Starting phenix.real_space_refine on Sun Feb 8 11:18:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nan_24275/02_2026/7nan_24275.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nan_24275/02_2026/7nan_24275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nan_24275/02_2026/7nan_24275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nan_24275/02_2026/7nan_24275.map" model { file = "/net/cci-nas-00/data/ceres_data/7nan_24275/02_2026/7nan_24275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nan_24275/02_2026/7nan_24275.cif" } resolution = 2.8 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= 1.000 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 290 5.16 5 C 29593 2.51 5 N 8164 2.21 5 O 8313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46360 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1665 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 13, 'ASN:plan1': 5, 'ASP:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1795 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 20, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "C" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1694 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 16, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1699 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 8, 'TRANS': 226} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 82 Planarities with less than four sites: {'GLU:plan': 12, 'TYR:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 76 Chain: "E" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1794 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 59 Chain: "F" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1783 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 11, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 68 Chain: "G" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1781 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 234} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 6, 'GLU:plan': 12, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "H" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1604 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "I" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1563 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1541 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1525 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "L" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1604 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "M" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1635 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 207} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "N" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1485 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "O" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1694 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 11, 'ASP:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 71 Chain: "P" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1850 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 5, 'TRANS': 245} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 15, 'PHE:plan': 1, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "Q" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1719 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 6, 'TRANS': 229} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 14, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 88 Chain: "R" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1688 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 8, 'TRANS': 226} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 12, 'TYR:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 79 Chain: "S" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 10, 'TRANS': 226} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 11, 'GLN:plan1': 2, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 84 Chain: "T" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1784 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 62 Chain: "U" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1781 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 8, 'TRANS': 234} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 6, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 72 Chain: "V" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1618 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "W" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1559 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "X" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1531 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "Y" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1522 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "Z" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1593 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 7, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 57 Chain: "a" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1624 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 7, 'TRANS': 206} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 40 Chain: "b" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1470 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 11.46, per 1000 atoms: 0.25 Number of scatterers: 46360 At special positions: 0 Unit cell: (136.147, 133.716, 179.909, 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 290 16.00 O 8313 8.00 N 8164 7.00 C 29593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.14 Conformation dependent library (CDL) restraints added in 2.0 seconds 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11508 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 76 sheets defined 40.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.715A pdb=" N VAL A 61 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 101 Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.743A pdb=" N HIS A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'B' and resid 18 through 31 removed outlier: 3.514A pdb=" N HIS B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 102 Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.543A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.955A pdb=" N GLN B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 251 Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 76 through 99 Processing helix chain 'C' and resid 103 through 121 Processing helix chain 'C' and resid 164 through 176 Processing helix chain 'C' and resid 179 through 182 Processing helix chain 'C' and resid 183 through 199 removed outlier: 3.563A pdb=" N VAL C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 236 Processing helix chain 'D' and resid 21 through 32 removed outlier: 3.765A pdb=" N LYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 81 through 104 removed outlier: 4.220A pdb=" N THR D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.713A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 185 removed outlier: 6.472A pdb=" N SER D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.549A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 100 Processing helix chain 'E' and resid 104 through 118 Processing helix chain 'E' and resid 119 through 122 Processing helix chain 'E' and resid 164 through 180 removed outlier: 4.274A pdb=" N ALA E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE E 179 " --> pdb=" O HIS E 175 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET E 180 " --> pdb=" O MET E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.693A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU E 199 " --> pdb=" O LEU E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 235 removed outlier: 3.531A pdb=" N LEU E 233 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY E 235 " --> pdb=" O PRO E 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 9 removed outlier: 3.898A pdb=" N ASP F 8 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU F 9 " --> pdb=" O GLY F 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 5 through 9' Processing helix chain 'F' and resid 20 through 32 removed outlier: 3.662A pdb=" N GLU F 24 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 103 Processing helix chain 'F' and resid 107 through 123 removed outlier: 3.915A pdb=" N TYR F 122 " --> pdb=" O TYR F 118 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 178 Processing helix chain 'F' and resid 185 through 201 removed outlier: 4.585A pdb=" N LYS F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU F 192 " --> pdb=" O ASP F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 228 through 244 removed outlier: 3.594A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.758A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 Processing helix chain 'G' and resid 171 through 185 removed outlier: 3.728A pdb=" N LYS G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS G 182 " --> pdb=" O PHE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 231 through 245 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 91 removed outlier: 3.829A pdb=" N ALA H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 147 through 164 Processing helix chain 'I' and resid 2 through 6 removed outlier: 3.847A pdb=" N ASN I 6 " --> pdb=" O MET I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 78 Processing helix chain 'I' and resid 82 through 97 removed outlier: 3.900A pdb=" N LYS I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 153 removed outlier: 3.802A pdb=" N GLY I 147 " --> pdb=" O GLU I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 175 Processing helix chain 'J' and resid 51 through 72 Processing helix chain 'J' and resid 76 through 94 removed outlier: 3.618A pdb=" N CYS J 91 " --> pdb=" O ASN J 87 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER J 94 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 147 removed outlier: 4.168A pdb=" N PHE J 137 " --> pdb=" O GLY J 133 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU J 138 " --> pdb=" O TYR J 134 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER J 141 " --> pdb=" O PHE J 137 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 171 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 89 removed outlier: 3.728A pdb=" N GLN K 89 " --> pdb=" O ASN K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 143 removed outlier: 3.880A pdb=" N GLY K 137 " --> pdb=" O VAL K 133 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 167 Processing helix chain 'K' and resid 192 through 199 Processing helix chain 'L' and resid 57 through 80 Processing helix chain 'L' and resid 84 through 98 Processing helix chain 'L' and resid 141 through 153 Proline residue: L 147 - end of helix Processing helix chain 'L' and resid 167 through 186 removed outlier: 3.605A pdb=" N ARG L 185 " --> pdb=" O SER L 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 77 Processing helix chain 'M' and resid 84 through 102 Processing helix chain 'M' and resid 141 through 157 removed outlier: 4.205A pdb=" N GLN M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) Proline residue: M 148 - end of helix Processing helix chain 'M' and resid 161 through 180 Processing helix chain 'M' and resid 209 through 215 removed outlier: 3.566A pdb=" N ILE M 215 " --> pdb=" O ALA M 212 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 Processing helix chain 'N' and resid 131 through 134 Processing helix chain 'N' and resid 135 through 143 Processing helix chain 'N' and resid 148 through 167 removed outlier: 3.576A pdb=" N ARG N 166 " --> pdb=" O LEU N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 194 Processing helix chain 'O' and resid 18 through 30 Processing helix chain 'O' and resid 58 through 61 Processing helix chain 'O' and resid 78 through 101 Processing helix chain 'O' and resid 105 through 123 Processing helix chain 'O' and resid 165 through 177 Processing helix chain 'O' and resid 182 through 198 removed outlier: 3.767A pdb=" N SER O 197 " --> pdb=" O THR O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 230 Processing helix chain 'P' and resid 18 through 31 removed outlier: 3.603A pdb=" N ALA P 31 " --> pdb=" O ALA P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 102 Processing helix chain 'P' and resid 106 through 124 Processing helix chain 'P' and resid 167 through 179 removed outlier: 3.943A pdb=" N GLN P 177 " --> pdb=" O SER P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 201 Processing helix chain 'P' and resid 229 through 252 Processing helix chain 'Q' and resid 16 through 29 Processing helix chain 'Q' and resid 76 through 99 Processing helix chain 'Q' and resid 103 through 121 Processing helix chain 'Q' and resid 164 through 176 Processing helix chain 'Q' and resid 183 through 199 removed outlier: 4.074A pdb=" N VAL Q 198 " --> pdb=" O ALA Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 202 through 204 No H-bonds generated for 'chain 'Q' and resid 202 through 204' Processing helix chain 'Q' and resid 221 through 237 Processing helix chain 'R' and resid 21 through 32 removed outlier: 3.700A pdb=" N LYS R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 64 removed outlier: 3.524A pdb=" N SER R 63 " --> pdb=" O GLU R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 104 removed outlier: 3.536A pdb=" N ALA R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 120 removed outlier: 3.852A pdb=" N LEU R 119 " --> pdb=" O ALA R 115 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA R 120 " --> pdb=" O VAL R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 185 Processing helix chain 'R' and resid 190 through 206 Processing helix chain 'R' and resid 230 through 241 Processing helix chain 'S' and resid 19 through 30 removed outlier: 3.646A pdb=" N GLU S 23 " --> pdb=" O ILE S 19 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL S 29 " --> pdb=" O ALA S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 100 Processing helix chain 'S' and resid 104 through 121 Proline residue: S 119 - end of helix Processing helix chain 'S' and resid 164 through 180 removed outlier: 4.282A pdb=" N ALA S 168 " --> pdb=" O ARG S 164 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER S 177 " --> pdb=" O GLU S 173 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU S 178 " --> pdb=" O ARG S 174 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE S 179 " --> pdb=" O HIS S 175 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N MET S 180 " --> pdb=" O MET S 176 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 199 removed outlier: 3.595A pdb=" N THR S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 229 through 235 removed outlier: 4.286A pdb=" N GLY S 235 " --> pdb=" O PRO S 231 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 32 removed outlier: 3.695A pdb=" N GLU T 24 " --> pdb=" O VAL T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 103 Processing helix chain 'T' and resid 107 through 125 removed outlier: 3.880A pdb=" N TYR T 122 " --> pdb=" O TYR T 118 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR T 123 " --> pdb=" O VAL T 119 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU T 124 " --> pdb=" O HIS T 120 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR T 125 " --> pdb=" O ALA T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 178 Processing helix chain 'T' and resid 185 through 201 removed outlier: 4.384A pdb=" N LYS T 191 " --> pdb=" O ARG T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 219 through 221 No H-bonds generated for 'chain 'T' and resid 219 through 221' Processing helix chain 'T' and resid 228 through 244 Processing helix chain 'U' and resid 22 through 33 removed outlier: 3.585A pdb=" N GLU U 26 " --> pdb=" O LEU U 22 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE U 32 " --> pdb=" O ALA U 28 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 36 No H-bonds generated for 'chain 'U' and resid 34 through 36' Processing helix chain 'U' and resid 83 through 106 Processing helix chain 'U' and resid 110 through 128 removed outlier: 3.758A pdb=" N TYR U 125 " --> pdb=" O ILE U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 171 through 186 Processing helix chain 'U' and resid 190 through 207 Processing helix chain 'U' and resid 231 through 245 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.616A pdb=" N ALA V 79 " --> pdb=" O ARG V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 Processing helix chain 'V' and resid 147 through 164 Processing helix chain 'W' and resid 2 through 6 removed outlier: 4.111A pdb=" N ASN W 6 " --> pdb=" O MET W 3 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 78 Processing helix chain 'W' and resid 82 through 97 removed outlier: 4.118A pdb=" N LYS W 97 " --> pdb=" O LEU W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 153 Processing helix chain 'W' and resid 158 through 175 Processing helix chain 'X' and resid 51 through 72 Processing helix chain 'X' and resid 76 through 93 removed outlier: 3.847A pdb=" N CYS X 91 " --> pdb=" O ASN X 87 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG X 93 " --> pdb=" O ALA X 89 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 147 removed outlier: 4.146A pdb=" N PHE X 137 " --> pdb=" O GLY X 133 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU X 138 " --> pdb=" O TYR X 134 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER X 141 " --> pdb=" O PHE X 137 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE X 142 " --> pdb=" O LEU X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 171 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 3.666A pdb=" N GLN Y 89 " --> pdb=" O ASN Y 85 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 131 through 143 removed outlier: 4.010A pdb=" N GLY Y 137 " --> pdb=" O VAL Y 133 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 167 Processing helix chain 'Y' and resid 191 through 200 Processing helix chain 'Z' and resid 57 through 80 Processing helix chain 'Z' and resid 84 through 99 removed outlier: 3.941A pdb=" N ARG Z 99 " --> pdb=" O ILE Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 141 through 153 Proline residue: Z 147 - end of helix Processing helix chain 'Z' and resid 167 through 185 Processing helix chain 'a' and resid 57 through 78 removed outlier: 3.921A pdb=" N GLY a 78 " --> pdb=" O GLU a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 102 Processing helix chain 'a' and resid 141 through 157 removed outlier: 4.294A pdb=" N GLN a 147 " --> pdb=" O ALA a 143 " (cutoff:3.500A) Proline residue: a 148 - end of helix Processing helix chain 'a' and resid 161 through 180 Processing helix chain 'a' and resid 209 through 214 removed outlier: 3.615A pdb=" N ALA a 212 " --> pdb=" O TRP a 209 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS a 213 " --> pdb=" O ASP a 210 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 71 Processing helix chain 'b' and resid 75 through 90 Processing helix chain 'b' and resid 129 through 134 removed outlier: 3.856A pdb=" N SER b 133 " --> pdb=" O SER b 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 135 through 143 Processing helix chain 'b' and resid 148 through 167 Processing helix chain 'b' and resid 190 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.523A pdb=" N SER C 130 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 131 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AA9, first strand: chain 'D' and resid 67 through 69 Processing sheet with id=AB1, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB2, first strand: chain 'E' and resid 63 through 67 removed outlier: 5.747A pdb=" N HIS E 65 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE E 72 " --> pdb=" O HIS E 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 162 through 165 removed outlier: 3.513A pdb=" N LYS F 51 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 66 through 70 removed outlier: 3.758A pdb=" N VAL F 69 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL F 73 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 134 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.398A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 69 through 70 removed outlier: 3.514A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.741A pdb=" N GLY H 11 " --> pdb=" O TYR H 8 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE H 173 " --> pdb=" O PRO H 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.120A pdb=" N GLU H 22 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AC1, first strand: chain 'H' and resid 211 through 218 removed outlier: 3.536A pdb=" N THR H 213 " --> pdb=" O THR I 198 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL I 184 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS I 18 " --> pdb=" O GLY I 15 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ALA I 9 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 27 through 28 removed outlier: 6.857A pdb=" N PHE I 27 " --> pdb=" O VAL I 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 41 through 43 removed outlier: 4.673A pdb=" N ILE I 120 " --> pdb=" O THR I 132 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR I 132 " --> pdb=" O ILE I 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 129 through 132 Processing sheet with id=AC5, first strand: chain 'J' and resid 129 through 132 Processing sheet with id=AC6, first strand: chain 'J' and resid 35 through 37 Processing sheet with id=AC7, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.635A pdb=" N SER K 188 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N HIS K 178 " --> pdb=" O ARG K 186 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ARG K 186 " --> pdb=" O HIS K 178 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.916A pdb=" N ALA K 20 " --> pdb=" O ALA K 27 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 34 through 35 removed outlier: 3.501A pdb=" N THR K 44 " --> pdb=" O MET K 100 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET K 100 " --> pdb=" O THR K 44 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 34 through 35 removed outlier: 3.501A pdb=" N THR K 44 " --> pdb=" O MET K 100 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET K 100 " --> pdb=" O THR K 44 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 135 through 139 removed outlier: 5.461A pdb=" N THR L 11 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 29 through 31 removed outlier: 6.908A pdb=" N LEU L 29 " --> pdb=" O HIS L 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 43 through 47 removed outlier: 6.633A pdb=" N THR L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL L 121 " --> pdb=" O ASP L 133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 7 through 8 removed outlier: 6.660A pdb=" N THR M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 7 through 8 Processing sheet with id=AD7, first strand: chain 'M' and resid 136 through 138 removed outlier: 6.021A pdb=" N PHE M 187 " --> pdb=" O PRO M 202 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE M 189 " --> pdb=" O GLU M 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 28 through 29 Processing sheet with id=AD9, first strand: chain 'N' and resid 125 through 129 Processing sheet with id=AE1, first strand: chain 'N' and resid 20 through 22 removed outlier: 7.420A pdb=" N THR N 20 " --> pdb=" O ALA N 27 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 35 through 36 removed outlier: 3.646A pdb=" N ILE N 99 " --> pdb=" O CYS N 44 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 159 through 162 Processing sheet with id=AE4, first strand: chain 'O' and resid 56 through 57 removed outlier: 4.720A pdb=" N GLY U 162 " --> pdb=" O ASP O 57 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 65 through 66 Processing sheet with id=AE6, first strand: chain 'P' and resid 161 through 164 Processing sheet with id=AE7, first strand: chain 'P' and resid 72 through 78 removed outlier: 3.942A pdb=" N LEU P 134 " --> pdb=" O SER P 150 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 158 through 161 Processing sheet with id=AE9, first strand: chain 'Q' and resid 62 through 66 removed outlier: 3.567A pdb=" N LEU Q 65 " --> pdb=" O VAL Q 69 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL Q 69 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA Q 131 " --> pdb=" O THR Q 147 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS Q 154 " --> pdb=" O GLN Q 146 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 167 through 170 removed outlier: 3.672A pdb=" N GLU R 216 " --> pdb=" O VAL R 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 67 through 69 Processing sheet with id=AF3, first strand: chain 'S' and resid 158 through 161 Processing sheet with id=AF4, first strand: chain 'S' and resid 63 through 67 removed outlier: 6.649A pdb=" N ILE S 63 " --> pdb=" O ILE S 74 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE S 74 " --> pdb=" O ILE S 63 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N HIS S 65 " --> pdb=" O ILE S 72 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE S 72 " --> pdb=" O HIS S 65 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU S 132 " --> pdb=" O THR S 147 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 162 through 165 Processing sheet with id=AF6, first strand: chain 'T' and resid 66 through 70 removed outlier: 3.524A pdb=" N VAL T 69 " --> pdb=" O VAL T 73 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL T 73 " --> pdb=" O VAL T 69 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 165 through 169 removed outlier: 6.083A pdb=" N THR U 38 " --> pdb=" O GLN U 53 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 69 through 71 Processing sheet with id=AF9, first strand: chain 'V' and resid 124 through 128 removed outlier: 6.854A pdb=" N ILE V 173 " --> pdb=" O PRO V 188 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.629A pdb=" N ALA V 20 " --> pdb=" O ALA V 27 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 34 through 38 removed outlier: 3.526A pdb=" N ILE V 37 " --> pdb=" O ILE V 41 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 211 through 218 removed outlier: 3.948A pdb=" N THR V 213 " --> pdb=" O THR W 198 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL W 184 " --> pdb=" O LEU W 199 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ALA W 9 " --> pdb=" O ASP W 24 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 27 through 28 removed outlier: 6.939A pdb=" N PHE W 27 " --> pdb=" O VAL W 34 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 41 through 43 removed outlier: 4.460A pdb=" N ILE W 120 " --> pdb=" O THR W 132 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 129 through 132 Processing sheet with id=AG7, first strand: chain 'X' and resid 129 through 132 Processing sheet with id=AG8, first strand: chain 'X' and resid 21 through 22 Processing sheet with id=AG9, first strand: chain 'X' and resid 35 through 36 Processing sheet with id=AH1, first strand: chain 'Y' and resid 125 through 126 removed outlier: 7.116A pdb=" N LEU Y 176 " --> pdb=" O VAL Y 187 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 20 through 22 removed outlier: 6.756A pdb=" N ALA Y 22 " --> pdb=" O ILE Y 26 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE Y 26 " --> pdb=" O ALA Y 22 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 41 through 42 Processing sheet with id=AH4, first strand: chain 'Z' and resid 135 through 139 removed outlier: 5.607A pdb=" N THR Z 11 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 29 through 31 removed outlier: 6.765A pdb=" N LEU Z 29 " --> pdb=" O HIS Z 36 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Z' and resid 43 through 47 removed outlier: 6.793A pdb=" N THR Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN Z 108 " --> pdb=" O PHE Z 124 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL Z 121 " --> pdb=" O ASP Z 133 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 7 through 8 removed outlier: 6.669A pdb=" N THR a 49 " --> pdb=" O VAL a 45 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 7 through 8 Processing sheet with id=AH9, first strand: chain 'a' and resid 136 through 138 Processing sheet with id=AI1, first strand: chain 'a' and resid 28 through 29 Processing sheet with id=AI2, first strand: chain 'b' and resid 125 through 128 Processing sheet with id=AI3, first strand: chain 'b' and resid 20 through 22 removed outlier: 7.178A pdb=" N THR b 20 " --> pdb=" O ALA b 27 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'b' and resid 34 through 36 2809 hydrogen bonds defined for protein. 8061 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: 13.67 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15164 1.34 - 1.46: 8867 1.46 - 1.57: 22711 1.57 - 1.69: 0 1.69 - 1.81: 478 Bond restraints: 47220 Sorted by residual: bond pdb=" N GLY T 6 " pdb=" CA GLY T 6 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.73e+00 bond pdb=" CA GLY b 172 " pdb=" C GLY b 172 " ideal model delta sigma weight residual 1.530 1.506 0.025 1.04e-02 9.25e+03 5.55e+00 bond pdb=" N GLY b 172 " pdb=" CA GLY b 172 " ideal model delta sigma weight residual 1.464 1.442 0.022 1.12e-02 7.97e+03 3.87e+00 bond pdb=" CA LEU X 102 " pdb=" CB LEU X 102 " ideal model delta sigma weight residual 1.533 1.503 0.030 1.60e-02 3.91e+03 3.63e+00 bond pdb=" CG1 ILE I 166 " pdb=" CD1 ILE I 166 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.57e+00 ... (remaining 47215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 63728 3.45 - 6.90: 327 6.90 - 10.35: 7 10.35 - 13.80: 0 13.80 - 17.25: 1 Bond angle restraints: 64063 Sorted by residual: angle pdb=" C MET Y 45 " pdb=" N ALA Y 46 " pdb=" CA ALA Y 46 " ideal model delta sigma weight residual 121.81 139.06 -17.25 2.16e+00 2.14e-01 6.38e+01 angle pdb=" N ILE W 29 " pdb=" CA ILE W 29 " pdb=" C ILE W 29 " ideal model delta sigma weight residual 109.34 101.19 8.15 2.08e+00 2.31e-01 1.54e+01 angle pdb=" N ALA C 51 " pdb=" CA ALA C 51 " pdb=" CB ALA C 51 " ideal model delta sigma weight residual 114.17 110.18 3.99 1.14e+00 7.69e-01 1.22e+01 angle pdb=" CA TRP F 215 " pdb=" CB TRP F 215 " pdb=" CG TRP F 215 " ideal model delta sigma weight residual 113.60 119.68 -6.08 1.90e+00 2.77e-01 1.02e+01 angle pdb=" C GLY H 170 " pdb=" N SER H 171 " pdb=" CA SER H 171 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.93e+00 ... (remaining 64058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 26230 17.97 - 35.94: 1590 35.94 - 53.92: 222 53.92 - 71.89: 41 71.89 - 89.86: 35 Dihedral angle restraints: 28118 sinusoidal: 10098 harmonic: 18020 Sorted by residual: dihedral pdb=" CA PRO E 149 " pdb=" C PRO E 149 " pdb=" N SER E 150 " pdb=" CA SER E 150 " ideal model delta harmonic sigma weight residual 180.00 157.04 22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA PRO S 149 " pdb=" C PRO S 149 " pdb=" N SER S 150 " pdb=" CA SER S 150 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLY V 170 " pdb=" C GLY V 170 " pdb=" N SER V 171 " pdb=" CA SER V 171 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 28115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 4767 0.040 - 0.080: 1856 0.080 - 0.120: 724 0.120 - 0.160: 91 0.160 - 0.200: 9 Chirality restraints: 7447 Sorted by residual: chirality pdb=" CB VAL O 86 " pdb=" CA VAL O 86 " pdb=" CG1 VAL O 86 " pdb=" CG2 VAL O 86 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB VAL U 91 " pdb=" CA VAL U 91 " pdb=" CG1 VAL U 91 " pdb=" CG2 VAL U 91 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CB VAL L 178 " pdb=" CA VAL L 178 " pdb=" CG1 VAL L 178 " pdb=" CG2 VAL L 178 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 7444 not shown) Planarity restraints: 8164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 105 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO B 106 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 106 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 106 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE P 105 " -0.050 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO P 106 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO P 106 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO P 106 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU S 103 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.67e+00 pdb=" N PRO S 104 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO S 104 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO S 104 " 0.036 5.00e-02 4.00e+02 ... (remaining 8161 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 471 2.63 - 3.20: 42907 3.20 - 3.77: 72202 3.77 - 4.33: 103354 4.33 - 4.90: 175261 Nonbonded interactions: 394195 Sorted by model distance: nonbonded pdb=" OH TYR E 6 " pdb=" OD2 ASP F 8 " model vdw 2.063 3.040 nonbonded pdb=" OG SER b 46 " pdb=" O GLY b 97 " model vdw 2.109 3.040 nonbonded pdb=" O VAL S 98 " pdb=" OG SER a 90 " model vdw 2.116 3.040 nonbonded pdb=" OG1 THR Q 8 " pdb=" O THR Q 119 " model vdw 2.117 3.040 nonbonded pdb=" O GLN C 116 " pdb=" OG1 THR C 119 " model vdw 2.119 3.040 ... (remaining 394190 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 3 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 231)) selection = (chain 'O' and (resid 3 through 21 or (resid 22 and (name N or name CA or name C \ or name O or name CB )) or resid 23 through 57 or (resid 58 through 60 and (nam \ e N or name CA or name C or name O or name CB )) or resid 61 through 138 or (res \ id 139 through 140 and (name N or name CA or name C or name O or name CB )) or r \ esid 141 through 163 or (resid 164 through 165 and (name N or name CA or name C \ or name O or name CB )) or resid 166 through 167 or (resid 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 205 or (resid 206 a \ nd (name N or name CA or name C or name O or name CB )) or resid 207 through 231 \ )) } ncs_group { reference = (chain 'B' and (resid 2 through 177 or (resid 178 and (name N or name CA or name \ C or name O or name CB )) or resid 179 through 251)) selection = (chain 'P' and (resid 2 through 21 or (resid 22 and (name N or name CA or name C \ or name O or name CB )) or resid 23 through 47 or (resid 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 50 or (resid 51 throug \ h 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throug \ h 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or re \ sid 58 through 70 or (resid 71 and (name N or name CA or name C or name O or nam \ e CB )) or resid 72 through 102 or (resid 103 and (name N or name CA or name C o \ r name O or name CB )) or resid 104 through 107 or (resid 108 and (name N or nam \ e CA or name C or name O or name CB )) or resid 109 through 184 or (resid 185 an \ d (name N or name CA or name C or name O or name CB )) or resid 186 or (resid 18 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 188 through \ 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) or re \ sid 211 through 218 or (resid 219 through 220 and (name N or name CA or name C o \ r name O or name CB )) or resid 221 or (resid 222 and (name N or name CA or name \ C or name O or name CB )) or resid 223 through 234 or (resid 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 through 251)) } ncs_group { reference = (chain 'C' and (resid 2 through 136 or (resid 137 and (name N or name CA or name \ C or name O or name CB )) or resid 138 through 140 or (resid 141 and (name N or \ name CA or name C or name O or name CB )) or resid 142 through 214 or (resid 21 \ 5 through 216 and (name N or name CA or name C or name O or name CB )) or resid \ 217 or (resid 218 and (name N or name CA or name C or name O or name CB )) or re \ sid 219 through 236)) selection = (chain 'Q' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 23 or (resid 24 through 25 and (name N \ or name CA or name C or name O or name CB )) or resid 26 through 49 or (resid 5 \ 0 through 52 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 3 through 149 or (resid 150 and (name N or name CA or name C or name O or name C \ B )) or resid 151 through 192 or (resid 193 through 194 and (name N or name CA o \ r name C or name O or name CB )) or resid 195 through 196 or (resid 197 through \ 198 and (name N or name CA or name C or name O or name CB )) or resid 199 throug \ h 220 or (resid 221 through 224 and (name N or name CA or name C or name O or na \ me CB )) or resid 225 through 236)) } ncs_group { reference = (chain 'D' and (resid 7 through 54 or (resid 55 through 56 and (name N or name C \ A or name C or name O or name CB )) or resid 57 through 156 or (resid 157 and (n \ ame N or name CA or name C or name O or name CB )) or resid 158 through 182 or ( \ resid 183 and (name N or name CA or name C or name O or name CB )) or resid 184 \ through 187 or (resid 188 and (name N or name CA or name C or name O or name CB \ )) or resid 189 through 191 or (resid 192 through 194 and (name N or name CA or \ name C or name O or name CB )) or resid 195 through 212 or (resid 213 and (name \ N or name CA or name C or name O or name CB )) or resid 214 through 238 or (resi \ d 239 through 241 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'R' and (resid 7 through 85 or (resid 86 and (name N or name CA or name C \ or name O or name CB )) or resid 87 through 124 or (resid 125 through 130 and ( \ name N or name CA or name C or name O or name CB )) or resid 131 through 215 or \ (resid 216 and (name N or name CA or name C or name O or name CB )) or resid 217 \ through 230 or (resid 231 through 232 and (name N or name CA or name C or name \ O or name CB )) or resid 233 through 241)) } ncs_group { reference = (chain 'E' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 8 or (resid 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 through 41 or (resid 42 and (name N or name CA or name C \ or name O or name CB )) or resid 43 through 54 or (resid 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 66 or (resid 67 and (n \ ame N or name CA or name C or name O or name CB )) or resid 68 through 79 or (re \ sid 80 through 81 and (name N or name CA or name C or name O or name CB )) or re \ sid 82 through 137 or (resid 138 through 139 and (name N or name CA or name C or \ name O or name CB )) or resid 140 through 185 or (resid 186 and (name N or name \ CA or name C or name O or name CB )) or resid 187 through 205 or (resid 206 and \ (name N or name CA or name C or name O or name CB )) or resid 207 through 236 o \ r (resid 237 through 238 and (name N or name CA or name C or name O or name CB ) \ ) or resid 239 through 240)) selection = (chain 'S' and (resid 4 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 240)) } ncs_group { reference = (chain 'F' and (resid 6 through 236 or (resid 237 and (name N or name CA or name \ C or name O or name CB )) or resid 238 through 244)) selection = (chain 'T' and (resid 6 through 55 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 142 or (resid 143 through 144 and ( \ name N or name CA or name C or name O or name CB )) or resid 145 through 244)) } ncs_group { reference = (chain 'G' and (resid 3 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 44 or (resid 45 through 48 a \ nd (name N or name CA or name C or name O or name CB )) or resid 49 through 55 o \ r (resid 56 through 59 and (name N or name CA or name C or name O or name CB )) \ or resid 60 through 63 or (resid 64 and (name N or name CA or name C or name O o \ r name CB )) or resid 65 through 129 or (resid 130 and (name N or name CA or nam \ e C or name O or name CB )) or resid 131 through 245)) selection = (chain 'U' and (resid 3 through 179 or (resid 180 and (name N or name CA or name \ C or name O or name CB )) or resid 181 through 186 or (resid 187 through 188 an \ d (name N or name CA or name C or name O or name CB )) or resid 189 through 210 \ or (resid 211 through 214 and (name N or name CA or name C or name O or name CB \ )) or resid 215 through 233 or (resid 234 and (name N or name CA or name C or na \ me O or name CB )) or resid 235 through 245)) } ncs_group { reference = (chain 'H' and (resid 1 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 180 or (resid 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 through 222)) selection = (chain 'V' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 148 or (resid 149 through 151 and ( \ name N or name CA or name C or name O or name CB )) or resid 152 through 156 or \ (resid 157 through 158 and (name N or name CA or name C or name O or name CB )) \ or resid 159 through 183 or (resid 184 and (name N or name CA or name C or name \ O or name CB )) or resid 185 through 222)) } ncs_group { reference = (chain 'I' and (resid 1 through 113 or (resid 114 and (name N or name CA or name \ C or name O or name CB )) or resid 115 through 148 or (resid 149 and (name N or \ name CA or name C or name O or name CB )) or resid 150 through 157 or (resid 15 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 159 through \ 189 or (resid 190 through 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 204)) selection = (chain 'W' and (resid 1 through 73 or (resid 74 and (name N or name CA or name C \ or name O or name CB )) or resid 75 through 190 or (resid 191 and (name N or na \ me CA or name C or name O or name CB )) or resid 192 through 204)) } ncs_group { reference = (chain 'J' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 196)) selection = (chain 'X' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 93 or (resid 94 through 95 and (nam \ e N or name CA or name C or name O or name CB )) or resid 96 through 196)) } ncs_group { reference = (chain 'K' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 71 or (resid 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 through 95 or (resid 96 and (n \ ame N or name CA or name C or name O or name CB )) or resid 97 through 105 or (r \ esid 106 and (name N or name CA or name C or name O or name CB )) or resid 107 t \ hrough 200)) selection = (chain 'Y' and (resid 1 through 114 or (resid 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 149 or (resid 150 and (name N or \ name CA or name C or name O or name CB )) or resid 151 through 200)) } ncs_group { reference = (chain 'L' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 38 or (resid 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 47 or (resid 48 and (n \ ame N or name CA or name C or name O or name CB )) or resid 49 through 124 or (r \ esid 125 and (name N or name CA or name C or name O or name CB )) or resid 126 t \ hrough 183 or (resid 184 and (name N or name CA or name C or name O or name CB ) \ ) or resid 185 through 213)) selection = (chain 'Z' and (resid 1 through 159 or (resid 160 through 162 and (name N or nam \ e CA or name C or name O or name CB )) or resid 163 through 213)) } ncs_group { reference = (chain 'M' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 154 or (resid 155 thro \ ugh 156 and (name N or name CA or name C or name O or name CB )) or resid 157 th \ rough 203 or (resid 204 and (name N or name CA or name C or name O or name CB )) \ or resid 205 through 209 or (resid 210 and (name N or name CA or name C or name \ O or name CB )) or resid 211 through 214)) selection = (chain 'a' and (resid 1 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB )) or resid 157 through 205 or (resid 206 through 207 an \ d (name N or name CA or name C or name O or name CB )) or resid 208 through 214) \ ) } ncs_group { reference = (chain 'N' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 31 or (resid 32 and (name N or name C \ A or name C or name O or name CB )) or resid 33 through 34 or (resid 35 and (nam \ e N or name CA or name C or name O or name CB )) or resid 36 through 38 or (resi \ d 39 and (name N or name CA or name C or name O or name CB )) or resid 40 throug \ h 139 or (resid 140 through 141 and (name N or name CA or name C or name O or na \ me CB )) or resid 142 through 195 or (resid 196 and (name N or name CA or name C \ or name O or name CB )) or resid 197 through 202)) selection = (chain 'b' and (resid 1 through 94 or (resid 95 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 47.960 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.010 0.088 47220 Z= 0.413 Angle : 0.726 17.253 64063 Z= 0.401 Chirality : 0.048 0.200 7447 Planarity : 0.005 0.075 8164 Dihedral : 12.417 89.860 16610 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.94 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: -0.69 (0.10), residues: 6188 helix: 0.18 (0.09), residues: 2321 sheet: -0.68 (0.12), residues: 1500 loop : -0.75 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 171 TYR 0.040 0.002 TYR I 146 PHE 0.030 0.002 PHE W 68 TRP 0.042 0.002 TRP F 215 HIS 0.008 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00958 (47220) covalent geometry : angle 0.72624 (64063) hydrogen bonds : bond 0.15024 ( 2773) hydrogen bonds : angle 7.06141 ( 8061) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1251 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7881 (ttt-90) cc_final: 0.7523 (ttt-90) REVERT: A 207 ILE cc_start: 0.9013 (pt) cc_final: 0.8749 (pp) REVERT: A 211 ILE cc_start: 0.9409 (pt) cc_final: 0.9159 (pp) REVERT: B 3 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.8161 (mtm110) REVERT: B 166 ASN cc_start: 0.9051 (t0) cc_final: 0.8779 (t0) REVERT: C 55 ASP cc_start: 0.8152 (t0) cc_final: 0.7747 (t0) REVERT: C 61 LYS cc_start: 0.8565 (mttm) cc_final: 0.8150 (mtmt) REVERT: C 66 ASP cc_start: 0.8631 (t0) cc_final: 0.8137 (t0) REVERT: C 96 LEU cc_start: 0.9080 (tp) cc_final: 0.8520 (tt) REVERT: C 116 GLN cc_start: 0.8528 (tm-30) cc_final: 0.7854 (tp40) REVERT: C 120 GLN cc_start: 0.8835 (tt0) cc_final: 0.8623 (tt0) REVERT: D 32 LYS cc_start: 0.9011 (mttt) cc_final: 0.8684 (mttm) REVERT: D 84 ASP cc_start: 0.8645 (m-30) cc_final: 0.7977 (m-30) REVERT: D 91 LYS cc_start: 0.8904 (tptp) cc_final: 0.8247 (tptm) REVERT: D 95 GLU cc_start: 0.8057 (tp30) cc_final: 0.7730 (tp30) REVERT: D 114 GLN cc_start: 0.8388 (tt0) cc_final: 0.8135 (tt0) REVERT: D 166 ASP cc_start: 0.8054 (m-30) cc_final: 0.7828 (m-30) REVERT: E 27 GLU cc_start: 0.8304 (tp30) cc_final: 0.8036 (tm-30) REVERT: E 30 LYS cc_start: 0.8711 (mttt) cc_final: 0.8480 (mttp) REVERT: E 50 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8537 (mtmp) REVERT: E 67 ASP cc_start: 0.8559 (t70) cc_final: 0.8199 (t0) REVERT: E 86 ASN cc_start: 0.8826 (m-40) cc_final: 0.8586 (m-40) REVERT: E 90 GLN cc_start: 0.8313 (tp40) cc_final: 0.7844 (mm-40) REVERT: E 94 ASP cc_start: 0.8106 (m-30) cc_final: 0.7816 (m-30) REVERT: E 100 ASP cc_start: 0.8140 (t0) cc_final: 0.7853 (t0) REVERT: E 180 MET cc_start: 0.8042 (mmm) cc_final: 0.7790 (tpt) REVERT: E 185 ASN cc_start: 0.8510 (p0) cc_final: 0.7384 (p0) REVERT: E 197 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8428 (mm-30) REVERT: F 27 MET cc_start: 0.7957 (ptp) cc_final: 0.7748 (ptp) REVERT: F 70 ASP cc_start: 0.8249 (t0) cc_final: 0.7728 (t0) REVERT: F 93 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7846 (mm-30) REVERT: F 225 GLU cc_start: 0.8603 (pt0) cc_final: 0.8382 (pp20) REVERT: G 10 ASP cc_start: 0.8416 (p0) cc_final: 0.8214 (p0) REVERT: G 11 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.8008 (mtt-85) REVERT: G 26 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7999 (mt-10) REVERT: G 80 MET cc_start: 0.8787 (mmm) cc_final: 0.8510 (mmm) REVERT: G 116 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8066 (ttmm) REVERT: G 120 ASP cc_start: 0.7983 (m-30) cc_final: 0.7766 (m-30) REVERT: G 131 MET cc_start: 0.8323 (ptp) cc_final: 0.8024 (ptp) REVERT: G 152 TYR cc_start: 0.8878 (m-80) cc_final: 0.8653 (m-80) REVERT: H 8 TYR cc_start: 0.8751 (p90) cc_final: 0.8507 (p90) REVERT: H 30 ASN cc_start: 0.8397 (t0) cc_final: 0.8153 (t0) REVERT: H 72 ARG cc_start: 0.8769 (ptp90) cc_final: 0.8363 (ptp-170) REVERT: I 24 ASP cc_start: 0.7443 (p0) cc_final: 0.7105 (p0) REVERT: I 40 LYS cc_start: 0.8550 (mttt) cc_final: 0.8037 (mttt) REVERT: I 67 LYS cc_start: 0.8691 (tptt) cc_final: 0.8427 (tptp) REVERT: I 71 ASN cc_start: 0.9066 (m-40) cc_final: 0.8858 (m-40) REVERT: I 112 ASP cc_start: 0.8509 (t70) cc_final: 0.8304 (t0) REVERT: I 175 ASP cc_start: 0.8404 (m-30) cc_final: 0.7902 (m-30) REVERT: I 176 ARG cc_start: 0.8573 (tpp-160) cc_final: 0.8201 (mmt180) REVERT: K 81 LYS cc_start: 0.8499 (tptt) cc_final: 0.8198 (tmtt) REVERT: L 130 TYR cc_start: 0.9068 (p90) cc_final: 0.8235 (p90) REVERT: L 152 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7812 (mm110) REVERT: L 177 ASP cc_start: 0.7689 (m-30) cc_final: 0.6966 (m-30) REVERT: L 184 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7926 (mp0) REVERT: L 205 GLU cc_start: 0.7738 (mp0) cc_final: 0.7480 (mp0) REVERT: M 64 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8654 (mtpp) REVERT: M 79 ASP cc_start: 0.8500 (p0) cc_final: 0.8255 (p0) REVERT: M 104 ASN cc_start: 0.9018 (t0) cc_final: 0.8422 (t0) REVERT: M 170 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7640 (mt-10) REVERT: M 180 ASP cc_start: 0.8486 (t70) cc_final: 0.8175 (t0) REVERT: M 200 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7377 (mt-10) REVERT: M 210 ASP cc_start: 0.8366 (p0) cc_final: 0.8140 (p0) REVERT: N 84 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8931 (ttpp) REVERT: N 87 CYS cc_start: 0.8452 (m) cc_final: 0.8152 (m) REVERT: O 57 ASP cc_start: 0.8080 (t0) cc_final: 0.7811 (t0) REVERT: O 108 GLN cc_start: 0.8347 (mm110) cc_final: 0.8043 (mm-40) REVERT: O 111 GLN cc_start: 0.8641 (mt0) cc_final: 0.8402 (mt0) REVERT: O 142 ARG cc_start: 0.8288 (ttt-90) cc_final: 0.8009 (ttt-90) REVERT: O 208 GLU cc_start: 0.7856 (tt0) cc_final: 0.7642 (tt0) REVERT: P 34 CYS cc_start: 0.7981 (t) cc_final: 0.7467 (t) REVERT: P 48 GLU cc_start: 0.8326 (tt0) cc_final: 0.7906 (tm-30) REVERT: P 57 ASP cc_start: 0.8619 (t70) cc_final: 0.8248 (t0) REVERT: P 75 SER cc_start: 0.8908 (t) cc_final: 0.8314 (t) REVERT: P 103 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7971 (mt-10) REVERT: P 166 ASN cc_start: 0.9036 (t0) cc_final: 0.8403 (t0) REVERT: P 167 ASN cc_start: 0.9135 (m110) cc_final: 0.8559 (m110) REVERT: Q 27 LYS cc_start: 0.9125 (mtpp) cc_final: 0.8676 (mtmm) REVERT: Q 116 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7457 (tp40) REVERT: Q 153 TYR cc_start: 0.9170 (p90) cc_final: 0.8914 (p90) REVERT: Q 157 LYS cc_start: 0.8749 (mttt) cc_final: 0.8498 (mtpt) REVERT: R 86 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8141 (mmmm) REVERT: R 135 ARG cc_start: 0.9166 (ptt90) cc_final: 0.8793 (ptt90) REVERT: R 227 HIS cc_start: 0.8541 (t-90) cc_final: 0.8302 (t70) REVERT: S 22 ILE cc_start: 0.8769 (pt) cc_final: 0.8494 (pp) REVERT: S 30 LYS cc_start: 0.9017 (mttt) cc_final: 0.8732 (mptt) REVERT: S 90 GLN cc_start: 0.8508 (tp40) cc_final: 0.7859 (tp-100) REVERT: S 94 ASP cc_start: 0.8070 (p0) cc_final: 0.7768 (p0) REVERT: T 70 ASP cc_start: 0.8087 (t70) cc_final: 0.7870 (t0) REVERT: U 5 SER cc_start: 0.9121 (t) cc_final: 0.8532 (p) REVERT: U 19 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8158 (mm-30) REVERT: U 104 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8660 (mtmm) REVERT: U 224 ASN cc_start: 0.8575 (p0) cc_final: 0.8352 (p0) REVERT: U 228 ARG cc_start: 0.8491 (mtm110) cc_final: 0.8240 (mtp-110) REVERT: V 30 ASN cc_start: 0.8728 (t0) cc_final: 0.8380 (t0) REVERT: V 54 MET cc_start: 0.8569 (mmt) cc_final: 0.8363 (mmm) REVERT: V 153 ASN cc_start: 0.8393 (m-40) cc_final: 0.7588 (m-40) REVERT: V 198 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7630 (ttm-80) REVERT: V 214 GLU cc_start: 0.8745 (tt0) cc_final: 0.8533 (tt0) REVERT: W 40 LYS cc_start: 0.8972 (mttp) cc_final: 0.8674 (mttm) REVERT: W 73 TYR cc_start: 0.9174 (t80) cc_final: 0.8804 (t80) REVERT: W 74 GLU cc_start: 0.8044 (pt0) cc_final: 0.7814 (tp30) REVERT: W 105 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8232 (mm-30) REVERT: W 154 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8146 (mt-10) REVERT: W 191 LYS cc_start: 0.9065 (ptmt) cc_final: 0.8682 (ptmm) REVERT: X 36 PHE cc_start: 0.8984 (m-80) cc_final: 0.8606 (m-80) REVERT: X 37 LYS cc_start: 0.8754 (tttm) cc_final: 0.8514 (tttp) REVERT: X 86 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7905 (ttm-80) REVERT: X 108 ASP cc_start: 0.8309 (t70) cc_final: 0.8014 (t70) REVERT: X 166 GLU cc_start: 0.8092 (tp30) cc_final: 0.7851 (tp30) REVERT: Y 26 ILE cc_start: 0.9254 (mt) cc_final: 0.8853 (mp) REVERT: Y 62 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8669 (mm-40) REVERT: Y 67 GLU cc_start: 0.8467 (tt0) cc_final: 0.8174 (tm-30) REVERT: Y 81 LYS cc_start: 0.9121 (tptt) cc_final: 0.8831 (tptm) REVERT: Y 119 ASN cc_start: 0.8759 (m-40) cc_final: 0.8503 (m110) REVERT: Z 105 TYR cc_start: 0.8591 (t80) cc_final: 0.8312 (t80) REVERT: Z 177 ASP cc_start: 0.7828 (m-30) cc_final: 0.7243 (m-30) REVERT: a 56 ASP cc_start: 0.8375 (t70) cc_final: 0.7847 (t70) REVERT: a 64 LYS cc_start: 0.9103 (mtpt) cc_final: 0.8797 (mtpm) REVERT: a 133 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7827 (mt-10) REVERT: b 7 GLN cc_start: 0.8505 (tt0) cc_final: 0.8039 (tt0) REVERT: b 193 GLN cc_start: 0.8846 (mt0) cc_final: 0.8605 (mt0) outliers start: 0 outliers final: 3 residues processed: 1251 average time/residue: 0.8853 time to fit residues: 1340.5574 Evaluate side-chains 985 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 982 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain Y residue 105 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 0.7980 chunk 497 optimal weight: 0.6980 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 0.9980 chunk 597 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 40 ASN B 69 ASN B 84 ASN B 240 HIS C 23 GLN C 85 ASN D 13 ASN D 122 GLN E 68 ASN G 53 GLN G 224 ASN H 153 ASN I 92 ASN I 161 HIS ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN J 168 GLN K 70 ASN K 89 GLN K 175 ASN K 191 ASN L 80 ASN L 146 GLN M 61 GLN M 108 ASN N 77 HIS N 154 GLN O 108 GLN O 139 ASN O 147 GLN P 69 ASN Q 23 GLN Q 54 GLN Q 175 ASN Q 221 ASN R 204 GLN T 63 ASN U 24 GLN U 53 GLN V 57 GLN V 80 ASN W 39 GLN W 156 ASN X 55 GLN X 65 GLN ** X 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 186 ASN X 189 HIS Y 89 GLN Y 175 ASN ** Y 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 152 GLN a 2 GLN b 110 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.082724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.068181 restraints weight = 94478.131| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.76 r_work: 0.2872 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 47220 Z= 0.138 Angle : 0.580 8.137 64063 Z= 0.312 Chirality : 0.043 0.169 7447 Planarity : 0.004 0.062 8164 Dihedral : 4.674 34.205 6851 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.36 % Allowed : 12.27 % Favored : 85.37 % 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: 0.48 (0.10), residues: 6188 helix: 1.50 (0.10), residues: 2334 sheet: -0.20 (0.12), residues: 1502 loop : -0.43 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 88 TYR 0.023 0.001 TYR U 160 PHE 0.019 0.001 PHE W 68 TRP 0.020 0.001 TRP F 215 HIS 0.007 0.001 HIS S 65 Details of bonding type rmsd covalent geometry : bond 0.00302 (47220) covalent geometry : angle 0.57966 (64063) hydrogen bonds : bond 0.04034 ( 2773) hydrogen bonds : angle 5.03428 ( 8061) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1130 time to evaluate : 1.790 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: A 158 LYS cc_start: 0.8869 (mttm) cc_final: 0.8555 (mttp) REVERT: A 176 ARG cc_start: 0.9044 (ttm110) cc_final: 0.8727 (ttm110) REVERT: A 195 LYS cc_start: 0.9582 (ttpp) cc_final: 0.9149 (ttmm) REVERT: A 208 GLU cc_start: 0.8517 (tt0) cc_final: 0.8302 (tt0) REVERT: B 166 ASN cc_start: 0.9178 (t0) cc_final: 0.8760 (t0) REVERT: B 167 ASN cc_start: 0.9414 (m110) cc_final: 0.8910 (m110) REVERT: B 180 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8699 (mmtm) REVERT: C 54 GLN cc_start: 0.8621 (mm110) cc_final: 0.8336 (mm110) REVERT: C 55 ASP cc_start: 0.8521 (t0) cc_final: 0.8085 (t0) REVERT: C 61 LYS cc_start: 0.8650 (mttm) cc_final: 0.8132 (mtmt) REVERT: C 66 ASP cc_start: 0.8961 (t0) cc_final: 0.8629 (t0) REVERT: C 116 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8195 (tp40) REVERT: C 120 GLN cc_start: 0.9203 (tt0) cc_final: 0.8849 (tt0) REVERT: D 32 LYS cc_start: 0.9057 (mttt) cc_final: 0.8782 (mttp) REVERT: D 84 ASP cc_start: 0.8927 (m-30) cc_final: 0.8446 (m-30) REVERT: D 91 LYS cc_start: 0.9189 (tptp) cc_final: 0.8786 (tmtm) REVERT: D 95 GLU cc_start: 0.8876 (tp30) cc_final: 0.8510 (tp30) REVERT: D 114 GLN cc_start: 0.8551 (tt0) cc_final: 0.8308 (pt0) REVERT: D 133 MET cc_start: 0.8700 (mpp) cc_final: 0.8464 (mmp) REVERT: D 178 GLN cc_start: 0.8211 (tp40) cc_final: 0.7926 (mm110) REVERT: D 182 GLN cc_start: 0.9026 (mt0) cc_final: 0.8750 (mt0) REVERT: D 196 LYS cc_start: 0.9355 (mtpp) cc_final: 0.9004 (mtmm) REVERT: D 239 LYS cc_start: 0.9153 (mtmm) cc_final: 0.8950 (mtmm) REVERT: E 27 GLU cc_start: 0.8486 (tp30) cc_final: 0.7983 (tp30) REVERT: E 67 ASP cc_start: 0.9082 (t70) cc_final: 0.8632 (t0) REVERT: E 86 ASN cc_start: 0.9019 (m-40) cc_final: 0.8720 (m-40) REVERT: E 90 GLN cc_start: 0.8848 (tp40) cc_final: 0.8423 (mm-40) REVERT: E 94 ASP cc_start: 0.8723 (m-30) cc_final: 0.8417 (m-30) REVERT: E 100 ASP cc_start: 0.8713 (t0) cc_final: 0.8397 (t0) REVERT: E 180 MET cc_start: 0.8743 (mmm) cc_final: 0.8350 (tpt) REVERT: E 185 ASN cc_start: 0.8447 (p0) cc_final: 0.8107 (p0) REVERT: E 189 LYS cc_start: 0.9495 (mttp) cc_final: 0.9103 (mttp) REVERT: E 197 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8854 (mm-30) REVERT: F 70 ASP cc_start: 0.8755 (t0) cc_final: 0.8202 (t0) REVERT: F 93 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8590 (mm-30) REVERT: F 97 ASN cc_start: 0.9091 (m-40) cc_final: 0.8806 (m110) REVERT: F 147 GLN cc_start: 0.8787 (mt0) cc_final: 0.8142 (mt0) REVERT: F 221 ASN cc_start: 0.9099 (m110) cc_final: 0.8774 (p0) REVERT: F 225 GLU cc_start: 0.9023 (pt0) cc_final: 0.8393 (pp20) REVERT: G 10 ASP cc_start: 0.8831 (p0) cc_final: 0.8551 (p0) REVERT: G 19 GLU cc_start: 0.8589 (mp0) cc_final: 0.8355 (mp0) REVERT: G 23 TYR cc_start: 0.8247 (m-80) cc_final: 0.7931 (m-80) REVERT: G 83 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8964 (mtm) REVERT: G 97 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8460 (mm-30) REVERT: G 104 LYS cc_start: 0.9236 (mtpp) cc_final: 0.8987 (mtpm) REVERT: G 112 ASP cc_start: 0.9034 (p0) cc_final: 0.8828 (p0) REVERT: G 116 LYS cc_start: 0.8817 (ttpt) cc_final: 0.8500 (ttmm) REVERT: G 138 MET cc_start: 0.8882 (ttp) cc_final: 0.8338 (tpp) REVERT: G 174 GLU cc_start: 0.9048 (mp0) cc_final: 0.8827 (pm20) REVERT: H 30 ASN cc_start: 0.9003 (t0) cc_final: 0.8546 (t0) REVERT: H 72 ARG cc_start: 0.8975 (ptp90) cc_final: 0.8522 (ptp-170) REVERT: I 65 ARG cc_start: 0.8534 (mtp85) cc_final: 0.8167 (mtp85) REVERT: I 112 ASP cc_start: 0.8919 (t70) cc_final: 0.8578 (t0) REVERT: I 150 GLU cc_start: 0.9296 (mm-30) cc_final: 0.9084 (mm-30) REVERT: I 175 ASP cc_start: 0.8699 (m-30) cc_final: 0.8281 (m-30) REVERT: J 100 VAL cc_start: 0.9404 (m) cc_final: 0.9165 (p) REVERT: J 108 ASP cc_start: 0.8581 (t70) cc_final: 0.8073 (t70) REVERT: J 155 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8187 (mtp85) REVERT: J 184 ASP cc_start: 0.8880 (p0) cc_final: 0.8602 (p0) REVERT: K 56 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8976 (mp0) REVERT: L 73 LYS cc_start: 0.9190 (mttt) cc_final: 0.8950 (mtmm) REVERT: L 152 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8107 (mm110) REVERT: L 177 ASP cc_start: 0.8396 (m-30) cc_final: 0.8121 (m-30) REVERT: L 186 ASP cc_start: 0.8626 (t0) cc_final: 0.8184 (t0) REVERT: L 205 GLU cc_start: 0.8081 (mp0) cc_final: 0.7813 (mp0) REVERT: L 206 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7754 (mm-30) REVERT: M 26 MET cc_start: 0.8972 (mtp) cc_final: 0.8682 (mtm) REVERT: M 47 ASN cc_start: 0.8805 (t0) cc_final: 0.8404 (t0) REVERT: M 56 ASP cc_start: 0.8654 (t0) cc_final: 0.8144 (t0) REVERT: M 59 ASP cc_start: 0.9008 (m-30) cc_final: 0.8747 (m-30) REVERT: M 64 LYS cc_start: 0.9106 (mtpt) cc_final: 0.8742 (mtpp) REVERT: M 79 ASP cc_start: 0.8320 (p0) cc_final: 0.8104 (p0) REVERT: M 104 ASN cc_start: 0.9240 (t0) cc_final: 0.8631 (t0) REVERT: M 170 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8136 (mp0) REVERT: M 180 ASP cc_start: 0.8975 (t70) cc_final: 0.8553 (t0) REVERT: M 200 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8165 (mt-10) REVERT: M 210 ASP cc_start: 0.8728 (p0) cc_final: 0.8209 (p0) REVERT: M 213 HIS cc_start: 0.9182 (m90) cc_final: 0.8901 (m-70) REVERT: N 84 LYS cc_start: 0.9395 (ttpt) cc_final: 0.9087 (ttpp) REVERT: N 90 TYR cc_start: 0.9034 (m-80) cc_final: 0.8629 (m-80) REVERT: N 144 ARG cc_start: 0.8192 (ptp90) cc_final: 0.7773 (ptt-90) REVERT: N 151 GLU cc_start: 0.8555 (tt0) cc_final: 0.7800 (tt0) REVERT: N 193 GLN cc_start: 0.8933 (mt0) cc_final: 0.8681 (mt0) REVERT: O 6 SER cc_start: 0.8665 (p) cc_final: 0.8108 (t) REVERT: O 48 GLU cc_start: 0.8083 (pp20) cc_final: 0.7800 (pp20) REVERT: O 57 ASP cc_start: 0.8167 (t0) cc_final: 0.7726 (t0) REVERT: O 108 GLN cc_start: 0.8871 (mm-40) cc_final: 0.7960 (mm-40) REVERT: O 111 GLN cc_start: 0.8916 (mt0) cc_final: 0.8645 (mt0) REVERT: O 142 ARG cc_start: 0.8614 (ttt-90) cc_final: 0.7978 (ttt-90) REVERT: O 189 THR cc_start: 0.9388 (p) cc_final: 0.9163 (t) REVERT: P 22 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8244 (mp0) REVERT: P 48 GLU cc_start: 0.8594 (tt0) cc_final: 0.7799 (tm-30) REVERT: P 57 ASP cc_start: 0.8672 (t70) cc_final: 0.8338 (t0) REVERT: P 75 SER cc_start: 0.9161 (t) cc_final: 0.8833 (t) REVERT: P 103 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8544 (mt-10) REVERT: P 166 ASN cc_start: 0.9144 (t0) cc_final: 0.8618 (t0) REVERT: P 167 ASN cc_start: 0.9344 (m110) cc_final: 0.8776 (m110) REVERT: Q 24 GLU cc_start: 0.8370 (tt0) cc_final: 0.8029 (tm-30) REVERT: Q 27 LYS cc_start: 0.9229 (mtpp) cc_final: 0.9011 (mtpt) REVERT: Q 28 LYS cc_start: 0.9270 (mttm) cc_final: 0.8894 (mtmt) REVERT: Q 55 ASP cc_start: 0.8398 (t0) cc_final: 0.8063 (t0) REVERT: Q 61 LYS cc_start: 0.8803 (mttm) cc_final: 0.8581 (tppt) REVERT: Q 96 LEU cc_start: 0.9229 (tt) cc_final: 0.8956 (tt) REVERT: Q 99 GLU cc_start: 0.8170 (mp0) cc_final: 0.7802 (mp0) REVERT: Q 116 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8050 (tp40) REVERT: Q 138 PHE cc_start: 0.8894 (t80) cc_final: 0.8649 (t80) REVERT: Q 146 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8298 (tm-30) REVERT: Q 153 TYR cc_start: 0.9355 (p90) cc_final: 0.9103 (p90) REVERT: Q 157 LYS cc_start: 0.8921 (mttt) cc_final: 0.8681 (mtpt) REVERT: Q 193 LYS cc_start: 0.9347 (mtpp) cc_final: 0.8994 (pttt) REVERT: R 32 LYS cc_start: 0.8851 (mttp) cc_final: 0.8566 (mttp) REVERT: R 206 MET cc_start: 0.8039 (mtm) cc_final: 0.7758 (mtm) REVERT: R 227 HIS cc_start: 0.8709 (t-90) cc_final: 0.8292 (t70) REVERT: S 6 TYR cc_start: 0.8919 (m-80) cc_final: 0.8717 (m-80) REVERT: S 26 MET cc_start: 0.8664 (mtp) cc_final: 0.8340 (mtp) REVERT: S 30 LYS cc_start: 0.8918 (mttt) cc_final: 0.8609 (mptt) REVERT: S 31 GLN cc_start: 0.8240 (pp30) cc_final: 0.8029 (pp30) REVERT: S 86 ASN cc_start: 0.9140 (m-40) cc_final: 0.8852 (m-40) REVERT: S 90 GLN cc_start: 0.9013 (tp40) cc_final: 0.8481 (mm-40) REVERT: S 94 ASP cc_start: 0.8533 (p0) cc_final: 0.8156 (p0) REVERT: S 178 GLU cc_start: 0.9026 (pm20) cc_final: 0.8768 (pm20) REVERT: T 70 ASP cc_start: 0.8560 (t70) cc_final: 0.8310 (t0) REVERT: T 180 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8290 (tp-100) REVERT: T 192 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8763 (mp0) REVERT: T 236 GLU cc_start: 0.9313 (mt-10) cc_final: 0.9007 (mm-30) REVERT: U 5 SER cc_start: 0.9120 (t) cc_final: 0.8505 (p) REVERT: U 19 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8589 (mm-30) REVERT: U 21 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.8185 (mmm-85) REVERT: U 104 LYS cc_start: 0.9209 (mtpt) cc_final: 0.8967 (mtmm) REVERT: U 155 ASP cc_start: 0.8376 (p0) cc_final: 0.8068 (p0) REVERT: U 187 PHE cc_start: 0.7376 (p90) cc_final: 0.6850 (p90) REVERT: U 189 TRP cc_start: 0.7254 (m-90) cc_final: 0.6957 (m-90) REVERT: U 216 GLU cc_start: 0.8372 (pt0) cc_final: 0.8138 (pt0) REVERT: U 224 ASN cc_start: 0.8972 (p0) cc_final: 0.8539 (p0) REVERT: U 228 ARG cc_start: 0.8662 (mtm110) cc_final: 0.8406 (mtp-110) REVERT: V 19 ARG cc_start: 0.8986 (ttm170) cc_final: 0.8571 (ttp-170) REVERT: V 30 ASN cc_start: 0.8866 (t0) cc_final: 0.8615 (OUTLIER) REVERT: V 150 GLU cc_start: 0.8512 (pm20) cc_final: 0.8273 (pm20) REVERT: V 153 ASN cc_start: 0.8467 (m-40) cc_final: 0.7988 (m-40) REVERT: V 184 ASP cc_start: 0.8772 (t0) cc_final: 0.8525 (t0) REVERT: V 202 TYR cc_start: 0.7526 (m-10) cc_final: 0.7170 (m-10) REVERT: V 214 GLU cc_start: 0.8891 (tt0) cc_final: 0.8573 (tt0) REVERT: W 60 GLN cc_start: 0.9211 (mt0) cc_final: 0.8988 (mt0) REVERT: W 64 GLN cc_start: 0.8884 (mt0) cc_final: 0.8635 (mt0) REVERT: W 74 GLU cc_start: 0.8407 (pt0) cc_final: 0.8146 (tp30) REVERT: W 77 GLU cc_start: 0.8651 (mm-30) cc_final: 0.7978 (mm-30) REVERT: W 105 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8671 (mm-30) REVERT: W 164 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8180 (mm-30) REVERT: X 36 PHE cc_start: 0.9255 (m-80) cc_final: 0.8993 (m-80) REVERT: X 37 LYS cc_start: 0.8914 (tttm) cc_final: 0.8678 (tttp) REVERT: X 87 ASN cc_start: 0.9069 (m-40) cc_final: 0.8217 (m110) REVERT: X 108 ASP cc_start: 0.8704 (t70) cc_final: 0.8275 (t70) REVERT: X 118 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8265 (mtp) REVERT: X 158 GLU cc_start: 0.8346 (tp30) cc_final: 0.8112 (tp30) REVERT: X 166 GLU cc_start: 0.8607 (tp30) cc_final: 0.8280 (tp30) REVERT: X 185 LYS cc_start: 0.9264 (ptmm) cc_final: 0.9063 (ptmm) REVERT: X 186 ASN cc_start: 0.9323 (m110) cc_final: 0.9026 (m-40) REVERT: Y 26 ILE cc_start: 0.9273 (mt) cc_final: 0.9003 (mp) REVERT: Y 62 GLN cc_start: 0.9388 (mm-40) cc_final: 0.9090 (mm-40) REVERT: Y 67 GLU cc_start: 0.8882 (tt0) cc_final: 0.8565 (tm-30) REVERT: Y 81 LYS cc_start: 0.9271 (tptt) cc_final: 0.9002 (tptm) REVERT: Y 89 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8768 (mm110) REVERT: Y 119 ASN cc_start: 0.8940 (m-40) cc_final: 0.8708 (m110) REVERT: Y 139 MET cc_start: 0.8769 (ttp) cc_final: 0.8497 (ttp) REVERT: Z 8 ASN cc_start: 0.9101 (m110) cc_final: 0.8784 (m110) REVERT: Z 159 GLN cc_start: 0.8452 (tp40) cc_final: 0.8111 (mt0) REVERT: Z 177 ASP cc_start: 0.8532 (m-30) cc_final: 0.8328 (m-30) REVERT: a 5 MET cc_start: 0.8481 (mmm) cc_final: 0.7803 (tpt) REVERT: a 56 ASP cc_start: 0.8839 (t70) cc_final: 0.8357 (t70) REVERT: a 133 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8325 (mt-10) REVERT: a 180 ASP cc_start: 0.8957 (t0) cc_final: 0.8733 (t0) REVERT: b 7 GLN cc_start: 0.8968 (tt0) cc_final: 0.8516 (tt0) REVERT: b 69 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8267 (mt-10) outliers start: 106 outliers final: 30 residues processed: 1165 average time/residue: 0.8275 time to fit residues: 1175.1963 Evaluate side-chains 1048 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 1014 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain J residue 158 GLU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 198 ASN Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 146 GLN Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain T residue 192 GLU Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 126 ILE Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain Z residue 148 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 206 optimal weight: 1.9990 chunk 369 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 563 optimal weight: 6.9990 chunk 319 optimal weight: 0.0020 chunk 222 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 chunk 414 optimal weight: 0.6980 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 111 GLN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN B 146 GLN C 23 GLN C 122 ASN E 65 HIS G 24 GLN G 100 ASN G 224 ASN H 153 ASN J 55 GLN J 193 ASN K 175 ASN L 146 GLN L 157 ASN M 89 HIS M 185 ASN O 139 ASN S 185 ASN T 101 ASN V 57 GLN V 85 GLN W 6 ASN W 32 GLN W 156 ASN X 63 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 146 GLN a 2 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.081329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.066667 restraints weight = 95093.527| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.77 r_work: 0.2819 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47220 Z= 0.154 Angle : 0.556 9.748 64063 Z= 0.298 Chirality : 0.043 0.160 7447 Planarity : 0.004 0.055 8164 Dihedral : 4.419 25.274 6849 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.67 % Allowed : 15.36 % Favored : 81.97 % 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: 0.85 (0.10), residues: 6188 helix: 1.81 (0.10), residues: 2338 sheet: 0.07 (0.12), residues: 1500 loop : -0.28 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 53 TYR 0.032 0.001 TYR U 160 PHE 0.023 0.001 PHE T 135 TRP 0.023 0.001 TRP F 215 HIS 0.006 0.001 HIS S 65 Details of bonding type rmsd covalent geometry : bond 0.00342 (47220) covalent geometry : angle 0.55598 (64063) hydrogen bonds : bond 0.03815 ( 2773) hydrogen bonds : angle 4.76834 ( 8061) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 1053 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLN cc_start: 0.8651 (tm130) cc_final: 0.8367 (tp40) REVERT: A 142 ARG cc_start: 0.8375 (tmt90) cc_final: 0.8012 (ttt-90) REVERT: A 147 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8601 (tm-30) REVERT: A 158 LYS cc_start: 0.8829 (mttm) cc_final: 0.8453 (mttp) REVERT: A 176 ARG cc_start: 0.9070 (ttm110) cc_final: 0.8335 (ttm110) REVERT: A 195 LYS cc_start: 0.9585 (ttpp) cc_final: 0.9273 (ttmm) REVERT: B 69 ASN cc_start: 0.8820 (t0) cc_final: 0.8585 (t0) REVERT: B 90 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9425 (mt) REVERT: B 166 ASN cc_start: 0.9212 (t0) cc_final: 0.8774 (t0) REVERT: B 167 ASN cc_start: 0.9429 (m110) cc_final: 0.8906 (m110) REVERT: B 229 LYS cc_start: 0.9195 (mtmm) cc_final: 0.8842 (mppt) REVERT: C 55 ASP cc_start: 0.8656 (t0) cc_final: 0.8249 (t0) REVERT: C 61 LYS cc_start: 0.8646 (mttm) cc_final: 0.8119 (mtmt) REVERT: C 66 ASP cc_start: 0.9068 (t0) cc_final: 0.8664 (t0) REVERT: C 99 GLU cc_start: 0.8279 (mp0) cc_final: 0.8031 (mp0) REVERT: C 116 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8393 (tp40) REVERT: C 120 GLN cc_start: 0.9219 (tt0) cc_final: 0.8899 (tt0) REVERT: D 32 LYS cc_start: 0.9033 (mttt) cc_final: 0.8712 (mttm) REVERT: D 52 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8209 (mtmm) REVERT: D 84 ASP cc_start: 0.9060 (m-30) cc_final: 0.8693 (m-30) REVERT: D 91 LYS cc_start: 0.9208 (tptp) cc_final: 0.8618 (tptt) REVERT: D 95 GLU cc_start: 0.8894 (tp30) cc_final: 0.8404 (tp30) REVERT: D 114 GLN cc_start: 0.8619 (tt0) cc_final: 0.8270 (tt0) REVERT: D 178 GLN cc_start: 0.8265 (tp40) cc_final: 0.7961 (mm110) REVERT: D 182 GLN cc_start: 0.8999 (mt0) cc_final: 0.8731 (mt0) REVERT: D 224 GLN cc_start: 0.8255 (tp40) cc_final: 0.8028 (tp40) REVERT: E 27 GLU cc_start: 0.8674 (tp30) cc_final: 0.8111 (tp30) REVERT: E 67 ASP cc_start: 0.9098 (t70) cc_final: 0.8645 (t0) REVERT: E 90 GLN cc_start: 0.8952 (tp40) cc_final: 0.8607 (mm-40) REVERT: E 94 ASP cc_start: 0.8760 (m-30) cc_final: 0.8485 (m-30) REVERT: E 100 ASP cc_start: 0.8735 (t0) cc_final: 0.8395 (t0) REVERT: E 180 MET cc_start: 0.8915 (mmm) cc_final: 0.8514 (tpt) REVERT: E 189 LYS cc_start: 0.9407 (mttp) cc_final: 0.9169 (mttp) REVERT: E 197 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8871 (mm-30) REVERT: F 27 MET cc_start: 0.8956 (mtt) cc_final: 0.8483 (mtt) REVERT: F 31 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: F 50 GLU cc_start: 0.7946 (tt0) cc_final: 0.7744 (tt0) REVERT: F 70 ASP cc_start: 0.8802 (t0) cc_final: 0.8263 (t0) REVERT: F 93 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8596 (mm-30) REVERT: F 97 ASN cc_start: 0.9089 (m-40) cc_final: 0.8814 (m110) REVERT: F 147 GLN cc_start: 0.8830 (mt0) cc_final: 0.8159 (mt0) REVERT: G 10 ASP cc_start: 0.8796 (p0) cc_final: 0.8519 (p0) REVERT: G 43 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7924 (ptt-90) REVERT: G 116 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8507 (ttmm) REVERT: G 120 ASP cc_start: 0.8496 (m-30) cc_final: 0.8255 (m-30) REVERT: G 174 GLU cc_start: 0.9089 (mp0) cc_final: 0.8840 (pm20) REVERT: G 224 ASN cc_start: 0.9174 (t0) cc_final: 0.8513 (p0) REVERT: H 30 ASN cc_start: 0.8974 (t0) cc_final: 0.8431 (t0) REVERT: H 72 ARG cc_start: 0.9010 (ptp90) cc_final: 0.8558 (ptp-170) REVERT: H 202 TYR cc_start: 0.7538 (m-80) cc_final: 0.7247 (m-10) REVERT: I 105 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8887 (mt-10) REVERT: I 112 ASP cc_start: 0.8882 (t70) cc_final: 0.8556 (t0) REVERT: I 145 MET cc_start: 0.8985 (mtm) cc_final: 0.8657 (mtp) REVERT: I 151 SER cc_start: 0.9432 (m) cc_final: 0.9218 (p) REVERT: I 157 MET cc_start: 0.9274 (mtm) cc_final: 0.9024 (mtm) REVERT: I 164 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: I 175 ASP cc_start: 0.8728 (m-30) cc_final: 0.8297 (m-30) REVERT: J 27 GLN cc_start: 0.8933 (tt0) cc_final: 0.8197 (tm130) REVERT: J 108 ASP cc_start: 0.8458 (t70) cc_final: 0.7940 (t70) REVERT: J 111 GLU cc_start: 0.8658 (mp0) cc_final: 0.8435 (mp0) REVERT: J 184 ASP cc_start: 0.8830 (p0) cc_final: 0.8584 (p0) REVERT: K 56 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.9051 (mp0) REVERT: K 72 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8135 (tm-30) REVERT: L 44 TYR cc_start: 0.8592 (m-80) cc_final: 0.8291 (m-80) REVERT: L 73 LYS cc_start: 0.9174 (mttt) cc_final: 0.8916 (mtmm) REVERT: L 131 GLN cc_start: 0.8637 (pt0) cc_final: 0.8346 (pt0) REVERT: L 177 ASP cc_start: 0.8523 (m-30) cc_final: 0.8267 (m-30) REVERT: L 186 ASP cc_start: 0.8725 (t0) cc_final: 0.8308 (t0) REVERT: L 205 GLU cc_start: 0.8251 (mp0) cc_final: 0.7887 (mp0) REVERT: L 206 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7742 (mm-30) REVERT: M 26 MET cc_start: 0.9021 (mtp) cc_final: 0.8647 (mtm) REVERT: M 56 ASP cc_start: 0.8898 (t0) cc_final: 0.8613 (t0) REVERT: M 64 LYS cc_start: 0.9075 (mtpt) cc_final: 0.8864 (mtpp) REVERT: M 79 ASP cc_start: 0.8387 (p0) cc_final: 0.8084 (p0) REVERT: M 104 ASN cc_start: 0.9231 (t0) cc_final: 0.8616 (t0) REVERT: M 170 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8203 (mp0) REVERT: M 180 ASP cc_start: 0.8966 (t70) cc_final: 0.8485 (t0) REVERT: M 200 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8050 (mt-10) REVERT: M 210 ASP cc_start: 0.8787 (p0) cc_final: 0.8414 (p0) REVERT: M 213 HIS cc_start: 0.9165 (m90) cc_final: 0.8837 (m-70) REVERT: N 84 LYS cc_start: 0.9422 (ttpt) cc_final: 0.9167 (ttpp) REVERT: N 107 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7023 (tp30) REVERT: N 167 ASP cc_start: 0.8462 (t0) cc_final: 0.8003 (t0) REVERT: N 193 GLN cc_start: 0.8894 (mt0) cc_final: 0.8651 (mt0) REVERT: O 48 GLU cc_start: 0.8172 (pp20) cc_final: 0.7807 (pp20) REVERT: O 57 ASP cc_start: 0.8273 (t0) cc_final: 0.7818 (t0) REVERT: O 108 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8692 (mm-40) REVERT: O 111 GLN cc_start: 0.8989 (mt0) cc_final: 0.8713 (mt0) REVERT: O 142 ARG cc_start: 0.8594 (ttt-90) cc_final: 0.7953 (ttt-90) REVERT: P 48 GLU cc_start: 0.8585 (tt0) cc_final: 0.7714 (tm-30) REVERT: P 57 ASP cc_start: 0.8708 (t70) cc_final: 0.8341 (t0) REVERT: P 75 SER cc_start: 0.9258 (t) cc_final: 0.8952 (t) REVERT: P 103 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8560 (mt-10) REVERT: P 166 ASN cc_start: 0.9166 (t0) cc_final: 0.8627 (t0) REVERT: P 167 ASN cc_start: 0.9422 (m110) cc_final: 0.8910 (m110) REVERT: P 184 MET cc_start: 0.8755 (mmm) cc_final: 0.8371 (mmm) REVERT: Q 24 GLU cc_start: 0.8404 (tt0) cc_final: 0.8007 (tm-30) REVERT: Q 27 LYS cc_start: 0.9228 (mtpp) cc_final: 0.9015 (mtpt) REVERT: Q 28 LYS cc_start: 0.9286 (mttm) cc_final: 0.8938 (mtmt) REVERT: Q 55 ASP cc_start: 0.8499 (t0) cc_final: 0.8088 (t0) REVERT: Q 99 GLU cc_start: 0.8169 (mp0) cc_final: 0.7887 (mp0) REVERT: Q 110 TYR cc_start: 0.8582 (t80) cc_final: 0.8346 (t80) REVERT: Q 116 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8127 (tp40) REVERT: Q 148 ASP cc_start: 0.8562 (t0) cc_final: 0.8319 (t0) REVERT: Q 153 TYR cc_start: 0.9408 (p90) cc_final: 0.9167 (p90) REVERT: Q 157 LYS cc_start: 0.8891 (mttt) cc_final: 0.8250 (mtmt) REVERT: R 32 LYS cc_start: 0.8819 (mttp) cc_final: 0.8471 (mttp) REVERT: R 206 MET cc_start: 0.8051 (mtm) cc_final: 0.7801 (mtm) REVERT: R 227 HIS cc_start: 0.8782 (t-90) cc_final: 0.8348 (t70) REVERT: R 231 LYS cc_start: 0.9286 (mtpm) cc_final: 0.8856 (tttp) REVERT: S 26 MET cc_start: 0.8625 (mtp) cc_final: 0.8258 (mtp) REVERT: S 30 LYS cc_start: 0.8882 (mttt) cc_final: 0.8463 (mptt) REVERT: S 31 GLN cc_start: 0.8351 (pp30) cc_final: 0.8093 (pp30) REVERT: S 90 GLN cc_start: 0.9031 (tp40) cc_final: 0.8691 (mm-40) REVERT: S 178 GLU cc_start: 0.9122 (pm20) cc_final: 0.8793 (pm20) REVERT: T 27 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8622 (mtt) REVERT: T 70 ASP cc_start: 0.8619 (t70) cc_final: 0.8332 (t0) REVERT: T 93 GLU cc_start: 0.8125 (pp20) cc_final: 0.7618 (pp20) REVERT: T 184 MET cc_start: 0.8695 (mtp) cc_final: 0.8276 (ptp) REVERT: T 192 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8774 (mp0) REVERT: T 236 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9069 (mm-30) REVERT: U 5 SER cc_start: 0.9070 (t) cc_final: 0.8316 (m) REVERT: U 21 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8122 (mmm-85) REVERT: U 104 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8955 (mtmm) REVERT: U 155 ASP cc_start: 0.8404 (p0) cc_final: 0.8022 (p0) REVERT: U 180 GLU cc_start: 0.8555 (pp20) cc_final: 0.8351 (pp20) REVERT: U 187 PHE cc_start: 0.7402 (p90) cc_final: 0.6934 (p90) REVERT: U 189 TRP cc_start: 0.7324 (m-90) cc_final: 0.6984 (m-90) REVERT: U 216 GLU cc_start: 0.8502 (pt0) cc_final: 0.8254 (pt0) REVERT: U 224 ASN cc_start: 0.9005 (p0) cc_final: 0.8601 (p0) REVERT: U 228 ARG cc_start: 0.8675 (mtm110) cc_final: 0.8377 (mtp-110) REVERT: U 234 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8362 (mp0) REVERT: V 19 ARG cc_start: 0.8963 (ttm170) cc_final: 0.8570 (ttm170) REVERT: V 30 ASN cc_start: 0.8965 (t0) cc_final: 0.8746 (t0) REVERT: V 53 ASP cc_start: 0.8113 (m-30) cc_final: 0.7836 (m-30) REVERT: V 85 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8647 (mt0) REVERT: V 150 GLU cc_start: 0.8513 (pm20) cc_final: 0.8233 (pm20) REVERT: V 184 ASP cc_start: 0.8709 (t0) cc_final: 0.8504 (t0) REVERT: V 214 GLU cc_start: 0.8933 (tt0) cc_final: 0.8604 (tt0) REVERT: W 64 GLN cc_start: 0.8923 (mt0) cc_final: 0.8715 (mt0) REVERT: W 74 GLU cc_start: 0.8432 (pt0) cc_final: 0.8193 (tp30) REVERT: W 105 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8633 (mm-30) REVERT: W 150 GLU cc_start: 0.8981 (tp30) cc_final: 0.8622 (tp30) REVERT: W 164 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8217 (mm-30) REVERT: X 36 PHE cc_start: 0.9216 (m-80) cc_final: 0.8890 (m-80) REVERT: X 37 LYS cc_start: 0.9033 (tttm) cc_final: 0.8764 (tttp) REVERT: X 87 ASN cc_start: 0.9091 (m-40) cc_final: 0.8705 (m-40) REVERT: X 108 ASP cc_start: 0.8722 (t70) cc_final: 0.8300 (t70) REVERT: X 118 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8293 (mtp) REVERT: X 158 GLU cc_start: 0.8548 (tp30) cc_final: 0.8281 (tp30) REVERT: X 166 GLU cc_start: 0.8682 (tp30) cc_final: 0.8305 (tp30) REVERT: X 168 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: X 184 ASP cc_start: 0.8960 (p0) cc_final: 0.8690 (p0) REVERT: X 185 LYS cc_start: 0.9289 (ptmm) cc_final: 0.9067 (ptmm) REVERT: X 186 ASN cc_start: 0.9387 (m110) cc_final: 0.8947 (m-40) REVERT: Y 26 ILE cc_start: 0.9278 (mt) cc_final: 0.8957 (mp) REVERT: Y 62 GLN cc_start: 0.9404 (mm-40) cc_final: 0.9138 (mm-40) REVERT: Y 67 GLU cc_start: 0.8925 (tt0) cc_final: 0.8568 (tm-30) REVERT: Y 70 ASN cc_start: 0.9506 (m-40) cc_final: 0.9169 (m110) REVERT: Y 81 LYS cc_start: 0.9307 (tptt) cc_final: 0.8961 (tptm) REVERT: Y 139 MET cc_start: 0.8822 (ttp) cc_final: 0.8571 (ttp) REVERT: Y 167 ASP cc_start: 0.8848 (t0) cc_final: 0.8596 (t0) REVERT: Z 157 ASN cc_start: 0.8592 (m-40) cc_final: 0.8285 (m110) REVERT: Z 159 GLN cc_start: 0.8466 (tp40) cc_final: 0.8092 (mt0) REVERT: Z 196 CYS cc_start: 0.8950 (m) cc_final: 0.7947 (m) REVERT: a 5 MET cc_start: 0.8548 (mmm) cc_final: 0.8004 (tpt) REVERT: a 56 ASP cc_start: 0.8891 (t70) cc_final: 0.8648 (t70) REVERT: a 59 ASP cc_start: 0.9337 (m-30) cc_final: 0.9092 (m-30) REVERT: a 133 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8461 (mt-10) REVERT: a 147 GLN cc_start: 0.9118 (tp-100) cc_final: 0.8894 (mm-40) REVERT: a 180 ASP cc_start: 0.9004 (t0) cc_final: 0.8633 (t0) REVERT: b 7 GLN cc_start: 0.8979 (tt0) cc_final: 0.8551 (tt0) REVERT: b 69 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8334 (mt-10) outliers start: 120 outliers final: 41 residues processed: 1100 average time/residue: 0.7715 time to fit residues: 1036.7631 Evaluate side-chains 1047 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 994 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 86 MET Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 192 GLU Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 161 CYS Chi-restraints excluded: chain V residue 85 GLN Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 168 GLN Chi-restraints excluded: chain Y residue 97 MET Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 172 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 135 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 330 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 491 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 366 optimal weight: 4.9990 chunk 320 optimal weight: 1.9990 chunk 513 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN C 23 GLN C 54 GLN D 122 GLN E 20 HIS F 120 HIS H 153 ASN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN J 63 ASN K 162 GLN K 175 ASN L 108 ASN L 159 GLN M 47 ASN N 7 GLN N 154 GLN O 139 ASN P 198 ASN S 21 GLN T 63 ASN ** T 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN U 100 ASN V 57 GLN V 80 ASN W 32 GLN W 156 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN Y 191 ASN ** Z 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 2 GLN a 47 ASN b 77 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.076835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.061894 restraints weight = 98243.842| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.74 r_work: 0.2741 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 47220 Z= 0.294 Angle : 0.639 9.670 64063 Z= 0.339 Chirality : 0.045 0.265 7447 Planarity : 0.004 0.064 8164 Dihedral : 4.595 33.550 6849 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.65 % Allowed : 16.31 % Favored : 80.04 % 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: 0.81 (0.10), residues: 6188 helix: 1.72 (0.10), residues: 2360 sheet: 0.03 (0.12), residues: 1505 loop : -0.25 (0.13), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 117 TYR 0.035 0.002 TYR U 160 PHE 0.018 0.002 PHE W 68 TRP 0.035 0.002 TRP F 215 HIS 0.005 0.001 HIS S 65 Details of bonding type rmsd covalent geometry : bond 0.00663 (47220) covalent geometry : angle 0.63851 (64063) hydrogen bonds : bond 0.04270 ( 2773) hydrogen bonds : angle 4.84883 ( 8061) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 1016 time to evaluate : 1.332 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: A 49 LYS cc_start: 0.9124 (ttpt) cc_final: 0.8797 (ttpt) REVERT: A 78 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8654 (mtp) REVERT: A 195 LYS cc_start: 0.9612 (ttpp) cc_final: 0.9325 (ttmm) REVERT: B 90 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9459 (mt) REVERT: B 166 ASN cc_start: 0.9280 (t0) cc_final: 0.9070 (t0) REVERT: B 232 GLU cc_start: 0.8410 (pm20) cc_final: 0.8138 (pm20) REVERT: C 28 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8878 (mtmm) REVERT: C 55 ASP cc_start: 0.8739 (t0) cc_final: 0.8286 (t0) REVERT: C 61 LYS cc_start: 0.8691 (mttm) cc_final: 0.8240 (mtmt) REVERT: C 66 ASP cc_start: 0.9031 (t0) cc_final: 0.8564 (t0) REVERT: C 99 GLU cc_start: 0.8583 (mp0) cc_final: 0.8175 (mp0) REVERT: C 120 GLN cc_start: 0.9251 (tt0) cc_final: 0.8963 (tt0) REVERT: D 32 LYS cc_start: 0.9066 (mttt) cc_final: 0.8739 (mttp) REVERT: D 91 LYS cc_start: 0.9285 (tptp) cc_final: 0.8755 (tptp) REVERT: D 95 GLU cc_start: 0.8952 (tp30) cc_final: 0.8507 (tp30) REVERT: D 114 GLN cc_start: 0.8753 (tt0) cc_final: 0.8487 (tt0) REVERT: D 178 GLN cc_start: 0.8542 (tp40) cc_final: 0.8126 (mm110) REVERT: D 182 GLN cc_start: 0.9027 (mt0) cc_final: 0.8766 (mt0) REVERT: D 196 LYS cc_start: 0.9346 (mtpp) cc_final: 0.8996 (mtmm) REVERT: D 224 GLN cc_start: 0.8265 (tp40) cc_final: 0.8034 (tp40) REVERT: E 27 GLU cc_start: 0.8889 (tp30) cc_final: 0.8172 (tm-30) REVERT: E 67 ASP cc_start: 0.9100 (t70) cc_final: 0.8695 (t0) REVERT: E 90 GLN cc_start: 0.9001 (tp40) cc_final: 0.8703 (mm-40) REVERT: E 94 ASP cc_start: 0.8731 (m-30) cc_final: 0.8496 (m-30) REVERT: E 100 ASP cc_start: 0.8719 (t0) cc_final: 0.8390 (t0) REVERT: E 180 MET cc_start: 0.8888 (mmm) cc_final: 0.8584 (tpt) REVERT: E 189 LYS cc_start: 0.9514 (mttp) cc_final: 0.9085 (mttp) REVERT: E 197 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8872 (mm-30) REVERT: F 27 MET cc_start: 0.8973 (mtt) cc_final: 0.8723 (mtt) REVERT: F 31 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: F 50 GLU cc_start: 0.8173 (tt0) cc_final: 0.7970 (tt0) REVERT: F 70 ASP cc_start: 0.8870 (t0) cc_final: 0.8340 (t0) REVERT: F 150 MET cc_start: 0.8665 (tmt) cc_final: 0.8459 (tmt) REVERT: F 202 ASP cc_start: 0.8019 (t0) cc_final: 0.7789 (p0) REVERT: G 10 ASP cc_start: 0.8882 (p0) cc_final: 0.8615 (p0) REVERT: G 11 ARG cc_start: 0.8545 (mtt90) cc_final: 0.7860 (mtt90) REVERT: G 80 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8723 (mmm) REVERT: G 81 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8685 (p) REVERT: G 112 ASP cc_start: 0.9140 (p0) cc_final: 0.8744 (p0) REVERT: G 116 LYS cc_start: 0.8963 (ttpt) cc_final: 0.8432 (ttmm) REVERT: G 120 ASP cc_start: 0.8555 (m-30) cc_final: 0.8263 (m-30) REVERT: G 174 GLU cc_start: 0.9081 (mp0) cc_final: 0.8842 (pm20) REVERT: G 224 ASN cc_start: 0.9145 (t0) cc_final: 0.8319 (p0) REVERT: H 30 ASN cc_start: 0.8884 (t0) cc_final: 0.8323 (t0) REVERT: I 105 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8682 (mt-10) REVERT: I 112 ASP cc_start: 0.8921 (t70) cc_final: 0.8678 (t0) REVERT: I 157 MET cc_start: 0.9254 (mtm) cc_final: 0.9050 (mtt) REVERT: I 175 ASP cc_start: 0.8863 (m-30) cc_final: 0.8481 (m-30) REVERT: J 27 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8336 (tm130) REVERT: J 68 LYS cc_start: 0.9203 (tttm) cc_final: 0.8826 (tppt) REVERT: J 108 ASP cc_start: 0.8624 (t70) cc_final: 0.8055 (t70) REVERT: J 111 GLU cc_start: 0.8676 (mp0) cc_final: 0.8414 (mp0) REVERT: J 184 ASP cc_start: 0.8819 (p0) cc_final: 0.8585 (p0) REVERT: K 56 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.9116 (mp0) REVERT: K 72 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8229 (tm-30) REVERT: K 81 LYS cc_start: 0.8965 (tptp) cc_final: 0.8615 (mtpt) REVERT: K 155 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8519 (tp) REVERT: L 39 ASP cc_start: 0.9020 (t70) cc_final: 0.8740 (t0) REVERT: L 47 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8815 (p) REVERT: L 48 ASP cc_start: 0.8675 (p0) cc_final: 0.8194 (t0) REVERT: L 73 LYS cc_start: 0.9192 (mttt) cc_final: 0.8992 (mtmm) REVERT: L 91 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8805 (ttp) REVERT: L 177 ASP cc_start: 0.8659 (m-30) cc_final: 0.8085 (m-30) REVERT: L 186 ASP cc_start: 0.8780 (t0) cc_final: 0.8461 (t0) REVERT: L 188 TYR cc_start: 0.9252 (m-80) cc_final: 0.8887 (m-80) REVERT: L 205 GLU cc_start: 0.8384 (mp0) cc_final: 0.8081 (mp0) REVERT: L 206 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7863 (mm-30) REVERT: M 26 MET cc_start: 0.9133 (mtp) cc_final: 0.8733 (mtm) REVERT: M 47 ASN cc_start: 0.9078 (t0) cc_final: 0.8607 (t0) REVERT: M 56 ASP cc_start: 0.9021 (t0) cc_final: 0.8598 (t0) REVERT: M 64 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8716 (ttmm) REVERT: M 79 ASP cc_start: 0.8507 (p0) cc_final: 0.8200 (p0) REVERT: M 104 ASN cc_start: 0.9229 (t0) cc_final: 0.8660 (t0) REVERT: M 170 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8266 (mp0) REVERT: M 180 ASP cc_start: 0.9084 (t70) cc_final: 0.8599 (t0) REVERT: M 200 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8179 (mt-10) REVERT: M 210 ASP cc_start: 0.8831 (p0) cc_final: 0.8472 (p0) REVERT: N 107 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: N 165 GLU cc_start: 0.8862 (tt0) cc_final: 0.8434 (tm-30) REVERT: N 167 ASP cc_start: 0.8500 (t0) cc_final: 0.8150 (t0) REVERT: N 193 GLN cc_start: 0.8908 (mt0) cc_final: 0.8633 (mt0) REVERT: O 48 GLU cc_start: 0.8258 (pp20) cc_final: 0.7817 (pp20) REVERT: O 57 ASP cc_start: 0.8307 (t0) cc_final: 0.7870 (t0) REVERT: O 108 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8914 (mm110) REVERT: O 118 GLN cc_start: 0.9250 (tm-30) cc_final: 0.9010 (tp40) REVERT: O 142 ARG cc_start: 0.8677 (ttt-90) cc_final: 0.8117 (ttt-90) REVERT: O 224 GLU cc_start: 0.9007 (mp0) cc_final: 0.8807 (pm20) REVERT: P 30 HIS cc_start: 0.8622 (OUTLIER) cc_final: 0.8295 (m-70) REVERT: P 48 GLU cc_start: 0.8529 (tt0) cc_final: 0.7771 (tm-30) REVERT: P 57 ASP cc_start: 0.8719 (t70) cc_final: 0.8342 (t0) REVERT: P 75 SER cc_start: 0.9367 (t) cc_final: 0.9126 (t) REVERT: P 166 ASN cc_start: 0.9224 (t0) cc_final: 0.8670 (t0) REVERT: P 167 ASN cc_start: 0.9413 (m110) cc_final: 0.8770 (m110) REVERT: Q 20 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8157 (mt-10) REVERT: Q 24 GLU cc_start: 0.8399 (tt0) cc_final: 0.7990 (tm-30) REVERT: Q 28 LYS cc_start: 0.9212 (mttm) cc_final: 0.8952 (mttt) REVERT: Q 55 ASP cc_start: 0.8644 (t0) cc_final: 0.8197 (t0) REVERT: Q 90 GLU cc_start: 0.8576 (tp30) cc_final: 0.8308 (tp30) REVERT: Q 99 GLU cc_start: 0.8173 (mp0) cc_final: 0.7915 (mp0) REVERT: Q 110 TYR cc_start: 0.8939 (t80) cc_final: 0.8583 (t80) REVERT: Q 116 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8326 (tp40) REVERT: Q 148 ASP cc_start: 0.9007 (t0) cc_final: 0.8452 (t0) REVERT: Q 157 LYS cc_start: 0.8933 (mttt) cc_final: 0.8430 (mtmp) REVERT: Q 193 LYS cc_start: 0.9419 (ptmt) cc_final: 0.9112 (ptmm) REVERT: R 86 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8499 (mptm) REVERT: R 206 MET cc_start: 0.8121 (mtm) cc_final: 0.7891 (mtm) REVERT: R 227 HIS cc_start: 0.8776 (t-90) cc_final: 0.8367 (t70) REVERT: R 231 LYS cc_start: 0.9296 (mtpm) cc_final: 0.8815 (tttp) REVERT: S 26 MET cc_start: 0.8736 (mtp) cc_final: 0.8508 (mtp) REVERT: S 30 LYS cc_start: 0.8962 (mttt) cc_final: 0.8593 (mptt) REVERT: S 31 GLN cc_start: 0.8328 (pp30) cc_final: 0.8094 (pp30) REVERT: S 90 GLN cc_start: 0.9169 (tp40) cc_final: 0.8367 (mm-40) REVERT: S 94 ASP cc_start: 0.8594 (m-30) cc_final: 0.7925 (m-30) REVERT: S 178 GLU cc_start: 0.9080 (pm20) cc_final: 0.8756 (pm20) REVERT: T 70 ASP cc_start: 0.8669 (t70) cc_final: 0.8406 (t0) REVERT: T 93 GLU cc_start: 0.8151 (pp20) cc_final: 0.7772 (pp20) REVERT: T 180 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8379 (tp-100) REVERT: T 184 MET cc_start: 0.8698 (mtp) cc_final: 0.8229 (ptp) REVERT: T 192 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.8864 (mp0) REVERT: T 236 GLU cc_start: 0.9373 (mt-10) cc_final: 0.9055 (mm-30) REVERT: U 5 SER cc_start: 0.9020 (t) cc_final: 0.8345 (m) REVERT: U 104 LYS cc_start: 0.9277 (mtpt) cc_final: 0.9042 (mtmm) REVERT: U 117 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8590 (mmp80) REVERT: U 155 ASP cc_start: 0.8442 (p0) cc_final: 0.8168 (p0) REVERT: U 187 PHE cc_start: 0.7424 (p90) cc_final: 0.6911 (p90) REVERT: U 189 TRP cc_start: 0.7360 (m-90) cc_final: 0.6894 (m-90) REVERT: U 224 ASN cc_start: 0.9045 (p0) cc_final: 0.8620 (p0) REVERT: U 228 ARG cc_start: 0.8670 (mtm110) cc_final: 0.8423 (mtp-110) REVERT: V 19 ARG cc_start: 0.8956 (ttm170) cc_final: 0.8342 (ttm-80) REVERT: V 30 ASN cc_start: 0.9166 (t0) cc_final: 0.8872 (t0) REVERT: V 150 GLU cc_start: 0.8471 (pm20) cc_final: 0.8141 (pm20) REVERT: V 153 ASN cc_start: 0.8648 (m-40) cc_final: 0.8296 (m110) REVERT: V 157 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8399 (mm-30) REVERT: V 184 ASP cc_start: 0.8804 (t0) cc_final: 0.8416 (t0) REVERT: V 202 TYR cc_start: 0.7373 (m-10) cc_final: 0.7055 (m-10) REVERT: V 214 GLU cc_start: 0.8927 (tt0) cc_final: 0.8639 (tt0) REVERT: W 64 GLN cc_start: 0.9042 (mt0) cc_final: 0.8832 (mt0) REVERT: W 98 ARG cc_start: 0.9093 (tpt-90) cc_final: 0.8689 (tpt-90) REVERT: W 105 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8688 (mm-30) REVERT: W 143 GLU cc_start: 0.8214 (pm20) cc_final: 0.7999 (pm20) REVERT: W 161 HIS cc_start: 0.8689 (m-70) cc_final: 0.8456 (m170) REVERT: W 164 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8441 (mm-30) REVERT: X 36 PHE cc_start: 0.9138 (m-80) cc_final: 0.8748 (m-80) REVERT: X 37 LYS cc_start: 0.9148 (tttm) cc_final: 0.8905 (tttp) REVERT: X 74 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: X 87 ASN cc_start: 0.9103 (m-40) cc_final: 0.8430 (m-40) REVERT: X 91 CYS cc_start: 0.9053 (m) cc_final: 0.8573 (m) REVERT: X 108 ASP cc_start: 0.8852 (t70) cc_final: 0.8517 (t70) REVERT: X 158 GLU cc_start: 0.8713 (tp30) cc_final: 0.8472 (tp30) REVERT: X 166 GLU cc_start: 0.8721 (tp30) cc_final: 0.8450 (tp30) REVERT: X 169 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8882 (ptmm) REVERT: Y 26 ILE cc_start: 0.9332 (mt) cc_final: 0.9023 (mp) REVERT: Y 34 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.8987 (t) REVERT: Y 62 GLN cc_start: 0.9477 (mm-40) cc_final: 0.9233 (mm-40) REVERT: Y 67 GLU cc_start: 0.8993 (tt0) cc_final: 0.8615 (tm-30) REVERT: Y 70 ASN cc_start: 0.9501 (m-40) cc_final: 0.9144 (m110) REVERT: Y 81 LYS cc_start: 0.9426 (tptt) cc_final: 0.9104 (tptm) REVERT: Z 172 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8820 (mtp) REVERT: Z 177 ASP cc_start: 0.8733 (m-30) cc_final: 0.8520 (m-30) REVERT: Z 196 CYS cc_start: 0.9099 (m) cc_final: 0.8673 (m) REVERT: Z 205 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7962 (tm-30) REVERT: Z 206 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: a 5 MET cc_start: 0.8672 (mmm) cc_final: 0.8211 (tpt) REVERT: a 25 ASP cc_start: 0.9036 (p0) cc_final: 0.8703 (p0) REVERT: a 56 ASP cc_start: 0.9037 (t70) cc_final: 0.8767 (t70) REVERT: a 133 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8479 (mt-10) REVERT: a 180 ASP cc_start: 0.9032 (t0) cc_final: 0.8724 (t0) REVERT: b 7 GLN cc_start: 0.9028 (tt0) cc_final: 0.8624 (tt0) REVERT: b 69 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8314 (mt-10) REVERT: b 151 GLU cc_start: 0.8960 (pt0) cc_final: 0.8709 (pt0) outliers start: 164 outliers final: 61 residues processed: 1087 average time/residue: 0.6095 time to fit residues: 814.2373 Evaluate side-chains 1060 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 978 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 154 ASP Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 86 MET Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain O residue 225 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 30 HIS Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain T residue 189 ILE Chi-restraints excluded: chain T residue 192 GLU Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain V residue 146 MET Chi-restraints excluded: chain W residue 88 SER Chi-restraints excluded: chain W residue 148 MET Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 74 GLU Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 206 GLU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 169 VAL Chi-restraints excluded: chain b residue 184 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 539 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 370 optimal weight: 0.2980 chunk 456 optimal weight: 2.9990 chunk 593 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 347 optimal weight: 6.9990 chunk 605 optimal weight: 0.9990 chunk 439 optimal weight: 4.9990 chunk 516 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN C 23 GLN E 43 HIS E 68 ASN F 97 ASN H 153 ASN I 80 GLN I 168 GLN J 55 GLN J 193 ASN L 108 ASN L 131 GLN L 157 ASN L 159 GLN M 185 ASN O 139 ASN O 147 GLN S 65 HIS T 63 ASN T 101 ASN V 57 GLN V 80 ASN W 32 GLN W 156 ASN X 27 GLN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 10 HIS Y 89 GLN Z 108 ASN Z 146 GLN Z 157 ASN a 61 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.078429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.063690 restraints weight = 97099.497| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.74 r_work: 0.2792 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 47220 Z= 0.148 Angle : 0.559 9.189 64063 Z= 0.299 Chirality : 0.043 0.239 7447 Planarity : 0.004 0.054 8164 Dihedral : 4.389 25.141 6847 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.82 % Allowed : 18.80 % Favored : 78.37 % 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: 0.95 (0.10), residues: 6188 helix: 1.91 (0.10), residues: 2356 sheet: 0.12 (0.13), residues: 1495 loop : -0.25 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 59 TYR 0.030 0.001 TYR U 160 PHE 0.018 0.001 PHE G 210 TRP 0.020 0.001 TRP F 215 HIS 0.005 0.001 HIS a 89 Details of bonding type rmsd covalent geometry : bond 0.00330 (47220) covalent geometry : angle 0.55896 (64063) hydrogen bonds : bond 0.03646 ( 2773) hydrogen bonds : angle 4.64191 ( 8061) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 1058 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8941 (pm20) cc_final: 0.8417 (pm20) REVERT: A 78 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8541 (mtp) REVERT: A 147 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8513 (tm-30) REVERT: A 158 LYS cc_start: 0.8907 (mttm) cc_final: 0.8498 (mttp) REVERT: A 176 ARG cc_start: 0.8787 (tpp-160) cc_final: 0.8562 (tpp-160) REVERT: A 195 LYS cc_start: 0.9604 (ttpp) cc_final: 0.9365 (ttmm) REVERT: B 69 ASN cc_start: 0.8809 (t0) cc_final: 0.8601 (t0) REVERT: B 114 LEU cc_start: 0.9399 (tp) cc_final: 0.9186 (tp) REVERT: B 232 GLU cc_start: 0.8377 (pm20) cc_final: 0.8176 (pm20) REVERT: C 28 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8841 (mtmm) REVERT: C 54 GLN cc_start: 0.9097 (tp40) cc_final: 0.8868 (tp40) REVERT: C 55 ASP cc_start: 0.8685 (t0) cc_final: 0.8268 (t0) REVERT: C 61 LYS cc_start: 0.8581 (mttm) cc_final: 0.8132 (mtpt) REVERT: C 66 ASP cc_start: 0.9050 (t0) cc_final: 0.8530 (t0) REVERT: C 99 GLU cc_start: 0.8602 (mp0) cc_final: 0.8140 (mp0) REVERT: C 116 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8532 (tp40) REVERT: C 157 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8696 (mtmm) REVERT: D 32 LYS cc_start: 0.9097 (mttt) cc_final: 0.8778 (mttp) REVERT: D 91 LYS cc_start: 0.9262 (tptp) cc_final: 0.8827 (tppt) REVERT: D 95 GLU cc_start: 0.8925 (tp30) cc_final: 0.8537 (tp30) REVERT: D 114 GLN cc_start: 0.8714 (tt0) cc_final: 0.8508 (tt0) REVERT: D 133 MET cc_start: 0.8672 (mpp) cc_final: 0.8391 (mmp) REVERT: D 178 GLN cc_start: 0.8527 (tp40) cc_final: 0.8152 (mm110) REVERT: D 182 GLN cc_start: 0.8977 (mt0) cc_final: 0.8721 (mt0) REVERT: D 225 ASN cc_start: 0.9052 (m-40) cc_final: 0.8802 (m110) REVERT: E 27 GLU cc_start: 0.8853 (tp30) cc_final: 0.8283 (tm-30) REVERT: E 67 ASP cc_start: 0.9102 (t70) cc_final: 0.8671 (t0) REVERT: E 90 GLN cc_start: 0.9036 (tp40) cc_final: 0.8722 (mm-40) REVERT: E 94 ASP cc_start: 0.8712 (m-30) cc_final: 0.8464 (m-30) REVERT: E 100 ASP cc_start: 0.8748 (t0) cc_final: 0.8399 (t0) REVERT: E 178 GLU cc_start: 0.8786 (pm20) cc_final: 0.8399 (pm20) REVERT: E 180 MET cc_start: 0.8916 (mmm) cc_final: 0.8704 (mmm) REVERT: E 189 LYS cc_start: 0.9510 (mttp) cc_final: 0.9113 (mttp) REVERT: E 197 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8859 (mm-30) REVERT: F 70 ASP cc_start: 0.8880 (t0) cc_final: 0.8375 (t0) REVERT: F 147 GLN cc_start: 0.8866 (mt0) cc_final: 0.8202 (mt0) REVERT: F 150 MET cc_start: 0.8598 (tmt) cc_final: 0.8096 (tmt) REVERT: F 179 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8458 (tm) REVERT: G 10 ASP cc_start: 0.8900 (p0) cc_final: 0.8604 (p0) REVERT: G 11 ARG cc_start: 0.8571 (mtt90) cc_final: 0.7813 (mtt90) REVERT: G 43 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7991 (ptt-90) REVERT: G 56 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8252 (t) REVERT: G 88 ARG cc_start: 0.8427 (mmm160) cc_final: 0.7972 (mmm-85) REVERT: G 112 ASP cc_start: 0.9087 (p0) cc_final: 0.8684 (p0) REVERT: G 116 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8369 (ttmm) REVERT: G 120 ASP cc_start: 0.8563 (m-30) cc_final: 0.8238 (m-30) REVERT: G 224 ASN cc_start: 0.9118 (t0) cc_final: 0.8265 (p0) REVERT: H 30 ASN cc_start: 0.8945 (t0) cc_final: 0.8342 (t0) REVERT: H 202 TYR cc_start: 0.7748 (m-80) cc_final: 0.7518 (m-80) REVERT: I 65 ARG cc_start: 0.8680 (mtp85) cc_final: 0.8191 (mtt-85) REVERT: I 105 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8817 (mt-10) REVERT: I 112 ASP cc_start: 0.8900 (t70) cc_final: 0.8660 (t0) REVERT: I 164 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: I 175 ASP cc_start: 0.8856 (m-30) cc_final: 0.8427 (m-30) REVERT: J 27 GLN cc_start: 0.8930 (tt0) cc_final: 0.8269 (tm130) REVERT: J 74 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8223 (mp0) REVERT: J 108 ASP cc_start: 0.8634 (t70) cc_final: 0.8037 (t70) REVERT: J 184 ASP cc_start: 0.8805 (p0) cc_final: 0.8578 (p0) REVERT: K 36 GLU cc_start: 0.8354 (mp0) cc_final: 0.8004 (mt-10) REVERT: K 56 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.9041 (mp0) REVERT: K 72 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8208 (tm-30) REVERT: K 81 LYS cc_start: 0.9008 (tptp) cc_final: 0.8735 (mtpt) REVERT: L 39 ASP cc_start: 0.9012 (t70) cc_final: 0.8734 (t0) REVERT: L 47 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8904 (p) REVERT: L 48 ASP cc_start: 0.8577 (p0) cc_final: 0.8148 (t0) REVERT: L 73 LYS cc_start: 0.9180 (mttt) cc_final: 0.8959 (mtmm) REVERT: L 177 ASP cc_start: 0.8687 (m-30) cc_final: 0.8328 (m-30) REVERT: L 186 ASP cc_start: 0.8744 (t0) cc_final: 0.8399 (t0) REVERT: L 188 TYR cc_start: 0.9325 (m-80) cc_final: 0.8877 (m-80) REVERT: L 205 GLU cc_start: 0.8322 (mp0) cc_final: 0.7930 (mp0) REVERT: L 206 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7769 (mm-30) REVERT: M 26 MET cc_start: 0.9070 (mtp) cc_final: 0.8709 (mtm) REVERT: M 47 ASN cc_start: 0.9039 (t0) cc_final: 0.8601 (t0) REVERT: M 56 ASP cc_start: 0.8973 (t0) cc_final: 0.8562 (t0) REVERT: M 64 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8900 (mtpp) REVERT: M 79 ASP cc_start: 0.8454 (p0) cc_final: 0.8114 (p0) REVERT: M 104 ASN cc_start: 0.9182 (t0) cc_final: 0.8631 (t0) REVERT: M 170 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8215 (mp0) REVERT: M 180 ASP cc_start: 0.8977 (t70) cc_final: 0.8491 (t0) REVERT: M 200 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8154 (mt-10) REVERT: M 210 ASP cc_start: 0.8856 (p0) cc_final: 0.8528 (p0) REVERT: N 104 ASP cc_start: 0.8363 (p0) cc_final: 0.7999 (p0) REVERT: N 107 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: N 144 ARG cc_start: 0.8546 (pmm150) cc_final: 0.8308 (pmm-80) REVERT: N 165 GLU cc_start: 0.8729 (tt0) cc_final: 0.8477 (tm-30) REVERT: N 167 ASP cc_start: 0.8455 (t0) cc_final: 0.8074 (t0) REVERT: N 193 GLN cc_start: 0.8874 (mt0) cc_final: 0.8588 (mt0) REVERT: O 48 GLU cc_start: 0.8240 (pp20) cc_final: 0.7776 (pp20) REVERT: O 57 ASP cc_start: 0.8240 (t0) cc_final: 0.7774 (t0) REVERT: O 108 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8910 (mm-40) REVERT: O 118 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8931 (tp40) REVERT: O 120 TYR cc_start: 0.8913 (m-80) cc_final: 0.8568 (m-80) REVERT: O 142 ARG cc_start: 0.8668 (ttt-90) cc_final: 0.8084 (ttt-90) REVERT: P 30 HIS cc_start: 0.8513 (OUTLIER) cc_final: 0.8299 (m-70) REVERT: P 48 GLU cc_start: 0.8428 (tt0) cc_final: 0.7684 (tm-30) REVERT: P 57 ASP cc_start: 0.8693 (t70) cc_final: 0.8348 (t0) REVERT: P 75 SER cc_start: 0.9346 (t) cc_final: 0.9105 (t) REVERT: P 166 ASN cc_start: 0.9236 (t0) cc_final: 0.8694 (t0) REVERT: P 167 ASN cc_start: 0.9389 (m110) cc_final: 0.8754 (m110) REVERT: P 184 MET cc_start: 0.8844 (mmm) cc_final: 0.8517 (mmm) REVERT: P 219 GLU cc_start: 0.8421 (mp0) cc_final: 0.8082 (mp0) REVERT: Q 24 GLU cc_start: 0.8391 (tt0) cc_final: 0.8104 (tm-30) REVERT: Q 55 ASP cc_start: 0.8664 (t0) cc_final: 0.8208 (t0) REVERT: Q 90 GLU cc_start: 0.8511 (tp30) cc_final: 0.8027 (tt0) REVERT: Q 99 GLU cc_start: 0.8258 (mp0) cc_final: 0.8057 (mp0) REVERT: Q 110 TYR cc_start: 0.8934 (t80) cc_final: 0.8733 (t80) REVERT: Q 116 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8302 (tp40) REVERT: Q 148 ASP cc_start: 0.9012 (t0) cc_final: 0.8515 (t0) REVERT: Q 157 LYS cc_start: 0.8903 (mttt) cc_final: 0.8387 (mtmp) REVERT: Q 193 LYS cc_start: 0.9389 (ptmt) cc_final: 0.9107 (ptmm) REVERT: R 32 LYS cc_start: 0.8890 (mttp) cc_final: 0.8626 (mptp) REVERT: R 206 MET cc_start: 0.8072 (mtm) cc_final: 0.7843 (mtm) REVERT: R 227 HIS cc_start: 0.8776 (t-90) cc_final: 0.8419 (t70) REVERT: R 231 LYS cc_start: 0.9287 (mtpm) cc_final: 0.8794 (tttp) REVERT: S 30 LYS cc_start: 0.8802 (mttt) cc_final: 0.8535 (mptt) REVERT: S 31 GLN cc_start: 0.8334 (pp30) cc_final: 0.8105 (pp30) REVERT: S 62 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8937 (mtpp) REVERT: S 90 GLN cc_start: 0.9071 (tp40) cc_final: 0.8219 (mm-40) REVERT: S 94 ASP cc_start: 0.8592 (m-30) cc_final: 0.7874 (m-30) REVERT: S 178 GLU cc_start: 0.9099 (pm20) cc_final: 0.8756 (pm20) REVERT: T 70 ASP cc_start: 0.8575 (t70) cc_final: 0.8323 (t0) REVERT: T 93 GLU cc_start: 0.8131 (pp20) cc_final: 0.7712 (pp20) REVERT: T 97 ASN cc_start: 0.8984 (m110) cc_final: 0.8447 (m-40) REVERT: T 180 GLN cc_start: 0.8774 (tp-100) cc_final: 0.8450 (tp-100) REVERT: T 184 MET cc_start: 0.8664 (mtp) cc_final: 0.8398 (ptp) REVERT: T 192 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8861 (mp0) REVERT: T 236 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8990 (mm-30) REVERT: U 5 SER cc_start: 0.9021 (t) cc_final: 0.8348 (m) REVERT: U 155 ASP cc_start: 0.8408 (p0) cc_final: 0.8104 (p0) REVERT: U 180 GLU cc_start: 0.8544 (pp20) cc_final: 0.8301 (pp20) REVERT: U 187 PHE cc_start: 0.7549 (p90) cc_final: 0.7092 (p90) REVERT: U 189 TRP cc_start: 0.7339 (m-90) cc_final: 0.6947 (m-90) REVERT: U 224 ASN cc_start: 0.9037 (p0) cc_final: 0.8609 (p0) REVERT: U 228 ARG cc_start: 0.8661 (mtm110) cc_final: 0.8319 (mtp-110) REVERT: V 19 ARG cc_start: 0.8935 (ttm170) cc_final: 0.8425 (ttm-80) REVERT: V 30 ASN cc_start: 0.9067 (t0) cc_final: 0.8865 (t0) REVERT: V 150 GLU cc_start: 0.8473 (pm20) cc_final: 0.8143 (pm20) REVERT: V 153 ASN cc_start: 0.8637 (m-40) cc_final: 0.8230 (m110) REVERT: V 157 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8493 (mm-30) REVERT: V 184 ASP cc_start: 0.8799 (t0) cc_final: 0.8460 (t0) REVERT: V 214 GLU cc_start: 0.8863 (tt0) cc_final: 0.8580 (tt0) REVERT: W 74 GLU cc_start: 0.8301 (tp30) cc_final: 0.7859 (tp30) REVERT: W 105 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8651 (mm-30) REVERT: W 143 GLU cc_start: 0.8225 (pm20) cc_final: 0.7991 (pm20) REVERT: W 161 HIS cc_start: 0.8712 (m-70) cc_final: 0.8494 (m170) REVERT: W 164 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8373 (mm-30) REVERT: W 172 ASN cc_start: 0.9379 (m-40) cc_final: 0.9152 (m110) REVERT: X 36 PHE cc_start: 0.9142 (m-80) cc_final: 0.8916 (m-80) REVERT: X 91 CYS cc_start: 0.9010 (m) cc_final: 0.8801 (m) REVERT: X 108 ASP cc_start: 0.8857 (t70) cc_final: 0.8501 (t70) REVERT: X 158 GLU cc_start: 0.8692 (tp30) cc_final: 0.8480 (tp30) REVERT: X 166 GLU cc_start: 0.8731 (tp30) cc_final: 0.8416 (tp30) REVERT: X 186 ASN cc_start: 0.9304 (m-40) cc_final: 0.9009 (m-40) REVERT: Y 26 ILE cc_start: 0.9275 (mt) cc_final: 0.8920 (mp) REVERT: Y 62 GLN cc_start: 0.9422 (mm-40) cc_final: 0.9222 (mm-40) REVERT: Y 67 GLU cc_start: 0.8923 (tt0) cc_final: 0.8606 (tm-30) REVERT: Y 70 ASN cc_start: 0.9501 (m-40) cc_final: 0.9140 (m110) REVERT: Y 81 LYS cc_start: 0.9400 (tptt) cc_final: 0.9071 (tptm) REVERT: Z 159 GLN cc_start: 0.8537 (tp40) cc_final: 0.8241 (mt0) REVERT: a 5 MET cc_start: 0.8604 (mmm) cc_final: 0.8156 (tpt) REVERT: a 25 ASP cc_start: 0.8937 (p0) cc_final: 0.8564 (p0) REVERT: a 59 ASP cc_start: 0.9368 (m-30) cc_final: 0.9116 (m-30) REVERT: a 133 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8474 (mt-10) REVERT: a 180 ASP cc_start: 0.8990 (t0) cc_final: 0.8685 (t0) REVERT: b 7 GLN cc_start: 0.8978 (tt0) cc_final: 0.8592 (tt0) REVERT: b 69 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8333 (mt-10) REVERT: b 151 GLU cc_start: 0.8928 (pt0) cc_final: 0.8693 (pt0) outliers start: 127 outliers final: 51 residues processed: 1115 average time/residue: 0.5125 time to fit residues: 704.1520 Evaluate side-chains 1054 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 990 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 43 MET Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 30 HIS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 62 LYS Chi-restraints excluded: chain T residue 192 GLU Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 161 CYS Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 148 MET Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 62 LYS Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain b residue 190 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 487 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 519 optimal weight: 0.9980 chunk 310 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 540 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 453 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 481 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 118 GLN C 23 GLN C 175 ASN D 118 ASN H 57 GLN H 153 ASN H 165 ASN I 168 GLN J 55 GLN J 193 ASN K 175 ASN L 108 ASN L 157 ASN N 154 GLN O 95 GLN O 139 ASN S 65 HIS T 101 ASN U 68 HIS V 57 GLN W 32 GLN W 60 GLN W 156 ASN X 27 GLN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN Y 162 GLN Z 108 ASN Z 146 GLN Z 157 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.078913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.064232 restraints weight = 97344.455| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.74 r_work: 0.2804 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 47220 Z= 0.142 Angle : 0.559 8.162 64063 Z= 0.299 Chirality : 0.042 0.225 7447 Planarity : 0.004 0.050 8164 Dihedral : 4.301 25.089 6847 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.89 % Allowed : 19.80 % Favored : 77.31 % 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: 0.99 (0.11), residues: 6188 helix: 1.97 (0.10), residues: 2342 sheet: 0.14 (0.13), residues: 1497 loop : -0.26 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 59 TYR 0.034 0.001 TYR G 160 PHE 0.018 0.001 PHE G 210 TRP 0.018 0.001 TRP Y 184 HIS 0.005 0.001 HIS a 89 Details of bonding type rmsd covalent geometry : bond 0.00321 (47220) covalent geometry : angle 0.55943 (64063) hydrogen bonds : bond 0.03492 ( 2773) hydrogen bonds : angle 4.55764 ( 8061) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1038 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8924 (pm20) cc_final: 0.8456 (pm20) REVERT: A 78 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8556 (mtp) REVERT: A 101 GLN cc_start: 0.9292 (mm-40) cc_final: 0.9054 (mm110) REVERT: A 147 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8497 (tm-30) REVERT: A 158 LYS cc_start: 0.8904 (mttm) cc_final: 0.8499 (mttp) REVERT: A 195 LYS cc_start: 0.9606 (ttpp) cc_final: 0.9386 (ttmm) REVERT: B 174 MET cc_start: 0.8894 (mtp) cc_final: 0.8487 (ttp) REVERT: C 28 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8828 (mtmm) REVERT: C 54 GLN cc_start: 0.9079 (tp40) cc_final: 0.8842 (tp40) REVERT: C 55 ASP cc_start: 0.8625 (t0) cc_final: 0.8077 (t0) REVERT: C 61 LYS cc_start: 0.8585 (mttm) cc_final: 0.8094 (mtpt) REVERT: C 66 ASP cc_start: 0.9043 (t0) cc_final: 0.8521 (t0) REVERT: C 67 ASP cc_start: 0.8673 (m-30) cc_final: 0.8456 (m-30) REVERT: C 99 GLU cc_start: 0.8704 (mp0) cc_final: 0.8284 (mp0) REVERT: C 116 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8579 (tp40) REVERT: D 32 LYS cc_start: 0.9098 (mttt) cc_final: 0.8811 (mttp) REVERT: D 91 LYS cc_start: 0.9271 (tptp) cc_final: 0.8871 (tppt) REVERT: D 95 GLU cc_start: 0.8905 (tp30) cc_final: 0.8524 (tp30) REVERT: D 178 GLN cc_start: 0.8552 (tp40) cc_final: 0.8182 (mm110) REVERT: D 182 GLN cc_start: 0.8968 (mt0) cc_final: 0.8713 (mt0) REVERT: D 196 LYS cc_start: 0.9305 (mmmm) cc_final: 0.9057 (mtmm) REVERT: E 27 GLU cc_start: 0.8888 (tp30) cc_final: 0.8292 (tm-30) REVERT: E 67 ASP cc_start: 0.9115 (t70) cc_final: 0.8707 (t0) REVERT: E 90 GLN cc_start: 0.9041 (tp40) cc_final: 0.8701 (mm-40) REVERT: E 94 ASP cc_start: 0.8706 (m-30) cc_final: 0.8450 (m-30) REVERT: E 100 ASP cc_start: 0.8720 (t0) cc_final: 0.8375 (t0) REVERT: E 178 GLU cc_start: 0.8809 (pm20) cc_final: 0.8395 (pm20) REVERT: E 180 MET cc_start: 0.8924 (mmm) cc_final: 0.8640 (tpt) REVERT: E 189 LYS cc_start: 0.9513 (mttp) cc_final: 0.9201 (mttp) REVERT: E 197 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8837 (mm-30) REVERT: F 50 GLU cc_start: 0.7990 (tt0) cc_final: 0.7509 (tm-30) REVERT: F 70 ASP cc_start: 0.8879 (t0) cc_final: 0.8379 (t0) REVERT: F 147 GLN cc_start: 0.8838 (mt0) cc_final: 0.8199 (mt0) REVERT: F 179 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8512 (tm) REVERT: G 10 ASP cc_start: 0.8907 (p0) cc_final: 0.8615 (p0) REVERT: G 11 ARG cc_start: 0.8596 (mtt90) cc_final: 0.7805 (mtt90) REVERT: G 56 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8216 (t) REVERT: G 80 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8656 (mmm) REVERT: G 83 MET cc_start: 0.9330 (mtm) cc_final: 0.9121 (mtm) REVERT: G 88 ARG cc_start: 0.8404 (mmm160) cc_final: 0.7964 (mmm-85) REVERT: G 97 GLU cc_start: 0.9071 (tp30) cc_final: 0.8756 (mm-30) REVERT: G 112 ASP cc_start: 0.9075 (p0) cc_final: 0.8567 (p0) REVERT: G 116 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8377 (ttmm) REVERT: G 117 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8422 (mmm-85) REVERT: G 120 ASP cc_start: 0.8555 (m-30) cc_final: 0.8244 (m-30) REVERT: H 30 ASN cc_start: 0.8974 (t0) cc_final: 0.8330 (t0) REVERT: I 105 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8733 (mp0) REVERT: I 112 ASP cc_start: 0.8886 (t70) cc_final: 0.8654 (t0) REVERT: I 164 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: I 175 ASP cc_start: 0.8849 (m-30) cc_final: 0.8412 (m-30) REVERT: J 108 ASP cc_start: 0.8502 (t70) cc_final: 0.8225 (t70) REVERT: J 155 ARG cc_start: 0.8380 (mtm-85) cc_final: 0.8093 (mpp-170) REVERT: J 184 ASP cc_start: 0.8788 (p0) cc_final: 0.8570 (p0) REVERT: K 36 GLU cc_start: 0.8424 (mp0) cc_final: 0.8076 (mt-10) REVERT: K 56 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.8913 (mp0) REVERT: K 72 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8122 (tm-30) REVERT: K 99 THR cc_start: 0.9069 (p) cc_final: 0.8687 (m) REVERT: L 47 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8987 (p) REVERT: L 48 ASP cc_start: 0.8578 (p0) cc_final: 0.8170 (t0) REVERT: L 131 GLN cc_start: 0.8726 (pt0) cc_final: 0.8456 (pt0) REVERT: L 177 ASP cc_start: 0.8696 (m-30) cc_final: 0.8324 (m-30) REVERT: L 186 ASP cc_start: 0.8706 (t0) cc_final: 0.8356 (t0) REVERT: L 188 TYR cc_start: 0.9343 (m-80) cc_final: 0.8882 (m-80) REVERT: L 205 GLU cc_start: 0.8311 (mp0) cc_final: 0.7919 (mp0) REVERT: L 206 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7778 (mm-30) REVERT: M 26 MET cc_start: 0.9072 (mtp) cc_final: 0.8731 (mtm) REVERT: M 47 ASN cc_start: 0.9041 (t0) cc_final: 0.8613 (t0) REVERT: M 56 ASP cc_start: 0.8999 (t0) cc_final: 0.8590 (t0) REVERT: M 79 ASP cc_start: 0.8422 (p0) cc_final: 0.8029 (p0) REVERT: M 104 ASN cc_start: 0.9176 (t0) cc_final: 0.8612 (t0) REVERT: M 170 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8181 (mp0) REVERT: M 180 ASP cc_start: 0.8984 (t70) cc_final: 0.8506 (t0) REVERT: M 200 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8115 (mt-10) REVERT: M 210 ASP cc_start: 0.8843 (p0) cc_final: 0.8578 (OUTLIER) REVERT: N 40 ARG cc_start: 0.8660 (mpt180) cc_final: 0.8422 (mpt-90) REVERT: N 71 ASN cc_start: 0.9222 (t0) cc_final: 0.9018 (t0) REVERT: N 107 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: N 165 GLU cc_start: 0.8692 (tt0) cc_final: 0.8471 (tm-30) REVERT: N 167 ASP cc_start: 0.8494 (t0) cc_final: 0.8152 (t0) REVERT: N 193 GLN cc_start: 0.8964 (mt0) cc_final: 0.8670 (mt0) REVERT: O 48 GLU cc_start: 0.8223 (pp20) cc_final: 0.7748 (pp20) REVERT: O 57 ASP cc_start: 0.8208 (t0) cc_final: 0.7645 (t0) REVERT: O 58 GLU cc_start: 0.8568 (pm20) cc_final: 0.8186 (pm20) REVERT: O 108 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8825 (mm110) REVERT: O 111 GLN cc_start: 0.9008 (mt0) cc_final: 0.8793 (mt0) REVERT: O 118 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8852 (tp40) REVERT: O 120 TYR cc_start: 0.8870 (m-80) cc_final: 0.8571 (m-80) REVERT: O 142 ARG cc_start: 0.8647 (ttt-90) cc_final: 0.8080 (ttt-90) REVERT: P 22 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: P 48 GLU cc_start: 0.8463 (tt0) cc_final: 0.7677 (tm-30) REVERT: P 57 ASP cc_start: 0.8670 (t70) cc_final: 0.8335 (t0) REVERT: P 75 SER cc_start: 0.9341 (t) cc_final: 0.9101 (t) REVERT: P 166 ASN cc_start: 0.9201 (t0) cc_final: 0.8663 (t0) REVERT: P 167 ASN cc_start: 0.9379 (m110) cc_final: 0.8762 (m110) REVERT: P 184 MET cc_start: 0.8862 (mmm) cc_final: 0.8571 (mmm) REVERT: Q 24 GLU cc_start: 0.8441 (tt0) cc_final: 0.8075 (tm-30) REVERT: Q 55 ASP cc_start: 0.8616 (t0) cc_final: 0.8224 (t0) REVERT: Q 90 GLU cc_start: 0.8455 (tp30) cc_final: 0.7997 (tt0) REVERT: Q 110 TYR cc_start: 0.8948 (t80) cc_final: 0.8735 (t80) REVERT: Q 116 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8267 (tp40) REVERT: Q 148 ASP cc_start: 0.9051 (t0) cc_final: 0.8650 (t0) REVERT: Q 157 LYS cc_start: 0.8928 (mttt) cc_final: 0.8403 (mtmp) REVERT: Q 193 LYS cc_start: 0.9386 (ptmt) cc_final: 0.9141 (ptmm) REVERT: Q 224 GLU cc_start: 0.8991 (tt0) cc_final: 0.8389 (tp30) REVERT: R 32 LYS cc_start: 0.8767 (mttp) cc_final: 0.8512 (mptp) REVERT: R 52 LYS cc_start: 0.8780 (mttt) cc_final: 0.8528 (mttp) REVERT: R 206 MET cc_start: 0.8041 (mtm) cc_final: 0.7817 (mtm) REVERT: R 227 HIS cc_start: 0.8813 (t-90) cc_final: 0.8448 (t70) REVERT: R 231 LYS cc_start: 0.9286 (mtpm) cc_final: 0.8871 (tttp) REVERT: S 26 MET cc_start: 0.8719 (mtp) cc_final: 0.8507 (mtp) REVERT: S 30 LYS cc_start: 0.8766 (mttt) cc_final: 0.8497 (mptt) REVERT: S 31 GLN cc_start: 0.8352 (pp30) cc_final: 0.8111 (pp30) REVERT: S 61 LYS cc_start: 0.9068 (pmtt) cc_final: 0.8856 (pttm) REVERT: S 90 GLN cc_start: 0.9066 (tp40) cc_final: 0.8256 (mm-40) REVERT: S 94 ASP cc_start: 0.8615 (m-30) cc_final: 0.7912 (m-30) REVERT: S 178 GLU cc_start: 0.9151 (pm20) cc_final: 0.8715 (pm20) REVERT: T 70 ASP cc_start: 0.8662 (t70) cc_final: 0.8397 (t0) REVERT: T 93 GLU cc_start: 0.8154 (pp20) cc_final: 0.7775 (pp20) REVERT: T 97 ASN cc_start: 0.8998 (m110) cc_final: 0.8438 (m-40) REVERT: T 184 MET cc_start: 0.8651 (mtp) cc_final: 0.8405 (ptm) REVERT: T 192 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8856 (mp0) REVERT: U 5 SER cc_start: 0.8965 (t) cc_final: 0.8282 (m) REVERT: U 155 ASP cc_start: 0.8460 (p0) cc_final: 0.8141 (p0) REVERT: U 187 PHE cc_start: 0.7578 (p90) cc_final: 0.7074 (p90) REVERT: U 189 TRP cc_start: 0.7314 (m-90) cc_final: 0.6965 (m-90) REVERT: U 224 ASN cc_start: 0.9051 (p0) cc_final: 0.8658 (p0) REVERT: U 228 ARG cc_start: 0.8591 (mtm110) cc_final: 0.8312 (mtp-110) REVERT: V 19 ARG cc_start: 0.8914 (ttm170) cc_final: 0.8387 (tmm-80) REVERT: V 30 ASN cc_start: 0.9075 (t0) cc_final: 0.8836 (t0) REVERT: V 150 GLU cc_start: 0.8509 (pm20) cc_final: 0.8217 (pm20) REVERT: V 153 ASN cc_start: 0.8690 (m-40) cc_final: 0.8472 (m110) REVERT: V 184 ASP cc_start: 0.8795 (t0) cc_final: 0.8470 (t0) REVERT: V 214 GLU cc_start: 0.8845 (tt0) cc_final: 0.8547 (tt0) REVERT: W 105 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8649 (mm-30) REVERT: W 150 GLU cc_start: 0.8971 (tp30) cc_final: 0.8664 (mm-30) REVERT: W 161 HIS cc_start: 0.8715 (m-70) cc_final: 0.8499 (m170) REVERT: W 164 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8354 (mm-30) REVERT: W 172 ASN cc_start: 0.9376 (m-40) cc_final: 0.9172 (m110) REVERT: X 36 PHE cc_start: 0.9097 (m-80) cc_final: 0.8861 (m-80) REVERT: X 68 LYS cc_start: 0.9529 (OUTLIER) cc_final: 0.8821 (tppt) REVERT: X 87 ASN cc_start: 0.9046 (m-40) cc_final: 0.8763 (m-40) REVERT: X 108 ASP cc_start: 0.8850 (t70) cc_final: 0.8487 (t70) REVERT: X 118 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8036 (mtp) REVERT: X 158 GLU cc_start: 0.8660 (tp30) cc_final: 0.8453 (tp30) REVERT: X 166 GLU cc_start: 0.8751 (tp30) cc_final: 0.8441 (tp30) REVERT: X 169 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8835 (ptmm) REVERT: X 186 ASN cc_start: 0.9316 (m-40) cc_final: 0.9021 (m-40) REVERT: Y 26 ILE cc_start: 0.9241 (mt) cc_final: 0.8854 (mp) REVERT: Y 34 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8800 (t) REVERT: Y 67 GLU cc_start: 0.8883 (tt0) cc_final: 0.8606 (tm-30) REVERT: Y 70 ASN cc_start: 0.9499 (m-40) cc_final: 0.9137 (m110) REVERT: Y 81 LYS cc_start: 0.9415 (tptt) cc_final: 0.9060 (tptm) REVERT: Z 159 GLN cc_start: 0.8519 (tp40) cc_final: 0.8231 (mt0) REVERT: a 5 MET cc_start: 0.8562 (mmm) cc_final: 0.8109 (tpt) REVERT: a 25 ASP cc_start: 0.8955 (p0) cc_final: 0.8580 (p0) REVERT: a 133 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8436 (mt-10) REVERT: a 164 GLU cc_start: 0.8748 (pt0) cc_final: 0.8340 (pm20) REVERT: a 180 ASP cc_start: 0.8977 (t0) cc_final: 0.8670 (t0) REVERT: a 200 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: b 7 GLN cc_start: 0.8980 (tt0) cc_final: 0.8608 (tt0) REVERT: b 69 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8345 (mt-10) REVERT: b 104 ASP cc_start: 0.8212 (p0) cc_final: 0.7988 (p0) REVERT: b 151 GLU cc_start: 0.8941 (pt0) cc_final: 0.8666 (pt0) outliers start: 130 outliers final: 57 residues processed: 1100 average time/residue: 0.5157 time to fit residues: 698.4998 Evaluate side-chains 1057 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 984 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain J residue 34 LYS Chi-restraints excluded: chain J residue 39 SER Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 43 MET Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 225 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain T residue 192 GLU Chi-restraints excluded: chain T residue 221 ASN Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 161 CYS Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 117 LYS Chi-restraints excluded: chain W residue 148 MET Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 62 LYS Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Y residue 34 VAL Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain a residue 169 VAL Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 190 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 132 optimal weight: 0.9990 chunk 541 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 309 optimal weight: 0.7980 chunk 145 optimal weight: 0.1980 chunk 401 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 409 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN C 23 GLN D 118 ASN E 65 HIS F 63 ASN F 97 ASN F 180 GLN H 153 ASN I 168 GLN J 55 GLN K 175 ASN L 108 ASN L 131 GLN L 157 ASN L 159 GLN O 139 ASN Q 54 GLN S 65 HIS T 101 ASN T 120 HIS V 57 GLN V 80 ASN W 32 GLN W 60 GLN X 27 GLN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN Z 108 ASN Z 146 GLN Z 157 ASN a 61 GLN b 110 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.079766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.064913 restraints weight = 96912.290| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.77 r_work: 0.2822 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 47220 Z= 0.126 Angle : 0.576 13.779 64063 Z= 0.306 Chirality : 0.042 0.287 7447 Planarity : 0.004 0.051 8164 Dihedral : 4.250 25.938 6847 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.80 % Allowed : 21.03 % Favored : 76.17 % 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: 1.05 (0.11), residues: 6188 helix: 2.05 (0.11), residues: 2327 sheet: 0.14 (0.13), residues: 1517 loop : -0.23 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG U 21 TYR 0.030 0.001 TYR U 160 PHE 0.022 0.001 PHE U 210 TRP 0.015 0.001 TRP P 159 HIS 0.009 0.001 HIS F 201 Details of bonding type rmsd covalent geometry : bond 0.00282 (47220) covalent geometry : angle 0.57608 (64063) hydrogen bonds : bond 0.03371 ( 2773) hydrogen bonds : angle 4.49727 ( 8061) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1015 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9050 (mtmm) cc_final: 0.8680 (mmtp) REVERT: A 48 GLU cc_start: 0.8894 (pm20) cc_final: 0.8483 (pm20) REVERT: A 78 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8567 (mtp) REVERT: A 147 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 158 LYS cc_start: 0.8904 (mttm) cc_final: 0.8505 (mttp) REVERT: A 176 ARG cc_start: 0.8698 (tpp-160) cc_final: 0.8240 (ttm110) REVERT: A 195 LYS cc_start: 0.9598 (ttpp) cc_final: 0.9388 (ttmm) REVERT: A 208 GLU cc_start: 0.8449 (tt0) cc_final: 0.8242 (tt0) REVERT: B 26 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7585 (pp20) REVERT: B 67 LYS cc_start: 0.9268 (ttmt) cc_final: 0.8726 (tttm) REVERT: B 174 MET cc_start: 0.8892 (mtp) cc_final: 0.8535 (ttp) REVERT: B 232 GLU cc_start: 0.8454 (pm20) cc_final: 0.8183 (pm20) REVERT: C 28 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8848 (mtmm) REVERT: C 54 GLN cc_start: 0.9052 (tp40) cc_final: 0.8838 (tp40) REVERT: C 55 ASP cc_start: 0.8604 (t0) cc_final: 0.8321 (t0) REVERT: C 61 LYS cc_start: 0.8605 (mttm) cc_final: 0.8147 (mtmt) REVERT: C 66 ASP cc_start: 0.9044 (t0) cc_final: 0.8515 (t0) REVERT: C 67 ASP cc_start: 0.8738 (m-30) cc_final: 0.8506 (m-30) REVERT: C 99 GLU cc_start: 0.8768 (mp0) cc_final: 0.8225 (mp0) REVERT: C 116 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8564 (tp40) REVERT: C 120 GLN cc_start: 0.9109 (tp40) cc_final: 0.8032 (tp40) REVERT: C 175 ASN cc_start: 0.8544 (p0) cc_final: 0.8314 (p0) REVERT: D 32 LYS cc_start: 0.9104 (mttt) cc_final: 0.8836 (mttp) REVERT: D 91 LYS cc_start: 0.9293 (tptp) cc_final: 0.8788 (tppt) REVERT: D 95 GLU cc_start: 0.8937 (tp30) cc_final: 0.8489 (tp30) REVERT: E 27 GLU cc_start: 0.8861 (tp30) cc_final: 0.8300 (tm-30) REVERT: E 67 ASP cc_start: 0.9157 (t70) cc_final: 0.8693 (t0) REVERT: E 90 GLN cc_start: 0.9046 (tp40) cc_final: 0.8729 (mm-40) REVERT: E 94 ASP cc_start: 0.8713 (m-30) cc_final: 0.8467 (m-30) REVERT: E 100 ASP cc_start: 0.8705 (t0) cc_final: 0.8365 (t0) REVERT: E 178 GLU cc_start: 0.8801 (pm20) cc_final: 0.8352 (pm20) REVERT: E 180 MET cc_start: 0.9064 (mmm) cc_final: 0.8775 (tpt) REVERT: E 189 LYS cc_start: 0.9524 (mttp) cc_final: 0.9233 (mttp) REVERT: E 197 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8813 (mm-30) REVERT: F 50 GLU cc_start: 0.8114 (tt0) cc_final: 0.7795 (tm-30) REVERT: F 70 ASP cc_start: 0.8854 (t0) cc_final: 0.8374 (t0) REVERT: F 147 GLN cc_start: 0.8832 (mt0) cc_final: 0.8217 (mt0) REVERT: G 10 ASP cc_start: 0.8906 (p0) cc_final: 0.8609 (p0) REVERT: G 11 ARG cc_start: 0.8596 (mtt90) cc_final: 0.7783 (mtt90) REVERT: G 56 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8175 (t) REVERT: G 80 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8762 (mmm) REVERT: G 83 MET cc_start: 0.9304 (mtm) cc_final: 0.9058 (mtm) REVERT: G 112 ASP cc_start: 0.9033 (p0) cc_final: 0.8611 (p0) REVERT: G 116 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8330 (ttmm) REVERT: G 120 ASP cc_start: 0.8585 (m-30) cc_final: 0.8250 (m-30) REVERT: H 30 ASN cc_start: 0.8996 (t0) cc_final: 0.8386 (t0) REVERT: H 104 ASP cc_start: 0.8705 (p0) cc_final: 0.8489 (p0) REVERT: I 65 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8094 (mtt-85) REVERT: I 105 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8731 (mp0) REVERT: I 112 ASP cc_start: 0.8860 (t70) cc_final: 0.8642 (t0) REVERT: I 164 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8247 (mt-10) REVERT: I 175 ASP cc_start: 0.8844 (m-30) cc_final: 0.8392 (m-30) REVERT: J 108 ASP cc_start: 0.8628 (t70) cc_final: 0.8291 (t70) REVERT: J 184 ASP cc_start: 0.8798 (p0) cc_final: 0.8567 (p0) REVERT: K 36 GLU cc_start: 0.8437 (mp0) cc_final: 0.8069 (mt-10) REVERT: K 56 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8935 (mp0) REVERT: K 72 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8123 (tm-30) REVERT: K 81 LYS cc_start: 0.8928 (tttp) cc_final: 0.8603 (mtpp) REVERT: K 99 THR cc_start: 0.9024 (p) cc_final: 0.8739 (m) REVERT: K 106 LYS cc_start: 0.9268 (mmmm) cc_final: 0.8988 (mmpt) REVERT: L 48 ASP cc_start: 0.8584 (p0) cc_final: 0.8151 (t0) REVERT: L 131 GLN cc_start: 0.8761 (pt0) cc_final: 0.8504 (pt0) REVERT: L 177 ASP cc_start: 0.8722 (m-30) cc_final: 0.8312 (m-30) REVERT: L 186 ASP cc_start: 0.8684 (t0) cc_final: 0.8350 (t0) REVERT: L 188 TYR cc_start: 0.9316 (m-80) cc_final: 0.8852 (m-80) REVERT: L 205 GLU cc_start: 0.8307 (mp0) cc_final: 0.7895 (mp0) REVERT: L 206 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7732 (mm-30) REVERT: M 26 MET cc_start: 0.9039 (mtp) cc_final: 0.8751 (mtm) REVERT: M 47 ASN cc_start: 0.9052 (t0) cc_final: 0.8632 (t0) REVERT: M 56 ASP cc_start: 0.9033 (t0) cc_final: 0.8635 (t0) REVERT: M 64 LYS cc_start: 0.9331 (ttmp) cc_final: 0.8904 (ttmm) REVERT: M 77 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8677 (pp) REVERT: M 79 ASP cc_start: 0.8354 (p0) cc_final: 0.7980 (p0) REVERT: M 104 ASN cc_start: 0.9150 (t0) cc_final: 0.8588 (t0) REVERT: M 170 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8286 (mp0) REVERT: M 180 ASP cc_start: 0.8945 (t70) cc_final: 0.8495 (t0) REVERT: M 200 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8100 (mt-10) REVERT: M 210 ASP cc_start: 0.8831 (p0) cc_final: 0.8575 (OUTLIER) REVERT: N 69 GLU cc_start: 0.8158 (pt0) cc_final: 0.7942 (pt0) REVERT: N 71 ASN cc_start: 0.9240 (t0) cc_final: 0.9028 (t0) REVERT: N 107 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: N 165 GLU cc_start: 0.8737 (tt0) cc_final: 0.8496 (tm-30) REVERT: N 167 ASP cc_start: 0.8506 (t0) cc_final: 0.8164 (t0) REVERT: N 193 GLN cc_start: 0.8960 (mt0) cc_final: 0.8656 (mt0) REVERT: O 48 GLU cc_start: 0.8236 (pp20) cc_final: 0.7764 (pp20) REVERT: O 57 ASP cc_start: 0.8213 (t0) cc_final: 0.7714 (t0) REVERT: O 120 TYR cc_start: 0.8765 (m-80) cc_final: 0.8518 (m-80) REVERT: O 142 ARG cc_start: 0.8657 (ttt-90) cc_final: 0.8088 (ttt-90) REVERT: O 208 GLU cc_start: 0.8131 (pt0) cc_final: 0.7861 (pt0) REVERT: P 22 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: P 34 CYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8546 (t) REVERT: P 48 GLU cc_start: 0.8443 (tt0) cc_final: 0.7627 (tm-30) REVERT: P 57 ASP cc_start: 0.8654 (t70) cc_final: 0.8333 (t0) REVERT: P 75 SER cc_start: 0.9380 (t) cc_final: 0.9057 (t) REVERT: P 166 ASN cc_start: 0.9256 (t0) cc_final: 0.8717 (t0) REVERT: P 167 ASN cc_start: 0.9374 (m110) cc_final: 0.8755 (m110) REVERT: Q 20 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8195 (mp0) REVERT: Q 24 GLU cc_start: 0.8442 (tt0) cc_final: 0.8146 (tm-30) REVERT: Q 55 ASP cc_start: 0.8608 (t0) cc_final: 0.8159 (t0) REVERT: Q 90 GLU cc_start: 0.8462 (tp30) cc_final: 0.7991 (tt0) REVERT: Q 116 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8415 (tp40) REVERT: Q 120 GLN cc_start: 0.8880 (tt0) cc_final: 0.8522 (tp40) REVERT: Q 148 ASP cc_start: 0.9067 (t0) cc_final: 0.8635 (t0) REVERT: Q 157 LYS cc_start: 0.8935 (mttt) cc_final: 0.8414 (mtmp) REVERT: Q 193 LYS cc_start: 0.9379 (ptmt) cc_final: 0.9173 (ptmm) REVERT: Q 224 GLU cc_start: 0.8989 (tt0) cc_final: 0.8403 (tp30) REVERT: R 32 LYS cc_start: 0.8773 (mttp) cc_final: 0.8514 (mptp) REVERT: R 52 LYS cc_start: 0.8790 (mttt) cc_final: 0.8559 (mttp) REVERT: R 206 MET cc_start: 0.7939 (mtm) cc_final: 0.7691 (mtm) REVERT: R 227 HIS cc_start: 0.8807 (t-90) cc_final: 0.8484 (t70) REVERT: R 231 LYS cc_start: 0.9279 (mtpm) cc_final: 0.8968 (tttm) REVERT: S 30 LYS cc_start: 0.8738 (mttt) cc_final: 0.8484 (mptt) REVERT: S 31 GLN cc_start: 0.8393 (pp30) cc_final: 0.8165 (pp30) REVERT: S 62 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8883 (mtpp) REVERT: S 90 GLN cc_start: 0.9085 (tp40) cc_final: 0.8323 (mm-40) REVERT: S 94 ASP cc_start: 0.8610 (m-30) cc_final: 0.7925 (m-30) REVERT: S 178 GLU cc_start: 0.9143 (pm20) cc_final: 0.8767 (pm20) REVERT: T 59 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8474 (mp0) REVERT: T 70 ASP cc_start: 0.8635 (t70) cc_final: 0.8375 (t0) REVERT: T 93 GLU cc_start: 0.8177 (pp20) cc_final: 0.7781 (pp20) REVERT: T 97 ASN cc_start: 0.9018 (m110) cc_final: 0.8443 (m-40) REVERT: T 184 MET cc_start: 0.8646 (mtp) cc_final: 0.8418 (ptm) REVERT: T 192 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8830 (mp0) REVERT: T 236 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8993 (mm-30) REVERT: U 5 SER cc_start: 0.8946 (t) cc_final: 0.8284 (m) REVERT: U 80 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8557 (mmm) REVERT: U 155 ASP cc_start: 0.8419 (p0) cc_final: 0.8105 (p0) REVERT: U 187 PHE cc_start: 0.7669 (p90) cc_final: 0.7176 (p90) REVERT: U 189 TRP cc_start: 0.7264 (m-90) cc_final: 0.6952 (m-90) REVERT: U 210 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8545 (m-80) REVERT: U 224 ASN cc_start: 0.9051 (p0) cc_final: 0.8652 (p0) REVERT: U 228 ARG cc_start: 0.8591 (mtm110) cc_final: 0.8330 (mtp-110) REVERT: V 19 ARG cc_start: 0.8871 (ttm170) cc_final: 0.8336 (tmm-80) REVERT: V 30 ASN cc_start: 0.9068 (t0) cc_final: 0.8822 (t0) REVERT: V 51 ASP cc_start: 0.8870 (m-30) cc_final: 0.8570 (m-30) REVERT: V 81 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.8873 (tpp-160) REVERT: V 85 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8540 (mt0) REVERT: V 150 GLU cc_start: 0.8477 (pm20) cc_final: 0.8188 (pm20) REVERT: V 153 ASN cc_start: 0.8610 (m-40) cc_final: 0.8291 (m110) REVERT: V 157 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8316 (mm-30) REVERT: V 184 ASP cc_start: 0.8779 (t0) cc_final: 0.8455 (t0) REVERT: V 214 GLU cc_start: 0.8820 (tt0) cc_final: 0.8522 (tt0) REVERT: W 105 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8648 (mm-30) REVERT: W 150 GLU cc_start: 0.8994 (tp30) cc_final: 0.8601 (mm-30) REVERT: W 161 HIS cc_start: 0.8705 (m-70) cc_final: 0.8497 (m170) REVERT: W 164 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8361 (mm-30) REVERT: W 172 ASN cc_start: 0.9323 (m-40) cc_final: 0.9086 (m110) REVERT: X 36 PHE cc_start: 0.9059 (m-80) cc_final: 0.8847 (m-80) REVERT: X 68 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.8880 (tppt) REVERT: X 108 ASP cc_start: 0.8831 (t70) cc_final: 0.8461 (t70) REVERT: X 118 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7971 (mtp) REVERT: X 158 GLU cc_start: 0.8676 (tp30) cc_final: 0.8468 (tp30) REVERT: X 166 GLU cc_start: 0.8732 (tp30) cc_final: 0.8423 (tp30) REVERT: X 186 ASN cc_start: 0.9333 (m-40) cc_final: 0.9076 (m-40) REVERT: Y 26 ILE cc_start: 0.9230 (mt) cc_final: 0.8841 (mp) REVERT: Y 62 GLN cc_start: 0.9417 (mm-40) cc_final: 0.9127 (mm110) REVERT: Y 67 GLU cc_start: 0.8917 (tt0) cc_final: 0.8560 (tm-30) REVERT: Y 70 ASN cc_start: 0.9497 (m-40) cc_final: 0.9132 (m110) REVERT: Z 157 ASN cc_start: 0.8883 (m-40) cc_final: 0.8582 (m-40) REVERT: Z 159 GLN cc_start: 0.8518 (tp40) cc_final: 0.8266 (mt0) REVERT: a 5 MET cc_start: 0.8550 (mmm) cc_final: 0.7954 (tpt) REVERT: a 25 ASP cc_start: 0.8945 (p0) cc_final: 0.8585 (p0) REVERT: a 133 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8456 (mt-10) REVERT: a 180 ASP cc_start: 0.8964 (t0) cc_final: 0.8617 (t0) REVERT: a 200 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: b 7 GLN cc_start: 0.8977 (tt0) cc_final: 0.8638 (tt0) REVERT: b 106 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: b 151 GLU cc_start: 0.8962 (pt0) cc_final: 0.8675 (pt0) outliers start: 126 outliers final: 50 residues processed: 1072 average time/residue: 0.4848 time to fit residues: 641.6845 Evaluate side-chains 1050 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 980 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 161 CYS Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 62 LYS Chi-restraints excluded: chain T residue 192 GLU Chi-restraints excluded: chain T residue 221 ASN Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 80 MET Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 210 PHE Chi-restraints excluded: chain V residue 81 ARG Chi-restraints excluded: chain V residue 85 GLN Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 117 LYS Chi-restraints excluded: chain W residue 148 MET Chi-restraints excluded: chain W residue 196 THR Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 41 LYS Chi-restraints excluded: chain X residue 62 LYS Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain Y residue 97 MET Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain a residue 169 VAL Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 106 GLN Chi-restraints excluded: chain b residue 190 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 420 optimal weight: 0.9980 chunk 549 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 533 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 298 optimal weight: 4.9990 chunk 446 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN C 23 GLN D 118 ASN E 65 HIS F 180 GLN H 153 ASN I 168 GLN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN K 175 ASN L 108 ASN L 159 GLN M 61 GLN N 154 GLN O 139 ASN S 65 HIS T 63 ASN T 68 ASN V 57 GLN V 80 ASN W 32 GLN W 60 GLN W 80 GLN W 156 ASN X 27 GLN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN Z 108 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.076258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.061161 restraints weight = 98969.973| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.79 r_work: 0.2733 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 47220 Z= 0.302 Angle : 0.676 12.825 64063 Z= 0.357 Chirality : 0.045 0.325 7447 Planarity : 0.004 0.051 8164 Dihedral : 4.508 27.432 6847 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.87 % Allowed : 21.38 % Favored : 75.75 % 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: 0.83 (0.11), residues: 6188 helix: 1.82 (0.10), residues: 2365 sheet: -0.03 (0.13), residues: 1530 loop : -0.28 (0.13), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 117 TYR 0.043 0.002 TYR C 110 PHE 0.020 0.002 PHE U 210 TRP 0.068 0.002 TRP Y 184 HIS 0.010 0.001 HIS F 201 Details of bonding type rmsd covalent geometry : bond 0.00683 (47220) covalent geometry : angle 0.67630 (64063) hydrogen bonds : bond 0.04078 ( 2773) hydrogen bonds : angle 4.72944 ( 8061) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 976 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8943 (pm20) cc_final: 0.8397 (pm20) REVERT: A 78 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8702 (mtp) REVERT: A 147 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8502 (tm-30) REVERT: A 176 ARG cc_start: 0.8754 (tpp-160) cc_final: 0.8258 (ttm110) REVERT: B 72 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8250 (mtm) REVERT: B 114 LEU cc_start: 0.9414 (tp) cc_final: 0.9099 (mp) REVERT: B 174 MET cc_start: 0.8908 (mtp) cc_final: 0.8537 (ttp) REVERT: C 28 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8878 (mtmm) REVERT: C 54 GLN cc_start: 0.9080 (tp40) cc_final: 0.8790 (tp40) REVERT: C 55 ASP cc_start: 0.8835 (t0) cc_final: 0.8473 (t0) REVERT: C 61 LYS cc_start: 0.8696 (mttm) cc_final: 0.8254 (mtmt) REVERT: C 66 ASP cc_start: 0.9080 (t0) cc_final: 0.8565 (t0) REVERT: C 99 GLU cc_start: 0.8914 (mp0) cc_final: 0.8313 (mp0) REVERT: C 120 GLN cc_start: 0.9190 (tp40) cc_final: 0.8144 (tp-100) REVERT: D 32 LYS cc_start: 0.9106 (mttt) cc_final: 0.8828 (mttp) REVERT: E 27 GLU cc_start: 0.8921 (tp30) cc_final: 0.8340 (tm-30) REVERT: E 67 ASP cc_start: 0.9182 (t70) cc_final: 0.8733 (t0) REVERT: E 90 GLN cc_start: 0.9048 (tp40) cc_final: 0.8789 (mm-40) REVERT: E 94 ASP cc_start: 0.8720 (m-30) cc_final: 0.8513 (m-30) REVERT: E 178 GLU cc_start: 0.8883 (pm20) cc_final: 0.8426 (pm20) REVERT: E 180 MET cc_start: 0.9095 (mmm) cc_final: 0.8782 (tpt) REVERT: E 189 LYS cc_start: 0.9535 (mttp) cc_final: 0.9151 (mtmp) REVERT: E 197 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8858 (mm-30) REVERT: F 50 GLU cc_start: 0.8235 (tt0) cc_final: 0.7845 (tm-30) REVERT: F 70 ASP cc_start: 0.8974 (t0) cc_final: 0.8451 (t0) REVERT: G 10 ASP cc_start: 0.8887 (p0) cc_final: 0.8633 (p0) REVERT: G 56 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8136 (t) REVERT: G 80 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8433 (mmm) REVERT: G 83 MET cc_start: 0.9435 (mtm) cc_final: 0.9202 (mtm) REVERT: G 112 ASP cc_start: 0.9158 (p0) cc_final: 0.8638 (p0) REVERT: G 116 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8382 (ttmm) REVERT: G 120 ASP cc_start: 0.8618 (m-30) cc_final: 0.8259 (m-30) REVERT: H 30 ASN cc_start: 0.8967 (t0) cc_final: 0.8301 (t0) REVERT: H 104 ASP cc_start: 0.8718 (p0) cc_final: 0.8502 (p0) REVERT: I 65 ARG cc_start: 0.8660 (mtp85) cc_final: 0.8159 (mtt-85) REVERT: I 105 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8740 (mp0) REVERT: I 112 ASP cc_start: 0.8878 (t70) cc_final: 0.8656 (t0) REVERT: I 175 ASP cc_start: 0.8916 (m-30) cc_final: 0.8522 (m-30) REVERT: J 108 ASP cc_start: 0.8780 (t70) cc_final: 0.8426 (t70) REVERT: J 155 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8115 (mpp-170) REVERT: J 165 GLU cc_start: 0.8518 (pt0) cc_final: 0.8200 (pt0) REVERT: J 184 ASP cc_start: 0.8816 (p0) cc_final: 0.8592 (p0) REVERT: K 36 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8160 (mt-10) REVERT: K 44 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8859 (m) REVERT: K 56 GLU cc_start: 0.9345 (OUTLIER) cc_final: 0.9044 (mp0) REVERT: K 72 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8224 (tm-30) REVERT: K 81 LYS cc_start: 0.9016 (tttp) cc_final: 0.8722 (mtpp) REVERT: K 106 LYS cc_start: 0.9302 (mmmm) cc_final: 0.9022 (mmpt) REVERT: L 39 ASP cc_start: 0.9052 (t70) cc_final: 0.8764 (t0) REVERT: L 48 ASP cc_start: 0.8734 (p0) cc_final: 0.8292 (t0) REVERT: L 177 ASP cc_start: 0.8687 (m-30) cc_final: 0.8109 (m-30) REVERT: L 186 ASP cc_start: 0.8738 (t0) cc_final: 0.8421 (t0) REVERT: L 188 TYR cc_start: 0.9377 (m-80) cc_final: 0.9023 (m-80) REVERT: L 205 GLU cc_start: 0.8387 (mp0) cc_final: 0.8060 (mp0) REVERT: L 206 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7684 (mm-30) REVERT: M 26 MET cc_start: 0.9137 (mtp) cc_final: 0.8754 (mtm) REVERT: M 47 ASN cc_start: 0.9186 (t0) cc_final: 0.8752 (t0) REVERT: M 56 ASP cc_start: 0.9084 (t0) cc_final: 0.8802 (t70) REVERT: M 64 LYS cc_start: 0.9372 (ttmp) cc_final: 0.8909 (ttmm) REVERT: M 79 ASP cc_start: 0.8499 (p0) cc_final: 0.8112 (p0) REVERT: M 104 ASN cc_start: 0.9161 (t0) cc_final: 0.8601 (t0) REVERT: M 170 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8228 (mp0) REVERT: M 180 ASP cc_start: 0.9050 (t70) cc_final: 0.8525 (t0) REVERT: M 200 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8204 (mt-10) REVERT: M 210 ASP cc_start: 0.8843 (p0) cc_final: 0.8560 (p0) REVERT: N 71 ASN cc_start: 0.9367 (t0) cc_final: 0.9120 (t0) REVERT: N 107 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: N 165 GLU cc_start: 0.8755 (tt0) cc_final: 0.8439 (tm-30) REVERT: N 167 ASP cc_start: 0.8481 (t0) cc_final: 0.8103 (t0) REVERT: N 193 GLN cc_start: 0.8997 (mt0) cc_final: 0.8677 (mt0) REVERT: O 48 GLU cc_start: 0.8306 (pp20) cc_final: 0.7797 (pp20) REVERT: O 57 ASP cc_start: 0.8327 (t0) cc_final: 0.7912 (t0) REVERT: O 58 GLU cc_start: 0.8903 (mp0) cc_final: 0.8466 (pm20) REVERT: O 59 ARG cc_start: 0.8596 (mpp80) cc_final: 0.8224 (mpp80) REVERT: O 122 GLN cc_start: 0.8884 (tp40) cc_final: 0.8420 (tp40) REVERT: O 142 ARG cc_start: 0.8693 (ttt-90) cc_final: 0.8115 (ttt-90) REVERT: O 208 GLU cc_start: 0.8273 (pt0) cc_final: 0.7994 (pt0) REVERT: O 224 GLU cc_start: 0.9050 (pm20) cc_final: 0.8840 (pm20) REVERT: P 34 CYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8572 (t) REVERT: P 48 GLU cc_start: 0.8546 (tt0) cc_final: 0.7801 (tm-30) REVERT: P 57 ASP cc_start: 0.8694 (t70) cc_final: 0.8347 (t0) REVERT: P 75 SER cc_start: 0.9396 (t) cc_final: 0.9130 (t) REVERT: P 166 ASN cc_start: 0.9252 (t0) cc_final: 0.8682 (t0) REVERT: P 167 ASN cc_start: 0.9392 (m110) cc_final: 0.8712 (m110) REVERT: P 184 MET cc_start: 0.8844 (mmm) cc_final: 0.8574 (mmm) REVERT: Q 20 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8152 (mt-10) REVERT: Q 55 ASP cc_start: 0.8676 (t0) cc_final: 0.8136 (t0) REVERT: Q 90 GLU cc_start: 0.8444 (tp30) cc_final: 0.7842 (tp30) REVERT: Q 99 GLU cc_start: 0.8412 (mp0) cc_final: 0.8074 (mp0) REVERT: Q 116 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8431 (tp40) REVERT: Q 148 ASP cc_start: 0.9099 (t0) cc_final: 0.8709 (t0) REVERT: Q 157 LYS cc_start: 0.8949 (mttt) cc_final: 0.8434 (mtmp) REVERT: Q 224 GLU cc_start: 0.9040 (tt0) cc_final: 0.8370 (tp30) REVERT: R 32 LYS cc_start: 0.8878 (mttp) cc_final: 0.8600 (mptp) REVERT: R 86 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8528 (mptm) REVERT: R 206 MET cc_start: 0.8050 (mtm) cc_final: 0.7798 (mtm) REVERT: R 227 HIS cc_start: 0.8819 (t-90) cc_final: 0.8452 (t70) REVERT: R 231 LYS cc_start: 0.9298 (mtpm) cc_final: 0.8949 (tttm) REVERT: S 26 MET cc_start: 0.8724 (mtp) cc_final: 0.8431 (mtp) REVERT: S 30 LYS cc_start: 0.8803 (mttt) cc_final: 0.8497 (mptt) REVERT: S 31 GLN cc_start: 0.8466 (pp30) cc_final: 0.8244 (pp30) REVERT: S 62 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8838 (mtpp) REVERT: S 90 GLN cc_start: 0.9187 (tp40) cc_final: 0.8402 (mm-40) REVERT: S 94 ASP cc_start: 0.8734 (m-30) cc_final: 0.7990 (m-30) REVERT: S 178 GLU cc_start: 0.9122 (pm20) cc_final: 0.8692 (pm20) REVERT: T 59 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8534 (mp0) REVERT: T 70 ASP cc_start: 0.8654 (t70) cc_final: 0.8358 (t0) REVERT: T 93 GLU cc_start: 0.8192 (pp20) cc_final: 0.7725 (pp20) REVERT: T 97 ASN cc_start: 0.9033 (m110) cc_final: 0.8457 (m-40) REVERT: T 184 MET cc_start: 0.8670 (mtp) cc_final: 0.8186 (ptp) REVERT: T 192 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.8908 (mp0) REVERT: T 236 GLU cc_start: 0.9316 (mt-10) cc_final: 0.9001 (mm-30) REVERT: U 5 SER cc_start: 0.8924 (t) cc_final: 0.8238 (m) REVERT: U 155 ASP cc_start: 0.8488 (p0) cc_final: 0.8183 (p0) REVERT: U 187 PHE cc_start: 0.7624 (p90) cc_final: 0.7134 (p90) REVERT: U 189 TRP cc_start: 0.7344 (m-90) cc_final: 0.6930 (m-90) REVERT: U 224 ASN cc_start: 0.9078 (p0) cc_final: 0.8668 (p0) REVERT: U 228 ARG cc_start: 0.8612 (mtm110) cc_final: 0.8303 (mtp-110) REVERT: V 19 ARG cc_start: 0.8922 (ttm170) cc_final: 0.8266 (tmm-80) REVERT: V 30 ASN cc_start: 0.9166 (t0) cc_final: 0.8815 (t0) REVERT: V 81 ARG cc_start: 0.9390 (OUTLIER) cc_final: 0.8866 (tpp-160) REVERT: V 85 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8683 (mt0) REVERT: V 150 GLU cc_start: 0.8475 (pm20) cc_final: 0.7804 (pm20) REVERT: V 153 ASN cc_start: 0.8614 (m-40) cc_final: 0.8240 (m110) REVERT: V 157 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8350 (mm-30) REVERT: V 184 ASP cc_start: 0.8872 (t0) cc_final: 0.8460 (t0) REVERT: V 198 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7689 (ttm110) REVERT: V 214 GLU cc_start: 0.8901 (tt0) cc_final: 0.8607 (tt0) REVERT: W 105 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8705 (mm-30) REVERT: W 143 GLU cc_start: 0.8228 (pm20) cc_final: 0.7947 (pm20) REVERT: W 164 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8476 (mm-30) REVERT: X 36 PHE cc_start: 0.9097 (m-80) cc_final: 0.8783 (m-80) REVERT: X 108 ASP cc_start: 0.8852 (t70) cc_final: 0.8461 (t70) REVERT: X 158 GLU cc_start: 0.8709 (tp30) cc_final: 0.8505 (tp30) REVERT: X 166 GLU cc_start: 0.8751 (tp30) cc_final: 0.8519 (tp30) REVERT: X 169 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8829 (ptmm) REVERT: X 186 ASN cc_start: 0.9386 (m-40) cc_final: 0.9173 (m-40) REVERT: Y 26 ILE cc_start: 0.9227 (mt) cc_final: 0.8795 (mp) REVERT: Y 62 GLN cc_start: 0.9480 (mm-40) cc_final: 0.9223 (mm110) REVERT: Y 67 GLU cc_start: 0.8935 (tt0) cc_final: 0.8530 (tm-30) REVERT: Y 70 ASN cc_start: 0.9480 (m-40) cc_final: 0.9047 (m110) REVERT: Z 146 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8807 (mm-40) REVERT: Z 159 GLN cc_start: 0.8541 (tp40) cc_final: 0.8241 (mt0) REVERT: Z 188 TYR cc_start: 0.9316 (m-80) cc_final: 0.9091 (m-80) REVERT: a 5 MET cc_start: 0.8698 (mmm) cc_final: 0.8166 (tpt) REVERT: a 25 ASP cc_start: 0.9014 (p0) cc_final: 0.8680 (p0) REVERT: a 110 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8663 (mpp) REVERT: a 133 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8553 (mt-10) REVERT: a 164 GLU cc_start: 0.8819 (pt0) cc_final: 0.8360 (pm20) REVERT: a 180 ASP cc_start: 0.9058 (t0) cc_final: 0.8708 (t0) REVERT: a 200 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: b 106 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8696 (pt0) REVERT: b 151 GLU cc_start: 0.8979 (pt0) cc_final: 0.8726 (pt0) outliers start: 129 outliers final: 70 residues processed: 1033 average time/residue: 0.4896 time to fit residues: 623.0746 Evaluate side-chains 1045 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 957 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 34 LYS Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 86 MET Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 62 LYS Chi-restraints excluded: chain T residue 192 GLU Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 161 CYS Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 81 ARG Chi-restraints excluded: chain V residue 85 GLN Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 88 SER Chi-restraints excluded: chain W residue 148 MET Chi-restraints excluded: chain W residue 196 THR Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 41 LYS Chi-restraints excluded: chain X residue 62 LYS Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Y residue 97 MET Chi-restraints excluded: chain Y residue 100 MET Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Y residue 167 ASP Chi-restraints excluded: chain Y residue 187 VAL Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 110 MET Chi-restraints excluded: chain a residue 169 VAL Chi-restraints excluded: chain a residue 200 GLU Chi-restraints excluded: chain b residue 84 LYS Chi-restraints excluded: chain b residue 106 GLN Chi-restraints excluded: chain b residue 184 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 84 optimal weight: 4.9990 chunk 289 optimal weight: 0.6980 chunk 398 optimal weight: 0.0570 chunk 96 optimal weight: 6.9990 chunk 183 optimal weight: 0.0000 chunk 364 optimal weight: 0.5980 chunk 184 optimal weight: 0.0770 chunk 147 optimal weight: 0.9980 chunk 372 optimal weight: 0.9990 chunk 373 optimal weight: 2.9990 chunk 562 optimal weight: 4.9990 overall best weight: 0.2860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 188 HIS C 23 GLN C 122 ASN D 118 ASN E 65 HIS E 68 ASN F 180 GLN H 153 ASN I 60 GLN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN J 193 ASN L 108 ASN L 131 GLN L 157 ASN L 159 GLN M 213 HIS O 108 GLN ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 HIS T 63 ASN V 57 GLN W 32 GLN W 60 GLN W 156 ASN X 27 GLN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 108 ASN Z 146 GLN Z 157 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.080170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.065570 restraints weight = 97014.500| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.74 r_work: 0.2832 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 47220 Z= 0.119 Angle : 0.602 11.730 64063 Z= 0.321 Chirality : 0.042 0.260 7447 Planarity : 0.004 0.051 8164 Dihedral : 4.311 21.383 6845 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.07 % Allowed : 22.81 % Favored : 75.13 % 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: 0.96 (0.11), residues: 6188 helix: 1.99 (0.11), residues: 2342 sheet: 0.06 (0.13), residues: 1514 loop : -0.27 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG V 143 TYR 0.028 0.001 TYR Q 110 PHE 0.019 0.001 PHE U 210 TRP 0.053 0.001 TRP Y 184 HIS 0.008 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00259 (47220) covalent geometry : angle 0.60175 (64063) hydrogen bonds : bond 0.03341 ( 2773) hydrogen bonds : angle 4.51858 ( 8061) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 1029 time to evaluate : 0.992 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: A 17 LYS cc_start: 0.9065 (mtmm) cc_final: 0.8709 (mmtp) REVERT: A 48 GLU cc_start: 0.8873 (pm20) cc_final: 0.8533 (pm20) REVERT: A 78 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8463 (mtp) REVERT: A 147 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8420 (tm-30) REVERT: A 158 LYS cc_start: 0.8895 (mttm) cc_final: 0.8476 (mttp) REVERT: A 176 ARG cc_start: 0.8673 (tpp-160) cc_final: 0.8300 (ttm110) REVERT: B 26 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7547 (pp20) REVERT: B 67 LYS cc_start: 0.9257 (ttmt) cc_final: 0.8713 (tttm) REVERT: B 174 MET cc_start: 0.8879 (mtp) cc_final: 0.8527 (ttp) REVERT: B 178 ASP cc_start: 0.9260 (m-30) cc_final: 0.8992 (m-30) REVERT: B 184 MET cc_start: 0.8534 (mmm) cc_final: 0.8193 (mmm) REVERT: C 28 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8834 (mtmm) REVERT: C 55 ASP cc_start: 0.8770 (t0) cc_final: 0.8428 (t0) REVERT: C 61 LYS cc_start: 0.8623 (mttm) cc_final: 0.8140 (mtmt) REVERT: C 66 ASP cc_start: 0.9042 (t0) cc_final: 0.8511 (t0) REVERT: C 67 ASP cc_start: 0.8671 (m-30) cc_final: 0.8442 (m-30) REVERT: C 99 GLU cc_start: 0.8783 (mp0) cc_final: 0.8202 (mp0) REVERT: C 116 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8537 (tp40) REVERT: D 32 LYS cc_start: 0.9084 (mttt) cc_final: 0.8820 (mttp) REVERT: D 91 LYS cc_start: 0.9347 (tptt) cc_final: 0.9075 (tppt) REVERT: D 95 GLU cc_start: 0.8938 (tp30) cc_final: 0.8706 (tp30) REVERT: E 27 GLU cc_start: 0.8884 (tp30) cc_final: 0.8293 (tm-30) REVERT: E 67 ASP cc_start: 0.9071 (t70) cc_final: 0.8657 (t0) REVERT: E 90 GLN cc_start: 0.9045 (tp40) cc_final: 0.8716 (mm-40) REVERT: E 94 ASP cc_start: 0.8712 (m-30) cc_final: 0.8464 (m-30) REVERT: E 178 GLU cc_start: 0.8815 (pm20) cc_final: 0.8356 (pm20) REVERT: E 180 MET cc_start: 0.9144 (mmm) cc_final: 0.8940 (mmm) REVERT: E 189 LYS cc_start: 0.9519 (mttp) cc_final: 0.9104 (mtmp) REVERT: E 197 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8895 (mm-30) REVERT: F 50 GLU cc_start: 0.8125 (tt0) cc_final: 0.7762 (tm-30) REVERT: F 70 ASP cc_start: 0.8868 (t0) cc_final: 0.8381 (t0) REVERT: F 147 GLN cc_start: 0.8807 (mt0) cc_final: 0.8207 (mt0) REVERT: G 10 ASP cc_start: 0.8927 (p0) cc_final: 0.8622 (p0) REVERT: G 56 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8141 (t) REVERT: G 80 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8739 (mmm) REVERT: G 83 MET cc_start: 0.9286 (mtm) cc_final: 0.9071 (mtm) REVERT: G 88 ARG cc_start: 0.8382 (mmm160) cc_final: 0.7957 (mmm-85) REVERT: G 97 GLU cc_start: 0.9058 (tp30) cc_final: 0.8782 (mm-30) REVERT: G 116 LYS cc_start: 0.8919 (ttpt) cc_final: 0.8270 (ttmm) REVERT: G 117 ARG cc_start: 0.8605 (mmm160) cc_final: 0.8313 (mmm-85) REVERT: G 120 ASP cc_start: 0.8573 (m-30) cc_final: 0.8235 (m-30) REVERT: H 30 ASN cc_start: 0.8989 (t0) cc_final: 0.8328 (t0) REVERT: I 33 MET cc_start: 0.9214 (tmm) cc_final: 0.8958 (tmm) REVERT: I 65 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8092 (mtt-85) REVERT: I 105 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8808 (mt-10) REVERT: I 112 ASP cc_start: 0.8860 (t70) cc_final: 0.8645 (t0) REVERT: I 164 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: I 175 ASP cc_start: 0.8854 (m-30) cc_final: 0.8429 (m-30) REVERT: J 108 ASP cc_start: 0.8862 (t70) cc_final: 0.8468 (t70) REVERT: J 184 ASP cc_start: 0.8795 (p0) cc_final: 0.8552 (p0) REVERT: K 36 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8085 (mt-10) REVERT: K 40 TYR cc_start: 0.8322 (p90) cc_final: 0.7903 (p90) REVERT: K 56 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8919 (mp0) REVERT: K 72 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8122 (tm-30) REVERT: K 81 LYS cc_start: 0.8989 (tttp) cc_final: 0.8713 (mtpp) REVERT: K 99 THR cc_start: 0.8964 (p) cc_final: 0.8763 (m) REVERT: K 106 LYS cc_start: 0.9312 (mmmm) cc_final: 0.9037 (mmpt) REVERT: K 151 GLN cc_start: 0.9039 (mp10) cc_final: 0.8681 (mp10) REVERT: L 48 ASP cc_start: 0.8601 (p0) cc_final: 0.8222 (t0) REVERT: L 131 GLN cc_start: 0.8753 (pt0) cc_final: 0.8514 (pt0) REVERT: L 157 ASN cc_start: 0.8284 (m110) cc_final: 0.8062 (m-40) REVERT: L 177 ASP cc_start: 0.8706 (m-30) cc_final: 0.8294 (m-30) REVERT: L 186 ASP cc_start: 0.8631 (t0) cc_final: 0.8286 (t0) REVERT: L 188 TYR cc_start: 0.9349 (m-80) cc_final: 0.8902 (m-80) REVERT: L 205 GLU cc_start: 0.8317 (mp0) cc_final: 0.7927 (mp0) REVERT: L 206 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7758 (mm-30) REVERT: M 26 MET cc_start: 0.8985 (mtp) cc_final: 0.8701 (mtm) REVERT: M 47 ASN cc_start: 0.9086 (t0) cc_final: 0.8677 (t0) REVERT: M 56 ASP cc_start: 0.9089 (t0) cc_final: 0.8808 (t70) REVERT: M 64 LYS cc_start: 0.9305 (ttmp) cc_final: 0.8790 (ttmm) REVERT: M 77 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8666 (pp) REVERT: M 79 ASP cc_start: 0.8333 (p0) cc_final: 0.7998 (p0) REVERT: M 104 ASN cc_start: 0.9145 (t0) cc_final: 0.8613 (t0) REVERT: M 180 ASP cc_start: 0.8883 (t70) cc_final: 0.8414 (t0) REVERT: M 200 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8118 (mt-10) REVERT: M 210 ASP cc_start: 0.8796 (p0) cc_final: 0.8546 (OUTLIER) REVERT: N 71 ASN cc_start: 0.9280 (t0) cc_final: 0.9038 (t0) REVERT: N 90 TYR cc_start: 0.8930 (m-80) cc_final: 0.8312 (m-80) REVERT: N 107 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: N 165 GLU cc_start: 0.8733 (tt0) cc_final: 0.8322 (tm-30) REVERT: N 167 ASP cc_start: 0.8480 (t0) cc_final: 0.8115 (t0) REVERT: N 193 GLN cc_start: 0.8945 (mt0) cc_final: 0.8644 (mt0) REVERT: O 48 GLU cc_start: 0.8250 (pp20) cc_final: 0.7768 (pp20) REVERT: O 57 ASP cc_start: 0.8249 (t0) cc_final: 0.7798 (t0) REVERT: O 58 GLU cc_start: 0.8840 (mp0) cc_final: 0.8390 (pm20) REVERT: O 59 ARG cc_start: 0.8541 (mpp80) cc_final: 0.8159 (mpp80) REVERT: O 120 TYR cc_start: 0.8757 (m-80) cc_final: 0.8488 (m-80) REVERT: O 122 GLN cc_start: 0.8792 (tp40) cc_final: 0.8381 (tp40) REVERT: O 208 GLU cc_start: 0.8291 (pt0) cc_final: 0.8032 (pt0) REVERT: O 218 ARG cc_start: 0.9191 (ptt90) cc_final: 0.8928 (ptt90) REVERT: P 22 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: P 34 CYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8446 (t) REVERT: P 48 GLU cc_start: 0.8400 (tt0) cc_final: 0.7625 (tm-30) REVERT: P 57 ASP cc_start: 0.8672 (t70) cc_final: 0.8393 (t0) REVERT: P 69 ASN cc_start: 0.8733 (t0) cc_final: 0.8410 (t0) REVERT: P 75 SER cc_start: 0.9339 (t) cc_final: 0.9069 (t) REVERT: P 166 ASN cc_start: 0.9266 (t0) cc_final: 0.8713 (t0) REVERT: P 167 ASN cc_start: 0.9362 (m110) cc_final: 0.8736 (m110) REVERT: P 184 MET cc_start: 0.8802 (mmm) cc_final: 0.8407 (mmm) REVERT: Q 20 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8130 (mp0) REVERT: Q 55 ASP cc_start: 0.8540 (t0) cc_final: 0.8042 (t0) REVERT: Q 79 ASP cc_start: 0.8624 (m-30) cc_final: 0.8116 (m-30) REVERT: Q 90 GLU cc_start: 0.8113 (tp30) cc_final: 0.7562 (tp30) REVERT: Q 116 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8453 (tp40) REVERT: Q 120 GLN cc_start: 0.8833 (tt0) cc_final: 0.8589 (tp40) REVERT: Q 148 ASP cc_start: 0.9068 (t0) cc_final: 0.8693 (t0) REVERT: Q 157 LYS cc_start: 0.8902 (mttt) cc_final: 0.8383 (mtmp) REVERT: Q 224 GLU cc_start: 0.8962 (tt0) cc_final: 0.8394 (tp30) REVERT: R 32 LYS cc_start: 0.8786 (mttp) cc_final: 0.8531 (mttp) REVERT: R 52 LYS cc_start: 0.8779 (mttt) cc_final: 0.8496 (mttp) REVERT: R 206 MET cc_start: 0.7889 (mtm) cc_final: 0.7652 (mtm) REVERT: R 216 GLU cc_start: 0.8021 (tt0) cc_final: 0.7683 (tt0) REVERT: R 227 HIS cc_start: 0.8815 (t-90) cc_final: 0.8506 (t70) REVERT: S 6 TYR cc_start: 0.8984 (m-80) cc_final: 0.8779 (m-80) REVERT: S 26 MET cc_start: 0.8637 (mtp) cc_final: 0.8369 (mtp) REVERT: S 30 LYS cc_start: 0.8748 (mttt) cc_final: 0.8478 (mptt) REVERT: S 62 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8807 (mtpp) REVERT: S 90 GLN cc_start: 0.9101 (tp40) cc_final: 0.8382 (mm-40) REVERT: S 94 ASP cc_start: 0.8729 (m-30) cc_final: 0.8057 (m-30) REVERT: S 122 ARG cc_start: 0.8683 (mtp85) cc_final: 0.8309 (mtp85) REVERT: S 176 MET cc_start: 0.8671 (ttp) cc_final: 0.8403 (mtp) REVERT: S 178 GLU cc_start: 0.9141 (pm20) cc_final: 0.8633 (pm20) REVERT: S 189 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8661 (mtpm) REVERT: T 59 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8512 (mp0) REVERT: T 70 ASP cc_start: 0.8630 (t70) cc_final: 0.8358 (t0) REVERT: T 93 GLU cc_start: 0.8155 (pp20) cc_final: 0.7762 (pp20) REVERT: T 97 ASN cc_start: 0.9002 (m110) cc_final: 0.8429 (m-40) REVERT: T 184 MET cc_start: 0.8643 (mtp) cc_final: 0.8302 (ptp) REVERT: T 236 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8971 (mm-30) REVERT: U 5 SER cc_start: 0.8938 (t) cc_final: 0.8274 (m) REVERT: U 80 MET cc_start: 0.9047 (mmm) cc_final: 0.8191 (mmt) REVERT: U 138 MET cc_start: 0.8777 (ttm) cc_final: 0.8311 (tpp) REVERT: U 155 ASP cc_start: 0.8353 (p0) cc_final: 0.8065 (p0) REVERT: U 187 PHE cc_start: 0.7661 (p90) cc_final: 0.7131 (p90) REVERT: U 189 TRP cc_start: 0.7280 (m-90) cc_final: 0.7007 (m-90) REVERT: U 224 ASN cc_start: 0.9078 (p0) cc_final: 0.8585 (p0) REVERT: U 228 ARG cc_start: 0.8583 (mtm110) cc_final: 0.8203 (ttp-110) REVERT: V 19 ARG cc_start: 0.8860 (ttm170) cc_final: 0.8420 (tmm-80) REVERT: V 30 ASN cc_start: 0.9040 (t0) cc_final: 0.8739 (t0) REVERT: V 81 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8926 (tpp-160) REVERT: V 149 GLU cc_start: 0.8342 (pp20) cc_final: 0.8136 (pp20) REVERT: V 150 GLU cc_start: 0.8389 (pm20) cc_final: 0.7876 (pm20) REVERT: V 153 ASN cc_start: 0.8648 (m-40) cc_final: 0.8287 (m110) REVERT: V 157 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8435 (mm-30) REVERT: V 184 ASP cc_start: 0.8757 (t0) cc_final: 0.8435 (t0) REVERT: V 214 GLU cc_start: 0.8839 (tt0) cc_final: 0.8560 (tt0) REVERT: W 105 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8642 (mm-30) REVERT: W 143 GLU cc_start: 0.8172 (pm20) cc_final: 0.7940 (pm20) REVERT: W 150 GLU cc_start: 0.8903 (tp30) cc_final: 0.8495 (mm-30) REVERT: W 164 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8359 (mm-30) REVERT: W 172 ASN cc_start: 0.9356 (m-40) cc_final: 0.9123 (m110) REVERT: X 36 PHE cc_start: 0.9022 (m-80) cc_final: 0.8799 (m-80) REVERT: X 68 LYS cc_start: 0.9505 (OUTLIER) cc_final: 0.8788 (tppt) REVERT: X 87 ASN cc_start: 0.9129 (m-40) cc_final: 0.8547 (m110) REVERT: X 108 ASP cc_start: 0.8895 (t70) cc_final: 0.8625 (t70) REVERT: X 118 MET cc_start: 0.8357 (ptm) cc_final: 0.8061 (mtp) REVERT: X 166 GLU cc_start: 0.8763 (tp30) cc_final: 0.8450 (tp30) REVERT: X 169 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8819 (ptmm) REVERT: X 186 ASN cc_start: 0.9345 (m-40) cc_final: 0.9124 (m-40) REVERT: Y 26 ILE cc_start: 0.9213 (mt) cc_final: 0.8896 (mp) REVERT: Y 62 GLN cc_start: 0.9405 (mm-40) cc_final: 0.9173 (mm110) REVERT: Y 67 GLU cc_start: 0.8900 (tt0) cc_final: 0.8548 (tm-30) REVERT: Y 70 ASN cc_start: 0.9480 (m-40) cc_final: 0.9085 (m110) REVERT: Z 159 GLN cc_start: 0.8557 (tp40) cc_final: 0.8284 (mt0) REVERT: a 5 MET cc_start: 0.8497 (mmm) cc_final: 0.8041 (tpt) REVERT: a 25 ASP cc_start: 0.8963 (p0) cc_final: 0.8637 (p0) REVERT: a 133 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8441 (mt-10) REVERT: a 164 GLU cc_start: 0.8750 (pt0) cc_final: 0.8348 (pm20) REVERT: a 180 ASP cc_start: 0.8942 (t0) cc_final: 0.8603 (t0) REVERT: a 200 GLU cc_start: 0.8334 (mp0) cc_final: 0.8018 (mp0) REVERT: b 7 GLN cc_start: 0.8928 (tt0) cc_final: 0.8594 (tt0) REVERT: b 106 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8493 (pt0) REVERT: b 151 GLU cc_start: 0.8975 (pt0) cc_final: 0.8680 (pt0) outliers start: 93 outliers final: 43 residues processed: 1072 average time/residue: 0.4735 time to fit residues: 627.0934 Evaluate side-chains 1038 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 980 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 62 LYS Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain V residue 81 ARG Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain W residue 148 MET Chi-restraints excluded: chain X residue 41 LYS Chi-restraints excluded: chain X residue 62 LYS Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 169 VAL Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 106 GLN Chi-restraints excluded: chain b residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 279 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 chunk 166 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 475 optimal weight: 5.9990 chunk 473 optimal weight: 0.0470 chunk 454 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 597 optimal weight: 4.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN D 118 ASN F 63 ASN F 180 GLN ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 ASN L 108 ASN L 151 ASN L 152 GLN L 159 GLN M 61 GLN O 108 GLN O 139 ASN R 104 ASN S 65 HIS V 57 GLN V 80 ASN W 32 GLN W 60 GLN X 27 GLN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN Z 146 GLN Z 157 ASN a 61 GLN a 81 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.079638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.064798 restraints weight = 97365.959| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.77 r_work: 0.2815 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 47220 Z= 0.142 Angle : 0.613 12.248 64063 Z= 0.325 Chirality : 0.043 0.310 7447 Planarity : 0.004 0.056 8164 Dihedral : 4.266 21.118 6845 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.80 % Allowed : 23.34 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.99 (0.11), residues: 6188 helix: 1.99 (0.11), residues: 2341 sheet: 0.07 (0.13), residues: 1531 loop : -0.22 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG V 143 TYR 0.032 0.001 TYR Z 75 PHE 0.026 0.001 PHE N 65 TRP 0.057 0.001 TRP Y 184 HIS 0.007 0.001 HIS F 201 Details of bonding type rmsd covalent geometry : bond 0.00325 (47220) covalent geometry : angle 0.61278 (64063) hydrogen bonds : bond 0.03403 ( 2773) hydrogen bonds : angle 4.52058 ( 8061) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 990 time to evaluate : 0.993 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: A 17 LYS cc_start: 0.9034 (mtmm) cc_final: 0.8667 (mmtp) REVERT: A 48 GLU cc_start: 0.8886 (pm20) cc_final: 0.8492 (pm20) REVERT: A 120 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.7668 (t80) REVERT: A 147 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8418 (tm-30) REVERT: A 158 LYS cc_start: 0.8906 (mttm) cc_final: 0.8520 (mttp) REVERT: A 202 MET cc_start: 0.8490 (ptm) cc_final: 0.8220 (pmm) REVERT: B 26 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7563 (pp20) REVERT: B 67 LYS cc_start: 0.9252 (ttmt) cc_final: 0.8713 (tttm) REVERT: B 72 MET cc_start: 0.8300 (mtm) cc_final: 0.8059 (mtm) REVERT: B 114 LEU cc_start: 0.9369 (tp) cc_final: 0.9158 (mp) REVERT: B 174 MET cc_start: 0.8889 (mtp) cc_final: 0.8543 (ttp) REVERT: B 178 ASP cc_start: 0.9289 (m-30) cc_final: 0.9020 (m-30) REVERT: B 184 MET cc_start: 0.8510 (mmm) cc_final: 0.8143 (mmm) REVERT: C 28 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8766 (mtmm) REVERT: C 55 ASP cc_start: 0.8806 (t0) cc_final: 0.8324 (t0) REVERT: C 61 LYS cc_start: 0.8660 (mttm) cc_final: 0.8212 (mtmt) REVERT: C 66 ASP cc_start: 0.9046 (t0) cc_final: 0.8514 (t0) REVERT: C 67 ASP cc_start: 0.8719 (m-30) cc_final: 0.8504 (m-30) REVERT: C 99 GLU cc_start: 0.8793 (mp0) cc_final: 0.8244 (mp0) REVERT: C 116 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8547 (tp40) REVERT: D 32 LYS cc_start: 0.9083 (mttt) cc_final: 0.8819 (mttp) REVERT: D 133 MET cc_start: 0.8642 (mpp) cc_final: 0.8434 (mmp) REVERT: E 27 GLU cc_start: 0.8892 (tp30) cc_final: 0.8302 (tm-30) REVERT: E 67 ASP cc_start: 0.9085 (t70) cc_final: 0.8671 (t0) REVERT: E 90 GLN cc_start: 0.9025 (tp40) cc_final: 0.8722 (mm-40) REVERT: E 94 ASP cc_start: 0.8698 (m-30) cc_final: 0.8471 (m-30) REVERT: E 178 GLU cc_start: 0.8801 (pm20) cc_final: 0.8332 (pm20) REVERT: E 189 LYS cc_start: 0.9525 (mttp) cc_final: 0.9104 (mtmp) REVERT: E 197 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8808 (mm-30) REVERT: F 50 GLU cc_start: 0.8138 (tt0) cc_final: 0.7759 (tm-30) REVERT: F 70 ASP cc_start: 0.8916 (t0) cc_final: 0.8434 (t0) REVERT: F 147 GLN cc_start: 0.8815 (mt0) cc_final: 0.8224 (mt0) REVERT: F 150 MET cc_start: 0.8623 (tmm) cc_final: 0.8221 (tmt) REVERT: G 10 ASP cc_start: 0.8887 (p0) cc_final: 0.8606 (p0) REVERT: G 43 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7871 (ptt-90) REVERT: G 56 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8130 (t) REVERT: G 80 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8808 (mmm) REVERT: G 83 MET cc_start: 0.9316 (mtm) cc_final: 0.9094 (mtm) REVERT: G 97 GLU cc_start: 0.9067 (tp30) cc_final: 0.8789 (mm-30) REVERT: G 116 LYS cc_start: 0.8927 (ttpt) cc_final: 0.8302 (ttmm) REVERT: G 117 ARG cc_start: 0.8619 (mmm160) cc_final: 0.8360 (mmm-85) REVERT: G 120 ASP cc_start: 0.8580 (m-30) cc_final: 0.8268 (m-30) REVERT: H 30 ASN cc_start: 0.9000 (t0) cc_final: 0.8327 (t0) REVERT: I 65 ARG cc_start: 0.8658 (mtp85) cc_final: 0.8141 (mtt-85) REVERT: I 105 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8803 (mp0) REVERT: I 112 ASP cc_start: 0.8858 (t70) cc_final: 0.8650 (t0) REVERT: I 164 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: I 175 ASP cc_start: 0.8872 (m-30) cc_final: 0.8455 (m-30) REVERT: I 177 ASP cc_start: 0.8554 (p0) cc_final: 0.8312 (p0) REVERT: J 18 ASP cc_start: 0.8417 (p0) cc_final: 0.8216 (p0) REVERT: J 108 ASP cc_start: 0.8846 (t70) cc_final: 0.8401 (t70) REVERT: J 119 ASP cc_start: 0.9046 (p0) cc_final: 0.8822 (p0) REVERT: J 184 ASP cc_start: 0.8822 (p0) cc_final: 0.8591 (p0) REVERT: K 36 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8097 (mt-10) REVERT: K 40 TYR cc_start: 0.8326 (p90) cc_final: 0.8026 (p90) REVERT: K 56 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8925 (mp0) REVERT: K 72 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8146 (tm-30) REVERT: K 81 LYS cc_start: 0.9055 (tttp) cc_final: 0.8790 (mtpp) REVERT: K 99 THR cc_start: 0.8973 (p) cc_final: 0.8757 (m) REVERT: K 106 LYS cc_start: 0.9329 (mmmm) cc_final: 0.9045 (mmpt) REVERT: K 151 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8653 (mp10) REVERT: L 48 ASP cc_start: 0.8624 (p0) cc_final: 0.8207 (t0) REVERT: L 131 GLN cc_start: 0.8781 (pt0) cc_final: 0.8549 (pt0) REVERT: L 144 MET cc_start: 0.9195 (mtp) cc_final: 0.8960 (tpp) REVERT: L 157 ASN cc_start: 0.8209 (m110) cc_final: 0.8005 (m-40) REVERT: L 177 ASP cc_start: 0.8673 (m-30) cc_final: 0.8098 (m-30) REVERT: L 186 ASP cc_start: 0.8618 (t0) cc_final: 0.8280 (t0) REVERT: L 188 TYR cc_start: 0.9341 (m-80) cc_final: 0.8890 (m-80) REVERT: L 205 GLU cc_start: 0.8321 (mp0) cc_final: 0.7939 (mp0) REVERT: L 206 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7777 (mm-30) REVERT: M 26 MET cc_start: 0.9020 (mtp) cc_final: 0.8745 (mtm) REVERT: M 47 ASN cc_start: 0.9115 (t0) cc_final: 0.8695 (t0) REVERT: M 56 ASP cc_start: 0.9056 (t0) cc_final: 0.8772 (t70) REVERT: M 64 LYS cc_start: 0.9315 (ttmp) cc_final: 0.8803 (ttmm) REVERT: M 79 ASP cc_start: 0.8338 (p0) cc_final: 0.7984 (p0) REVERT: M 104 ASN cc_start: 0.9151 (t0) cc_final: 0.8619 (t0) REVERT: M 180 ASP cc_start: 0.8926 (t70) cc_final: 0.8483 (t0) REVERT: M 200 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8142 (mt-10) REVERT: M 210 ASP cc_start: 0.8811 (p0) cc_final: 0.8565 (OUTLIER) REVERT: N 71 ASN cc_start: 0.9288 (t0) cc_final: 0.9038 (t0) REVERT: N 90 TYR cc_start: 0.8922 (m-80) cc_final: 0.8678 (m-80) REVERT: N 107 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: N 165 GLU cc_start: 0.8740 (tt0) cc_final: 0.8281 (tm-30) REVERT: N 167 ASP cc_start: 0.8531 (t0) cc_final: 0.8185 (t0) REVERT: N 193 GLN cc_start: 0.8964 (mt0) cc_final: 0.8646 (mt0) REVERT: O 48 GLU cc_start: 0.8241 (pp20) cc_final: 0.7753 (pp20) REVERT: O 57 ASP cc_start: 0.8295 (t0) cc_final: 0.7814 (t0) REVERT: O 58 GLU cc_start: 0.8857 (mp0) cc_final: 0.8370 (pm20) REVERT: O 59 ARG cc_start: 0.8564 (mpp80) cc_final: 0.8155 (mpp80) REVERT: O 108 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8870 (mm110) REVERT: O 120 TYR cc_start: 0.8769 (m-80) cc_final: 0.8477 (m-80) REVERT: O 122 GLN cc_start: 0.8799 (tp40) cc_final: 0.8397 (tp40) REVERT: O 208 GLU cc_start: 0.8259 (pt0) cc_final: 0.7995 (pt0) REVERT: O 218 ARG cc_start: 0.9192 (ptt90) cc_final: 0.8938 (ptt90) REVERT: P 34 CYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8436 (t) REVERT: P 48 GLU cc_start: 0.8447 (tt0) cc_final: 0.7626 (tm-30) REVERT: P 57 ASP cc_start: 0.8598 (t70) cc_final: 0.8309 (t0) REVERT: P 69 ASN cc_start: 0.8763 (t0) cc_final: 0.8451 (t0) REVERT: P 75 SER cc_start: 0.9362 (t) cc_final: 0.9096 (t) REVERT: P 166 ASN cc_start: 0.9276 (t0) cc_final: 0.8729 (t0) REVERT: P 167 ASN cc_start: 0.9367 (m110) cc_final: 0.8722 (m110) REVERT: P 184 MET cc_start: 0.8822 (mmm) cc_final: 0.8477 (mmm) REVERT: Q 20 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8159 (mt-10) REVERT: Q 55 ASP cc_start: 0.8566 (t0) cc_final: 0.8061 (t0) REVERT: Q 79 ASP cc_start: 0.8637 (m-30) cc_final: 0.8151 (m-30) REVERT: Q 90 GLU cc_start: 0.8100 (tp30) cc_final: 0.7526 (tp30) REVERT: Q 116 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8337 (tp40) REVERT: Q 120 GLN cc_start: 0.8825 (tt0) cc_final: 0.8535 (tp40) REVERT: Q 148 ASP cc_start: 0.9081 (t0) cc_final: 0.8700 (t0) REVERT: Q 157 LYS cc_start: 0.8913 (mttt) cc_final: 0.8403 (mtmp) REVERT: Q 224 GLU cc_start: 0.9002 (tt0) cc_final: 0.8393 (tp30) REVERT: R 32 LYS cc_start: 0.8789 (mttp) cc_final: 0.8536 (mttp) REVERT: R 52 LYS cc_start: 0.8802 (mttt) cc_final: 0.8521 (mttp) REVERT: R 206 MET cc_start: 0.7924 (mtm) cc_final: 0.7685 (mtm) REVERT: R 216 GLU cc_start: 0.8075 (tt0) cc_final: 0.7759 (tt0) REVERT: R 227 HIS cc_start: 0.8830 (t-90) cc_final: 0.8526 (t70) REVERT: R 231 LYS cc_start: 0.9170 (tppt) cc_final: 0.8929 (tttp) REVERT: S 26 MET cc_start: 0.8623 (mtp) cc_final: 0.8327 (mtp) REVERT: S 30 LYS cc_start: 0.8776 (mttt) cc_final: 0.8494 (mptt) REVERT: S 62 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8862 (mtpp) REVERT: S 90 GLN cc_start: 0.9123 (tp40) cc_final: 0.8395 (mm-40) REVERT: S 94 ASP cc_start: 0.8701 (m-30) cc_final: 0.8021 (m-30) REVERT: S 176 MET cc_start: 0.8728 (ttp) cc_final: 0.8461 (mtp) REVERT: S 178 GLU cc_start: 0.9104 (pm20) cc_final: 0.8604 (pm20) REVERT: T 59 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8512 (mp0) REVERT: T 70 ASP cc_start: 0.8618 (t70) cc_final: 0.8365 (t0) REVERT: T 93 GLU cc_start: 0.8159 (pp20) cc_final: 0.7762 (pp20) REVERT: T 97 ASN cc_start: 0.9025 (m110) cc_final: 0.8434 (m-40) REVERT: T 184 MET cc_start: 0.8595 (mtp) cc_final: 0.8257 (ptp) REVERT: T 236 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8988 (mm-30) REVERT: U 5 SER cc_start: 0.8924 (t) cc_final: 0.8259 (m) REVERT: U 80 MET cc_start: 0.9058 (mmm) cc_final: 0.8602 (mmt) REVERT: U 155 ASP cc_start: 0.8332 (p0) cc_final: 0.8042 (p0) REVERT: U 187 PHE cc_start: 0.7646 (p90) cc_final: 0.7126 (p90) REVERT: U 189 TRP cc_start: 0.7309 (m-90) cc_final: 0.7006 (m-90) REVERT: U 224 ASN cc_start: 0.9066 (p0) cc_final: 0.8572 (p0) REVERT: U 228 ARG cc_start: 0.8577 (mtm110) cc_final: 0.8197 (ttp-110) REVERT: V 19 ARG cc_start: 0.8865 (ttm170) cc_final: 0.8418 (tmm-80) REVERT: V 30 ASN cc_start: 0.9072 (t0) cc_final: 0.8770 (t0) REVERT: V 81 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.8940 (tpp-160) REVERT: V 150 GLU cc_start: 0.8401 (pm20) cc_final: 0.8001 (pm20) REVERT: V 153 ASN cc_start: 0.8653 (m-40) cc_final: 0.8252 (m110) REVERT: V 157 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8449 (mm-30) REVERT: V 184 ASP cc_start: 0.8758 (t0) cc_final: 0.8434 (t0) REVERT: V 214 GLU cc_start: 0.8827 (tt0) cc_final: 0.8545 (tt0) REVERT: W 105 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8657 (mm-30) REVERT: W 143 GLU cc_start: 0.8201 (pm20) cc_final: 0.7894 (pm20) REVERT: W 150 GLU cc_start: 0.8917 (tp30) cc_final: 0.8528 (mm-30) REVERT: W 164 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8419 (mm-30) REVERT: X 36 PHE cc_start: 0.9042 (m-80) cc_final: 0.8794 (m-80) REVERT: X 87 ASN cc_start: 0.9120 (m-40) cc_final: 0.8536 (m110) REVERT: X 108 ASP cc_start: 0.8857 (t70) cc_final: 0.8503 (t70) REVERT: X 118 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8085 (mtp) REVERT: X 166 GLU cc_start: 0.8768 (tp30) cc_final: 0.8507 (tp30) REVERT: Y 26 ILE cc_start: 0.9232 (mt) cc_final: 0.8929 (mp) REVERT: Y 62 GLN cc_start: 0.9407 (mm-40) cc_final: 0.9158 (mm110) REVERT: Y 67 GLU cc_start: 0.8904 (tt0) cc_final: 0.8589 (tm-30) REVERT: Y 70 ASN cc_start: 0.9479 (m-40) cc_final: 0.9080 (m110) REVERT: a 5 MET cc_start: 0.8497 (mmm) cc_final: 0.8067 (tpt) REVERT: a 25 ASP cc_start: 0.8979 (p0) cc_final: 0.8684 (p0) REVERT: a 133 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8457 (mt-10) REVERT: a 164 GLU cc_start: 0.8728 (pt0) cc_final: 0.8363 (pm20) REVERT: a 200 GLU cc_start: 0.8355 (mp0) cc_final: 0.8036 (mp0) REVERT: b 7 GLN cc_start: 0.8949 (tt0) cc_final: 0.8608 (tt0) REVERT: b 106 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8489 (pt0) REVERT: b 151 GLU cc_start: 0.8972 (pt0) cc_final: 0.8611 (pm20) outliers start: 81 outliers final: 50 residues processed: 1031 average time/residue: 0.4739 time to fit residues: 600.2819 Evaluate side-chains 1041 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 976 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 168 GLN Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 151 GLN Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 108 GLN Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 70 CYS Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 62 LYS Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 81 ARG Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 149 GLU Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain W residue 148 MET Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 41 LYS Chi-restraints excluded: chain X residue 62 LYS Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain Z residue 114 ASP Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 169 VAL Chi-restraints excluded: chain b residue 106 GLN Chi-restraints excluded: chain b residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 1 optimal weight: 0.9980 chunk 256 optimal weight: 6.9990 chunk 557 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 499 optimal weight: 2.9990 chunk 550 optimal weight: 4.9990 chunk 334 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 291 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 54 GLN F 63 ASN F 180 GLN ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 ASN I 32 GLN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 ASN K 175 ASN L 108 ASN L 157 ASN ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN S 65 HIS T 63 ASN V 57 GLN V 80 ASN W 32 GLN W 60 GLN W 80 GLN W 156 ASN W 172 ASN X 27 GLN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 108 ASN Z 146 GLN Z 157 ASN Z 159 GLN a 61 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.064251 restraints weight = 97368.452| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.75 r_work: 0.2801 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 47220 Z= 0.175 Angle : 0.663 31.711 64063 Z= 0.346 Chirality : 0.043 0.302 7447 Planarity : 0.004 0.131 8164 Dihedral : 4.294 21.024 6845 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.91 % Allowed : 23.52 % Favored : 74.57 % 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: 0.95 (0.11), residues: 6188 helix: 1.97 (0.11), residues: 2351 sheet: 0.04 (0.13), residues: 1530 loop : -0.28 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG V 143 TYR 0.053 0.001 TYR Y 40 PHE 0.030 0.001 PHE N 65 TRP 0.059 0.002 TRP Y 184 HIS 0.007 0.001 HIS F 201 Details of bonding type rmsd covalent geometry : bond 0.00401 (47220) covalent geometry : angle 0.66311 (64063) hydrogen bonds : bond 0.03499 ( 2773) hydrogen bonds : angle 4.54443 ( 8061) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13760.78 seconds wall clock time: 234 minutes 32.93 seconds (14072.93 seconds total)