_start: 0.8761 (t0) cc_final: 0.8462 (t0) REVERT: I 91 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8243 (tm-30) REVERT: I 139 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8702 (mm-30) REVERT: J 32 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8307 (tm-30) REVERT: J 88 SER cc_start: 0.9397 (m) cc_final: 0.8980 (t) REVERT: J 108 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8691 (pp) REVERT: J 144 GLN cc_start: 0.9497 (mp10) cc_final: 0.8344 (mp10) REVERT: J 164 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8248 (mm-30) REVERT: J 177 ASP cc_start: 0.8393 (t0) cc_final: 0.8132 (t0) REVERT: J 203 MET cc_start: 0.8339 (mmm) cc_final: 0.8121 (mmp) REVERT: K 37 LYS cc_start: 0.8835 (ptmm) cc_final: 0.8327 (tttm) REVERT: K 160 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9304 (mt) REVERT: K 163 CYS cc_start: 0.9302 (m) cc_final: 0.8838 (m) REVERT: M 196 CYS cc_start: 0.8951 (m) cc_final: 0.8724 (m) REVERT: N 25 ASP cc_start: 0.8772 (p0) cc_final: 0.8501 (p0) REVERT: N 110 MET cc_start: 0.8513 (mmm) cc_final: 0.8248 (mmm) REVERT: N 170 GLU cc_start: 0.8536 (pp20) cc_final: 0.8186 (pp20) REVERT: N 180 ASP cc_start: 0.9134 (t0) cc_final: 0.8793 (t0) REVERT: O 19 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8599 (mp0) REVERT: O 224 ASN cc_start: 0.8643 (p0) cc_final: 0.8377 (p0) REVERT: P 48 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8249 (tm-30) REVERT: P 63 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8316 (mtpt) REVERT: P 78 MET cc_start: 0.8295 (mtp) cc_final: 0.7668 (ptm) REVERT: P 81 ASP cc_start: 0.8607 (m-30) cc_final: 0.7579 (m-30) REVERT: P 122 GLN cc_start: 0.9031 (tt0) cc_final: 0.8423 (tp40) REVERT: P 224 GLU cc_start: 0.9304 (mp0) cc_final: 0.8963 (mp0) REVERT: Q 30 HIS cc_start: 0.8380 (m90) cc_final: 0.7997 (m90) REVERT: Q 66 TYR cc_start: 0.8323 (m-80) cc_final: 0.8020 (m-80) REVERT: R 90 GLU cc_start: 0.9258 (tp30) cc_final: 0.8710 (tt0) REVERT: R 157 LYS cc_start: 0.9278 (mttt) cc_final: 0.8912 (mtmt) REVERT: S 133 MET cc_start: 0.8312 (mmp) cc_final: 0.8065 (mmm) REVERT: S 164 GLN cc_start: 0.7415 (tm-30) cc_final: 0.7163 (tm-30) REVERT: S 192 LYS cc_start: 0.9491 (ptmm) cc_final: 0.9189 (ptpp) REVERT: S 225 ASN cc_start: 0.9336 (p0) cc_final: 0.8985 (p0) REVERT: T 26 MET cc_start: 0.8986 (tpp) cc_final: 0.8627 (tpp) REVERT: T 27 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8197 (tm-30) REVERT: T 176 MET cc_start: 0.8465 (tmm) cc_final: 0.8096 (tmm) REVERT: T 189 LYS cc_start: 0.9663 (OUTLIER) cc_final: 0.9314 (mmmt) REVERT: U 175 GLU cc_start: 0.9269 (mp0) cc_final: 0.9013 (mp0) REVERT: U 179 LEU cc_start: 0.9246 (tt) cc_final: 0.8949 (tt) REVERT: U 184 MET cc_start: 0.7723 (mtp) cc_final: 0.7465 (mtp) REVERT: U 236 GLU cc_start: 0.9465 (mt-10) cc_final: 0.8934 (mt-10) REVERT: V 95 MET cc_start: 0.7276 (tmm) cc_final: 0.6090 (tmm) REVERT: V 107 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8015 (tm-30) REVERT: W 19 ARG cc_start: 0.9199 (ttm170) cc_final: 0.8854 (ttm170) REVERT: W 202 TYR cc_start: 0.7418 (m-10) cc_final: 0.7136 (m-80) REVERT: X 3 MET cc_start: 0.8785 (mmm) cc_final: 0.8389 (mmm) REVERT: X 105 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: X 130 MET cc_start: 0.8003 (tpp) cc_final: 0.7475 (tpp) REVERT: X 150 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8220 (tt0) REVERT: Y 52 ASP cc_start: 0.8716 (m-30) cc_final: 0.8167 (t0) REVERT: Y 86 ARG cc_start: 0.9132 (tpp80) cc_final: 0.8768 (tpp80) REVERT: Y 90 ASP cc_start: 0.8845 (p0) cc_final: 0.8617 (p0) REVERT: a 127 VAL cc_start: 0.9476 (m) cc_final: 0.9181 (p) REVERT: a 131 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7483 (tm-30) REVERT: a 146 GLN cc_start: 0.9484 (mm110) cc_final: 0.8950 (mm-40) REVERT: a 196 CYS cc_start: 0.9085 (m) cc_final: 0.8817 (m) REVERT: b 76 LEU cc_start: 0.9192 (mt) cc_final: 0.8851 (mt) REVERT: b 104 ASN cc_start: 0.8646 (t0) cc_final: 0.8176 (t0) REVERT: b 170 GLU cc_start: 0.8336 (pp20) cc_final: 0.8131 (tm-30) REVERT: b 173 MET cc_start: 0.8976 (tpt) cc_final: 0.8610 (mmt) REVERT: b 180 ASP cc_start: 0.9019 (t0) cc_final: 0.8393 (t0) REVERT: b 200 GLU cc_start: 0.7651 (mp0) cc_final: 0.7269 (mp0) outliers start: 132 outliers final: 94 residues processed: 1031 average time/residue: 0.2625 time to fit residues: 444.7186 Evaluate side-chains 1011 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 911 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 130 TYR Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 160 TYR Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 221 ASN Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 79 ARG Chi-restraints excluded: chain X residue 105 GLU Chi-restraints excluded: chain X residue 156 ASN Chi-restraints excluded: chain Y residue 34 LYS Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 96 MET Chi-restraints excluded: chain b residue 98 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 34 optimal weight: 0.9990 chunk 341 optimal weight: 0.7980 chunk 506 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 428 optimal weight: 4.9990 chunk 436 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 225 optimal weight: 0.1980 chunk 457 optimal weight: 6.9990 chunk 455 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 20 GLN B 94 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN F 166 GLN G 32 ASN H 106 GLN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN K 71 ASN M 8 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN S 204 GLN ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 ASN Y 32 HIS b 65 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.063841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.052219 restraints weight = 143347.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.054457 restraints weight = 64342.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.055977 restraints weight = 37340.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.057012 restraints weight = 25299.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.057656 restraints weight = 18992.501| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46168 Z= 0.132 Angle : 0.636 10.120 62689 Z= 0.329 Chirality : 0.044 0.252 7344 Planarity : 0.004 0.057 7971 Dihedral : 4.397 31.345 6785 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.37 % Allowed : 18.81 % Favored : 78.82 % 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: 0.61 (0.11), residues: 6139 helix: 1.52 (0.11), residues: 2244 sheet: -0.05 (0.13), residues: 1450 loop : -0.25 (0.13), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG W 89 TYR 0.029 0.001 TYR C 97 PHE 0.026 0.001 PHE A 191 TRP 0.020 0.001 TRP G 215 HIS 0.008 0.001 HIS S 227 Details of bonding type rmsd covalent geometry : bond 0.00302 (46168) covalent geometry : angle 0.63632 (62689) hydrogen bonds : bond 0.03255 ( 2420) hydrogen bonds : angle 4.62222 ( 6927) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 997 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8631 (mtm110) cc_final: 0.8401 (ptm-80) REVERT: A 23 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.6936 (t80) REVERT: A 80 MET cc_start: 0.8598 (mmm) cc_final: 0.8307 (mmm) REVERT: A 93 ARG cc_start: 0.9252 (mmm-85) cc_final: 0.8987 (tpp80) REVERT: A 123 GLN cc_start: 0.9491 (tm-30) cc_final: 0.8929 (tm-30) REVERT: A 152 TYR cc_start: 0.8157 (m-80) cc_final: 0.7761 (m-10) REVERT: A 224 ASN cc_start: 0.8825 (p0) cc_final: 0.8607 (p0) REVERT: B 48 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7830 (tm-30) REVERT: B 122 GLN cc_start: 0.8768 (tp40) cc_final: 0.8474 (tp40) REVERT: B 147 GLN cc_start: 0.8348 (tt0) cc_final: 0.7726 (tm-30) REVERT: B 155 PHE cc_start: 0.8588 (m-80) cc_final: 0.8132 (m-10) REVERT: B 208 GLU cc_start: 0.8298 (tp30) cc_final: 0.7921 (tp30) REVERT: B 218 ARG cc_start: 0.9226 (tmm-80) cc_final: 0.8863 (tmm-80) REVERT: B 224 GLU cc_start: 0.9305 (mp0) cc_final: 0.9082 (pm20) REVERT: C 25 MET cc_start: 0.8970 (mmt) cc_final: 0.8623 (mmp) REVERT: C 26 GLU cc_start: 0.8552 (tp30) cc_final: 0.8166 (tp30) REVERT: C 93 ILE cc_start: 0.9614 (mt) cc_final: 0.9394 (mm) REVERT: D 5 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7002 (ttt-90) REVERT: D 23 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8268 (pp30) REVERT: D 120 GLN cc_start: 0.8451 (tt0) cc_final: 0.8167 (tt0) REVERT: D 146 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8131 (tm-30) REVERT: E 51 GLU cc_start: 0.7768 (tt0) cc_final: 0.7277 (pt0) REVERT: E 118 ASN cc_start: 0.9137 (m-40) cc_final: 0.8917 (m-40) REVERT: E 133 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.6506 (mmm) REVERT: E 216 GLU cc_start: 0.6751 (tt0) cc_final: 0.6456 (tt0) REVERT: E 225 ASN cc_start: 0.9021 (p0) cc_final: 0.8739 (p0) REVERT: F 26 MET cc_start: 0.8585 (ttm) cc_final: 0.8346 (mmt) REVERT: F 146 GLN cc_start: 0.7874 (tt0) cc_final: 0.7267 (tm-30) REVERT: F 179 PHE cc_start: 0.8945 (m-80) cc_final: 0.8684 (m-80) REVERT: F 182 CYS cc_start: 0.7779 (m) cc_final: 0.7150 (m) REVERT: G 27 MET cc_start: 0.8388 (ppp) cc_final: 0.8070 (mtp) REVERT: G 150 MET cc_start: 0.8275 (tmm) cc_final: 0.7883 (tmm) REVERT: G 175 GLU cc_start: 0.9132 (mp0) cc_final: 0.8902 (mm-30) REVERT: G 225 GLU cc_start: 0.7771 (mp0) cc_final: 0.7193 (mp0) REVERT: H 51 ASP cc_start: 0.8808 (m-30) cc_final: 0.8560 (p0) REVERT: H 90 TYR cc_start: 0.8739 (m-10) cc_final: 0.8470 (m-10) REVERT: H 95 MET cc_start: 0.8022 (tmm) cc_final: 0.6855 (tmm) REVERT: H 116 MET cc_start: 0.8159 (mmm) cc_final: 0.7840 (mmm) REVERT: H 120 MET cc_start: 0.8583 (ttm) cc_final: 0.8248 (ttm) REVERT: H 165 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8610 (tm-30) REVERT: H 167 ASP cc_start: 0.8730 (t0) cc_final: 0.8355 (t0) REVERT: I 30 ASN cc_start: 0.8870 (t0) cc_final: 0.8132 (t0) REVERT: I 91 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: I 135 MET cc_start: 0.9063 (mmm) cc_final: 0.8758 (tpp) REVERT: J 3 MET cc_start: 0.7928 (mmm) cc_final: 0.7482 (mmm) REVERT: J 88 SER cc_start: 0.9301 (m) cc_final: 0.8865 (t) REVERT: J 108 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8661 (pp) REVERT: J 143 GLU cc_start: 0.8749 (pm20) cc_final: 0.8527 (pm20) REVERT: J 144 GLN cc_start: 0.9453 (mp10) cc_final: 0.8245 (mp10) REVERT: J 164 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8317 (mm-30) REVERT: J 177 ASP cc_start: 0.8366 (t0) cc_final: 0.8055 (t0) REVERT: K 31 ASP cc_start: 0.8547 (p0) cc_final: 0.8306 (p0) REVERT: K 37 LYS cc_start: 0.9046 (ptmm) cc_final: 0.8513 (tttm) REVERT: K 65 GLN cc_start: 0.9268 (mm-40) cc_final: 0.9045 (mm-40) REVERT: K 163 CYS cc_start: 0.9285 (m) cc_final: 0.8831 (m) REVERT: L 44 THR cc_start: 0.8308 (p) cc_final: 0.8040 (t) REVERT: L 99 THR cc_start: 0.8077 (t) cc_final: 0.7870 (t) REVERT: L 167 ASP cc_start: 0.8840 (t70) cc_final: 0.8580 (t0) REVERT: M 8 ASN cc_start: 0.8975 (m110) cc_final: 0.8488 (m110) REVERT: M 196 CYS cc_start: 0.8944 (m) cc_final: 0.8706 (m) REVERT: M 205 GLU cc_start: 0.7150 (tp30) cc_final: 0.6809 (tp30) REVERT: N 25 ASP cc_start: 0.8692 (p0) cc_final: 0.8367 (p0) REVERT: N 110 MET cc_start: 0.8487 (mmm) cc_final: 0.8256 (mmm) REVERT: N 170 GLU cc_start: 0.8464 (pp20) cc_final: 0.8194 (pp20) REVERT: N 180 ASP cc_start: 0.9089 (t0) cc_final: 0.8682 (t0) REVERT: O 19 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8651 (mp0) REVERT: O 174 GLU cc_start: 0.9055 (mp0) cc_final: 0.8831 (mp0) REVERT: O 224 ASN cc_start: 0.8652 (p0) cc_final: 0.8343 (p0) REVERT: P 48 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8116 (tm-30) REVERT: P 50 LYS cc_start: 0.9023 (tppt) cc_final: 0.8516 (tppt) REVERT: P 63 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8396 (mtpt) REVERT: P 78 MET cc_start: 0.8298 (mtp) cc_final: 0.8002 (ptm) REVERT: P 81 ASP cc_start: 0.8627 (m-30) cc_final: 0.7690 (m-30) REVERT: P 102 GLU cc_start: 0.8236 (tm-30) cc_final: 0.8002 (tm-30) REVERT: P 118 GLN cc_start: 0.9334 (tm-30) cc_final: 0.8849 (tm-30) REVERT: P 122 GLN cc_start: 0.8931 (tt0) cc_final: 0.8147 (tp40) REVERT: P 208 GLU cc_start: 0.8188 (tp30) cc_final: 0.7657 (tp30) REVERT: P 219 ARG cc_start: 0.9155 (ptp90) cc_final: 0.8813 (ttp-110) REVERT: P 224 GLU cc_start: 0.9300 (mp0) cc_final: 0.9000 (mp0) REVERT: Q 66 TYR cc_start: 0.8235 (m-80) cc_final: 0.7877 (m-80) REVERT: Q 88 ASN cc_start: 0.8705 (p0) cc_final: 0.8398 (p0) REVERT: Q 167 ASN cc_start: 0.9033 (m-40) cc_final: 0.8819 (m-40) REVERT: R 90 GLU cc_start: 0.9197 (tp30) cc_final: 0.8646 (tt0) REVERT: R 157 LYS cc_start: 0.9254 (mttt) cc_final: 0.8906 (mtmt) REVERT: S 107 MET cc_start: 0.8964 (ttm) cc_final: 0.8688 (ttm) REVERT: S 143 PHE cc_start: 0.9030 (m-80) cc_final: 0.8563 (m-80) REVERT: S 156 MET cc_start: 0.7857 (ttm) cc_final: 0.6749 (ttt) REVERT: S 164 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7215 (tm-30) REVERT: S 182 GLN cc_start: 0.8920 (pp30) cc_final: 0.8599 (pp30) REVERT: S 206 MET cc_start: 0.8722 (mmm) cc_final: 0.8065 (mmp) REVERT: S 225 ASN cc_start: 0.9348 (p0) cc_final: 0.9045 (p0) REVERT: T 26 MET cc_start: 0.8991 (tpp) cc_final: 0.8629 (tpp) REVERT: T 27 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8264 (tm-30) REVERT: T 176 MET cc_start: 0.8423 (tmm) cc_final: 0.8057 (tmm) REVERT: T 189 LYS cc_start: 0.9635 (OUTLIER) cc_final: 0.9368 (mmmt) REVERT: U 175 GLU cc_start: 0.9285 (mp0) cc_final: 0.8971 (mp0) REVERT: U 179 LEU cc_start: 0.9238 (tt) cc_final: 0.8899 (tt) REVERT: U 236 GLU cc_start: 0.9436 (mt-10) cc_final: 0.8898 (mt-10) REVERT: V 90 TYR cc_start: 0.8946 (m-80) cc_final: 0.8676 (m-80) REVERT: V 95 MET cc_start: 0.6993 (tmm) cc_final: 0.5922 (tmm) REVERT: V 107 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8043 (tm-30) REVERT: W 19 ARG cc_start: 0.9114 (ttm170) cc_final: 0.8762 (ttm170) REVERT: W 139 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8512 (mm-30) REVERT: X 3 MET cc_start: 0.8821 (mmm) cc_final: 0.8432 (mmm) REVERT: X 98 ARG cc_start: 0.9027 (tpt-90) cc_final: 0.8800 (tpt-90) REVERT: X 105 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: X 117 LYS cc_start: 0.9308 (mmmm) cc_final: 0.9015 (mmtt) REVERT: X 130 MET cc_start: 0.7913 (tpp) cc_final: 0.7367 (tpp) REVERT: X 150 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8360 (tt0) REVERT: Y 18 ASP cc_start: 0.8723 (t0) cc_final: 0.8267 (t0) REVERT: Y 34 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8582 (ptpp) REVERT: Y 52 ASP cc_start: 0.8637 (m-30) cc_final: 0.8159 (t0) REVERT: Y 55 GLN cc_start: 0.9256 (mm-40) cc_final: 0.9023 (mm-40) REVERT: Y 86 ARG cc_start: 0.9060 (tpp80) cc_final: 0.8736 (tpp80) REVERT: Y 186 ASN cc_start: 0.9506 (m-40) cc_final: 0.9300 (m-40) REVERT: a 54 CYS cc_start: 0.8217 (m) cc_final: 0.7749 (m) REVERT: a 127 VAL cc_start: 0.9459 (m) cc_final: 0.9220 (p) REVERT: a 131 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7968 (tm-30) REVERT: b 50 MET cc_start: 0.8590 (ptp) cc_final: 0.8390 (ptp) REVERT: b 76 LEU cc_start: 0.9136 (mt) cc_final: 0.8805 (mt) REVERT: b 104 ASN cc_start: 0.8634 (t0) cc_final: 0.8219 (t0) REVERT: b 173 MET cc_start: 0.8991 (tpt) cc_final: 0.8679 (mmt) REVERT: b 180 ASP cc_start: 0.8979 (t0) cc_final: 0.8369 (t0) REVERT: b 200 GLU cc_start: 0.7642 (mp0) cc_final: 0.7319 (mp0) outliers start: 101 outliers final: 74 residues processed: 1046 average time/residue: 0.2654 time to fit residues: 453.9962 Evaluate side-chains 1020 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 938 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 144 MET Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 79 ARG Chi-restraints excluded: chain X residue 105 GLU Chi-restraints excluded: chain Y residue 34 LYS Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 159 LEU Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 96 MET Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 36 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 463 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 580 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 552 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 482 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN H 106 GLN J 71 ASN L 89 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN S 204 GLN T 86 ASN ** V 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 ASN ** a 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.063519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.051904 restraints weight = 144065.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.054129 restraints weight = 64775.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.055635 restraints weight = 37654.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.056663 restraints weight = 25540.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.057349 restraints weight = 19164.338| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 46168 Z= 0.149 Angle : 0.654 12.568 62689 Z= 0.338 Chirality : 0.044 0.271 7344 Planarity : 0.004 0.058 7971 Dihedral : 4.355 30.897 6785 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.46 % Allowed : 19.59 % Favored : 77.95 % 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: 0.66 (0.11), residues: 6139 helix: 1.61 (0.11), residues: 2204 sheet: -0.04 (0.13), residues: 1464 loop : -0.23 (0.13), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG W 89 TYR 0.035 0.001 TYR D 110 PHE 0.022 0.001 PHE C 124 TRP 0.022 0.001 TRP G 215 HIS 0.007 0.001 HIS S 227 Details of bonding type rmsd covalent geometry : bond 0.00340 (46168) covalent geometry : angle 0.65374 (62689) hydrogen bonds : bond 0.03247 ( 2420) hydrogen bonds : angle 4.59589 ( 6927) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 969 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8626 (mtm110) cc_final: 0.8419 (ptm-80) REVERT: A 23 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.6902 (t80) REVERT: A 80 MET cc_start: 0.8745 (mmm) cc_final: 0.8504 (mmm) REVERT: A 93 ARG cc_start: 0.9245 (mmm-85) cc_final: 0.8989 (tpp80) REVERT: A 123 GLN cc_start: 0.9490 (tm-30) cc_final: 0.8933 (tm-30) REVERT: A 224 ASN cc_start: 0.8833 (p0) cc_final: 0.8605 (p0) REVERT: B 48 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 101 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8572 (mm-40) REVERT: B 122 GLN cc_start: 0.8822 (tp40) cc_final: 0.8529 (tp40) REVERT: B 147 GLN cc_start: 0.8331 (tt0) cc_final: 0.7727 (tm-30) REVERT: B 155 PHE cc_start: 0.8615 (m-80) cc_final: 0.8170 (m-10) REVERT: B 218 ARG cc_start: 0.9148 (tmm-80) cc_final: 0.8793 (tmm-80) REVERT: C 25 MET cc_start: 0.8971 (mmt) cc_final: 0.8578 (mmp) REVERT: C 26 GLU cc_start: 0.8516 (tp30) cc_final: 0.8178 (tp30) REVERT: C 93 ILE cc_start: 0.9611 (mt) cc_final: 0.9381 (mm) REVERT: D 120 GLN cc_start: 0.8498 (tt0) cc_final: 0.8149 (tt0) REVERT: D 146 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8161 (tm-30) REVERT: E 32 LYS cc_start: 0.9039 (mtmm) cc_final: 0.8687 (mtmm) REVERT: E 51 GLU cc_start: 0.7771 (tt0) cc_final: 0.7381 (pt0) REVERT: E 118 ASN cc_start: 0.9056 (m-40) cc_final: 0.8774 (m-40) REVERT: E 125 GLU cc_start: 0.8109 (pm20) cc_final: 0.7806 (pm20) REVERT: E 133 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.6463 (mmm) REVERT: E 216 GLU cc_start: 0.6817 (tt0) cc_final: 0.6472 (tt0) REVERT: E 225 ASN cc_start: 0.9037 (p0) cc_final: 0.8758 (p0) REVERT: F 26 MET cc_start: 0.8570 (ttm) cc_final: 0.8357 (mmm) REVERT: F 90 GLN cc_start: 0.9301 (tp40) cc_final: 0.9095 (tp40) REVERT: F 146 GLN cc_start: 0.7961 (tt0) cc_final: 0.7372 (tm-30) REVERT: F 166 GLN cc_start: 0.9179 (tp40) cc_final: 0.8969 (tp-100) REVERT: F 182 CYS cc_start: 0.7768 (m) cc_final: 0.7148 (m) REVERT: G 150 MET cc_start: 0.8364 (tmm) cc_final: 0.7943 (tmm) REVERT: G 175 GLU cc_start: 0.9118 (mp0) cc_final: 0.8884 (mm-30) REVERT: H 51 ASP cc_start: 0.8804 (m-30) cc_final: 0.8583 (p0) REVERT: H 90 TYR cc_start: 0.8644 (m-10) cc_final: 0.8342 (m-10) REVERT: H 165 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8519 (tm-30) REVERT: H 167 ASP cc_start: 0.8855 (t0) cc_final: 0.8490 (t0) REVERT: I 30 ASN cc_start: 0.8907 (t0) cc_final: 0.8176 (t0) REVERT: I 53 ASP cc_start: 0.8860 (t0) cc_final: 0.8644 (t0) REVERT: I 91 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8251 (tm-30) REVERT: I 135 MET cc_start: 0.9056 (mmm) cc_final: 0.8739 (tpp) REVERT: J 88 SER cc_start: 0.9269 (m) cc_final: 0.8875 (t) REVERT: J 108 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8662 (pp) REVERT: J 144 GLN cc_start: 0.9447 (mp10) cc_final: 0.8264 (mp10) REVERT: J 150 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8341 (tt0) REVERT: J 164 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8372 (mm-30) REVERT: J 177 ASP cc_start: 0.8406 (t0) cc_final: 0.8080 (t0) REVERT: J 203 MET cc_start: 0.8728 (mmp) cc_final: 0.8415 (mmm) REVERT: K 37 LYS cc_start: 0.9129 (ptmm) cc_final: 0.8669 (tttm) REVERT: K 38 MET cc_start: 0.8647 (mmm) cc_final: 0.7740 (mmm) REVERT: K 59 TYR cc_start: 0.8914 (t80) cc_final: 0.8365 (t80) REVERT: K 163 CYS cc_start: 0.9264 (m) cc_final: 0.8800 (m) REVERT: L 167 ASP cc_start: 0.8842 (t70) cc_final: 0.8531 (t0) REVERT: M 8 ASN cc_start: 0.9088 (m110) cc_final: 0.8447 (m110) REVERT: N 110 MET cc_start: 0.8495 (mmm) cc_final: 0.8272 (mmm) REVERT: N 170 GLU cc_start: 0.8449 (pp20) cc_final: 0.8188 (pp20) REVERT: N 180 ASP cc_start: 0.9097 (t0) cc_final: 0.8691 (t0) REVERT: O 224 ASN cc_start: 0.8653 (p0) cc_final: 0.8364 (p0) REVERT: P 48 GLU cc_start: 0.8652 (tm-30) cc_final: 0.7954 (tm-30) REVERT: P 50 LYS cc_start: 0.8803 (tppt) cc_final: 0.7976 (tppt) REVERT: P 63 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8428 (mtpt) REVERT: P 78 MET cc_start: 0.8345 (mtp) cc_final: 0.8029 (ptm) REVERT: P 81 ASP cc_start: 0.8655 (m-30) cc_final: 0.7751 (m-30) REVERT: P 122 GLN cc_start: 0.8982 (tt0) cc_final: 0.8303 (tp40) REVERT: P 208 GLU cc_start: 0.8168 (tp30) cc_final: 0.7642 (tp30) REVERT: P 219 ARG cc_start: 0.9178 (ptp90) cc_final: 0.8911 (ttp-110) REVERT: P 224 GLU cc_start: 0.9272 (mp0) cc_final: 0.8971 (mp0) REVERT: Q 30 HIS cc_start: 0.8363 (m90) cc_final: 0.8126 (m90) REVERT: Q 66 TYR cc_start: 0.8296 (m-80) cc_final: 0.7973 (m-80) REVERT: Q 88 ASN cc_start: 0.8748 (p0) cc_final: 0.8441 (p0) REVERT: Q 167 ASN cc_start: 0.9012 (m-40) cc_final: 0.8784 (m-40) REVERT: R 90 GLU cc_start: 0.9173 (tp30) cc_final: 0.8599 (tt0) REVERT: R 157 LYS cc_start: 0.9265 (mttt) cc_final: 0.8921 (mtmt) REVERT: S 107 MET cc_start: 0.9001 (ttm) cc_final: 0.8795 (ttm) REVERT: S 156 MET cc_start: 0.7969 (ttm) cc_final: 0.7062 (ttt) REVERT: S 164 GLN cc_start: 0.7455 (tm-30) cc_final: 0.7131 (tm-30) REVERT: S 182 GLN cc_start: 0.8898 (pp30) cc_final: 0.8561 (pp30) REVERT: S 225 ASN cc_start: 0.9368 (p0) cc_final: 0.9101 (p0) REVERT: T 26 MET cc_start: 0.9025 (tpp) cc_final: 0.8726 (tpp) REVERT: T 27 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8285 (tm-30) REVERT: T 176 MET cc_start: 0.8476 (tmm) cc_final: 0.8118 (tmm) REVERT: T 189 LYS cc_start: 0.9639 (OUTLIER) cc_final: 0.9330 (mmmt) REVERT: U 135 PHE cc_start: 0.8780 (p90) cc_final: 0.8493 (p90) REVERT: U 175 GLU cc_start: 0.9283 (mp0) cc_final: 0.8967 (mp0) REVERT: U 179 LEU cc_start: 0.9259 (tt) cc_final: 0.8981 (tt) REVERT: U 236 GLU cc_start: 0.9437 (mt-10) cc_final: 0.8912 (mt-10) REVERT: V 53 GLN cc_start: 0.9078 (mt0) cc_final: 0.8810 (mt0) REVERT: V 95 MET cc_start: 0.7100 (tmm) cc_final: 0.6070 (tmm) REVERT: V 107 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8157 (tm-30) REVERT: W 19 ARG cc_start: 0.9120 (ttm170) cc_final: 0.8814 (ttm170) REVERT: X 3 MET cc_start: 0.8807 (mmm) cc_final: 0.8401 (mmm) REVERT: X 105 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: X 117 LYS cc_start: 0.9292 (mmmm) cc_final: 0.9041 (mmtt) REVERT: X 130 MET cc_start: 0.7915 (tpp) cc_final: 0.7430 (tpp) REVERT: X 150 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: X 182 MET cc_start: 0.8310 (mmm) cc_final: 0.7621 (mmp) REVERT: Y 18 ASP cc_start: 0.8725 (t0) cc_final: 0.8512 (t0) REVERT: Y 34 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8619 (ptpp) REVERT: Y 52 ASP cc_start: 0.8628 (m-30) cc_final: 0.8148 (t0) REVERT: Y 55 GLN cc_start: 0.9250 (mm-40) cc_final: 0.9020 (mm-40) REVERT: a 54 CYS cc_start: 0.8159 (m) cc_final: 0.7684 (m) REVERT: a 91 MET cc_start: 0.9002 (tmm) cc_final: 0.8497 (tmm) REVERT: a 127 VAL cc_start: 0.9462 (m) cc_final: 0.9203 (p) REVERT: a 131 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8002 (tm-30) REVERT: a 193 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8945 (tp) REVERT: b 76 LEU cc_start: 0.9118 (mt) cc_final: 0.8779 (mt) REVERT: b 104 ASN cc_start: 0.8585 (t0) cc_final: 0.8158 (t0) REVERT: b 173 MET cc_start: 0.8979 (tpt) cc_final: 0.8642 (mmt) REVERT: b 180 ASP cc_start: 0.8976 (t0) cc_final: 0.8360 (t0) outliers start: 105 outliers final: 80 residues processed: 1021 average time/residue: 0.2608 time to fit residues: 437.1878 Evaluate side-chains 1022 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 934 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 144 MET Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 79 ARG Chi-restraints excluded: chain X residue 105 GLU Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain Y residue 34 LYS Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 96 MET Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 290 optimal weight: 4.9990 chunk 317 optimal weight: 3.9990 chunk 541 optimal weight: 2.9990 chunk 603 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 195 optimal weight: 0.0670 chunk 192 optimal weight: 0.0570 chunk 226 optimal weight: 6.9990 chunk 535 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 GLN ** V 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 ASN ** a 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.063653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.052029 restraints weight = 143823.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.054259 restraints weight = 64776.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.055762 restraints weight = 37720.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.056760 restraints weight = 25618.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.057470 restraints weight = 19413.228| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 46168 Z= 0.138 Angle : 0.666 11.624 62689 Z= 0.344 Chirality : 0.044 0.219 7344 Planarity : 0.004 0.057 7971 Dihedral : 4.340 29.430 6785 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.25 % Allowed : 19.80 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.63 (0.11), residues: 6139 helix: 1.55 (0.11), residues: 2231 sheet: -0.02 (0.13), residues: 1456 loop : -0.26 (0.13), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG W 89 TYR 0.034 0.001 TYR D 110 PHE 0.025 0.001 PHE A 191 TRP 0.021 0.001 TRP G 215 HIS 0.007 0.001 HIS S 227 Details of bonding type rmsd covalent geometry : bond 0.00320 (46168) covalent geometry : angle 0.66635 (62689) hydrogen bonds : bond 0.03189 ( 2420) hydrogen bonds : angle 4.56879 ( 6927) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 967 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.6907 (t80) REVERT: A 80 MET cc_start: 0.8737 (mmm) cc_final: 0.8522 (mmm) REVERT: A 93 ARG cc_start: 0.9232 (mmm-85) cc_final: 0.8990 (tpp80) REVERT: A 123 GLN cc_start: 0.9488 (tm-30) cc_final: 0.8928 (tm-30) REVERT: B 48 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7752 (tm-30) REVERT: B 50 LYS cc_start: 0.9171 (tppt) cc_final: 0.8785 (ttmt) REVERT: B 122 GLN cc_start: 0.8798 (tp40) cc_final: 0.8523 (tp40) REVERT: B 147 GLN cc_start: 0.8271 (tt0) cc_final: 0.7761 (tm-30) REVERT: B 155 PHE cc_start: 0.8620 (m-80) cc_final: 0.8183 (m-10) REVERT: B 218 ARG cc_start: 0.9116 (tmm-80) cc_final: 0.8773 (tmm-80) REVERT: C 25 MET cc_start: 0.8988 (mmt) cc_final: 0.8574 (mmp) REVERT: C 26 GLU cc_start: 0.8532 (tp30) cc_final: 0.8206 (tp30) REVERT: C 93 ILE cc_start: 0.9587 (mt) cc_final: 0.9375 (mm) REVERT: D 5 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7274 (ttt-90) REVERT: D 120 GLN cc_start: 0.8471 (tt0) cc_final: 0.8092 (tt0) REVERT: D 146 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8169 (tm-30) REVERT: E 32 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8577 (mtmm) REVERT: E 51 GLU cc_start: 0.7804 (tt0) cc_final: 0.7435 (pt0) REVERT: E 59 MET cc_start: 0.8605 (ptp) cc_final: 0.7932 (pmm) REVERT: E 118 ASN cc_start: 0.9048 (m-40) cc_final: 0.8767 (m-40) REVERT: E 125 GLU cc_start: 0.8159 (pm20) cc_final: 0.7831 (pm20) REVERT: E 133 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.6415 (mmm) REVERT: E 216 GLU cc_start: 0.6644 (tt0) cc_final: 0.6286 (tt0) REVERT: E 225 ASN cc_start: 0.9055 (p0) cc_final: 0.8779 (p0) REVERT: F 90 GLN cc_start: 0.9310 (tp40) cc_final: 0.9100 (tp40) REVERT: F 146 GLN cc_start: 0.8011 (tt0) cc_final: 0.7382 (tm-30) REVERT: F 166 GLN cc_start: 0.9218 (tp40) cc_final: 0.9015 (tp-100) REVERT: F 182 CYS cc_start: 0.8041 (m) cc_final: 0.7189 (m) REVERT: G 70 ASP cc_start: 0.9005 (t70) cc_final: 0.8769 (t70) REVERT: G 150 MET cc_start: 0.8403 (tmm) cc_final: 0.7959 (tmm) REVERT: G 175 GLU cc_start: 0.9101 (mp0) cc_final: 0.8829 (mm-30) REVERT: H 51 ASP cc_start: 0.8793 (m-30) cc_final: 0.8573 (p0) REVERT: H 90 TYR cc_start: 0.8588 (m-10) cc_final: 0.8153 (m-10) REVERT: H 165 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8494 (tm-30) REVERT: H 167 ASP cc_start: 0.8851 (t0) cc_final: 0.8478 (t0) REVERT: I 30 ASN cc_start: 0.8921 (t0) cc_final: 0.8206 (t0) REVERT: I 53 ASP cc_start: 0.8765 (t0) cc_final: 0.7918 (t0) REVERT: I 91 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8302 (tm-30) REVERT: I 135 MET cc_start: 0.9058 (mmm) cc_final: 0.8779 (mmm) REVERT: J 71 ASN cc_start: 0.9383 (m-40) cc_final: 0.9173 (m110) REVERT: J 88 SER cc_start: 0.9230 (m) cc_final: 0.8842 (t) REVERT: J 108 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8686 (pp) REVERT: J 144 GLN cc_start: 0.9457 (mp10) cc_final: 0.8284 (mp10) REVERT: J 150 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8361 (tt0) REVERT: J 157 MET cc_start: 0.8120 (mtp) cc_final: 0.7875 (mmm) REVERT: J 164 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8351 (mm-30) REVERT: J 177 ASP cc_start: 0.8451 (t0) cc_final: 0.8091 (t0) REVERT: K 37 LYS cc_start: 0.9103 (ptmm) cc_final: 0.8554 (tttp) REVERT: K 38 MET cc_start: 0.8607 (mmm) cc_final: 0.8131 (mmm) REVERT: K 59 TYR cc_start: 0.8905 (t80) cc_final: 0.8353 (t80) REVERT: K 163 CYS cc_start: 0.9261 (m) cc_final: 0.8910 (m) REVERT: L 167 ASP cc_start: 0.8871 (t70) cc_final: 0.8544 (t0) REVERT: M 8 ASN cc_start: 0.9091 (m110) cc_final: 0.8489 (m110) REVERT: N 110 MET cc_start: 0.8493 (mmm) cc_final: 0.8267 (mmm) REVERT: N 170 GLU cc_start: 0.8405 (pp20) cc_final: 0.8151 (pp20) REVERT: N 180 ASP cc_start: 0.9065 (t0) cc_final: 0.8642 (t0) REVERT: O 172 GLN cc_start: 0.9427 (pp30) cc_final: 0.9116 (pp30) REVERT: O 174 GLU cc_start: 0.9005 (mp0) cc_final: 0.8691 (mp0) REVERT: O 224 ASN cc_start: 0.8642 (p0) cc_final: 0.8355 (p0) REVERT: P 48 GLU cc_start: 0.8694 (tm-30) cc_final: 0.7913 (tm-30) REVERT: P 50 LYS cc_start: 0.8684 (tppt) cc_final: 0.7623 (tppt) REVERT: P 63 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8452 (mtpt) REVERT: P 78 MET cc_start: 0.8329 (mtp) cc_final: 0.8030 (ptm) REVERT: P 81 ASP cc_start: 0.8647 (m-30) cc_final: 0.7750 (m-30) REVERT: P 118 GLN cc_start: 0.9315 (tm-30) cc_final: 0.8813 (tm-30) REVERT: P 122 GLN cc_start: 0.8936 (tt0) cc_final: 0.8020 (tp40) REVERT: P 208 GLU cc_start: 0.8195 (tp30) cc_final: 0.7679 (tp30) REVERT: P 219 ARG cc_start: 0.9168 (ptp90) cc_final: 0.8932 (ttp-110) REVERT: P 224 GLU cc_start: 0.9257 (mp0) cc_final: 0.8966 (mp0) REVERT: Q 30 HIS cc_start: 0.8388 (m90) cc_final: 0.8101 (m90) REVERT: Q 66 TYR cc_start: 0.8323 (m-80) cc_final: 0.8032 (m-80) REVERT: Q 88 ASN cc_start: 0.8764 (p0) cc_final: 0.8491 (p0) REVERT: Q 167 ASN cc_start: 0.9005 (m-40) cc_final: 0.8768 (m-40) REVERT: R 90 GLU cc_start: 0.9169 (tp30) cc_final: 0.8442 (tt0) REVERT: R 157 LYS cc_start: 0.9267 (mttt) cc_final: 0.8942 (mtmt) REVERT: S 133 MET cc_start: 0.8281 (mmp) cc_final: 0.8073 (mmm) REVERT: S 156 MET cc_start: 0.7966 (ttm) cc_final: 0.6962 (ttt) REVERT: S 164 GLN cc_start: 0.7442 (tm-30) cc_final: 0.7070 (tm-30) REVERT: S 182 GLN cc_start: 0.8938 (pp30) cc_final: 0.8643 (pp30) REVERT: S 225 ASN cc_start: 0.9336 (p0) cc_final: 0.9059 (p0) REVERT: T 26 MET cc_start: 0.9032 (tpp) cc_final: 0.8756 (tpp) REVERT: T 27 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8355 (tm-30) REVERT: T 87 PHE cc_start: 0.9450 (t80) cc_final: 0.9221 (t80) REVERT: T 176 MET cc_start: 0.8490 (tmm) cc_final: 0.8136 (tmm) REVERT: T 189 LYS cc_start: 0.9634 (OUTLIER) cc_final: 0.9337 (mmmt) REVERT: U 135 PHE cc_start: 0.8796 (p90) cc_final: 0.8512 (p90) REVERT: U 175 GLU cc_start: 0.9281 (mp0) cc_final: 0.8948 (mp0) REVERT: U 179 LEU cc_start: 0.9272 (tt) cc_final: 0.9039 (tt) REVERT: U 236 GLU cc_start: 0.9438 (mt-10) cc_final: 0.8913 (mt-10) REVERT: V 95 MET cc_start: 0.7511 (tmm) cc_final: 0.5701 (tmm) REVERT: V 107 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8040 (tm-30) REVERT: V 119 MET cc_start: 0.7613 (ttp) cc_final: 0.7374 (ttp) REVERT: W 19 ARG cc_start: 0.9130 (ttm170) cc_final: 0.8605 (ttm170) REVERT: W 89 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8420 (tmm-80) REVERT: X 3 MET cc_start: 0.8799 (mmm) cc_final: 0.8382 (mmm) REVERT: X 11 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8491 (ttp) REVERT: X 105 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: X 117 LYS cc_start: 0.9286 (mmmm) cc_final: 0.9056 (mmtt) REVERT: X 130 MET cc_start: 0.7824 (tpp) cc_final: 0.7361 (tpp) REVERT: X 145 MET cc_start: 0.8966 (ptp) cc_final: 0.8523 (pmm) REVERT: X 150 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: Y 18 ASP cc_start: 0.8649 (t0) cc_final: 0.8303 (t0) REVERT: Y 52 ASP cc_start: 0.8599 (m-30) cc_final: 0.8126 (t0) REVERT: Y 55 GLN cc_start: 0.9229 (mm-40) cc_final: 0.9029 (mm-40) REVERT: Y 108 ASP cc_start: 0.8351 (p0) cc_final: 0.8114 (p0) REVERT: Y 166 GLU cc_start: 0.8538 (tp30) cc_final: 0.8208 (tp30) REVERT: a 54 CYS cc_start: 0.8142 (m) cc_final: 0.7661 (m) REVERT: a 83 MET cc_start: 0.8852 (mmm) cc_final: 0.8604 (mmm) REVERT: a 91 MET cc_start: 0.9039 (tmm) cc_final: 0.8521 (tmm) REVERT: a 127 VAL cc_start: 0.9464 (m) cc_final: 0.9208 (p) REVERT: a 131 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7995 (tm-30) REVERT: a 193 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8936 (tp) REVERT: b 56 ASP cc_start: 0.8337 (t0) cc_final: 0.8054 (t0) REVERT: b 76 LEU cc_start: 0.9102 (mt) cc_final: 0.8762 (mt) REVERT: b 104 ASN cc_start: 0.8626 (t0) cc_final: 0.8169 (t0) REVERT: b 173 MET cc_start: 0.8991 (tpt) cc_final: 0.8709 (mmt) REVERT: b 180 ASP cc_start: 0.8948 (t0) cc_final: 0.8345 (t0) outliers start: 96 outliers final: 74 residues processed: 1017 average time/residue: 0.2523 time to fit residues: 421.6013 Evaluate side-chains 1013 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 930 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 144 MET Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 188 GLN Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 79 ARG Chi-restraints excluded: chain X residue 105 GLU Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 96 MET Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 359 optimal weight: 7.9990 chunk 443 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 389 optimal weight: 9.9990 chunk 466 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 264 optimal weight: 6.9990 chunk 509 optimal weight: 4.9990 chunk 428 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN H 106 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 GLN V 53 GLN X 92 ASN a 146 GLN b 65 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.061968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.050411 restraints weight = 146362.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.052590 restraints weight = 66110.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.054062 restraints weight = 38573.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.055043 restraints weight = 26303.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.055747 restraints weight = 19947.967| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 46168 Z= 0.211 Angle : 0.716 13.110 62689 Z= 0.369 Chirality : 0.045 0.279 7344 Planarity : 0.004 0.060 7971 Dihedral : 4.430 29.946 6785 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.25 % Allowed : 19.96 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.60 (0.11), residues: 6139 helix: 1.51 (0.11), residues: 2233 sheet: -0.07 (0.13), residues: 1474 loop : -0.23 (0.13), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG W 89 TYR 0.038 0.002 TYR C 97 PHE 0.024 0.001 PHE C 124 TRP 0.030 0.002 TRP G 215 HIS 0.007 0.001 HIS S 227 Details of bonding type rmsd covalent geometry : bond 0.00479 (46168) covalent geometry : angle 0.71636 (62689) hydrogen bonds : bond 0.03480 ( 2420) hydrogen bonds : angle 4.66932 ( 6927) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12278 Ramachandran restraints generated. 6139 Oldfield, 0 Emsley, 6139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 924 time to evaluate : 2.061 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: A 19 GLU cc_start: 0.8414 (mp0) cc_final: 0.7798 (mp0) REVERT: A 23 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.6672 (t80) REVERT: A 80 MET cc_start: 0.8714 (mmm) cc_final: 0.8484 (mmm) REVERT: A 93 ARG cc_start: 0.9254 (mmm-85) cc_final: 0.9032 (tpp80) REVERT: A 123 GLN cc_start: 0.9514 (tm-30) cc_final: 0.8968 (tm-30) REVERT: B 48 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7746 (tm-30) REVERT: B 50 LYS cc_start: 0.9176 (tppt) cc_final: 0.8807 (ttmt) REVERT: B 101 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8600 (mm110) REVERT: B 117 MET cc_start: 0.8903 (ttm) cc_final: 0.8561 (ttm) REVERT: B 122 GLN cc_start: 0.8861 (tp40) cc_final: 0.8579 (tp40) REVERT: B 147 GLN cc_start: 0.8314 (tt0) cc_final: 0.7711 (tm-30) REVERT: B 155 PHE cc_start: 0.8677 (m-80) cc_final: 0.8230 (m-10) REVERT: B 218 ARG cc_start: 0.9098 (tmm-80) cc_final: 0.8740 (tmm-80) REVERT: C 25 MET cc_start: 0.9000 (mmt) cc_final: 0.8580 (mmp) REVERT: C 26 GLU cc_start: 0.8552 (tp30) cc_final: 0.8249 (tp30) REVERT: C 93 ILE cc_start: 0.9586 (mt) cc_final: 0.9348 (mm) REVERT: D 5 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6859 (ttt180) REVERT: D 120 GLN cc_start: 0.8507 (tt0) cc_final: 0.8157 (tt0) REVERT: D 146 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8207 (tm-30) REVERT: E 51 GLU cc_start: 0.7900 (tt0) cc_final: 0.7596 (pt0) REVERT: E 118 ASN cc_start: 0.9082 (m-40) cc_final: 0.8797 (m-40) REVERT: E 125 GLU cc_start: 0.8199 (pm20) cc_final: 0.7819 (pm20) REVERT: E 133 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.6444 (mmm) REVERT: E 225 ASN cc_start: 0.9101 (p0) cc_final: 0.8815 (p0) REVERT: F 26 MET cc_start: 0.8951 (mmm) cc_final: 0.8644 (mmm) REVERT: F 90 GLN cc_start: 0.9342 (tp40) cc_final: 0.9111 (tp40) REVERT: F 166 GLN cc_start: 0.9198 (tp40) cc_final: 0.8988 (tp-100) REVERT: F 182 CYS cc_start: 0.7837 (m) cc_final: 0.7045 (m) REVERT: G 70 ASP cc_start: 0.9082 (t70) cc_final: 0.8857 (t70) REVERT: G 83 ASP cc_start: 0.8921 (m-30) cc_final: 0.8655 (m-30) REVERT: G 150 MET cc_start: 0.8407 (tmm) cc_final: 0.7967 (tmm) REVERT: G 175 GLU cc_start: 0.9084 (mp0) cc_final: 0.8846 (mp0) REVERT: H 90 TYR cc_start: 0.8646 (m-10) cc_final: 0.8319 (m-10) REVERT: H 165 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8467 (tm-30) REVERT: H 167 ASP cc_start: 0.8800 (t0) cc_final: 0.8414 (t0) REVERT: I 30 ASN cc_start: 0.8865 (t0) cc_final: 0.8205 (t0) REVERT: I 91 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8387 (tm-30) REVERT: I 135 MET cc_start: 0.9055 (mmm) cc_final: 0.8763 (mmm) REVERT: J 88 SER cc_start: 0.9297 (m) cc_final: 0.8970 (t) REVERT: J 108 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8686 (pp) REVERT: J 144 GLN cc_start: 0.9475 (mp10) cc_final: 0.8327 (mp10) REVERT: J 150 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8272 (tt0) REVERT: J 164 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8233 (mm-30) REVERT: J 177 ASP cc_start: 0.8543 (t0) cc_final: 0.8146 (t0) REVERT: J 182 MET cc_start: 0.8606 (mmp) cc_final: 0.8389 (mmt) REVERT: K 37 LYS cc_start: 0.9058 (ptmm) cc_final: 0.8667 (tttm) REVERT: K 38 MET cc_start: 0.8473 (mmm) cc_final: 0.8046 (mmm) REVERT: K 163 CYS cc_start: 0.9225 (m) cc_final: 0.8893 (m) REVERT: L 44 THR cc_start: 0.8849 (p) cc_final: 0.8642 (t) REVERT: L 91 LYS cc_start: 0.9118 (ttpt) cc_final: 0.8782 (ptpt) REVERT: L 139 MET cc_start: 0.8898 (ttp) cc_final: 0.8619 (ttp) REVERT: M 8 ASN cc_start: 0.9158 (m110) cc_final: 0.8565 (m110) REVERT: N 110 MET cc_start: 0.8525 (mmm) cc_final: 0.8273 (mmm) REVERT: N 170 GLU cc_start: 0.8479 (pp20) cc_final: 0.8225 (pp20) REVERT: N 180 ASP cc_start: 0.9093 (t0) cc_final: 0.8692 (t0) REVERT: O 224 ASN cc_start: 0.8623 (p0) cc_final: 0.8360 (p0) REVERT: P 48 GLU cc_start: 0.8710 (tm-30) cc_final: 0.7905 (tm-30) REVERT: P 50 LYS cc_start: 0.8672 (tppt) cc_final: 0.7813 (tppt) REVERT: P 63 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8456 (mtpt) REVERT: P 78 MET cc_start: 0.8419 (mtp) cc_final: 0.7795 (ptm) REVERT: P 81 ASP cc_start: 0.8629 (m-30) cc_final: 0.7616 (m-30) REVERT: P 122 GLN cc_start: 0.8969 (tt0) cc_final: 0.8388 (tp40) REVERT: P 208 GLU cc_start: 0.8202 (tp30) cc_final: 0.7648 (tp30) REVERT: P 219 ARG cc_start: 0.9186 (ptp90) cc_final: 0.8898 (ttp-110) REVERT: P 224 GLU cc_start: 0.9267 (mp0) cc_final: 0.8982 (mp0) REVERT: Q 30 HIS cc_start: 0.8396 (m90) cc_final: 0.8117 (m90) REVERT: Q 66 TYR cc_start: 0.8401 (m-80) cc_final: 0.8165 (m-80) REVERT: Q 88 ASN cc_start: 0.8790 (p0) cc_final: 0.8445 (p0) REVERT: Q 167 ASN cc_start: 0.9079 (m-40) cc_final: 0.8833 (m-40) REVERT: R 90 GLU cc_start: 0.9220 (tp30) cc_final: 0.8654 (tt0) REVERT: R 157 LYS cc_start: 0.9299 (mttt) cc_final: 0.8946 (mtmt) REVERT: S 156 MET cc_start: 0.7985 (ttm) cc_final: 0.7073 (ttt) REVERT: S 164 GLN cc_start: 0.7490 (tm-30) cc_final: 0.7187 (tm-30) REVERT: S 182 GLN cc_start: 0.9010 (pp30) cc_final: 0.8688 (pp30) REVERT: S 206 MET cc_start: 0.8567 (mmm) cc_final: 0.7866 (mmp) REVERT: T 27 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8414 (tm-30) REVERT: T 189 LYS cc_start: 0.9632 (OUTLIER) cc_final: 0.9374 (mmmt) REVERT: U 175 GLU cc_start: 0.9273 (mp0) cc_final: 0.8941 (mp0) REVERT: U 179 LEU cc_start: 0.9258 (tt) cc_final: 0.8964 (tt) REVERT: U 236 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9004 (mt-10) REVERT: V 95 MET cc_start: 0.7099 (tmm) cc_final: 0.6317 (tmm) REVERT: V 107 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8056 (tm-30) REVERT: W 19 ARG cc_start: 0.9160 (ttm170) cc_final: 0.8832 (ttm170) REVERT: W 57 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8229 (mt0) REVERT: W 89 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8443 (tmm-80) REVERT: X 3 MET cc_start: 0.8788 (mmm) cc_final: 0.8378 (mmm) REVERT: X 88 SER cc_start: 0.9261 (m) cc_final: 0.8948 (t) REVERT: X 105 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8202 (mp0) REVERT: X 117 LYS cc_start: 0.9305 (mmmm) cc_final: 0.9096 (mmtt) REVERT: X 150 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: Y 52 ASP cc_start: 0.8686 (m-30) cc_final: 0.8099 (t0) REVERT: a 54 CYS cc_start: 0.8143 (m) cc_final: 0.7705 (m) REVERT: a 91 MET cc_start: 0.9005 (tmm) cc_final: 0.8469 (tmm) REVERT: a 127 VAL cc_start: 0.9489 (m) cc_final: 0.9236 (p) REVERT: a 131 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8024 (tm-30) REVERT: b 104 ASN cc_start: 0.8594 (t0) cc_final: 0.8106 (t0) REVERT: b 157 GLN cc_start: 0.8419 (tp-100) cc_final: 0.8092 (tm-30) REVERT: b 173 MET cc_start: 0.8996 (tpt) cc_final: 0.8696 (mmt) REVERT: b 180 ASP cc_start: 0.9028 (t0) cc_final: 0.8435 (t0) outliers start: 96 outliers final: 83 residues processed: 969 average time/residue: 0.2353 time to fit residues: 374.3466 Evaluate side-chains 998 residues out of total 5144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 909 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 24 ASP Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 146 TYR Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 63 CYS Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 130 TYR Chi-restraints excluded: chain M residue 144 MET Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain N residue 188 GLN Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 78 CYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 131 MET Chi-restraints excluded: chain O residue 137 CYS Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 147 THR Chi-restraints excluded: chain T residue 189 LYS Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 186 CYS Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 79 ARG Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain Y residue 46 CYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 91 CYS Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain a residue 95 ILE Chi-restraints excluded: chain a residue 130 TYR Chi-restraints excluded: chain a residue 146 GLN Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 96 MET Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 596 optimal weight: 4.9990 chunk 539 optimal weight: 0.9990 chunk 330 optimal weight: 5.9990 chunk 371 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 494 optimal weight: 1.9990 chunk 351 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 101 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN I 57 GLN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 GLN X 92 ASN a 146 GLN b 65 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.062467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.050987 restraints weight = 145926.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.053172 restraints weight = 65492.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.054644 restraints weight = 38007.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.055646 restraints weight = 25840.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.056356 restraints weight = 19367.358| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 46168 Z= 0.170 Angle : 0.719 13.521 62689 Z= 0.370 Chirality : 0.045 0.293 7344 Planarity : 0.004 0.067 7971 Dihedral : 4.439 30.481 6785 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.27 % Allowed : 20.55 % Favored : 77.18 % 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: 0.58 (0.11), residues: 6139 helix: 1.51 (0.11), residues: 2213 sheet: -0.07 (0.13), residues: 1474 loop : -0.24 (0.13), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG W 89 TYR 0.038 0.001 TYR C 97 PHE 0.036 0.001 PHE F 87 TRP 0.025 0.001 TRP G 215 HIS 0.007 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00393 (46168) covalent geometry : angle 0.71893 (62689) hydrogen bonds : bond 0.03387 ( 2420) hydrogen bonds : angle 4.63750 ( 6927) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9184.14 seconds wall clock time: 158 minutes 53.74 seconds (9533.74 seconds total)