Starting phenix.real_space_refine on Thu Dec 26 15:48:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nan_24275/12_2024/7nan_24275.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nan_24275/12_2024/7nan_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_24275/12_2024/7nan_24275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nan_24275/12_2024/7nan_24275.map" model { file = "/net/cci-nas-00/data/ceres_data/7nan_24275/12_2024/7nan_24275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nan_24275/12_2024/7nan_24275.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} 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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 20, '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: {'GLN:plan1': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ASP:plan': 8} 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: {'TYR:plan': 1, 'GLU:plan': 12, '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: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 1, '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: {'GLU:plan': 11, 'ASN:plan1': 1, 'ASP:plan': 7} 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: {'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 2, 'ASP:plan': 6} 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, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} 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: {'GLU:plan': 2, 'ASP:plan': 5} 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, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLU:plan': 4, 'ASP: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: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5} 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: {'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLN:plan1': 2, 'GLU:plan': 14, 'ASP:plan': 8} 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: {'TYR:plan': 1, 'GLU:plan': 12, '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: {'GLN:plan1': 2, 'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 11} 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: {'GLU:plan': 11, 'ASP:plan': 6} 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: {'GLU:plan': 11, 'ARG:plan': 2, 'ASP:plan': 6} 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, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP: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: {'GLU:plan': 2, 'ASP:plan': 6} 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, 'ARG:plan': 1, 'ASP:plan': 3} 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: {'GLU:plan': 7, 'ARG:plan': 1, '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: {'GLU:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 28.21, per 1000 atoms: 0.61 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: 12.98 Conformation dependent library (CDL) restraints added in 5.7 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: 7.56 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: 21.63 Time building geometry restraints manager: 14.81 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.600 Check model and map are aligned: 0.330 Set scattering table: 0.380 Process input model: 107.830 Find NCS groups from input model: 4.510 Set up NCS constraints: 0.410 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: 0.020 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.030 ------------------------------------------------------------------------------- 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= 0.632 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (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 TRP 0.042 0.002 TRP F 215 HIS 0.008 0.001 HIS C 94 PHE 0.030 0.002 PHE W 68 TYR 0.040 0.002 TYR I 146 ARG 0.014 0.001 ARG M 171 *********************** 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 : 5.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 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: 0.8077 (t0) REVERT: C 96 LEU cc_start: 0.9080 (tp) cc_final: 0.8535 (tt) REVERT: C 116 GLN cc_start: 0.8528 (tm-30) cc_final: 0.7869 (tp40) REVERT: D 32 LYS cc_start: 0.9011 (mttt) cc_final: 0.8685 (mttm) REVERT: D 84 ASP cc_start: 0.8645 (m-30) cc_final: 0.7998 (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: 0.8136 (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: 0.8040 (tm-30) REVERT: E 30 LYS cc_start: 0.8711 (mttt) cc_final: 0.8482 (mttp) REVERT: E 50 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8536 (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: 0.8555 (m-40) REVERT: E 90 GLN cc_start: 0.8313 (tp40) cc_final: 0.7845 (mm-40) REVERT: E 94 ASP cc_start: 0.8106 (m-30) cc_final: 0.7815 (m-30) REVERT: E 100 ASP cc_start: 0.8140 (t0) cc_final: 0.7852 (t0) REVERT: E 180 MET cc_start: 0.8041 (mmm) cc_final: 0.7790 (tpt) REVERT: E 185 ASN cc_start: 0.8510 (p0) cc_final: 0.7372 (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: 0.7845 (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: 0.8030 (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: 0.7442 (p0) cc_final: 0.7104 (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: 0.7900 (m-30) REVERT: I 176 ARG cc_start: 0.8573 (tpp-160) cc_final: 0.8203 (mmt180) REVERT: J 68 LYS cc_start: 0.9015 (tttm) cc_final: 0.8718 (tptp) REVERT: J 74 GLU cc_start: 0.7757 (mp0) cc_final: 0.7281 (mp0) 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: 0.7819 (mm110) REVERT: L 177 ASP cc_start: 0.7689 (m-30) cc_final: 0.7015 (m-30) REVERT: L 184 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7921 (mp0) REVERT: L 205 GLU cc_start: 0.7738 (mp0) cc_final: 0.7479 (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: 0.8256 (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: 0.8174 (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: 0.8141 (p0) REVERT: N 84 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8932 (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: 0.8057 (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: 0.7468 (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: 0.8315 (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: 0.8382 (t0) REVERT: P 167 ASN cc_start: 0.9135 (m110) cc_final: 0.8532 (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: 0.8499 (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: 0.8533 (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: 0.7474 (m-40) REVERT: V 198 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7635 (ttm-80) REVERT: V 202 TYR cc_start: 0.7076 (m-10) cc_final: 0.6850 (m-10) 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: 0.8673 (mttm) REVERT: W 73 TYR cc_start: 0.9174 (t80) cc_final: 0.8774 (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: 0.8233 (mm-30) REVERT: W 150 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8106 (tp30) REVERT: W 154 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8145 (mt-10) REVERT: W 191 LYS cc_start: 0.9065 (ptmt) cc_final: 0.8680 (ptmm) REVERT: X 36 PHE cc_start: 0.8984 (m-80) cc_final: 0.8604 (m-80) REVERT: X 37 LYS cc_start: 0.8754 (tttm) cc_final: 0.8512 (tttp) REVERT: X 86 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7926 (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: 0.8670 (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: 0.7829 (m-30) cc_final: 0.7195 (m-30) REVERT: a 56 ASP cc_start: 0.8375 (t70) cc_final: 0.7818 (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: 0.7826 (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: 0.8590 (mt0) outliers start: 0 outliers final: 3 residues processed: 1251 average time/residue: 1.8706 time to fit residues: 2822.4181 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 : 5.505 ------------------------------------------------------------------------------- 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 517 optimal weight: 0.6980 chunk 464 optimal weight: 0.8980 chunk 257 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 313 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 480 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 292 optimal weight: 0.8980 chunk 357 optimal weight: 2.9990 chunk 556 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 C 116 GLN C 120 GLN D 13 ASN D 122 GLN E 21 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 29 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 154 HIS 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 47220 Z= 0.199 Angle : 0.585 8.505 64063 Z= 0.314 Chirality : 0.043 0.167 7447 Planarity : 0.004 0.063 8164 Dihedral : 4.717 40.467 6851 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.38 % Allowed : 12.45 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.10), residues: 6188 helix: 1.46 (0.10), residues: 2337 sheet: -0.21 (0.12), residues: 1507 loop : -0.44 (0.12), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 215 HIS 0.007 0.001 HIS S 65 PHE 0.019 0.001 PHE W 68 TYR 0.022 0.001 TYR U 160 ARG 0.008 0.001 ARG U 88 *********************** 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 1224 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1117 time to evaluate : 5.991 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 158 LYS cc_start: 0.8902 (mttm) cc_final: 0.8479 (mttp) REVERT: A 176 ARG cc_start: 0.8877 (ttm110) cc_final: 0.8608 (ttm110) REVERT: B 166 ASN cc_start: 0.9071 (t0) cc_final: 0.8603 (t0) REVERT: B 167 ASN cc_start: 0.9345 (m110) cc_final: 0.8716 (m110) REVERT: C 54 GLN cc_start: 0.8606 (mm110) cc_final: 0.8371 (mm110) REVERT: C 55 ASP cc_start: 0.8159 (t0) cc_final: 0.7783 (t0) REVERT: C 61 LYS cc_start: 0.8542 (mttm) cc_final: 0.8058 (mtmt) REVERT: C 66 ASP cc_start: 0.8592 (t0) cc_final: 0.8286 (t0) REVERT: C 99 GLU cc_start: 0.7564 (mp0) cc_final: 0.7356 (mp0) REVERT: C 116 GLN cc_start: 0.8426 (tm130) cc_final: 0.8034 (tp40) REVERT: C 157 LYS cc_start: 0.8886 (mppt) cc_final: 0.8511 (mtmm) REVERT: D 32 LYS cc_start: 0.9079 (mttt) cc_final: 0.8834 (mttp) REVERT: D 52 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8153 (mtmm) REVERT: D 84 ASP cc_start: 0.8658 (m-30) cc_final: 0.8123 (m-30) REVERT: D 91 LYS cc_start: 0.9054 (tptp) cc_final: 0.8368 (tmtm) REVERT: D 95 GLU cc_start: 0.8188 (tp30) cc_final: 0.7779 (tp30) REVERT: D 178 GLN cc_start: 0.8295 (tp40) cc_final: 0.8027 (mm110) REVERT: D 182 GLN cc_start: 0.8839 (mt0) cc_final: 0.8616 (mt0) REVERT: D 196 LYS cc_start: 0.9250 (mtpp) cc_final: 0.8920 (mtmm) REVERT: E 26 MET cc_start: 0.8211 (mmm) cc_final: 0.7804 (mmm) REVERT: E 67 ASP cc_start: 0.8735 (t70) cc_final: 0.8333 (t0) REVERT: E 86 ASN cc_start: 0.8882 (m-40) cc_final: 0.8569 (m-40) REVERT: E 90 GLN cc_start: 0.8441 (tp40) cc_final: 0.7914 (mm-40) REVERT: E 94 ASP cc_start: 0.8091 (m-30) cc_final: 0.7752 (m-30) REVERT: E 100 ASP cc_start: 0.8067 (t0) cc_final: 0.7776 (t0) REVERT: E 180 MET cc_start: 0.8324 (mmm) cc_final: 0.7999 (tpt) REVERT: E 189 LYS cc_start: 0.9331 (mttp) cc_final: 0.8990 (mttp) REVERT: F 70 ASP cc_start: 0.8307 (t0) cc_final: 0.7767 (t0) REVERT: F 93 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7823 (mm-30) REVERT: F 97 ASN cc_start: 0.9012 (m-40) cc_final: 0.8683 (m110) REVERT: F 147 GLN cc_start: 0.8566 (mt0) cc_final: 0.7899 (mt0) REVERT: F 150 MET cc_start: 0.7832 (tmt) cc_final: 0.7257 (tmt) REVERT: F 221 ASN cc_start: 0.8924 (m110) cc_final: 0.8714 (p0) REVERT: F 225 GLU cc_start: 0.8586 (pt0) cc_final: 0.8253 (pp20) REVERT: G 10 ASP cc_start: 0.8618 (p0) cc_final: 0.8348 (p0) REVERT: G 23 TYR cc_start: 0.8077 (m-80) cc_final: 0.7757 (m-80) REVERT: G 104 LYS cc_start: 0.9081 (mtpp) cc_final: 0.8802 (mtpm) REVERT: G 112 ASP cc_start: 0.8818 (p0) cc_final: 0.8561 (p0) REVERT: G 116 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8377 (ttmm) REVERT: G 138 MET cc_start: 0.8680 (ttp) cc_final: 0.8134 (tpp) REVERT: H 30 ASN cc_start: 0.8788 (t0) cc_final: 0.8396 (t0) REVERT: H 72 ARG cc_start: 0.8768 (ptp90) cc_final: 0.8345 (ptp-170) REVERT: I 65 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7620 (mtp85) REVERT: I 175 ASP cc_start: 0.8257 (m-30) cc_final: 0.7852 (m-30) REVERT: J 108 ASP cc_start: 0.8169 (t70) cc_final: 0.7875 (t70) REVERT: J 184 ASP cc_start: 0.8546 (p0) cc_final: 0.8288 (p0) REVERT: K 56 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8577 (mp0) REVERT: L 73 LYS cc_start: 0.8934 (mttt) cc_final: 0.8644 (mtmm) REVERT: L 186 ASP cc_start: 0.8417 (t0) cc_final: 0.8057 (t0) REVERT: L 188 TYR cc_start: 0.9039 (m-80) cc_final: 0.8807 (m-80) REVERT: L 205 GLU cc_start: 0.7797 (mp0) cc_final: 0.7509 (mp0) REVERT: M 26 MET cc_start: 0.8461 (mtp) cc_final: 0.8153 (mtm) REVERT: M 47 ASN cc_start: 0.8443 (t0) cc_final: 0.8053 (t0) REVERT: M 56 ASP cc_start: 0.8340 (t0) cc_final: 0.7827 (t0) REVERT: M 59 ASP cc_start: 0.8778 (m-30) cc_final: 0.8530 (m-30) REVERT: M 64 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8613 (mtpp) REVERT: M 65 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8690 (pt0) REVERT: M 104 ASN cc_start: 0.9045 (t0) cc_final: 0.8487 (t0) REVERT: M 170 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7777 (mp0) REVERT: M 173 MET cc_start: 0.8835 (mmm) cc_final: 0.8604 (mmt) REVERT: M 180 ASP cc_start: 0.8662 (t70) cc_final: 0.8252 (t0) REVERT: M 200 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7435 (mt-10) REVERT: M 210 ASP cc_start: 0.8458 (p0) cc_final: 0.7980 (p0) REVERT: N 84 LYS cc_start: 0.9296 (ttpt) cc_final: 0.8971 (ttpp) REVERT: N 90 TYR cc_start: 0.8923 (m-80) cc_final: 0.8555 (m-80) REVERT: O 6 SER cc_start: 0.8642 (p) cc_final: 0.8127 (t) REVERT: O 48 GLU cc_start: 0.7777 (pp20) cc_final: 0.7541 (pp20) REVERT: O 57 ASP cc_start: 0.8107 (t0) cc_final: 0.7729 (t0) REVERT: O 108 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8264 (mm-40) REVERT: O 111 GLN cc_start: 0.8646 (mt0) cc_final: 0.8370 (mt0) REVERT: O 142 ARG cc_start: 0.8236 (ttt-90) cc_final: 0.7715 (ttt-90) REVERT: O 189 THR cc_start: 0.9410 (p) cc_final: 0.9181 (t) REVERT: P 48 GLU cc_start: 0.8289 (tt0) cc_final: 0.7721 (tm-30) REVERT: P 57 ASP cc_start: 0.8511 (t70) cc_final: 0.8179 (t0) REVERT: P 75 SER cc_start: 0.9047 (t) cc_final: 0.8673 (t) REVERT: P 103 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7946 (mt-10) REVERT: P 166 ASN cc_start: 0.9048 (t0) cc_final: 0.8487 (t0) REVERT: P 167 ASN cc_start: 0.9196 (m110) cc_final: 0.8602 (m110) REVERT: Q 24 GLU cc_start: 0.7931 (tt0) cc_final: 0.7602 (tm-30) REVERT: Q 28 LYS cc_start: 0.9194 (mttm) cc_final: 0.8565 (mttt) REVERT: Q 55 ASP cc_start: 0.8165 (t0) cc_final: 0.7869 (t0) REVERT: Q 61 LYS cc_start: 0.8721 (mttm) cc_final: 0.8514 (tppt) REVERT: Q 96 LEU cc_start: 0.9216 (tt) cc_final: 0.8940 (tt) REVERT: Q 99 GLU cc_start: 0.7875 (mp0) cc_final: 0.7668 (mp0) REVERT: Q 116 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7786 (tp40) REVERT: Q 153 TYR cc_start: 0.9214 (p90) cc_final: 0.8968 (p90) REVERT: Q 157 LYS cc_start: 0.8782 (mttt) cc_final: 0.8556 (mtpt) REVERT: Q 193 LYS cc_start: 0.9485 (ptpt) cc_final: 0.9160 (ptmt) REVERT: Q 224 GLU cc_start: 0.7979 (tp30) cc_final: 0.7762 (tp30) REVERT: R 32 LYS cc_start: 0.8805 (mttp) cc_final: 0.8534 (mttp) REVERT: R 227 HIS cc_start: 0.8475 (t-90) cc_final: 0.8230 (t70) REVERT: S 30 LYS cc_start: 0.8992 (mttt) cc_final: 0.8719 (mptt) REVERT: S 86 ASN cc_start: 0.9006 (m-40) cc_final: 0.8698 (m-40) REVERT: S 90 GLN cc_start: 0.8562 (tp40) cc_final: 0.7981 (tp-100) REVERT: S 94 ASP cc_start: 0.8085 (p0) cc_final: 0.7767 (p0) REVERT: T 180 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7901 (tp-100) REVERT: T 236 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8809 (mm-30) REVERT: U 5 SER cc_start: 0.9156 (t) cc_final: 0.8743 (p) REVERT: U 19 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8126 (mm-30) REVERT: U 104 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8807 (mtmm) REVERT: U 155 ASP cc_start: 0.8199 (p0) cc_final: 0.7925 (p0) REVERT: U 187 PHE cc_start: 0.7244 (p90) cc_final: 0.6835 (p90) REVERT: U 189 TRP cc_start: 0.7201 (m-90) cc_final: 0.7001 (m-90) REVERT: U 216 GLU cc_start: 0.8274 (pt0) cc_final: 0.8041 (pt0) REVERT: U 224 ASN cc_start: 0.8750 (p0) cc_final: 0.8367 (p0) REVERT: U 228 ARG cc_start: 0.8441 (mtm110) cc_final: 0.8146 (mtp-110) REVERT: V 30 ASN cc_start: 0.8714 (t0) cc_final: 0.8445 (OUTLIER) REVERT: V 153 ASN cc_start: 0.8328 (m-40) cc_final: 0.7703 (m-40) REVERT: V 214 GLU cc_start: 0.8662 (tt0) cc_final: 0.8445 (tt0) REVERT: W 73 TYR cc_start: 0.9279 (t80) cc_final: 0.8968 (t80) REVERT: W 77 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8251 (mm-30) REVERT: W 97 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8752 (mtpp) REVERT: W 105 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8172 (mm-30) REVERT: W 164 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7595 (mm-30) REVERT: X 36 PHE cc_start: 0.9002 (m-80) cc_final: 0.8792 (m-80) REVERT: X 37 LYS cc_start: 0.8750 (tttm) cc_final: 0.8544 (tttp) REVERT: X 87 ASN cc_start: 0.8813 (m-40) cc_final: 0.8343 (m110) REVERT: X 108 ASP cc_start: 0.8357 (t70) cc_final: 0.8043 (t70) REVERT: X 118 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7512 (mtp) REVERT: X 166 GLU cc_start: 0.8384 (tp30) cc_final: 0.8037 (tp30) REVERT: Y 26 ILE cc_start: 0.9267 (mt) cc_final: 0.9008 (mp) REVERT: Y 62 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8849 (mm110) REVERT: Y 70 ASN cc_start: 0.9302 (m-40) cc_final: 0.9089 (m110) REVERT: Y 81 LYS cc_start: 0.9161 (tptt) cc_final: 0.8870 (tptm) REVERT: Y 119 ASN cc_start: 0.8734 (m-40) cc_final: 0.8462 (m110) REVERT: Y 139 MET cc_start: 0.8173 (ttp) cc_final: 0.7926 (ttp) REVERT: Z 8 ASN cc_start: 0.9016 (m110) cc_final: 0.8725 (m110) REVERT: Z 105 TYR cc_start: 0.8633 (t80) cc_final: 0.8406 (t80) REVERT: Z 157 ASN cc_start: 0.8520 (m-40) cc_final: 0.8147 (m110) REVERT: Z 177 ASP cc_start: 0.7916 (m-30) cc_final: 0.7709 (m-30) REVERT: a 5 MET cc_start: 0.7801 (mmm) cc_final: 0.7339 (tpt) REVERT: a 56 ASP cc_start: 0.8554 (t70) cc_final: 0.8085 (t70) REVERT: a 59 ASP cc_start: 0.8899 (m-30) cc_final: 0.8682 (m-30) REVERT: a 133 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7719 (mt-10) REVERT: b 7 GLN cc_start: 0.8597 (tt0) cc_final: 0.8240 (tt0) REVERT: b 69 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7854 (mt-10) outliers start: 107 outliers final: 26 residues processed: 1153 average time/residue: 1.7601 time to fit residues: 2470.0651 Evaluate side-chains 1028 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 998 time to evaluate : 5.734 ------------------------------------------------------------------------------- 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 137 ASP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain J residue 26 VAL 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 65 GLN 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 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 R residue 47 CYS Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 97 LYS Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain a residue 168 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 309 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 463 optimal weight: 5.9990 chunk 379 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 557 optimal weight: 4.9990 chunk 602 optimal weight: 0.7980 chunk 496 optimal weight: 1.9990 chunk 553 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 447 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 C 23 GLN C 122 ASN E 65 HIS G 24 GLN G 100 ASN H 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN J 193 ASN K 175 ASN L 146 GLN L 157 ASN M 89 HIS N 154 GLN O 139 ASN O 147 GLN S 185 ASN T 63 ASN T 101 ASN V 57 GLN V 80 ASN V 85 GLN W 6 ASN W 32 GLN W 80 GLN W 156 ASN X 63 ASN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 186 ASN Y 10 HIS Y 191 ASN Z 146 GLN a 2 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 47220 Z= 0.271 Angle : 0.577 10.325 64063 Z= 0.310 Chirality : 0.044 0.153 7447 Planarity : 0.004 0.070 8164 Dihedral : 4.488 25.303 6849 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.91 % Allowed : 15.05 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.10), residues: 6188 helix: 1.74 (0.10), residues: 2353 sheet: 0.04 (0.12), residues: 1495 loop : -0.32 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 215 HIS 0.006 0.001 HIS S 65 PHE 0.018 0.001 PHE W 68 TYR 0.036 0.001 TYR U 160 ARG 0.011 0.001 ARG C 213 *********************** 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 1180 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1049 time to evaluate : 5.709 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: 0.8511 (tm130) cc_final: 0.8072 (tm-30) REVERT: A 147 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8537 (tm-30) REVERT: A 158 LYS cc_start: 0.8927 (mttm) cc_final: 0.8583 (mttp) REVERT: A 195 LYS cc_start: 0.9505 (ttpp) cc_final: 0.9293 (ttmm) REVERT: A 202 MET cc_start: 0.7913 (mtm) cc_final: 0.7689 (mtt) REVERT: B 72 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8036 (ptp) REVERT: B 90 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9409 (mt) REVERT: B 166 ASN cc_start: 0.9183 (t0) cc_final: 0.8920 (t0) REVERT: C 55 ASP cc_start: 0.8376 (t0) cc_final: 0.8056 (t0) REVERT: C 61 LYS cc_start: 0.8565 (mttm) cc_final: 0.8087 (mtmt) REVERT: C 66 ASP cc_start: 0.8650 (t0) cc_final: 0.8284 (t0) REVERT: C 116 GLN cc_start: 0.8733 (tm130) cc_final: 0.8202 (tp40) REVERT: D 32 LYS cc_start: 0.9065 (mttt) cc_final: 0.8819 (mttp) REVERT: D 66 LYS cc_start: 0.8569 (mttt) cc_final: 0.8339 (mmtp) REVERT: D 84 ASP cc_start: 0.8856 (m-30) cc_final: 0.8487 (m-30) REVERT: D 91 LYS cc_start: 0.9116 (tptp) cc_final: 0.8322 (tptt) REVERT: D 93 ARG cc_start: 0.8930 (mtt180) cc_final: 0.8717 (mtt180) REVERT: D 95 GLU cc_start: 0.8192 (tp30) cc_final: 0.7647 (tp30) REVERT: E 26 MET cc_start: 0.8210 (mmm) cc_final: 0.7908 (mmm) REVERT: E 27 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7445 (tm-30) REVERT: E 67 ASP cc_start: 0.8722 (t70) cc_final: 0.8292 (t0) REVERT: E 90 GLN cc_start: 0.8593 (tp40) cc_final: 0.8169 (mm-40) REVERT: E 94 ASP cc_start: 0.8139 (m-30) cc_final: 0.7834 (m-30) REVERT: E 100 ASP cc_start: 0.8108 (t0) cc_final: 0.7795 (t0) REVERT: E 176 MET cc_start: 0.8210 (ttp) cc_final: 0.7955 (ttt) REVERT: E 180 MET cc_start: 0.8387 (mmm) cc_final: 0.8069 (tpt) REVERT: F 27 MET cc_start: 0.8484 (mtt) cc_final: 0.8066 (mtt) REVERT: F 31 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: F 70 ASP cc_start: 0.8452 (t0) cc_final: 0.7922 (t0) REVERT: F 93 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7847 (mm-30) REVERT: F 97 ASN cc_start: 0.9015 (m-40) cc_final: 0.8713 (m110) REVERT: F 147 GLN cc_start: 0.8597 (mt0) cc_final: 0.7897 (mt0) REVERT: F 150 MET cc_start: 0.7985 (tmt) cc_final: 0.7481 (tmt) REVERT: G 10 ASP cc_start: 0.8616 (p0) cc_final: 0.8336 (p0) REVERT: G 43 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.7746 (ptt-90) REVERT: G 81 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8469 (p) REVERT: G 104 LYS cc_start: 0.9110 (mtpp) cc_final: 0.8854 (mtpm) REVERT: G 112 ASP cc_start: 0.8861 (p0) cc_final: 0.8615 (p0) REVERT: G 116 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8321 (ttmm) REVERT: G 120 ASP cc_start: 0.8154 (m-30) cc_final: 0.7873 (m-30) REVERT: G 224 ASN cc_start: 0.8976 (t0) cc_final: 0.8247 (p0) REVERT: H 30 ASN cc_start: 0.8712 (t0) cc_final: 0.8227 (t0) REVERT: H 72 ARG cc_start: 0.8831 (ptp90) cc_final: 0.8410 (ptp-170) REVERT: H 202 TYR cc_start: 0.7383 (m-80) cc_final: 0.7161 (m-10) REVERT: I 49 TYR cc_start: 0.8764 (m-80) cc_final: 0.8491 (m-80) REVERT: I 105 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8194 (mt-10) REVERT: I 112 ASP cc_start: 0.8562 (t0) cc_final: 0.8302 (t0) REVERT: I 145 MET cc_start: 0.8663 (mtm) cc_final: 0.8441 (mtp) REVERT: I 157 MET cc_start: 0.9202 (mtm) cc_final: 0.8995 (mtm) REVERT: I 175 ASP cc_start: 0.8433 (m-30) cc_final: 0.8027 (m-30) REVERT: J 68 LYS cc_start: 0.9094 (tptp) cc_final: 0.8840 (tptp) REVERT: J 101 ASN cc_start: 0.9028 (m110) cc_final: 0.8823 (m-40) REVERT: J 108 ASP cc_start: 0.8112 (t70) cc_final: 0.7702 (t70) REVERT: J 184 ASP cc_start: 0.8503 (p0) cc_final: 0.8290 (p0) REVERT: K 44 THR cc_start: 0.9115 (m) cc_final: 0.8772 (m) REVERT: K 56 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8714 (mp0) REVERT: K 81 LYS cc_start: 0.8662 (tptt) cc_final: 0.8304 (tmtt) REVERT: L 73 LYS cc_start: 0.8949 (mttt) cc_final: 0.8716 (mtmm) REVERT: L 186 ASP cc_start: 0.8522 (t0) cc_final: 0.8197 (t0) REVERT: L 205 GLU cc_start: 0.7908 (mp0) cc_final: 0.7584 (mp0) REVERT: M 26 MET cc_start: 0.8570 (mtp) cc_final: 0.8249 (mtm) REVERT: M 56 ASP cc_start: 0.8577 (t0) cc_final: 0.8349 (t0) REVERT: M 64 LYS cc_start: 0.9010 (mtpt) cc_final: 0.8653 (mtpp) REVERT: M 79 ASP cc_start: 0.8259 (p0) cc_final: 0.7597 (p0) REVERT: M 81 HIS cc_start: 0.8022 (m90) cc_final: 0.7737 (m90) REVERT: M 104 ASN cc_start: 0.9104 (t0) cc_final: 0.8468 (t0) REVERT: M 170 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7873 (mp0) REVERT: M 180 ASP cc_start: 0.8697 (t70) cc_final: 0.8241 (t0) REVERT: M 200 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7493 (mt-10) REVERT: M 210 ASP cc_start: 0.8520 (p0) cc_final: 0.8265 (p0) REVERT: N 84 LYS cc_start: 0.9382 (ttpt) cc_final: 0.9086 (ttpp) REVERT: N 151 GLU cc_start: 0.7929 (tt0) cc_final: 0.7698 (tt0) REVERT: N 167 ASP cc_start: 0.8176 (t0) cc_final: 0.7852 (t0) REVERT: O 48 GLU cc_start: 0.7862 (pp20) cc_final: 0.7544 (pp20) REVERT: O 57 ASP cc_start: 0.8221 (t0) cc_final: 0.7862 (t0) REVERT: O 108 GLN cc_start: 0.8878 (mm-40) cc_final: 0.7783 (mm-40) REVERT: O 111 GLN cc_start: 0.8743 (mt0) cc_final: 0.8453 (mt0) REVERT: O 142 ARG cc_start: 0.8225 (ttt-90) cc_final: 0.7716 (ttt-90) REVERT: O 147 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: P 22 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: P 48 GLU cc_start: 0.8223 (tt0) cc_final: 0.7643 (tm-30) REVERT: P 57 ASP cc_start: 0.8552 (t70) cc_final: 0.8192 (t0) REVERT: P 75 SER cc_start: 0.9117 (t) cc_final: 0.8768 (t) REVERT: P 166 ASN cc_start: 0.9087 (t0) cc_final: 0.8594 (t0) REVERT: P 167 ASN cc_start: 0.9274 (m110) cc_final: 0.8778 (m110) REVERT: Q 23 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: Q 24 GLU cc_start: 0.8096 (tt0) cc_final: 0.7878 (tm-30) REVERT: Q 28 LYS cc_start: 0.9200 (mttm) cc_final: 0.8872 (mtpt) REVERT: Q 55 ASP cc_start: 0.8303 (t0) cc_final: 0.7994 (t0) REVERT: Q 61 LYS cc_start: 0.8739 (mttm) cc_final: 0.8515 (tppt) REVERT: Q 116 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7906 (tp40) REVERT: Q 148 ASP cc_start: 0.8482 (t0) cc_final: 0.8132 (t0) REVERT: Q 153 TYR cc_start: 0.9293 (p90) cc_final: 0.9070 (p90) REVERT: Q 157 LYS cc_start: 0.8784 (mttt) cc_final: 0.8246 (mtmp) REVERT: Q 193 LYS cc_start: 0.9501 (ptpt) cc_final: 0.9172 (ptmt) REVERT: Q 224 GLU cc_start: 0.7979 (tp30) cc_final: 0.7771 (tp30) REVERT: R 32 LYS cc_start: 0.8823 (mttp) cc_final: 0.8496 (mttp) REVERT: R 227 HIS cc_start: 0.8529 (t-90) cc_final: 0.8316 (t70) REVERT: R 231 LYS cc_start: 0.9261 (mtpm) cc_final: 0.8890 (tttp) REVERT: S 26 MET cc_start: 0.8483 (mtp) cc_final: 0.8190 (mtp) REVERT: S 30 LYS cc_start: 0.8942 (mttt) cc_final: 0.8587 (mptt) REVERT: S 31 GLN cc_start: 0.7837 (pp30) cc_final: 0.7612 (pp30) REVERT: S 90 GLN cc_start: 0.8798 (tp40) cc_final: 0.8272 (mm-40) REVERT: S 94 ASP cc_start: 0.8087 (p0) cc_final: 0.7742 (p0) REVERT: T 93 GLU cc_start: 0.7650 (pp20) cc_final: 0.7169 (pp20) REVERT: U 5 SER cc_start: 0.9119 (t) cc_final: 0.8526 (m) REVERT: U 104 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8833 (mtmm) REVERT: U 155 ASP cc_start: 0.8264 (p0) cc_final: 0.7924 (p0) REVERT: U 187 PHE cc_start: 0.7298 (p90) cc_final: 0.6983 (p90) REVERT: U 189 TRP cc_start: 0.7284 (m-90) cc_final: 0.7022 (m-90) REVERT: U 216 GLU cc_start: 0.8370 (pt0) cc_final: 0.8146 (pt0) REVERT: U 224 ASN cc_start: 0.8755 (p0) cc_final: 0.8369 (p0) REVERT: U 228 ARG cc_start: 0.8456 (mtm110) cc_final: 0.8080 (mtp-110) REVERT: V 51 ASP cc_start: 0.8673 (m-30) cc_final: 0.8434 (m-30) REVERT: V 53 ASP cc_start: 0.7744 (m-30) cc_final: 0.7399 (m-30) REVERT: V 85 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: V 157 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8036 (mm-30) REVERT: V 214 GLU cc_start: 0.8682 (tt0) cc_final: 0.8461 (tt0) REVERT: W 64 GLN cc_start: 0.8741 (mt0) cc_final: 0.8519 (mt0) REVERT: W 74 GLU cc_start: 0.7137 (tp30) cc_final: 0.6823 (tp30) REVERT: W 77 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7886 (mm-30) REVERT: W 164 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7749 (mm-30) REVERT: X 36 PHE cc_start: 0.8983 (m-80) cc_final: 0.8692 (m-80) REVERT: X 37 LYS cc_start: 0.8894 (tttm) cc_final: 0.8650 (tttp) REVERT: X 108 ASP cc_start: 0.8404 (t70) cc_final: 0.8122 (t70) REVERT: X 118 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7627 (mtp) REVERT: X 166 GLU cc_start: 0.8446 (tp30) cc_final: 0.8105 (tp30) REVERT: X 168 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: Y 26 ILE cc_start: 0.9344 (mt) cc_final: 0.9046 (mp) REVERT: Y 62 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8896 (mm-40) REVERT: Y 67 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8255 (tm-30) REVERT: Y 70 ASN cc_start: 0.9382 (m-40) cc_final: 0.9087 (m110) REVERT: Y 81 LYS cc_start: 0.9264 (tptt) cc_final: 0.8841 (tptm) REVERT: Z 157 ASN cc_start: 0.8548 (m-40) cc_final: 0.8305 (m110) REVERT: Z 196 CYS cc_start: 0.8487 (m) cc_final: 0.7328 (m) REVERT: a 5 MET cc_start: 0.7976 (mmm) cc_final: 0.7668 (tpt) REVERT: a 56 ASP cc_start: 0.8720 (t70) cc_final: 0.8298 (t70) REVERT: a 133 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7814 (mt-10) REVERT: a 180 ASP cc_start: 0.8687 (t0) cc_final: 0.8443 (t0) REVERT: b 61 TYR cc_start: 0.9215 (t80) cc_final: 0.9012 (t80) REVERT: b 69 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7917 (mt-10) outliers start: 131 outliers final: 45 residues processed: 1104 average time/residue: 1.6417 time to fit residues: 2213.7334 Evaluate side-chains 1043 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 986 time to evaluate : 4.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 95 ARG 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 G residue 43 ARG Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain I residue 137 VAL 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 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 99 ILE Chi-restraints excluded: chain O residue 147 GLN 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 81 SER Chi-restraints excluded: chain P residue 150 SER Chi-restraints excluded: chain Q residue 23 GLN 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 U residue 112 ASP Chi-restraints excluded: chain U residue 161 CYS Chi-restraints excluded: chain V residue 85 GLN Chi-restraints excluded: chain X residue 41 LYS Chi-restraints excluded: chain X residue 46 CYS 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 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 550 optimal weight: 4.9990 chunk 419 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 266 optimal weight: 9.9990 chunk 374 optimal weight: 4.9990 chunk 559 optimal weight: 5.9990 chunk 592 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 530 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN C 54 GLN D 225 ASN E 20 HIS E 68 ASN F 120 HIS H 153 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN J 63 ASN J 99 HIS K 162 GLN K 175 ASN L 108 ASN L 157 ASN L 159 GLN M 47 ASN N 110 GLN N 193 GLN O 139 ASN P 198 ASN S 21 GLN S 175 HIS ** T 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN V 57 GLN V 80 ASN V 85 GLN W 32 GLN W 60 GLN W 80 GLN W 156 ASN X 65 GLN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN ** 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: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 47220 Z= 0.481 Angle : 0.659 9.480 64063 Z= 0.350 Chirality : 0.046 0.281 7447 Planarity : 0.004 0.070 8164 Dihedral : 4.639 27.129 6847 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.62 % Allowed : 16.71 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.10), residues: 6188 helix: 1.69 (0.10), residues: 2357 sheet: -0.02 (0.12), residues: 1511 loop : -0.28 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 215 HIS 0.005 0.001 HIS S 65 PHE 0.018 0.002 PHE W 68 TYR 0.036 0.002 TYR U 160 ARG 0.010 0.001 ARG G 117 *********************** 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 1170 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1007 time to evaluate : 4.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8614 (ttpm) REVERT: A 147 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 176 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8420 (tpp-160) REVERT: A 195 LYS cc_start: 0.9505 (ttpp) cc_final: 0.9304 (ttmm) REVERT: A 202 MET cc_start: 0.7984 (mtm) cc_final: 0.7752 (mtt) REVERT: B 72 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8234 (ptp) REVERT: B 90 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9391 (mt) REVERT: C 28 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8886 (mtmm) REVERT: C 55 ASP cc_start: 0.8434 (t0) cc_final: 0.8040 (t0) REVERT: C 61 LYS cc_start: 0.8630 (mttm) cc_final: 0.8181 (mtpt) REVERT: C 66 ASP cc_start: 0.8703 (t0) cc_final: 0.7705 (t0) REVERT: C 95 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7719 (ttp-170) REVERT: C 99 GLU cc_start: 0.7972 (mp0) cc_final: 0.7708 (mp0) REVERT: C 120 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8019 (tp-100) REVERT: D 32 LYS cc_start: 0.9078 (mttt) cc_final: 0.8821 (mttp) REVERT: D 91 LYS cc_start: 0.9176 (tptp) cc_final: 0.8398 (tptp) REVERT: D 95 GLU cc_start: 0.8281 (tp30) cc_final: 0.7745 (tp30) REVERT: D 196 LYS cc_start: 0.9272 (mtpp) cc_final: 0.8935 (mtmp) REVERT: E 26 MET cc_start: 0.8382 (mmm) cc_final: 0.7977 (mmm) REVERT: E 67 ASP cc_start: 0.8769 (t70) cc_final: 0.8349 (t0) REVERT: E 90 GLN cc_start: 0.8695 (tp40) cc_final: 0.8345 (mm-40) REVERT: E 94 ASP cc_start: 0.8147 (m-30) cc_final: 0.7903 (m-30) REVERT: E 100 ASP cc_start: 0.8146 (t0) cc_final: 0.7824 (t0) REVERT: E 178 GLU cc_start: 0.8449 (pm20) cc_final: 0.8146 (pm20) REVERT: E 180 MET cc_start: 0.8427 (mmm) cc_final: 0.8188 (tpt) REVERT: E 189 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.8910 (mttp) REVERT: F 27 MET cc_start: 0.8590 (mtt) cc_final: 0.8315 (mtt) REVERT: F 31 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: F 70 ASP cc_start: 0.8511 (t0) cc_final: 0.7985 (t0) REVERT: F 150 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7498 (tmt) REVERT: G 10 ASP cc_start: 0.8688 (p0) cc_final: 0.8424 (p0) REVERT: G 11 ARG cc_start: 0.8300 (mtt90) cc_final: 0.7592 (mtt90) REVERT: G 104 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8915 (mtpm) REVERT: G 112 ASP cc_start: 0.8915 (p0) cc_final: 0.8674 (p0) REVERT: G 116 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8220 (ttmm) REVERT: G 120 ASP cc_start: 0.8196 (m-30) cc_final: 0.7839 (m-30) REVERT: H 30 ASN cc_start: 0.8696 (t0) cc_final: 0.8190 (t0) REVERT: H 72 ARG cc_start: 0.8826 (ptp90) cc_final: 0.8527 (ptp-170) REVERT: H 118 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8941 (p) REVERT: I 79 ARG cc_start: 0.8828 (ptt-90) cc_final: 0.8567 (ptt90) REVERT: I 105 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: I 112 ASP cc_start: 0.8647 (t0) cc_final: 0.8389 (t0) REVERT: I 130 MET cc_start: 0.8110 (tmm) cc_final: 0.7561 (tmm) REVERT: I 164 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: I 175 ASP cc_start: 0.8480 (m-30) cc_final: 0.8086 (m-30) REVERT: J 27 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8132 (tm130) REVERT: J 68 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8267 (tppt) REVERT: J 101 ASN cc_start: 0.9026 (m110) cc_final: 0.8823 (m-40) REVERT: J 108 ASP cc_start: 0.8164 (t70) cc_final: 0.7845 (t70) REVERT: J 184 ASP cc_start: 0.8501 (p0) cc_final: 0.8278 (p0) REVERT: K 44 THR cc_start: 0.9193 (m) cc_final: 0.8885 (m) REVERT: K 56 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8775 (mp0) REVERT: K 155 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8411 (tp) REVERT: L 39 ASP cc_start: 0.8548 (t70) cc_final: 0.8309 (t0) REVERT: L 47 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8841 (p) REVERT: L 177 ASP cc_start: 0.7896 (m-30) cc_final: 0.7474 (m-30) REVERT: L 186 ASP cc_start: 0.8534 (t0) cc_final: 0.8293 (t0) REVERT: L 188 TYR cc_start: 0.9168 (m-80) cc_final: 0.8863 (m-80) REVERT: L 205 GLU cc_start: 0.7993 (mp0) cc_final: 0.7769 (mp0) REVERT: M 26 MET cc_start: 0.8703 (mtp) cc_final: 0.8351 (mtm) REVERT: M 47 ASN cc_start: 0.8692 (t0) cc_final: 0.8190 (t0) REVERT: M 56 ASP cc_start: 0.8767 (t0) cc_final: 0.8375 (t0) REVERT: M 64 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8811 (mtpp) REVERT: M 79 ASP cc_start: 0.8779 (p0) cc_final: 0.8413 (p0) REVERT: M 104 ASN cc_start: 0.9087 (t0) cc_final: 0.8480 (t0) REVERT: M 170 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7866 (mp0) REVERT: M 180 ASP cc_start: 0.8760 (t70) cc_final: 0.8288 (t0) REVERT: M 200 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7586 (mt-10) REVERT: N 165 GLU cc_start: 0.8293 (tt0) cc_final: 0.8051 (tm-30) REVERT: N 167 ASP cc_start: 0.8224 (t0) cc_final: 0.7959 (t0) REVERT: O 48 GLU cc_start: 0.7940 (pp20) cc_final: 0.7552 (pp20) REVERT: O 57 ASP cc_start: 0.8192 (t0) cc_final: 0.7873 (t0) REVERT: O 108 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8576 (mm110) REVERT: O 118 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8859 (tp40) REVERT: O 142 ARG cc_start: 0.8314 (ttt-90) cc_final: 0.7816 (ttt-90) REVERT: P 22 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: P 30 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.8164 (m-70) REVERT: P 48 GLU cc_start: 0.8191 (tt0) cc_final: 0.7698 (tm-30) REVERT: P 57 ASP cc_start: 0.8572 (t70) cc_final: 0.8202 (t0) REVERT: P 75 SER cc_start: 0.9236 (t) cc_final: 0.8947 (t) REVERT: P 166 ASN cc_start: 0.9158 (t0) cc_final: 0.8547 (t0) REVERT: P 167 ASN cc_start: 0.9237 (m110) cc_final: 0.8496 (m110) REVERT: P 184 MET cc_start: 0.8507 (mmm) cc_final: 0.8266 (mmm) REVERT: Q 23 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: Q 55 ASP cc_start: 0.8413 (t0) cc_final: 0.8100 (t0) REVERT: Q 110 TYR cc_start: 0.8626 (t80) cc_final: 0.8228 (t80) REVERT: Q 116 GLN cc_start: 0.8607 (tm-30) cc_final: 0.7957 (tp40) REVERT: Q 148 ASP cc_start: 0.8741 (t0) cc_final: 0.8239 (t0) REVERT: Q 153 TYR cc_start: 0.9308 (p90) cc_final: 0.9087 (p90) REVERT: Q 157 LYS cc_start: 0.8810 (mttt) cc_final: 0.8281 (mtmp) REVERT: Q 193 LYS cc_start: 0.9471 (ptpt) cc_final: 0.9162 (ptmm) REVERT: Q 224 GLU cc_start: 0.8048 (tp30) cc_final: 0.7814 (tp30) REVERT: R 32 LYS cc_start: 0.8908 (mttp) cc_final: 0.8625 (mttp) REVERT: R 86 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8377 (mptm) REVERT: R 227 HIS cc_start: 0.8581 (t-90) cc_final: 0.8291 (t70) REVERT: R 231 LYS cc_start: 0.9261 (mtpm) cc_final: 0.8802 (tttp) REVERT: S 30 LYS cc_start: 0.8941 (mttt) cc_final: 0.8579 (mptt) REVERT: S 31 GLN cc_start: 0.8117 (pp30) cc_final: 0.7822 (pp30) REVERT: S 90 GLN cc_start: 0.8898 (tp40) cc_final: 0.8439 (mm-40) REVERT: S 94 ASP cc_start: 0.8155 (p0) cc_final: 0.7846 (p0) REVERT: T 93 GLU cc_start: 0.7653 (pp20) cc_final: 0.7298 (pp20) REVERT: T 192 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8827 (mm-30) REVERT: U 5 SER cc_start: 0.9107 (t) cc_final: 0.8545 (m) REVERT: U 80 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8368 (mmm) REVERT: U 83 MET cc_start: 0.8811 (mtp) cc_final: 0.8504 (mtt) REVERT: U 104 LYS cc_start: 0.9101 (mtpt) cc_final: 0.8883 (mtmm) REVERT: U 117 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8297 (mmp80) REVERT: U 155 ASP cc_start: 0.8229 (p0) cc_final: 0.7968 (p0) REVERT: U 187 PHE cc_start: 0.7432 (p90) cc_final: 0.7057 (p90) REVERT: U 189 TRP cc_start: 0.7291 (m-90) cc_final: 0.6902 (m-90) REVERT: U 224 ASN cc_start: 0.8830 (p0) cc_final: 0.8445 (p0) REVERT: U 228 ARG cc_start: 0.8429 (mtm110) cc_final: 0.8123 (mtp-110) REVERT: V 198 ARG cc_start: 0.8190 (ptp-110) cc_final: 0.7925 (ttm110) REVERT: V 214 GLU cc_start: 0.8713 (tt0) cc_final: 0.8500 (tt0) REVERT: W 98 ARG cc_start: 0.9078 (tpt-90) cc_final: 0.8699 (tpt-90) REVERT: W 161 HIS cc_start: 0.8346 (m-70) cc_final: 0.8130 (m170) REVERT: W 164 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7922 (mm-30) REVERT: X 36 PHE cc_start: 0.8923 (m-80) cc_final: 0.8597 (m-80) REVERT: X 37 LYS cc_start: 0.8971 (tttm) cc_final: 0.8703 (tttp) REVERT: X 108 ASP cc_start: 0.8502 (t70) cc_final: 0.8232 (t70) REVERT: X 166 GLU cc_start: 0.8510 (tp30) cc_final: 0.8249 (tp30) REVERT: X 169 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8872 (ptmm) REVERT: X 186 ASN cc_start: 0.9026 (m-40) cc_final: 0.8818 (m-40) REVERT: Y 26 ILE cc_start: 0.9363 (mt) cc_final: 0.9073 (mp) REVERT: Y 62 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8970 (mm-40) REVERT: Y 67 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8383 (tm-30) REVERT: Z 157 ASN cc_start: 0.8651 (m-40) cc_final: 0.8445 (m110) REVERT: Z 172 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8359 (mtp) REVERT: Z 177 ASP cc_start: 0.8192 (m-30) cc_final: 0.7947 (m-30) REVERT: Z 196 CYS cc_start: 0.8542 (m) cc_final: 0.8213 (m) REVERT: a 5 MET cc_start: 0.7995 (mmm) cc_final: 0.7706 (tpt) REVERT: a 25 ASP cc_start: 0.8811 (p0) cc_final: 0.8469 (p0) REVERT: a 56 ASP cc_start: 0.8755 (t70) cc_final: 0.8506 (t70) REVERT: a 59 ASP cc_start: 0.9093 (m-30) cc_final: 0.8810 (m-30) REVERT: a 180 ASP cc_start: 0.8772 (t0) cc_final: 0.8492 (t0) REVERT: b 7 GLN cc_start: 0.8711 (tt0) cc_final: 0.8305 (tt0) REVERT: b 69 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7903 (mt-10) REVERT: b 71 ASN cc_start: 0.8844 (t0) cc_final: 0.8627 (t0) REVERT: b 106 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8383 (pt0) outliers start: 163 outliers final: 66 residues processed: 1074 average time/residue: 1.5391 time to fit residues: 2017.0857 Evaluate side-chains 1046 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 956 time to evaluate : 4.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 72 MET 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 93 SER Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 120 GLN 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 E residue 189 LYS Chi-restraints excluded: chain F residue 20 VAL 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 F residue 150 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 118 SER 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 164 GLU 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 68 LYS 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 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 L residue 47 THR 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 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 99 ILE Chi-restraints excluded: chain O residue 102 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 22 GLU Chi-restraints excluded: chain P residue 30 HIS Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 150 SER Chi-restraints excluded: chain Q residue 23 GLN 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 147 THR Chi-restraints excluded: chain T residue 189 ILE 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 117 ARG 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 41 LYS Chi-restraints excluded: chain X residue 46 CYS 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 99 THR Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 158 MET Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain a residue 14 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 493 optimal weight: 0.9980 chunk 336 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 441 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 505 optimal weight: 2.9990 chunk 409 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 302 optimal weight: 1.9990 chunk 531 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 B 146 GLN D 204 GLN D 225 ASN E 43 HIS E 68 ASN F 97 ASN H 57 GLN H 153 ASN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 ASN L 108 ASN L 131 GLN L 157 ASN L 159 GLN M 185 ASN O 139 ASN S 65 HIS T 63 ASN T 101 ASN V 57 GLN V 80 ASN V 153 ASN W 32 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 Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 47220 Z= 0.240 Angle : 0.577 7.946 64063 Z= 0.309 Chirality : 0.043 0.258 7447 Planarity : 0.004 0.068 8164 Dihedral : 4.475 25.649 6847 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.98 % Allowed : 18.54 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.10), residues: 6188 helix: 1.84 (0.10), residues: 2362 sheet: 0.08 (0.13), residues: 1496 loop : -0.27 (0.13), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 215 HIS 0.005 0.001 HIS a 89 PHE 0.018 0.001 PHE G 210 TYR 0.031 0.001 TYR G 160 ARG 0.010 0.000 ARG O 59 *********************** 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 1183 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1049 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8515 (ttpm) REVERT: A 78 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8012 (mtp) REVERT: A 147 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 158 LYS cc_start: 0.8941 (mttm) cc_final: 0.8553 (mttp) REVERT: A 202 MET cc_start: 0.8025 (mtm) cc_final: 0.7809 (mtm) REVERT: B 72 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8181 (ptp) REVERT: B 184 MET cc_start: 0.8210 (mmm) cc_final: 0.7850 (mmm) REVERT: B 229 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8907 (mppt) REVERT: C 28 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8826 (mtmm) REVERT: C 55 ASP cc_start: 0.8387 (t0) cc_final: 0.8003 (t0) REVERT: C 61 LYS cc_start: 0.8557 (mttm) cc_final: 0.8103 (mtpt) REVERT: C 66 ASP cc_start: 0.8670 (t0) cc_final: 0.8234 (t0) REVERT: C 116 GLN cc_start: 0.8836 (tm130) cc_final: 0.8257 (tp40) REVERT: C 120 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.7934 (tp-100) REVERT: C 157 LYS cc_start: 0.8862 (mtpt) cc_final: 0.8601 (mtmm) REVERT: D 32 LYS cc_start: 0.9116 (mttt) cc_final: 0.8838 (mttp) REVERT: D 91 LYS cc_start: 0.9145 (tptp) cc_final: 0.8574 (tppt) REVERT: D 93 ARG cc_start: 0.8914 (mtt180) cc_final: 0.8680 (mtt180) REVERT: D 95 GLU cc_start: 0.8261 (tp30) cc_final: 0.7842 (tp30) REVERT: E 26 MET cc_start: 0.8281 (mmm) cc_final: 0.8039 (mmm) REVERT: E 27 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7408 (tm-30) REVERT: E 67 ASP cc_start: 0.8746 (t70) cc_final: 0.8307 (t0) REVERT: E 90 GLN cc_start: 0.8704 (tp40) cc_final: 0.8317 (mm-40) REVERT: E 94 ASP cc_start: 0.8122 (m-30) cc_final: 0.7848 (m-30) REVERT: E 100 ASP cc_start: 0.8124 (t0) cc_final: 0.7774 (t0) REVERT: E 178 GLU cc_start: 0.8418 (pm20) cc_final: 0.8094 (pm20) REVERT: E 180 MET cc_start: 0.8387 (mmm) cc_final: 0.8117 (tpt) REVERT: E 189 LYS cc_start: 0.9347 (mttp) cc_final: 0.8903 (mttp) REVERT: F 70 ASP cc_start: 0.8513 (t0) cc_final: 0.8003 (t0) REVERT: F 147 GLN cc_start: 0.8628 (mt0) cc_final: 0.7914 (mt0) REVERT: F 150 MET cc_start: 0.8080 (tmt) cc_final: 0.7323 (tmt) REVERT: F 179 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8585 (tm) REVERT: G 10 ASP cc_start: 0.8700 (p0) cc_final: 0.8420 (p0) REVERT: G 11 ARG cc_start: 0.8289 (mtt90) cc_final: 0.7546 (mtt90) REVERT: G 43 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7772 (ptt-90) REVERT: G 56 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8241 (t) REVERT: G 80 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8194 (mmm) REVERT: G 104 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8913 (mtpm) REVERT: G 112 ASP cc_start: 0.8829 (p0) cc_final: 0.8422 (p0) REVERT: G 116 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8151 (ttmm) REVERT: G 120 ASP cc_start: 0.8200 (m-30) cc_final: 0.7808 (m-30) REVERT: H 30 ASN cc_start: 0.8721 (t0) cc_final: 0.8174 (t0) REVERT: H 118 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8988 (p) REVERT: I 65 ARG cc_start: 0.8126 (mtp85) cc_final: 0.7859 (mtt-85) REVERT: I 105 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: I 112 ASP cc_start: 0.8618 (t0) cc_final: 0.8406 (t0) REVERT: I 130 MET cc_start: 0.8078 (tmm) cc_final: 0.7528 (tmm) REVERT: I 164 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: I 175 ASP cc_start: 0.8470 (m-30) cc_final: 0.8043 (m-30) REVERT: J 101 ASN cc_start: 0.9028 (m110) cc_final: 0.8827 (m-40) REVERT: J 184 ASP cc_start: 0.8473 (p0) cc_final: 0.8254 (p0) REVERT: K 36 GLU cc_start: 0.8047 (mp0) cc_final: 0.7711 (mt-10) REVERT: K 44 THR cc_start: 0.9019 (m) cc_final: 0.8659 (m) REVERT: K 56 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8667 (mp0) REVERT: K 81 LYS cc_start: 0.8837 (tptp) cc_final: 0.8427 (tttm) REVERT: L 39 ASP cc_start: 0.8529 (t70) cc_final: 0.8282 (t0) REVERT: L 131 GLN cc_start: 0.8375 (pt0) cc_final: 0.8130 (pt0) REVERT: L 184 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8522 (tp30) REVERT: L 186 ASP cc_start: 0.8486 (t0) cc_final: 0.8195 (t0) REVERT: L 188 TYR cc_start: 0.9181 (m-80) cc_final: 0.8876 (m-80) REVERT: L 205 GLU cc_start: 0.7897 (mp0) cc_final: 0.7650 (mp0) REVERT: M 26 MET cc_start: 0.8593 (mtp) cc_final: 0.8315 (mtm) REVERT: M 47 ASN cc_start: 0.8692 (t0) cc_final: 0.8237 (t0) REVERT: M 56 ASP cc_start: 0.8721 (t0) cc_final: 0.8332 (t0) REVERT: M 64 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8798 (mtpp) REVERT: M 79 ASP cc_start: 0.8693 (p0) cc_final: 0.8312 (p0) REVERT: M 104 ASN cc_start: 0.9034 (t0) cc_final: 0.8450 (t0) REVERT: M 170 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7764 (mp0) REVERT: M 180 ASP cc_start: 0.8677 (t70) cc_final: 0.8231 (t0) REVERT: M 200 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7522 (mt-10) REVERT: N 167 ASP cc_start: 0.8223 (t0) cc_final: 0.7952 (t0) REVERT: O 48 GLU cc_start: 0.7919 (pp20) cc_final: 0.7503 (pp20) REVERT: O 57 ASP cc_start: 0.8122 (t0) cc_final: 0.7761 (t0) REVERT: O 108 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8226 (mm-40) REVERT: O 118 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8841 (tp40) REVERT: O 142 ARG cc_start: 0.8294 (ttt-90) cc_final: 0.7795 (ttt-90) REVERT: P 22 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: P 30 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.8145 (m-70) REVERT: P 48 GLU cc_start: 0.8113 (tt0) cc_final: 0.7655 (tm-30) REVERT: P 57 ASP cc_start: 0.8537 (t70) cc_final: 0.8156 (t0) REVERT: P 75 SER cc_start: 0.9194 (t) cc_final: 0.8904 (t) REVERT: P 166 ASN cc_start: 0.9134 (t0) cc_final: 0.8536 (t0) REVERT: P 167 ASN cc_start: 0.9234 (m110) cc_final: 0.8594 (m110) REVERT: Q 23 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: Q 55 ASP cc_start: 0.8412 (t0) cc_final: 0.8033 (t0) REVERT: Q 99 GLU cc_start: 0.8149 (mp0) cc_final: 0.7724 (mp0) REVERT: Q 116 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8017 (tp40) REVERT: Q 148 ASP cc_start: 0.8810 (t0) cc_final: 0.8307 (t0) REVERT: Q 157 LYS cc_start: 0.8766 (mttt) cc_final: 0.8225 (mtmp) REVERT: Q 193 LYS cc_start: 0.9459 (ptpt) cc_final: 0.9171 (ptmm) REVERT: Q 224 GLU cc_start: 0.8151 (tp30) cc_final: 0.7902 (tp30) REVERT: R 227 HIS cc_start: 0.8566 (t-90) cc_final: 0.8326 (t70) REVERT: R 231 LYS cc_start: 0.9280 (mtpm) cc_final: 0.8878 (tttp) REVERT: S 30 LYS cc_start: 0.8860 (mttt) cc_final: 0.8640 (mptt) REVERT: S 31 GLN cc_start: 0.8055 (pp30) cc_final: 0.7793 (pp30) REVERT: S 90 GLN cc_start: 0.8769 (tp40) cc_final: 0.8046 (mm-40) REVERT: S 94 ASP cc_start: 0.8109 (p0) cc_final: 0.7651 (p0) REVERT: T 93 GLU cc_start: 0.7677 (pp20) cc_final: 0.7276 (pp20) REVERT: T 97 ASN cc_start: 0.8910 (m110) cc_final: 0.8328 (m-40) REVERT: T 192 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8790 (mm-30) REVERT: T 236 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8808 (mm-30) REVERT: U 5 SER cc_start: 0.9089 (t) cc_final: 0.8521 (m) REVERT: U 21 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.7948 (mmm-85) REVERT: U 80 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8245 (mmm) REVERT: U 83 MET cc_start: 0.8824 (mtp) cc_final: 0.8517 (mtt) REVERT: U 104 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8831 (mtmm) REVERT: U 155 ASP cc_start: 0.8215 (p0) cc_final: 0.7921 (p0) REVERT: U 187 PHE cc_start: 0.7399 (p90) cc_final: 0.7090 (p90) REVERT: U 189 TRP cc_start: 0.7231 (m-90) cc_final: 0.6964 (m-90) REVERT: U 224 ASN cc_start: 0.8841 (p0) cc_final: 0.8451 (p0) REVERT: U 228 ARG cc_start: 0.8410 (mtm110) cc_final: 0.8099 (mtp-110) REVERT: V 150 GLU cc_start: 0.8376 (pm20) cc_final: 0.6883 (pm20) REVERT: V 153 ASN cc_start: 0.8547 (m-40) cc_final: 0.8103 (m110) REVERT: V 198 ARG cc_start: 0.8138 (ptp-110) cc_final: 0.7916 (ttm110) REVERT: V 214 GLU cc_start: 0.8682 (tt0) cc_final: 0.8471 (tt0) REVERT: W 77 GLU cc_start: 0.8562 (mm-30) cc_final: 0.7954 (mm-30) REVERT: W 126 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8772 (pp) REVERT: W 150 GLU cc_start: 0.8573 (tp30) cc_final: 0.8288 (mm-30) REVERT: W 161 HIS cc_start: 0.8297 (m-70) cc_final: 0.8077 (m170) REVERT: W 164 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7873 (mm-30) REVERT: X 37 LYS cc_start: 0.8950 (tttm) cc_final: 0.8748 (tttp) REVERT: X 68 LYS cc_start: 0.9315 (tttm) cc_final: 0.9075 (tptt) REVERT: X 108 ASP cc_start: 0.8476 (t70) cc_final: 0.8210 (t70) REVERT: X 166 GLU cc_start: 0.8504 (tp30) cc_final: 0.8211 (tp30) REVERT: X 186 ASN cc_start: 0.9012 (m-40) cc_final: 0.8799 (m-40) REVERT: Y 26 ILE cc_start: 0.9315 (mt) cc_final: 0.8983 (mp) REVERT: Y 62 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8952 (mm110) REVERT: Y 67 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8350 (tm-30) REVERT: Y 70 ASN cc_start: 0.9457 (m-40) cc_final: 0.9134 (m110) REVERT: Z 157 ASN cc_start: 0.8662 (m-40) cc_final: 0.8449 (m110) REVERT: Z 196 CYS cc_start: 0.8674 (m) cc_final: 0.8450 (m) REVERT: a 5 MET cc_start: 0.7918 (mmm) cc_final: 0.7546 (tpt) REVERT: a 25 ASP cc_start: 0.8748 (p0) cc_final: 0.8382 (p0) REVERT: a 56 ASP cc_start: 0.8665 (t70) cc_final: 0.8463 (t70) REVERT: a 133 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7821 (mt-10) REVERT: a 180 ASP cc_start: 0.8712 (t0) cc_final: 0.8431 (t0) REVERT: b 7 GLN cc_start: 0.8665 (tt0) cc_final: 0.8244 (tt0) REVERT: b 69 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7914 (mt-10) REVERT: b 71 ASN cc_start: 0.8850 (t0) cc_final: 0.8584 (t0) outliers start: 134 outliers final: 51 residues processed: 1106 average time/residue: 1.3978 time to fit residues: 1886.7398 Evaluate side-chains 1057 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 988 time to evaluate : 4.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS 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 B residue 72 MET 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 95 ARG Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 218 LYS 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 80 MET Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 118 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 39 SER 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 56 GLU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain L residue 184 GLU 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 191 THR Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain N residue 20 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 22 GLU Chi-restraints excluded: chain P residue 30 HIS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 150 SER Chi-restraints excluded: chain Q residue 23 GLN 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 U residue 79 VAL Chi-restraints excluded: chain U residue 80 MET Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 126 ILE 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 Y residue 121 ILE Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 158 MET 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 199 optimal weight: 6.9990 chunk 533 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 347 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 593 optimal weight: 5.9990 chunk 492 optimal weight: 10.0000 chunk 274 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 196 optimal weight: 0.6980 chunk 311 optimal weight: 5.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- 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 54 GLN D 225 ASN E 65 HIS E 166 GLN ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 ASN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN J 193 ASN K 175 ASN L 79 ASN L 108 ASN L 157 ASN N 154 GLN O 95 GLN O 139 ASN S 65 HIS T 101 ASN V 57 GLN V 80 ASN V 85 GLN 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** Y 89 GLN Z 108 ASN Z 146 GLN a 61 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 47220 Z= 0.382 Angle : 0.628 10.872 64063 Z= 0.334 Chirality : 0.044 0.250 7447 Planarity : 0.004 0.071 8164 Dihedral : 4.532 26.746 6847 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.42 % Allowed : 19.36 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.11), residues: 6188 helix: 1.80 (0.10), residues: 2356 sheet: -0.02 (0.13), residues: 1511 loop : -0.26 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 215 HIS 0.004 0.001 HIS a 89 PHE 0.017 0.001 PHE W 68 TYR 0.031 0.001 TYR U 160 ARG 0.011 0.001 ARG O 59 *********************** 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 1160 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1006 time to evaluate : 4.056 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: A 49 LYS cc_start: 0.8804 (ttpt) cc_final: 0.8548 (ttpm) REVERT: A 78 MET cc_start: 0.8503 (mtt) cc_final: 0.8216 (mtp) REVERT: A 101 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8749 (mm110) REVERT: A 147 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8376 (tm-30) REVERT: A 176 ARG cc_start: 0.8593 (tpp-160) cc_final: 0.8159 (ttm110) REVERT: A 202 MET cc_start: 0.7977 (mtm) cc_final: 0.7703 (mtm) REVERT: B 72 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8246 (ptp) REVERT: B 229 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8934 (mtmm) REVERT: B 232 GLU cc_start: 0.8266 (pm20) cc_final: 0.7925 (pm20) REVERT: C 28 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8860 (mtmm) REVERT: C 55 ASP cc_start: 0.8509 (t0) cc_final: 0.8121 (t0) REVERT: C 61 LYS cc_start: 0.8614 (mttm) cc_final: 0.8172 (mtmt) REVERT: C 66 ASP cc_start: 0.8696 (t0) cc_final: 0.8282 (t0) REVERT: C 116 GLN cc_start: 0.8921 (tm130) cc_final: 0.8487 (tm-30) REVERT: D 32 LYS cc_start: 0.9129 (mttt) cc_final: 0.8903 (mttp) REVERT: D 93 ARG cc_start: 0.8958 (mtt180) cc_final: 0.8727 (mtt180) REVERT: E 26 MET cc_start: 0.8353 (mmm) cc_final: 0.8048 (mmm) REVERT: E 67 ASP cc_start: 0.8796 (t70) cc_final: 0.8338 (t0) REVERT: E 90 GLN cc_start: 0.8733 (tp40) cc_final: 0.8387 (mm-40) REVERT: E 94 ASP cc_start: 0.8119 (m-30) cc_final: 0.7888 (m-30) REVERT: E 100 ASP cc_start: 0.8095 (t0) cc_final: 0.7763 (t0) REVERT: E 178 GLU cc_start: 0.8384 (pm20) cc_final: 0.8071 (pm20) REVERT: E 180 MET cc_start: 0.8502 (mmm) cc_final: 0.8237 (tpt) REVERT: E 189 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9041 (mttp) REVERT: F 70 ASP cc_start: 0.8575 (t0) cc_final: 0.8070 (t0) REVERT: F 150 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7452 (tmt) REVERT: G 10 ASP cc_start: 0.8717 (p0) cc_final: 0.8467 (p0) REVERT: G 11 ARG cc_start: 0.8300 (mtt90) cc_final: 0.7527 (mtt90) REVERT: G 56 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8196 (t) REVERT: G 80 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8147 (mmm) REVERT: G 104 LYS cc_start: 0.9143 (mtpp) cc_final: 0.8939 (mtpm) REVERT: G 112 ASP cc_start: 0.8856 (p0) cc_final: 0.8451 (p0) REVERT: G 116 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8170 (ttmm) REVERT: G 120 ASP cc_start: 0.8247 (m-30) cc_final: 0.7834 (m-30) REVERT: H 30 ASN cc_start: 0.8731 (t0) cc_final: 0.8184 (t0) REVERT: I 105 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: I 112 ASP cc_start: 0.8637 (t0) cc_final: 0.8434 (t0) REVERT: I 130 MET cc_start: 0.8108 (tmm) cc_final: 0.7622 (tmm) REVERT: I 164 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: I 175 ASP cc_start: 0.8520 (m-30) cc_final: 0.8164 (m-30) REVERT: J 184 ASP cc_start: 0.8487 (p0) cc_final: 0.8222 (p0) REVERT: K 36 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7763 (mt-10) REVERT: K 44 THR cc_start: 0.9084 (m) cc_final: 0.8783 (m) REVERT: K 56 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8670 (mp0) REVERT: K 155 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8365 (tp) REVERT: L 39 ASP cc_start: 0.8549 (t70) cc_final: 0.8252 (t0) REVERT: L 131 GLN cc_start: 0.8402 (pt0) cc_final: 0.8133 (pt0) REVERT: L 177 ASP cc_start: 0.7906 (m-30) cc_final: 0.7699 (m-30) REVERT: L 186 ASP cc_start: 0.8526 (t0) cc_final: 0.8264 (t0) REVERT: L 205 GLU cc_start: 0.8018 (mp0) cc_final: 0.7815 (mp0) REVERT: M 26 MET cc_start: 0.8664 (mtp) cc_final: 0.8315 (mtm) REVERT: M 47 ASN cc_start: 0.8747 (t0) cc_final: 0.8292 (t0) REVERT: M 56 ASP cc_start: 0.8792 (t0) cc_final: 0.8563 (t70) REVERT: M 64 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8791 (mtpp) REVERT: M 79 ASP cc_start: 0.8802 (p0) cc_final: 0.8412 (p0) REVERT: M 104 ASN cc_start: 0.9037 (t0) cc_final: 0.8452 (t0) REVERT: M 170 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7858 (mp0) REVERT: M 180 ASP cc_start: 0.8734 (t70) cc_final: 0.8256 (t0) REVERT: M 200 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7518 (mt-10) REVERT: N 167 ASP cc_start: 0.8202 (t0) cc_final: 0.7925 (t0) REVERT: O 48 GLU cc_start: 0.7948 (pp20) cc_final: 0.7518 (pp20) REVERT: O 57 ASP cc_start: 0.8132 (t0) cc_final: 0.7802 (t0) REVERT: O 108 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8660 (mm110) REVERT: O 111 GLN cc_start: 0.8744 (mt0) cc_final: 0.8500 (mt0) REVERT: O 118 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8930 (tp40) REVERT: O 142 ARG cc_start: 0.8305 (ttt-90) cc_final: 0.7961 (ttt-90) REVERT: P 22 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: P 30 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.8097 (m-70) REVERT: P 48 GLU cc_start: 0.8142 (tt0) cc_final: 0.7671 (tm-30) REVERT: P 57 ASP cc_start: 0.8539 (t70) cc_final: 0.8206 (t0) REVERT: P 75 SER cc_start: 0.9269 (t) cc_final: 0.9017 (t) REVERT: P 166 ASN cc_start: 0.9191 (t0) cc_final: 0.8586 (t0) REVERT: P 167 ASN cc_start: 0.9239 (m110) cc_final: 0.8608 (m110) REVERT: P 184 MET cc_start: 0.8598 (mmm) cc_final: 0.8159 (mmm) REVERT: Q 23 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: Q 55 ASP cc_start: 0.8441 (t0) cc_final: 0.8074 (t0) REVERT: Q 110 TYR cc_start: 0.8660 (t80) cc_final: 0.8120 (t80) REVERT: Q 116 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8303 (tp40) REVERT: Q 148 ASP cc_start: 0.8811 (t0) cc_final: 0.8331 (t0) REVERT: Q 157 LYS cc_start: 0.8798 (mttt) cc_final: 0.8283 (mtmp) REVERT: Q 193 LYS cc_start: 0.9456 (ptpt) cc_final: 0.9219 (ptmm) REVERT: Q 224 GLU cc_start: 0.8179 (tp30) cc_final: 0.7950 (tp30) REVERT: R 32 LYS cc_start: 0.8800 (mttp) cc_final: 0.8552 (mptp) REVERT: R 227 HIS cc_start: 0.8588 (t-90) cc_final: 0.8355 (t70) REVERT: R 231 LYS cc_start: 0.9262 (mtpm) cc_final: 0.8913 (tttm) REVERT: S 30 LYS cc_start: 0.8819 (mttt) cc_final: 0.8594 (mptt) REVERT: S 90 GLN cc_start: 0.8870 (tp40) cc_final: 0.8404 (mm-40) REVERT: S 94 ASP cc_start: 0.8156 (p0) cc_final: 0.7847 (p0) REVERT: T 93 GLU cc_start: 0.7693 (pp20) cc_final: 0.7288 (pp20) REVERT: T 97 ASN cc_start: 0.8927 (m110) cc_final: 0.8349 (m-40) REVERT: U 5 SER cc_start: 0.9087 (t) cc_final: 0.8555 (p) REVERT: U 19 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7929 (mm-30) REVERT: U 21 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.8058 (mmm-85) REVERT: U 83 MET cc_start: 0.8883 (mtp) cc_final: 0.8578 (mtt) REVERT: U 104 LYS cc_start: 0.9098 (mtpt) cc_final: 0.8832 (mtmm) REVERT: U 155 ASP cc_start: 0.8282 (p0) cc_final: 0.7968 (p0) REVERT: U 187 PHE cc_start: 0.7501 (p90) cc_final: 0.7173 (p90) REVERT: U 189 TRP cc_start: 0.7228 (m-90) cc_final: 0.6895 (m-90) REVERT: U 224 ASN cc_start: 0.8857 (p0) cc_final: 0.8503 (p0) REVERT: U 228 ARG cc_start: 0.8417 (mtm110) cc_final: 0.8087 (mtp-110) REVERT: V 85 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8579 (mt0) REVERT: V 135 MET cc_start: 0.9087 (tpt) cc_final: 0.8876 (tpt) REVERT: V 153 ASN cc_start: 0.8467 (m-40) cc_final: 0.8197 (m110) REVERT: V 198 ARG cc_start: 0.8170 (ptp-110) cc_final: 0.7891 (ttm110) REVERT: W 161 HIS cc_start: 0.8342 (m-70) cc_final: 0.8127 (m170) REVERT: W 164 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7942 (mm-30) REVERT: W 172 ASN cc_start: 0.9390 (m110) cc_final: 0.9139 (m110) REVERT: X 68 LYS cc_start: 0.9328 (tttm) cc_final: 0.9040 (tptt) REVERT: X 108 ASP cc_start: 0.8502 (t70) cc_final: 0.8219 (t70) REVERT: X 166 GLU cc_start: 0.8534 (tp30) cc_final: 0.8277 (tp30) REVERT: X 169 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8825 (ptmm) REVERT: Y 26 ILE cc_start: 0.9328 (mt) cc_final: 0.8986 (mp) REVERT: Y 62 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8968 (mm-40) REVERT: Y 67 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8441 (tm-30) REVERT: Y 70 ASN cc_start: 0.9457 (m-40) cc_final: 0.9132 (m110) REVERT: Z 159 GLN cc_start: 0.8613 (mt0) cc_final: 0.8391 (mt0) REVERT: Z 196 CYS cc_start: 0.8665 (m) cc_final: 0.8444 (m) REVERT: a 5 MET cc_start: 0.7960 (mmm) cc_final: 0.7672 (tpt) REVERT: a 25 ASP cc_start: 0.8814 (p0) cc_final: 0.8478 (p0) REVERT: a 164 GLU cc_start: 0.8284 (pt0) cc_final: 0.7955 (pm20) REVERT: a 180 ASP cc_start: 0.8740 (t0) cc_final: 0.8469 (t0) REVERT: a 200 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: b 69 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7969 (mt-10) REVERT: b 71 ASN cc_start: 0.8926 (t0) cc_final: 0.8675 (t0) REVERT: b 106 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8295 (pt0) outliers start: 154 outliers final: 76 residues processed: 1082 average time/residue: 1.3596 time to fit residues: 1808.0061 Evaluate side-chains 1076 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 983 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 106 THR 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 155 ASN Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 95 ARG 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 E residue 166 GLN Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 150 MET 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 131 MET Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 34 LYS Chi-restraints excluded: chain J residue 65 GLN 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 99 THR Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 73 ASP 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 99 ILE Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 223 THR 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 30 HIS 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 P residue 150 SER Chi-restraints excluded: chain Q residue 23 GLN 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 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 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 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 169 LYS Chi-restraints excluded: chain Y residue 42 LEU 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 Y residue 187 VAL Chi-restraints excluded: chain Z residue 158 MET 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 a residue 200 GLU Chi-restraints excluded: chain b residue 51 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 613 random chunks: chunk 571 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 337 optimal weight: 6.9990 chunk 433 optimal weight: 0.7980 chunk 335 optimal weight: 0.9990 chunk 499 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 chunk 590 optimal weight: 0.9990 chunk 369 optimal weight: 6.9990 chunk 360 optimal weight: 0.9990 chunk 272 optimal weight: 2.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN C 23 GLN D 118 ASN D 225 ASN E 65 HIS E 68 ASN F 97 ASN F 180 GLN H 153 ASN I 60 GLN I 168 GLN I 172 ASN J 55 GLN L 157 ASN L 159 GLN ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 GLN S 65 HIS T 63 ASN T 101 ASN V 57 GLN 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 Z 157 ASN a 81 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 47220 Z= 0.210 Angle : 0.594 10.053 64063 Z= 0.318 Chirality : 0.043 0.309 7447 Planarity : 0.004 0.066 8164 Dihedral : 4.421 25.618 6847 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.96 % Allowed : 20.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.11), residues: 6188 helix: 1.91 (0.11), residues: 2351 sheet: 0.09 (0.13), residues: 1494 loop : -0.29 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 159 HIS 0.005 0.001 HIS a 89 PHE 0.018 0.001 PHE G 210 TYR 0.030 0.001 TYR U 160 ARG 0.012 0.000 ARG O 59 *********************** 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 1185 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 1052 time to evaluate : 4.234 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: A 49 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8460 (ttpm) REVERT: A 78 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8084 (mtp) REVERT: A 101 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8907 (mm110) REVERT: A 147 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 158 LYS cc_start: 0.8944 (mttm) cc_final: 0.8544 (mttp) REVERT: A 195 LYS cc_start: 0.9434 (mtpt) cc_final: 0.9206 (ttmm) REVERT: B 67 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8530 (tttm) REVERT: B 72 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8210 (ptp) REVERT: B 184 MET cc_start: 0.8217 (mmm) cc_final: 0.7885 (mmm) REVERT: C 28 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8806 (mtmm) REVERT: C 55 ASP cc_start: 0.8451 (t0) cc_final: 0.8051 (t0) REVERT: C 61 LYS cc_start: 0.8555 (mttm) cc_final: 0.8113 (mtmt) REVERT: C 66 ASP cc_start: 0.8690 (t0) cc_final: 0.8248 (t0) REVERT: C 95 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8488 (ttp-170) REVERT: C 99 GLU cc_start: 0.8163 (mp0) cc_final: 0.7906 (mp0) REVERT: C 116 GLN cc_start: 0.8869 (tm130) cc_final: 0.8303 (tp40) REVERT: C 120 GLN cc_start: 0.9031 (tp40) cc_final: 0.8101 (tp40) REVERT: D 32 LYS cc_start: 0.9112 (mttt) cc_final: 0.8838 (mttp) REVERT: D 91 LYS cc_start: 0.9210 (tptt) cc_final: 0.8719 (tppt) REVERT: D 93 ARG cc_start: 0.8916 (mtt180) cc_final: 0.8687 (mtt180) REVERT: D 95 GLU cc_start: 0.8372 (tp30) cc_final: 0.7987 (tp30) REVERT: E 26 MET cc_start: 0.8304 (mmm) cc_final: 0.7930 (mmm) REVERT: E 27 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7466 (tm-30) REVERT: E 30 LYS cc_start: 0.8310 (mttp) cc_final: 0.8087 (mttp) REVERT: E 67 ASP cc_start: 0.8706 (t70) cc_final: 0.8290 (t0) REVERT: E 90 GLN cc_start: 0.8740 (tp40) cc_final: 0.8368 (mm-40) REVERT: E 94 ASP cc_start: 0.8104 (m-30) cc_final: 0.7844 (m-30) REVERT: E 178 GLU cc_start: 0.8365 (pm20) cc_final: 0.8050 (pm20) REVERT: E 180 MET cc_start: 0.8500 (mmm) cc_final: 0.8270 (tpt) REVERT: E 189 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8965 (mttp) REVERT: F 70 ASP cc_start: 0.8519 (t0) cc_final: 0.8026 (t0) REVERT: F 147 GLN cc_start: 0.8620 (mt0) cc_final: 0.7933 (mt0) REVERT: F 150 MET cc_start: 0.8060 (tmt) cc_final: 0.7461 (tmt) REVERT: G 10 ASP cc_start: 0.8712 (p0) cc_final: 0.8449 (p0) REVERT: G 11 ARG cc_start: 0.8367 (mtt90) cc_final: 0.7687 (mtt90) REVERT: G 56 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8117 (t) REVERT: G 80 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8333 (mmm) REVERT: G 88 ARG cc_start: 0.8112 (mmm160) cc_final: 0.7663 (mmm-85) REVERT: G 112 ASP cc_start: 0.8796 (p0) cc_final: 0.8404 (p0) REVERT: G 116 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8130 (ttmm) REVERT: G 120 ASP cc_start: 0.8182 (m-30) cc_final: 0.7830 (m-30) REVERT: H 30 ASN cc_start: 0.8758 (t0) cc_final: 0.8193 (t0) REVERT: I 65 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7760 (mtt-85) REVERT: I 112 ASP cc_start: 0.8565 (t0) cc_final: 0.8326 (t0) REVERT: I 130 MET cc_start: 0.8130 (tmm) cc_final: 0.7619 (tmm) REVERT: I 164 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: I 175 ASP cc_start: 0.8533 (m-30) cc_final: 0.8132 (m-30) REVERT: J 184 ASP cc_start: 0.8445 (p0) cc_final: 0.8235 (p0) REVERT: K 36 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7787 (mt-10) REVERT: K 56 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: K 81 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8056 (ttmm) REVERT: K 99 THR cc_start: 0.8892 (p) cc_final: 0.8542 (m) REVERT: L 131 GLN cc_start: 0.8345 (pt0) cc_final: 0.8080 (pt0) REVERT: L 157 ASN cc_start: 0.8385 (m110) cc_final: 0.8140 (m-40) REVERT: L 186 ASP cc_start: 0.8458 (t0) cc_final: 0.8182 (t0) REVERT: L 188 TYR cc_start: 0.9119 (m-80) cc_final: 0.8741 (m-80) REVERT: L 205 GLU cc_start: 0.7920 (mp0) cc_final: 0.7657 (mp0) REVERT: M 26 MET cc_start: 0.8581 (mtp) cc_final: 0.8299 (mtm) REVERT: M 47 ASN cc_start: 0.8698 (t0) cc_final: 0.8254 (t0) REVERT: M 56 ASP cc_start: 0.8768 (t0) cc_final: 0.8535 (t70) REVERT: M 64 LYS cc_start: 0.9010 (mtpt) cc_final: 0.8525 (ttmm) REVERT: M 79 ASP cc_start: 0.8719 (p0) cc_final: 0.8284 (p0) REVERT: M 104 ASN cc_start: 0.8999 (t0) cc_final: 0.8405 (t0) REVERT: M 170 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7768 (mp0) REVERT: M 180 ASP cc_start: 0.8656 (t0) cc_final: 0.8221 (t0) REVERT: M 200 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7492 (mt-10) REVERT: N 167 ASP cc_start: 0.8198 (t0) cc_final: 0.7927 (t0) REVERT: O 48 GLU cc_start: 0.7896 (pp20) cc_final: 0.7453 (pp20) REVERT: O 57 ASP cc_start: 0.8018 (t0) cc_final: 0.7680 (t0) REVERT: O 58 GLU cc_start: 0.8356 (pm20) cc_final: 0.7888 (pm20) REVERT: O 108 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8149 (mm-40) REVERT: O 118 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8811 (tp40) REVERT: O 120 TYR cc_start: 0.8720 (m-80) cc_final: 0.8408 (m-80) REVERT: O 142 ARG cc_start: 0.8290 (ttt-90) cc_final: 0.7946 (ttt-90) REVERT: P 22 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: P 34 CYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8203 (t) REVERT: P 48 GLU cc_start: 0.8070 (tt0) cc_final: 0.7624 (tm-30) REVERT: P 57 ASP cc_start: 0.8506 (t70) cc_final: 0.8202 (t0) REVERT: P 75 SER cc_start: 0.9243 (t) cc_final: 0.8867 (t) REVERT: P 166 ASN cc_start: 0.9176 (t0) cc_final: 0.8559 (t0) REVERT: P 167 ASN cc_start: 0.9216 (m110) cc_final: 0.8568 (m110) REVERT: Q 23 GLN cc_start: 0.8307 (mt0) cc_final: 0.7782 (mt0) REVERT: Q 24 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8084 (tm-30) REVERT: Q 55 ASP cc_start: 0.8380 (t0) cc_final: 0.7936 (t0) REVERT: Q 90 GLU cc_start: 0.8116 (tp30) cc_final: 0.7838 (tm-30) REVERT: Q 116 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8109 (tp40) REVERT: Q 148 ASP cc_start: 0.8855 (t0) cc_final: 0.8372 (t0) REVERT: Q 157 LYS cc_start: 0.8769 (mttt) cc_final: 0.8230 (mtmp) REVERT: Q 193 LYS cc_start: 0.9434 (ptpt) cc_final: 0.9223 (ptmm) REVERT: Q 224 GLU cc_start: 0.8106 (tp30) cc_final: 0.7879 (tp30) REVERT: R 32 LYS cc_start: 0.8787 (mttp) cc_final: 0.8527 (mptp) REVERT: R 227 HIS cc_start: 0.8620 (t-90) cc_final: 0.8394 (t70) REVERT: R 231 LYS cc_start: 0.9269 (mtpm) cc_final: 0.8974 (tttm) REVERT: S 30 LYS cc_start: 0.8778 (mttt) cc_final: 0.8572 (mptt) REVERT: S 61 LYS cc_start: 0.9045 (pmtt) cc_final: 0.8805 (pttm) REVERT: S 90 GLN cc_start: 0.8695 (tp40) cc_final: 0.7997 (mm-40) REVERT: S 94 ASP cc_start: 0.8124 (p0) cc_final: 0.7690 (p0) REVERT: T 93 GLU cc_start: 0.7718 (pp20) cc_final: 0.7360 (pp20) REVERT: T 97 ASN cc_start: 0.8931 (m110) cc_final: 0.8304 (m-40) REVERT: U 5 SER cc_start: 0.9073 (t) cc_final: 0.8485 (m) REVERT: U 21 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.7936 (mmm-85) REVERT: U 80 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8408 (mmt) REVERT: U 83 MET cc_start: 0.8852 (mtp) cc_final: 0.8559 (mtt) REVERT: U 155 ASP cc_start: 0.8203 (p0) cc_final: 0.7877 (p0) REVERT: U 187 PHE cc_start: 0.7554 (p90) cc_final: 0.7189 (p90) REVERT: U 189 TRP cc_start: 0.7209 (m-90) cc_final: 0.6986 (m-90) REVERT: U 224 ASN cc_start: 0.8860 (p0) cc_final: 0.8515 (p0) REVERT: U 228 ARG cc_start: 0.8397 (mtm110) cc_final: 0.8108 (mtp-110) REVERT: V 19 ARG cc_start: 0.8966 (ttm170) cc_final: 0.8306 (tmm-80) REVERT: V 51 ASP cc_start: 0.8654 (m-30) cc_final: 0.8366 (m-30) REVERT: V 150 GLU cc_start: 0.8243 (pm20) cc_final: 0.7971 (pm20) REVERT: W 77 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7528 (mm-30) REVERT: W 105 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8113 (mm-30) REVERT: W 150 GLU cc_start: 0.8540 (tp30) cc_final: 0.8300 (mm-30) REVERT: W 161 HIS cc_start: 0.8301 (m-70) cc_final: 0.8096 (m170) REVERT: W 164 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7909 (mm-30) REVERT: W 172 ASN cc_start: 0.9280 (m110) cc_final: 0.8982 (m110) REVERT: X 108 ASP cc_start: 0.8462 (t70) cc_final: 0.8193 (t70) REVERT: X 118 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7387 (mtp) REVERT: X 166 GLU cc_start: 0.8520 (tp30) cc_final: 0.8227 (tp30) REVERT: X 169 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8835 (ptmm) REVERT: X 184 ASP cc_start: 0.8526 (p0) cc_final: 0.8315 (p0) REVERT: Y 26 ILE cc_start: 0.9279 (mt) cc_final: 0.8917 (mp) REVERT: Y 62 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8985 (mm-40) REVERT: Y 67 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8430 (tm-30) REVERT: Y 70 ASN cc_start: 0.9466 (m-40) cc_final: 0.9104 (m110) REVERT: a 5 MET cc_start: 0.7879 (mmm) cc_final: 0.7486 (tpt) REVERT: a 25 ASP cc_start: 0.8765 (p0) cc_final: 0.8419 (p0) REVERT: a 133 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7826 (mt-10) REVERT: a 180 ASP cc_start: 0.8691 (t0) cc_final: 0.8392 (t0) REVERT: a 200 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: b 7 GLN cc_start: 0.8708 (tt0) cc_final: 0.8322 (tt0) REVERT: b 69 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7902 (mt-10) REVERT: b 71 ASN cc_start: 0.8912 (t0) cc_final: 0.8646 (t0) outliers start: 133 outliers final: 60 residues processed: 1110 average time/residue: 1.2191 time to fit residues: 1654.9380 Evaluate side-chains 1063 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 988 time to evaluate : 3.657 ------------------------------------------------------------------------------- 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 B residue 21 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 79 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 H residue 129 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain J residue 14 LEU 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 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 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 92 LEU Chi-restraints excluded: chain P residue 150 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 U residue 79 VAL Chi-restraints excluded: chain U residue 80 MET Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 57 THR 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 118 MET Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Y residue 97 MET Chi-restraints excluded: chain Y residue 167 ASP Chi-restraints excluded: chain Z residue 172 MET 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 a residue 200 GLU Chi-restraints excluded: chain b residue 86 MET 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 365 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 352 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 375 optimal weight: 9.9990 chunk 402 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 464 optimal weight: 0.0170 overall best weight: 2.6026 ------------------------------------------------------------------------------- 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 ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN C 23 GLN C 122 ASN C 175 ASN D 118 ASN D 225 ASN E 65 HIS E 166 GLN F 63 ASN ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 GLN H 153 ASN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN J 55 GLN J 193 ASN K 175 ASN L 159 GLN O 139 ASN S 65 HIS T 68 ASN V 57 GLN V 80 ASN V 153 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 Z 157 ASN a 61 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 47220 Z= 0.372 Angle : 0.658 14.776 64063 Z= 0.350 Chirality : 0.045 0.357 7447 Planarity : 0.004 0.064 8164 Dihedral : 4.524 27.227 6847 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.91 % Allowed : 21.72 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.11), residues: 6188 helix: 1.79 (0.11), residues: 2352 sheet: -0.02 (0.13), residues: 1510 loop : -0.29 (0.13), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 215 HIS 0.009 0.001 HIS F 201 PHE 0.034 0.001 PHE N 65 TYR 0.040 0.001 TYR C 110 ARG 0.012 0.001 ARG V 143 *********************** 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 1118 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 987 time to evaluate : 3.577 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: 0.8817 (ttpt) cc_final: 0.8542 (ttpm) REVERT: A 78 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8214 (mtp) REVERT: A 101 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8920 (mm110) REVERT: A 147 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 158 LYS cc_start: 0.8972 (mttm) cc_final: 0.8568 (mttp) REVERT: A 176 ARG cc_start: 0.8454 (tpp-160) cc_final: 0.8244 (ttm110) REVERT: B 72 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8235 (ptp) REVERT: B 184 MET cc_start: 0.8280 (mmm) cc_final: 0.7919 (mmm) REVERT: C 55 ASP cc_start: 0.8611 (t0) cc_final: 0.8288 (t0) REVERT: C 61 LYS cc_start: 0.8628 (mttm) cc_final: 0.8181 (mtmt) REVERT: C 66 ASP cc_start: 0.8689 (t0) cc_final: 0.8271 (t0) REVERT: C 116 GLN cc_start: 0.8920 (tm130) cc_final: 0.8492 (tm-30) REVERT: D 32 LYS cc_start: 0.9127 (mttt) cc_final: 0.8833 (mttp) REVERT: D 93 ARG cc_start: 0.8956 (mtt180) cc_final: 0.8726 (mtt180) REVERT: E 26 MET cc_start: 0.8334 (mmm) cc_final: 0.8048 (mmm) REVERT: E 27 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7530 (tm-30) REVERT: E 67 ASP cc_start: 0.8793 (t70) cc_final: 0.8348 (t0) REVERT: E 90 GLN cc_start: 0.8745 (tp40) cc_final: 0.8398 (mm-40) REVERT: E 94 ASP cc_start: 0.8119 (m-30) cc_final: 0.7891 (m-30) REVERT: E 178 GLU cc_start: 0.8383 (pm20) cc_final: 0.8049 (pm20) REVERT: E 180 MET cc_start: 0.8540 (mmm) cc_final: 0.8315 (tpt) REVERT: E 189 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9006 (mttp) REVERT: F 70 ASP cc_start: 0.8581 (t0) cc_final: 0.8087 (t0) REVERT: F 150 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7443 (tmt) REVERT: G 10 ASP cc_start: 0.8721 (p0) cc_final: 0.8467 (p0) REVERT: G 56 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8124 (t) REVERT: G 80 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8284 (mmm) REVERT: G 112 ASP cc_start: 0.8856 (p0) cc_final: 0.8447 (p0) REVERT: G 116 LYS cc_start: 0.8903 (ttpt) cc_final: 0.8161 (ttmm) REVERT: G 120 ASP cc_start: 0.8231 (m-30) cc_final: 0.7863 (m-30) REVERT: H 30 ASN cc_start: 0.8747 (t0) cc_final: 0.8175 (t0) REVERT: I 65 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7716 (mtt-85) REVERT: I 105 GLU cc_start: 0.8559 (mp0) cc_final: 0.8186 (mp0) REVERT: I 112 ASP cc_start: 0.8596 (t0) cc_final: 0.8348 (t0) REVERT: I 164 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: I 175 ASP cc_start: 0.8552 (m-30) cc_final: 0.8174 (m-30) REVERT: J 165 GLU cc_start: 0.8128 (pt0) cc_final: 0.7840 (pt0) REVERT: J 184 ASP cc_start: 0.8462 (p0) cc_final: 0.8259 (p0) REVERT: K 36 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7832 (mt-10) REVERT: K 56 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8687 (mp0) REVERT: K 81 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8387 (mtpp) REVERT: L 39 ASP cc_start: 0.8550 (t70) cc_final: 0.8283 (t0) REVERT: L 186 ASP cc_start: 0.8506 (t0) cc_final: 0.8239 (t0) REVERT: L 188 TYR cc_start: 0.9148 (m-80) cc_final: 0.8891 (m-80) REVERT: M 26 MET cc_start: 0.8655 (mtp) cc_final: 0.8342 (mtm) REVERT: M 47 ASN cc_start: 0.8782 (t0) cc_final: 0.8314 (t0) REVERT: M 56 ASP cc_start: 0.8785 (t0) cc_final: 0.8544 (t70) REVERT: M 64 LYS cc_start: 0.9068 (mtpt) cc_final: 0.8637 (mtpp) REVERT: M 79 ASP cc_start: 0.8773 (p0) cc_final: 0.8360 (p0) REVERT: M 104 ASN cc_start: 0.9029 (t0) cc_final: 0.8445 (t0) REVERT: M 170 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7775 (mp0) REVERT: M 180 ASP cc_start: 0.8735 (t0) cc_final: 0.8257 (t0) REVERT: M 200 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7554 (mt-10) REVERT: N 167 ASP cc_start: 0.8195 (t0) cc_final: 0.7913 (t0) REVERT: O 48 GLU cc_start: 0.7963 (pp20) cc_final: 0.7512 (pp20) REVERT: O 57 ASP cc_start: 0.8227 (t0) cc_final: 0.7742 (t0) REVERT: O 108 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8824 (mm-40) REVERT: O 111 GLN cc_start: 0.8725 (mt0) cc_final: 0.8454 (mt0) REVERT: O 118 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8864 (tp40) REVERT: O 142 ARG cc_start: 0.8314 (ttt-90) cc_final: 0.7966 (ttt-90) REVERT: O 208 GLU cc_start: 0.7963 (pt0) cc_final: 0.7762 (pt0) REVERT: P 34 CYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8150 (t) REVERT: P 48 GLU cc_start: 0.8163 (tt0) cc_final: 0.7661 (tm-30) REVERT: P 57 ASP cc_start: 0.8538 (t70) cc_final: 0.8239 (t0) REVERT: P 75 SER cc_start: 0.9279 (t) cc_final: 0.8962 (t) REVERT: P 166 ASN cc_start: 0.9210 (t0) cc_final: 0.8584 (t0) REVERT: P 167 ASN cc_start: 0.9233 (m110) cc_final: 0.8578 (m110) REVERT: Q 55 ASP cc_start: 0.8364 (t0) cc_final: 0.7926 (t0) REVERT: Q 120 GLN cc_start: 0.8793 (tt0) cc_final: 0.8483 (tp-100) REVERT: Q 148 ASP cc_start: 0.8824 (t0) cc_final: 0.8359 (t0) REVERT: Q 157 LYS cc_start: 0.8777 (mttt) cc_final: 0.8229 (mtmp) REVERT: Q 224 GLU cc_start: 0.8150 (tp30) cc_final: 0.7917 (tp30) REVERT: R 32 LYS cc_start: 0.8807 (mttp) cc_final: 0.8567 (mptp) REVERT: R 86 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8409 (mptm) REVERT: R 227 HIS cc_start: 0.8617 (t-90) cc_final: 0.8389 (t70) REVERT: R 231 LYS cc_start: 0.9292 (mtpm) cc_final: 0.8978 (tttm) REVERT: S 30 LYS cc_start: 0.8817 (mttt) cc_final: 0.8598 (mptt) REVERT: S 90 GLN cc_start: 0.8796 (tp40) cc_final: 0.8323 (mm-40) REVERT: S 94 ASP cc_start: 0.8158 (p0) cc_final: 0.7858 (p0) REVERT: T 93 GLU cc_start: 0.7731 (pp20) cc_final: 0.7382 (pp20) REVERT: T 97 ASN cc_start: 0.8999 (m110) cc_final: 0.8385 (m-40) REVERT: U 5 SER cc_start: 0.9072 (t) cc_final: 0.8495 (m) REVERT: U 80 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.7919 (mmt) REVERT: U 83 MET cc_start: 0.8910 (mtp) cc_final: 0.8620 (mtt) REVERT: U 138 MET cc_start: 0.8451 (ttm) cc_final: 0.7814 (tpp) REVERT: U 155 ASP cc_start: 0.8242 (p0) cc_final: 0.7951 (p0) REVERT: U 187 PHE cc_start: 0.7493 (p90) cc_final: 0.7153 (p90) REVERT: U 189 TRP cc_start: 0.7276 (m-90) cc_final: 0.6976 (m-90) REVERT: U 224 ASN cc_start: 0.8872 (p0) cc_final: 0.8519 (p0) REVERT: U 228 ARG cc_start: 0.8403 (mtm110) cc_final: 0.8073 (mtp-110) REVERT: V 153 ASN cc_start: 0.8502 (m-40) cc_final: 0.8292 (m110) REVERT: W 150 GLU cc_start: 0.8568 (tp30) cc_final: 0.8258 (mm-30) REVERT: W 161 HIS cc_start: 0.8337 (m-70) cc_final: 0.8130 (m170) REVERT: W 164 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7985 (mm-30) REVERT: W 172 ASN cc_start: 0.9353 (m110) cc_final: 0.9124 (m110) REVERT: X 68 LYS cc_start: 0.9339 (tttm) cc_final: 0.9025 (tptt) REVERT: X 108 ASP cc_start: 0.8511 (t70) cc_final: 0.8236 (t70) REVERT: X 166 GLU cc_start: 0.8535 (tp30) cc_final: 0.8273 (tp30) REVERT: X 169 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8852 (ptmm) REVERT: Y 26 ILE cc_start: 0.9308 (mt) cc_final: 0.8940 (mp) REVERT: Y 62 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8966 (mm-40) REVERT: Y 67 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8420 (tm-30) REVERT: a 5 MET cc_start: 0.7980 (mmm) cc_final: 0.7646 (tpt) REVERT: a 25 ASP cc_start: 0.8812 (p0) cc_final: 0.8480 (p0) REVERT: a 133 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7843 (mt-10) REVERT: a 164 GLU cc_start: 0.8279 (pt0) cc_final: 0.7960 (pm20) REVERT: a 180 ASP cc_start: 0.8728 (t0) cc_final: 0.8424 (t0) REVERT: a 200 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: b 71 ASN cc_start: 0.8960 (t0) cc_final: 0.8670 (t0) outliers start: 131 outliers final: 80 residues processed: 1052 average time/residue: 1.1820 time to fit residues: 1516.7329 Evaluate side-chains 1052 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 960 time to evaluate : 3.559 ------------------------------------------------------------------------------- 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 B residue 21 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 95 ARG 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 E residue 166 GLN Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 79 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 H residue 129 SER Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 164 GLU 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 118 MET 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 K residue 182 ASP Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 65 GLN 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 O residue 102 GLU Chi-restraints excluded: chain O residue 225 VAL 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 P residue 150 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 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 V residue 37 ILE 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 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 118 MET Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 97 MET Chi-restraints excluded: chain Y residue 121 ILE Chi-restraints excluded: chain Y residue 174 VAL Chi-restraints excluded: chain Y residue 187 VAL Chi-restraints excluded: chain Z residue 172 MET 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 a residue 200 GLU Chi-restraints excluded: chain b residue 84 LYS Chi-restraints excluded: chain b residue 86 MET 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 537 optimal weight: 3.9990 chunk 566 optimal weight: 6.9990 chunk 516 optimal weight: 0.9990 chunk 550 optimal weight: 2.9990 chunk 565 optimal weight: 0.9980 chunk 331 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 432 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 497 optimal weight: 0.8980 chunk 520 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN C 23 GLN D 118 ASN D 225 ASN E 65 HIS E 68 ASN E 166 GLN F 180 GLN H 153 ASN I 60 GLN J 55 GLN L 131 GLN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 GLN ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 HIS 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 Z 157 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 47220 Z= 0.217 Angle : 0.633 14.014 64063 Z= 0.338 Chirality : 0.043 0.347 7447 Planarity : 0.004 0.063 8164 Dihedral : 4.437 20.523 6845 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.47 % Allowed : 22.74 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.11), residues: 6188 helix: 1.87 (0.11), residues: 2342 sheet: 0.04 (0.13), residues: 1514 loop : -0.31 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 215 HIS 0.007 0.001 HIS F 201 PHE 0.031 0.001 PHE N 65 TYR 0.033 0.001 TYR Y 40 ARG 0.013 0.001 ARG K 166 *********************** 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 1129 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1018 time to evaluate : 3.644 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 49 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8545 (ttpp) REVERT: A 78 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8001 (mtp) REVERT: A 147 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8319 (tm-30) REVERT: A 158 LYS cc_start: 0.8937 (mttm) cc_final: 0.8539 (mttp) REVERT: A 208 GLU cc_start: 0.8098 (tt0) cc_final: 0.7848 (tt0) REVERT: B 26 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7500 (pp20) REVERT: B 67 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8546 (tttm) REVERT: B 72 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8204 (ptp) REVERT: B 184 MET cc_start: 0.8285 (mmm) cc_final: 0.7929 (mmm) REVERT: C 55 ASP cc_start: 0.8568 (t0) cc_final: 0.8238 (t0) REVERT: C 61 LYS cc_start: 0.8565 (mttm) cc_final: 0.8087 (mtmt) REVERT: C 66 ASP cc_start: 0.8682 (t0) cc_final: 0.8242 (t0) REVERT: C 95 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8526 (ttp-170) REVERT: C 116 GLN cc_start: 0.8872 (tm130) cc_final: 0.8311 (tp40) REVERT: C 120 GLN cc_start: 0.9041 (tp40) cc_final: 0.8053 (tp40) REVERT: D 32 LYS cc_start: 0.9115 (mttt) cc_final: 0.8868 (mttp) REVERT: D 91 LYS cc_start: 0.9251 (tmtm) cc_final: 0.8487 (tptt) REVERT: D 93 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8687 (mtt180) REVERT: D 95 GLU cc_start: 0.8394 (tp30) cc_final: 0.8019 (tp30) REVERT: E 26 MET cc_start: 0.8244 (mmm) cc_final: 0.7877 (mmm) REVERT: E 27 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7559 (tm-30) REVERT: E 30 LYS cc_start: 0.8257 (mttp) cc_final: 0.8027 (mttp) REVERT: E 67 ASP cc_start: 0.8701 (t70) cc_final: 0.8292 (t0) REVERT: E 90 GLN cc_start: 0.8721 (tp40) cc_final: 0.8332 (mm-40) REVERT: E 94 ASP cc_start: 0.8102 (m-30) cc_final: 0.7844 (m-30) REVERT: E 178 GLU cc_start: 0.8349 (pm20) cc_final: 0.8024 (pm20) REVERT: E 180 MET cc_start: 0.8557 (mmm) cc_final: 0.8329 (tpt) REVERT: E 189 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8966 (mttp) REVERT: F 70 ASP cc_start: 0.8524 (t0) cc_final: 0.8025 (t0) REVERT: F 147 GLN cc_start: 0.8593 (mt0) cc_final: 0.7975 (mt0) REVERT: F 150 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7506 (tmt) REVERT: F 179 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8557 (tm) REVERT: G 10 ASP cc_start: 0.8729 (p0) cc_final: 0.8447 (p0) REVERT: G 43 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7692 (ptt-90) REVERT: G 56 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8053 (t) REVERT: G 88 ARG cc_start: 0.8178 (mmm160) cc_final: 0.7976 (mmm-85) REVERT: G 112 ASP cc_start: 0.8794 (p0) cc_final: 0.8415 (p0) REVERT: G 116 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8120 (ttmm) REVERT: G 120 ASP cc_start: 0.8185 (m-30) cc_final: 0.7824 (m-30) REVERT: H 30 ASN cc_start: 0.8747 (t0) cc_final: 0.8160 (t0) REVERT: I 65 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7674 (mtt-85) REVERT: I 112 ASP cc_start: 0.8555 (t0) cc_final: 0.8307 (t0) REVERT: I 164 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: I 175 ASP cc_start: 0.8532 (m-30) cc_final: 0.8120 (m-30) REVERT: K 36 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7786 (mt-10) REVERT: K 56 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8566 (mp0) REVERT: K 81 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8449 (mtpp) REVERT: K 99 THR cc_start: 0.8865 (p) cc_final: 0.8601 (m) REVERT: K 151 GLN cc_start: 0.8906 (mp10) cc_final: 0.8296 (pm20) REVERT: L 131 GLN cc_start: 0.8423 (pt0) cc_final: 0.8210 (pt0) REVERT: L 186 ASP cc_start: 0.8435 (t0) cc_final: 0.8163 (t0) REVERT: L 188 TYR cc_start: 0.9124 (m-80) cc_final: 0.8815 (m-80) REVERT: M 26 MET cc_start: 0.8559 (mtp) cc_final: 0.8273 (mtm) REVERT: M 47 ASN cc_start: 0.8737 (t0) cc_final: 0.8284 (t0) REVERT: M 56 ASP cc_start: 0.8763 (t0) cc_final: 0.8525 (t70) REVERT: M 64 LYS cc_start: 0.9038 (mtpt) cc_final: 0.8546 (ttmm) REVERT: M 79 ASP cc_start: 0.8700 (p0) cc_final: 0.8270 (p0) REVERT: M 104 ASN cc_start: 0.8989 (t0) cc_final: 0.8414 (t0) REVERT: M 170 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7765 (mp0) REVERT: M 180 ASP cc_start: 0.8671 (t0) cc_final: 0.8224 (t0) REVERT: M 200 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7547 (mt-10) REVERT: N 90 TYR cc_start: 0.8734 (m-80) cc_final: 0.8196 (m-80) REVERT: N 167 ASP cc_start: 0.8207 (t0) cc_final: 0.7937 (t0) REVERT: O 48 GLU cc_start: 0.7944 (pp20) cc_final: 0.7491 (pp20) REVERT: O 57 ASP cc_start: 0.8176 (t0) cc_final: 0.7847 (t0) REVERT: O 58 GLU cc_start: 0.8601 (mp0) cc_final: 0.8280 (pm20) REVERT: O 59 ARG cc_start: 0.8116 (mpp80) cc_final: 0.7680 (mpp80) REVERT: O 108 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8222 (mm-40) REVERT: O 120 TYR cc_start: 0.8698 (m-80) cc_final: 0.8413 (m-80) REVERT: O 142 ARG cc_start: 0.8303 (ttt-90) cc_final: 0.7953 (ttt-90) REVERT: P 22 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: P 34 CYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8217 (t) REVERT: P 48 GLU cc_start: 0.8105 (tt0) cc_final: 0.7624 (tm-30) REVERT: P 57 ASP cc_start: 0.8490 (t70) cc_final: 0.8190 (t0) REVERT: P 75 SER cc_start: 0.9204 (t) cc_final: 0.8893 (t) REVERT: P 166 ASN cc_start: 0.9195 (t0) cc_final: 0.8587 (t0) REVERT: P 167 ASN cc_start: 0.9209 (m110) cc_final: 0.8562 (m110) REVERT: Q 55 ASP cc_start: 0.8340 (t0) cc_final: 0.7904 (t0) REVERT: Q 120 GLN cc_start: 0.8696 (tt0) cc_final: 0.8378 (tp-100) REVERT: Q 148 ASP cc_start: 0.8820 (t0) cc_final: 0.8391 (t0) REVERT: Q 157 LYS cc_start: 0.8775 (mttt) cc_final: 0.8231 (mtmp) REVERT: R 32 LYS cc_start: 0.8791 (mttp) cc_final: 0.8533 (mptp) REVERT: R 86 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8380 (mptm) REVERT: R 231 LYS cc_start: 0.9275 (mtpm) cc_final: 0.8979 (tttm) REVERT: S 30 LYS cc_start: 0.8769 (mttt) cc_final: 0.8550 (mptt) REVERT: S 90 GLN cc_start: 0.8772 (tp40) cc_final: 0.8142 (mm-40) REVERT: S 94 ASP cc_start: 0.8116 (p0) cc_final: 0.7687 (p0) REVERT: T 93 GLU cc_start: 0.7734 (pp20) cc_final: 0.7377 (pp20) REVERT: T 97 ASN cc_start: 0.8964 (m110) cc_final: 0.8351 (m-40) REVERT: U 5 SER cc_start: 0.9059 (t) cc_final: 0.8448 (m) REVERT: U 80 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8393 (mmt) REVERT: U 83 MET cc_start: 0.8861 (mtp) cc_final: 0.8576 (mtt) REVERT: U 155 ASP cc_start: 0.8120 (p0) cc_final: 0.7834 (p0) REVERT: U 187 PHE cc_start: 0.7598 (p90) cc_final: 0.7284 (p90) REVERT: U 189 TRP cc_start: 0.7177 (m-90) cc_final: 0.6953 (m-90) REVERT: U 224 ASN cc_start: 0.8873 (p0) cc_final: 0.8519 (p0) REVERT: U 228 ARG cc_start: 0.8391 (mtm110) cc_final: 0.8116 (mtp-110) REVERT: V 19 ARG cc_start: 0.8966 (ttm170) cc_final: 0.8357 (tmm-80) REVERT: V 150 GLU cc_start: 0.8339 (pm20) cc_final: 0.8101 (pm20) REVERT: W 77 GLU cc_start: 0.8347 (mp0) cc_final: 0.7791 (mm-30) REVERT: W 105 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8065 (mm-30) REVERT: W 125 LEU cc_start: 0.9133 (mp) cc_final: 0.8685 (mm) REVERT: W 150 GLU cc_start: 0.8609 (tp30) cc_final: 0.8306 (mm-30) REVERT: W 164 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7950 (mm-30) REVERT: W 172 ASN cc_start: 0.9298 (m110) cc_final: 0.8987 (m110) REVERT: X 108 ASP cc_start: 0.8493 (t70) cc_final: 0.8244 (t70) REVERT: X 118 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7413 (mtp) REVERT: X 166 GLU cc_start: 0.8524 (tp30) cc_final: 0.8253 (tp30) REVERT: X 169 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8841 (ptmm) REVERT: Y 26 ILE cc_start: 0.9276 (mt) cc_final: 0.8914 (mp) REVERT: Y 62 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8976 (mm-40) REVERT: Y 67 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8389 (tm-30) REVERT: Y 70 ASN cc_start: 0.9451 (m-40) cc_final: 0.9057 (m110) REVERT: Z 83 MET cc_start: 0.8311 (mtp) cc_final: 0.7816 (ttt) REVERT: a 5 MET cc_start: 0.7852 (mmm) cc_final: 0.7550 (tpt) REVERT: a 25 ASP cc_start: 0.8812 (p0) cc_final: 0.8487 (p0) REVERT: a 133 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7820 (mt-10) REVERT: a 164 GLU cc_start: 0.8218 (pt0) cc_final: 0.7882 (pm20) REVERT: a 180 ASP cc_start: 0.8669 (t0) cc_final: 0.8380 (t0) REVERT: a 200 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: b 7 GLN cc_start: 0.8649 (tt0) cc_final: 0.8363 (tt0) REVERT: b 71 ASN cc_start: 0.8948 (t0) cc_final: 0.8653 (t0) REVERT: b 104 ASP cc_start: 0.7851 (p0) cc_final: 0.7595 (p0) REVERT: b 119 MET cc_start: 0.8296 (ptm) cc_final: 0.8073 (ptm) outliers start: 111 outliers final: 63 residues processed: 1079 average time/residue: 1.1314 time to fit residues: 1492.2051 Evaluate side-chains 1052 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 973 time to evaluate : 3.376 ------------------------------------------------------------------------------- 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 B residue 21 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain G residue 56 VAL 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 H residue 129 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 118 MET 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 179 VAL 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 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 92 LEU Chi-restraints excluded: chain P residue 150 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 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 161 CYS Chi-restraints excluded: chain V residue 37 ILE 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 88 SER Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 148 MET Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 26 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 X residue 169 LYS Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 97 MET Chi-restraints excluded: chain Y residue 167 ASP Chi-restraints excluded: chain Y residue 174 VAL 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 a residue 200 GLU Chi-restraints excluded: chain b residue 86 MET 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 548 optimal weight: 0.8980 chunk 361 optimal weight: 7.9990 chunk 582 optimal weight: 2.9990 chunk 355 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 404 optimal weight: 2.9990 chunk 610 optimal weight: 5.9990 chunk 562 optimal weight: 6.9990 chunk 486 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 375 optimal weight: 0.0270 overall best weight: 1.7844 ------------------------------------------------------------------------------- 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN C 23 GLN D 118 ASN D 225 ASN E 166 GLN F 63 ASN F 180 GLN H 153 ASN I 60 GLN J 55 GLN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 GLN ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 HIS S 146 GLN T 63 ASN V 57 GLN V 80 ASN V 153 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** Z 108 ASN Z 157 ASN a 61 GLN b 110 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 47220 Z= 0.293 Angle : 0.661 13.848 64063 Z= 0.352 Chirality : 0.044 0.340 7447 Planarity : 0.004 0.066 8164 Dihedral : 4.471 19.426 6845 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.18 % Allowed : 23.34 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.11), residues: 6188 helix: 1.83 (0.11), residues: 2351 sheet: -0.01 (0.13), residues: 1516 loop : -0.32 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 215 HIS 0.007 0.001 HIS F 201 PHE 0.025 0.001 PHE N 65 TYR 0.038 0.001 TYR Q 110 ARG 0.013 0.001 ARG A 176 ********************** 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 1076 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 978 time to evaluate : 3.404 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 49 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8551 (ttpp) REVERT: A 78 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8121 (mtp) REVERT: A 147 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8332 (tm-30) REVERT: A 158 LYS cc_start: 0.8945 (mttm) cc_final: 0.8547 (mttp) REVERT: A 208 GLU cc_start: 0.8113 (tt0) cc_final: 0.7907 (tt0) REVERT: B 26 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7415 (pp20) REVERT: B 72 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8195 (ptp) REVERT: B 184 MET cc_start: 0.8301 (mmm) cc_final: 0.7937 (mmm) REVERT: C 55 ASP cc_start: 0.8601 (t0) cc_final: 0.8264 (t0) REVERT: C 61 LYS cc_start: 0.8606 (mttm) cc_final: 0.8151 (mtmt) REVERT: C 66 ASP cc_start: 0.8691 (t0) cc_final: 0.8266 (t0) REVERT: C 116 GLN cc_start: 0.8896 (tm130) cc_final: 0.8457 (tm-30) REVERT: C 120 GLN cc_start: 0.9038 (tp40) cc_final: 0.8086 (tp40) REVERT: D 32 LYS cc_start: 0.9119 (mttt) cc_final: 0.8871 (mttp) REVERT: D 91 LYS cc_start: 0.9277 (tmtm) cc_final: 0.8583 (tptt) REVERT: D 93 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8690 (mtt180) REVERT: D 95 GLU cc_start: 0.8417 (tp30) cc_final: 0.8008 (tp30) REVERT: E 26 MET cc_start: 0.8270 (mmm) cc_final: 0.7901 (mmm) REVERT: E 27 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7598 (tm-30) REVERT: E 30 LYS cc_start: 0.8271 (mttp) cc_final: 0.8041 (mttp) REVERT: E 67 ASP cc_start: 0.8712 (t70) cc_final: 0.8302 (t0) REVERT: E 90 GLN cc_start: 0.8707 (tp40) cc_final: 0.8328 (mm-40) REVERT: E 94 ASP cc_start: 0.8101 (m-30) cc_final: 0.7861 (m-30) REVERT: E 189 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8978 (mttp) REVERT: F 70 ASP cc_start: 0.8551 (t0) cc_final: 0.8060 (t0) REVERT: F 147 GLN cc_start: 0.8636 (mt0) cc_final: 0.7993 (mt0) REVERT: F 150 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7412 (tmt) REVERT: F 179 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8581 (tm) REVERT: G 10 ASP cc_start: 0.8679 (p0) cc_final: 0.8415 (p0) REVERT: G 43 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7675 (ptt-90) REVERT: G 56 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.8050 (t) REVERT: G 88 ARG cc_start: 0.8189 (mmm160) cc_final: 0.7969 (mmm-85) REVERT: G 112 ASP cc_start: 0.8829 (p0) cc_final: 0.8433 (p0) REVERT: G 116 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8159 (ttmm) REVERT: G 120 ASP cc_start: 0.8189 (m-30) cc_final: 0.7834 (m-30) REVERT: H 30 ASN cc_start: 0.8753 (t0) cc_final: 0.8161 (t0) REVERT: I 65 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7679 (mtt-85) REVERT: I 112 ASP cc_start: 0.8556 (t0) cc_final: 0.8294 (t0) REVERT: I 175 ASP cc_start: 0.8530 (m-30) cc_final: 0.8137 (m-30) REVERT: J 37 LYS cc_start: 0.8942 (ptmm) cc_final: 0.8448 (tttp) REVERT: J 165 GLU cc_start: 0.8128 (pt0) cc_final: 0.7834 (pt0) REVERT: K 36 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7806 (mt-10) REVERT: K 56 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: K 81 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8537 (mtpp) REVERT: K 99 THR cc_start: 0.8857 (p) cc_final: 0.8603 (m) REVERT: K 151 GLN cc_start: 0.8906 (mp10) cc_final: 0.8280 (pm20) REVERT: L 39 ASP cc_start: 0.8545 (t70) cc_final: 0.8257 (t0) REVERT: L 131 GLN cc_start: 0.8403 (pt0) cc_final: 0.8155 (pt0) REVERT: L 151 ASN cc_start: 0.9434 (t0) cc_final: 0.9151 (t0) REVERT: L 186 ASP cc_start: 0.8461 (t0) cc_final: 0.8190 (t0) REVERT: L 188 TYR cc_start: 0.9146 (m-80) cc_final: 0.8872 (m-80) REVERT: M 26 MET cc_start: 0.8606 (mtp) cc_final: 0.8314 (mtm) REVERT: M 47 ASN cc_start: 0.8772 (t0) cc_final: 0.8314 (t0) REVERT: M 56 ASP cc_start: 0.8787 (t0) cc_final: 0.8505 (t70) REVERT: M 64 LYS cc_start: 0.9063 (mtpt) cc_final: 0.8547 (ttmm) REVERT: M 79 ASP cc_start: 0.8711 (p0) cc_final: 0.8285 (p0) REVERT: M 104 ASN cc_start: 0.9020 (t0) cc_final: 0.8443 (t0) REVERT: M 170 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7755 (mp0) REVERT: M 180 ASP cc_start: 0.8668 (t0) cc_final: 0.8214 (t0) REVERT: M 200 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7568 (mt-10) REVERT: N 86 MET cc_start: 0.8692 (ttm) cc_final: 0.8349 (ttm) REVERT: N 90 TYR cc_start: 0.8812 (m-80) cc_final: 0.8394 (m-80) REVERT: N 167 ASP cc_start: 0.8182 (t0) cc_final: 0.7909 (t0) REVERT: O 48 GLU cc_start: 0.7961 (pp20) cc_final: 0.7511 (pp20) REVERT: O 57 ASP cc_start: 0.8174 (t0) cc_final: 0.7805 (t0) REVERT: O 58 GLU cc_start: 0.8594 (mp0) cc_final: 0.8294 (pm20) REVERT: O 59 ARG cc_start: 0.8190 (mpp80) cc_final: 0.7922 (mpp80) REVERT: O 108 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8673 (mm-40) REVERT: O 120 TYR cc_start: 0.8726 (m-80) cc_final: 0.8430 (m-80) REVERT: O 142 ARG cc_start: 0.8319 (ttt-90) cc_final: 0.7965 (ttt-90) REVERT: P 34 CYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8114 (t) REVERT: P 48 GLU cc_start: 0.8118 (tt0) cc_final: 0.7641 (tm-30) REVERT: P 57 ASP cc_start: 0.8501 (t70) cc_final: 0.8211 (t0) REVERT: P 75 SER cc_start: 0.9250 (t) cc_final: 0.8901 (t) REVERT: P 166 ASN cc_start: 0.9213 (t0) cc_final: 0.8606 (t0) REVERT: P 167 ASN cc_start: 0.9216 (m110) cc_final: 0.8576 (m110) REVERT: Q 55 ASP cc_start: 0.8358 (t0) cc_final: 0.7921 (t0) REVERT: Q 120 GLN cc_start: 0.8681 (tt0) cc_final: 0.8373 (tp-100) REVERT: Q 148 ASP cc_start: 0.8790 (t0) cc_final: 0.8347 (t0) REVERT: Q 157 LYS cc_start: 0.8771 (mttt) cc_final: 0.8234 (mtmp) REVERT: R 32 LYS cc_start: 0.8803 (mttp) cc_final: 0.8541 (mptp) REVERT: R 86 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8416 (mptm) REVERT: R 231 LYS cc_start: 0.9282 (mtpm) cc_final: 0.8987 (tttm) REVERT: S 26 MET cc_start: 0.8407 (mtp) cc_final: 0.8189 (mtp) REVERT: S 30 LYS cc_start: 0.8783 (mttt) cc_final: 0.8559 (mptt) REVERT: S 90 GLN cc_start: 0.8801 (tp40) cc_final: 0.8364 (mm-40) REVERT: S 94 ASP cc_start: 0.8148 (p0) cc_final: 0.7856 (p0) REVERT: S 159 MET cc_start: 0.8536 (tpp) cc_final: 0.8318 (tpt) REVERT: T 93 GLU cc_start: 0.7739 (pp20) cc_final: 0.7376 (pp20) REVERT: T 97 ASN cc_start: 0.8973 (m110) cc_final: 0.8344 (m-40) REVERT: U 5 SER cc_start: 0.9054 (t) cc_final: 0.8452 (m) REVERT: U 80 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8279 (mmt) REVERT: U 83 MET cc_start: 0.8875 (mtp) cc_final: 0.8586 (mtt) REVERT: U 138 MET cc_start: 0.8358 (ttm) cc_final: 0.8145 (mmt) REVERT: U 155 ASP cc_start: 0.8149 (p0) cc_final: 0.7868 (p0) REVERT: U 187 PHE cc_start: 0.7591 (p90) cc_final: 0.7195 (p90) REVERT: U 189 TRP cc_start: 0.7245 (m-90) cc_final: 0.7009 (m-90) REVERT: U 224 ASN cc_start: 0.8879 (p0) cc_final: 0.8528 (p0) REVERT: U 228 ARG cc_start: 0.8400 (mtm110) cc_final: 0.8143 (mtp-110) REVERT: V 19 ARG cc_start: 0.8965 (ttm170) cc_final: 0.8358 (tmm-80) REVERT: W 80 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8416 (mm-40) REVERT: W 105 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8076 (mm-30) REVERT: W 125 LEU cc_start: 0.9152 (mp) cc_final: 0.8705 (mm) REVERT: W 172 ASN cc_start: 0.9362 (m110) cc_final: 0.9088 (m110) REVERT: X 108 ASP cc_start: 0.8504 (t70) cc_final: 0.8247 (t70) REVERT: X 166 GLU cc_start: 0.8548 (tp30) cc_final: 0.8299 (tp30) REVERT: X 169 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8835 (ptmm) REVERT: Y 26 ILE cc_start: 0.9299 (mt) cc_final: 0.8931 (mp) REVERT: Y 62 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8987 (mm-40) REVERT: Y 67 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8382 (tm-30) REVERT: Z 83 MET cc_start: 0.8153 (mtp) cc_final: 0.7931 (ttt) REVERT: a 5 MET cc_start: 0.7899 (mmm) cc_final: 0.7612 (tpt) REVERT: a 25 ASP cc_start: 0.8839 (p0) cc_final: 0.8549 (p0) REVERT: a 133 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7827 (mt-10) REVERT: a 164 GLU cc_start: 0.8242 (pt0) cc_final: 0.7913 (pm20) REVERT: a 200 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: b 71 ASN cc_start: 0.8962 (t0) cc_final: 0.8666 (t0) REVERT: b 119 MET cc_start: 0.8369 (ptm) cc_final: 0.8168 (ptm) outliers start: 98 outliers final: 65 residues processed: 1033 average time/residue: 1.1184 time to fit residues: 1409.3096 Evaluate side-chains 1044 residues out of total 5190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 967 time to evaluate : 3.361 ------------------------------------------------------------------------------- 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 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 217 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 69 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 E residue 189 LYS Chi-restraints excluded: chain F residue 24 GLU Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain G residue 56 VAL 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 H residue 129 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain J residue 118 MET 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 91 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 M residue 191 THR Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain N residue 20 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 92 LEU Chi-restraints excluded: chain P residue 150 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 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 161 CYS Chi-restraints excluded: chain V residue 37 ILE 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 88 SER Chi-restraints excluded: chain W residue 137 VAL 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 169 LYS Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 97 MET Chi-restraints excluded: chain Y residue 167 ASP Chi-restraints excluded: chain Y residue 174 VAL 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 a residue 200 GLU Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 86 MET 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 298 optimal weight: 0.6980 chunk 386 optimal weight: 0.8980 chunk 518 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 448 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 487 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 500 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 118 GLN A 188 HIS B 69 ASN C 23 GLN D 118 ASN F 63 ASN F 180 GLN H 153 ASN I 60 GLN J 55 GLN ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 GLN N 66 HIS O 122 GLN ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 HIS S 146 GLN T 63 ASN T 120 HIS U 92 GLN V 57 GLN V 80 ASN V 153 ASN W 32 GLN W 156 ASN X 27 GLN ** X 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN Z 108 ASN Z 157 ASN a 61 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.079565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.064728 restraints weight = 96665.044| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.76 r_work: 0.2816 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 47220 Z= 0.218 Angle : 0.648 13.778 64063 Z= 0.345 Chirality : 0.043 0.324 7447 Planarity : 0.004 0.064 8164 Dihedral : 4.410 19.172 6845 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.98 % Allowed : 23.69 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.11), residues: 6188 helix: 1.89 (0.11), residues: 2340 sheet: 0.04 (0.13), residues: 1526 loop : -0.29 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 215 HIS 0.008 0.001 HIS A 188 PHE 0.026 0.001 PHE N 65 TYR 0.046 0.001 TYR Y 40 ARG 0.018 0.001 ARG A 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23145.91 seconds wall clock time: 402 minutes 3.02 seconds (24123.02 seconds total)