Starting phenix.real_space_refine on Wed Jul 30 12:16:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r69_4733/07_2025/6r69_4733.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r69_4733/07_2025/6r69_4733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r69_4733/07_2025/6r69_4733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r69_4733/07_2025/6r69_4733.map" model { file = "/net/cci-nas-00/data/ceres_data/6r69_4733/07_2025/6r69_4733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r69_4733/07_2025/6r69_4733.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 99 5.16 5 C 8390 2.51 5 N 1934 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12541 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "B" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "C" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "D" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "E" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "F" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1986 Classifications: {'peptide': 258} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 240} Chain: "G" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "H" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "I" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "J" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Time building chain proxies: 8.43, per 1000 atoms: 0.67 Number of scatterers: 12541 At special positions: 0 Unit cell: (105.4, 101.15, 130.9, 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 99 16.00 O 2118 8.00 N 1934 7.00 C 8390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.8 seconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3094 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.714A pdb=" N PHE A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Proline residue: A 55 - end of helix Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.637A pdb=" N THR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.957A pdb=" N GLU A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 140 Proline residue: A 133 - end of helix removed outlier: 3.556A pdb=" N ARG A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.806A pdb=" N LEU A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 208 Proline residue: A 172 - end of helix removed outlier: 3.874A pdb=" N GLN A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Proline residue: A 192 - end of helix removed outlier: 3.525A pdb=" N LEU A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.767A pdb=" N LEU A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Proline residue: A 220 - end of helix removed outlier: 4.348A pdb=" N PHE A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.628A pdb=" N LEU A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 63 Proline residue: B 55 - end of helix removed outlier: 3.964A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 removed outlier: 3.765A pdb=" N ALA B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 119 removed outlier: 3.598A pdb=" N GLY B 91 " --> pdb=" O GLN B 87 " (cutoff:3.500A) Proline residue: B 103 - end of helix removed outlier: 4.825A pdb=" N GLN B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix removed outlier: 3.811A pdb=" N GLU B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 142 Proline residue: B 133 - end of helix removed outlier: 3.688A pdb=" N GLN B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 153 removed outlier: 3.803A pdb=" N LEU B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 166 through 205 Proline residue: B 172 - end of helix removed outlier: 4.127A pdb=" N ILE B 191 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Proline residue: B 192 - end of helix Processing helix chain 'B' and resid 217 through 229 removed outlier: 4.061A pdb=" N PHE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 245 removed outlier: 3.620A pdb=" N LEU B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.743A pdb=" N ILE C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Proline residue: C 55 - end of helix removed outlier: 3.755A pdb=" N THR C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 75 removed outlier: 3.879A pdb=" N ILE C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 101 through 117 removed outlier: 4.766A pdb=" N GLN C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 123 through 140 removed outlier: 4.063A pdb=" N LEU C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Proline residue: C 133 - end of helix removed outlier: 3.555A pdb=" N ALA C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 154 removed outlier: 3.956A pdb=" N LEU C 147 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 154 " --> pdb=" O PHE C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 190 removed outlier: 3.665A pdb=" N LEU C 170 " --> pdb=" O PRO C 166 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 171 " --> pdb=" O MET C 167 " (cutoff:3.500A) Proline residue: C 172 - end of helix removed outlier: 3.609A pdb=" N PHE C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 208 Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 217 through 228 removed outlier: 4.269A pdb=" N PHE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 245 removed outlier: 3.614A pdb=" N LEU C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 235 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 236 " --> pdb=" O TRP C 232 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 62 removed outlier: 3.675A pdb=" N ILE D 48 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 52 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Proline residue: D 55 - end of helix removed outlier: 3.994A pdb=" N THR D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 75 Processing helix chain 'D' and resid 87 through 112 Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 127 through 140 Proline residue: D 133 - end of helix Processing helix chain 'D' and resid 143 through 153 removed outlier: 3.637A pdb=" N LEU D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 190 removed outlier: 3.701A pdb=" N LEU D 171 " --> pdb=" O MET D 167 " (cutoff:3.500A) Proline residue: D 172 - end of helix Processing helix chain 'D' and resid 190 through 208 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.543A pdb=" N ILE D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Proline residue: D 220 - end of helix Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.522A pdb=" N VAL D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 63 removed outlier: 4.414A pdb=" N ILE E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) Proline residue: E 55 - end of helix removed outlier: 3.847A pdb=" N THR E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 77 removed outlier: 3.809A pdb=" N VAL E 70 " --> pdb=" O ARG E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 117 removed outlier: 4.234A pdb=" N ALA E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Proline residue: E 103 - end of helix removed outlier: 4.593A pdb=" N GLN E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 124 through 140 Proline residue: E 133 - end of helix Processing helix chain 'E' and resid 143 through 155 removed outlier: 3.949A pdb=" N LEU E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 208 removed outlier: 3.509A pdb=" N LEU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU E 171 " --> pdb=" O MET E 167 " (cutoff:3.500A) Proline residue: E 172 - end of helix removed outlier: 3.730A pdb=" N ILE E 191 " --> pdb=" O PHE E 187 " (cutoff:3.500A) Proline residue: E 192 - end of helix removed outlier: 3.589A pdb=" N LEU E 207 " --> pdb=" O VAL E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 228 removed outlier: 4.564A pdb=" N PHE E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 245 removed outlier: 3.861A pdb=" N LEU E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE E 243 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 14 removed outlier: 4.248A pdb=" N LEU F 10 " --> pdb=" O SER F 6 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR F 11 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TRP F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 29 Processing helix chain 'F' and resid 44 through 55 removed outlier: 3.834A pdb=" N ILE F 48 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL F 53 " --> pdb=" O MET F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 89 removed outlier: 3.662A pdb=" N MET F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN F 76 " --> pdb=" O TRP F 72 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 104 removed outlier: 4.063A pdb=" N VAL F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 141 removed outlier: 3.808A pdb=" N MET F 131 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE F 137 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU F 138 " --> pdb=" O MET F 134 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 157 removed outlier: 3.535A pdb=" N HIS F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 removed outlier: 4.297A pdb=" N GLY F 176 " --> pdb=" O LEU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 206 removed outlier: 4.097A pdb=" N LEU F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) Proline residue: F 189 - end of helix removed outlier: 3.658A pdb=" N GLY F 202 " --> pdb=" O ASN F 198 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG F 206 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 212 removed outlier: 3.641A pdb=" N LEU F 211 " --> pdb=" O ALA F 208 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER F 212 " --> pdb=" O PRO F 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 212' Processing helix chain 'F' and resid 216 through 232 removed outlier: 4.197A pdb=" N THR F 223 " --> pdb=" O PRO F 219 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET F 229 " --> pdb=" O GLY F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 261 removed outlier: 3.573A pdb=" N PHE F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS F 242 " --> pdb=" O PRO F 238 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Proline residue: F 259 - end of helix Processing helix chain 'G' and resid 2 through 40 removed outlier: 3.585A pdb=" N MET G 7 " --> pdb=" O PRO G 3 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY G 10 " --> pdb=" O VAL G 6 " (cutoff:3.500A) Proline residue: G 23 - end of helix Processing helix chain 'G' and resid 50 through 66 removed outlier: 3.782A pdb=" N VAL G 58 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE G 63 " --> pdb=" O PHE G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 89 removed outlier: 3.997A pdb=" N LEU G 73 " --> pdb=" O MET G 69 " (cutoff:3.500A) Proline residue: G 85 - end of helix removed outlier: 3.693A pdb=" N ILE G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY G 89 " --> pdb=" O PRO G 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 40 Proline residue: H 23 - end of helix removed outlier: 3.705A pdb=" N LEU H 38 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 66 removed outlier: 3.631A pdb=" N VAL H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE H 63 " --> pdb=" O PHE H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 84 removed outlier: 4.083A pdb=" N LEU H 73 " --> pdb=" O MET H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'I' and resid 2 through 39 Proline residue: I 23 - end of helix Processing helix chain 'I' and resid 50 through 66 removed outlier: 3.531A pdb=" N VAL I 58 " --> pdb=" O LYS I 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE I 63 " --> pdb=" O PHE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 88 Proline residue: I 85 - end of helix removed outlier: 4.104A pdb=" N ILE I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 38 removed outlier: 4.157A pdb=" N GLY J 10 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS J 15 " --> pdb=" O THR J 11 " (cutoff:3.500A) Proline residue: J 23 - end of helix removed outlier: 3.701A pdb=" N LEU J 38 " --> pdb=" O ILE J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 66 removed outlier: 4.011A pdb=" N LYS J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE J 63 " --> pdb=" O PHE J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 88 removed outlier: 3.815A pdb=" N LEU J 73 " --> pdb=" O MET J 69 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Proline residue: J 85 - end of helix removed outlier: 3.619A pdb=" N ILE J 88 " --> pdb=" O LEU J 84 " (cutoff:3.500A) 788 hydrogen bonds defined for protein. 2349 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: 3.44 Time building geometry restraints manager: 4.01 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: 3717 1.34 - 1.46: 1593 1.46 - 1.57: 7313 1.57 - 1.69: 0 1.69 - 1.81: 197 Bond restraints: 12820 Sorted by residual: bond pdb=" N PHE F 140 " pdb=" CA PHE F 140 " ideal model delta sigma weight residual 1.468 1.451 0.018 1.24e-02 6.50e+03 2.00e+00 bond pdb=" CG1 ILE B 68 " pdb=" CD1 ILE B 68 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.76e+00 bond pdb=" C GLU I 46 " pdb=" O GLU I 46 " ideal model delta sigma weight residual 1.234 1.245 -0.011 8.30e-03 1.45e+04 1.72e+00 bond pdb=" N GLU J 46 " pdb=" CA GLU J 46 " ideal model delta sigma weight residual 1.468 1.452 0.016 1.24e-02 6.50e+03 1.71e+00 bond pdb=" CB TRP C 232 " pdb=" CG TRP C 232 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.64e+00 ... (remaining 12815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 17198 2.93 - 5.85: 258 5.85 - 8.78: 18 8.78 - 11.70: 1 11.70 - 14.63: 1 Bond angle restraints: 17476 Sorted by residual: angle pdb=" C THR J 42 " pdb=" N GLN J 43 " pdb=" CA GLN J 43 " ideal model delta sigma weight residual 120.38 126.95 -6.57 1.46e+00 4.69e-01 2.02e+01 angle pdb=" CA LEU F 150 " pdb=" CB LEU F 150 " pdb=" CG LEU F 150 " ideal model delta sigma weight residual 116.30 101.67 14.63 3.50e+00 8.16e-02 1.75e+01 angle pdb=" C ILE F 159 " pdb=" N GLY F 160 " pdb=" CA GLY F 160 " ideal model delta sigma weight residual 121.41 113.52 7.89 1.96e+00 2.60e-01 1.62e+01 angle pdb=" N PHE B 64 " pdb=" CA PHE B 64 " pdb=" CB PHE B 64 " ideal model delta sigma weight residual 114.27 107.74 6.53 1.64e+00 3.72e-01 1.58e+01 angle pdb=" N PHE D 64 " pdb=" CA PHE D 64 " pdb=" CB PHE D 64 " ideal model delta sigma weight residual 114.17 110.02 4.15 1.14e+00 7.69e-01 1.33e+01 ... (remaining 17471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 6847 17.38 - 34.75: 745 34.75 - 52.13: 114 52.13 - 69.50: 16 69.50 - 86.88: 9 Dihedral angle restraints: 7731 sinusoidal: 2988 harmonic: 4743 Sorted by residual: dihedral pdb=" CA ALA I 41 " pdb=" C ALA I 41 " pdb=" N THR I 42 " pdb=" CA THR I 42 " ideal model delta harmonic sigma weight residual -180.00 -140.71 -39.29 0 5.00e+00 4.00e-02 6.17e+01 dihedral pdb=" CA ALA G 41 " pdb=" C ALA G 41 " pdb=" N THR G 42 " pdb=" CA THR G 42 " ideal model delta harmonic sigma weight residual -180.00 -141.80 -38.20 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA LEU F 211 " pdb=" C LEU F 211 " pdb=" N SER F 212 " pdb=" CA SER F 212 " ideal model delta harmonic sigma weight residual 180.00 142.14 37.86 0 5.00e+00 4.00e-02 5.73e+01 ... (remaining 7728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1309 0.035 - 0.070: 610 0.070 - 0.105: 222 0.105 - 0.140: 39 0.140 - 0.175: 9 Chirality restraints: 2189 Sorted by residual: chirality pdb=" CA PRO G 67 " pdb=" N PRO G 67 " pdb=" C PRO G 67 " pdb=" CB PRO G 67 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CG LEU D 223 " pdb=" CB LEU D 223 " pdb=" CD1 LEU D 223 " pdb=" CD2 LEU D 223 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA PRO E 81 " pdb=" N PRO E 81 " pdb=" C PRO E 81 " pdb=" CB PRO E 81 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 2186 not shown) Planarity restraints: 2130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 84 " 0.051 5.00e-02 4.00e+02 7.82e-02 9.79e+00 pdb=" N PRO C 85 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 213 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO D 214 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 214 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 214 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 84 " 0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO D 85 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 85 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 85 " 0.039 5.00e-02 4.00e+02 ... (remaining 2127 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1146 2.73 - 3.27: 13976 3.27 - 3.82: 19782 3.82 - 4.36: 23427 4.36 - 4.90: 39753 Nonbonded interactions: 98084 Sorted by model distance: nonbonded pdb=" OE1 GLU G 46 " pdb=" OG SER H 50 " model vdw 2.191 3.040 nonbonded pdb=" O ALA D 131 " pdb=" N ARG D 135 " model vdw 2.195 3.120 nonbonded pdb=" OG1 THR D 65 " pdb=" OE1 GLU D 178 " model vdw 2.199 3.040 nonbonded pdb=" O ALA F 83 " pdb=" OG1 THR F 87 " model vdw 2.201 3.040 nonbonded pdb=" O MET C 138 " pdb=" OG1 THR C 142 " model vdw 2.203 3.040 ... (remaining 98079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.330 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.005 0.052 12820 Z= 0.232 Angle : 0.896 14.628 17476 Z= 0.506 Chirality : 0.045 0.175 2189 Planarity : 0.007 0.078 2130 Dihedral : 14.420 86.876 4637 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.82 % Favored : 89.81 % Rotamer: Outliers : 0.15 % Allowed : 5.38 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -3.99 (0.18), residues: 1609 helix: -1.98 (0.12), residues: 1203 sheet: None (None), residues: 0 loop : -4.27 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 68 HIS 0.003 0.001 HIS F 14 PHE 0.030 0.002 PHE B 64 TYR 0.013 0.001 TYR A 113 ARG 0.007 0.001 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.17116 ( 788) hydrogen bonds : angle 6.84625 ( 2349) covalent geometry : bond 0.00539 (12820) covalent geometry : angle 0.89633 (17476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 386 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 MET cc_start: 0.7711 (ptm) cc_final: 0.7419 (ptt) REVERT: B 47 PHE cc_start: 0.7840 (t80) cc_final: 0.7616 (t80) REVERT: C 60 MET cc_start: 0.8002 (mmp) cc_final: 0.7786 (mmt) outliers start: 2 outliers final: 0 residues processed: 387 average time/residue: 0.2534 time to fit residues: 137.9653 Evaluate side-chains 250 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 1.9990 chunk 118 optimal weight: 0.0170 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 0.0570 chunk 142 optimal weight: 4.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN B 241 GLN C 76 ASN C 184 GLN C 241 GLN D 87 GLN E 76 ASN E 155 ASN F 105 GLN F 121 ASN F 143 HIS F 165 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 ASN J 39 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.075662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.060612 restraints weight = 47030.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062443 restraints weight = 26434.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.063689 restraints weight = 18076.895| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12820 Z= 0.163 Angle : 0.814 11.382 17476 Z= 0.398 Chirality : 0.045 0.181 2189 Planarity : 0.007 0.075 2130 Dihedral : 6.106 42.934 1695 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.02 % Favored : 91.86 % Rotamer: Outliers : 2.11 % Allowed : 14.75 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.21), residues: 1609 helix: -0.45 (0.14), residues: 1239 sheet: None (None), residues: 0 loop : -3.61 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 232 HIS 0.007 0.001 HIS F 14 PHE 0.037 0.002 PHE B 64 TYR 0.018 0.002 TYR E 174 ARG 0.011 0.001 ARG E 152 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 788) hydrogen bonds : angle 4.68869 ( 2349) covalent geometry : bond 0.00356 (12820) covalent geometry : angle 0.81398 (17476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 297 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 THR cc_start: 0.7660 (OUTLIER) cc_final: 0.7195 (t) REVERT: A 87 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7050 (mm-40) REVERT: A 129 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8437 (tttm) REVERT: B 129 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8692 (mmtm) REVERT: B 174 TYR cc_start: 0.8293 (t80) cc_final: 0.7850 (t80) REVERT: B 178 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7586 (mt-10) REVERT: B 211 MET cc_start: 0.8197 (mmm) cc_final: 0.7987 (mmm) REVERT: B 224 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6560 (ttm) REVERT: C 123 MET cc_start: 0.7624 (tmm) cc_final: 0.7301 (tmm) REVERT: D 73 LEU cc_start: 0.9192 (mp) cc_final: 0.8916 (mp) REVERT: D 76 ASN cc_start: 0.8736 (m-40) cc_final: 0.8535 (m110) REVERT: D 101 MET cc_start: 0.9051 (tpp) cc_final: 0.8776 (tpp) REVERT: D 123 MET cc_start: 0.8341 (mpp) cc_final: 0.6920 (ptm) REVERT: E 123 MET cc_start: 0.8359 (mtp) cc_final: 0.7949 (mtp) REVERT: E 160 GLN cc_start: 0.8681 (pm20) cc_final: 0.8084 (pp30) REVERT: F 210 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: I 45 ASN cc_start: 0.6728 (OUTLIER) cc_final: 0.5830 (t0) REVERT: J 7 MET cc_start: 0.8911 (tpp) cc_final: 0.8482 (tpp) REVERT: J 14 MET cc_start: 0.7399 (mmt) cc_final: 0.6802 (ttm) outliers start: 29 outliers final: 6 residues processed: 312 average time/residue: 0.2371 time to fit residues: 105.9987 Evaluate side-chains 250 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 239 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain I residue 45 ASN Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 84 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 53 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 23 optimal weight: 0.0050 chunk 152 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 76 ASN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.077170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.061912 restraints weight = 47948.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.063871 restraints weight = 26306.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.065182 restraints weight = 17695.819| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 12820 Z= 0.148 Angle : 0.802 12.212 17476 Z= 0.384 Chirality : 0.045 0.334 2189 Planarity : 0.006 0.068 2130 Dihedral : 5.849 42.806 1695 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.40 % Favored : 92.48 % Rotamer: Outliers : 2.62 % Allowed : 16.93 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.21), residues: 1609 helix: 0.16 (0.15), residues: 1223 sheet: None (None), residues: 0 loop : -3.66 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 232 HIS 0.004 0.001 HIS F 143 PHE 0.033 0.001 PHE B 64 TYR 0.024 0.002 TYR A 174 ARG 0.006 0.001 ARG C 140 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 788) hydrogen bonds : angle 4.30126 ( 2349) covalent geometry : bond 0.00331 (12820) covalent geometry : angle 0.80197 (17476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 THR cc_start: 0.7740 (OUTLIER) cc_final: 0.7348 (t) REVERT: A 66 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7426 (ptp-170) REVERT: A 87 GLN cc_start: 0.7355 (mm-40) cc_final: 0.6978 (mm-40) REVERT: A 211 MET cc_start: 0.8083 (mtp) cc_final: 0.7695 (mtp) REVERT: B 129 LYS cc_start: 0.8987 (mmtm) cc_final: 0.8693 (mmtm) REVERT: B 152 ARG cc_start: 0.9080 (tmm-80) cc_final: 0.8761 (tmm-80) REVERT: B 174 TYR cc_start: 0.8293 (t80) cc_final: 0.7887 (t80) REVERT: B 178 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7607 (mt-10) REVERT: B 205 MET cc_start: 0.8228 (ttm) cc_final: 0.7744 (mtm) REVERT: C 95 PHE cc_start: 0.9011 (m-10) cc_final: 0.8733 (m-80) REVERT: C 123 MET cc_start: 0.7469 (tmm) cc_final: 0.6753 (tmm) REVERT: D 129 LYS cc_start: 0.8678 (mptt) cc_final: 0.8405 (pttt) REVERT: E 123 MET cc_start: 0.8186 (mtp) cc_final: 0.7858 (mtp) REVERT: E 160 GLN cc_start: 0.8753 (pm20) cc_final: 0.8083 (pp30) REVERT: F 52 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8532 (mm) REVERT: F 229 MET cc_start: 0.9079 (tpp) cc_final: 0.8788 (tpp) REVERT: G 14 MET cc_start: 0.9125 (mmm) cc_final: 0.8914 (mmm) REVERT: H 1 MET cc_start: 0.6715 (mmt) cc_final: 0.6136 (mmt) REVERT: I 45 ASN cc_start: 0.7189 (p0) cc_final: 0.6110 (t0) REVERT: I 84 LEU cc_start: 0.9636 (tp) cc_final: 0.9411 (tt) REVERT: J 7 MET cc_start: 0.8818 (tpp) cc_final: 0.8197 (tpp) REVERT: J 14 MET cc_start: 0.7229 (mmt) cc_final: 0.6818 (ttm) REVERT: J 26 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9192 (mt) outliers start: 36 outliers final: 11 residues processed: 307 average time/residue: 0.2277 time to fit residues: 102.2613 Evaluate side-chains 261 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 246 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain J residue 26 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 152 optimal weight: 8.9990 chunk 23 optimal weight: 0.0060 chunk 153 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN F 121 ASN F 143 HIS ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.075853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.060779 restraints weight = 47813.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.062691 restraints weight = 26141.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.063990 restraints weight = 17505.720| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12820 Z= 0.164 Angle : 0.800 11.689 17476 Z= 0.385 Chirality : 0.045 0.175 2189 Planarity : 0.006 0.066 2130 Dihedral : 5.706 43.121 1695 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.96 % Favored : 91.98 % Rotamer: Outliers : 2.33 % Allowed : 19.19 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.71 (0.21), residues: 1609 helix: 0.42 (0.15), residues: 1241 sheet: None (None), residues: 0 loop : -3.51 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 72 HIS 0.005 0.001 HIS F 14 PHE 0.033 0.001 PHE B 64 TYR 0.025 0.002 TYR J 76 ARG 0.006 0.001 ARG C 152 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 788) hydrogen bonds : angle 4.23428 ( 2349) covalent geometry : bond 0.00378 (12820) covalent geometry : angle 0.79963 (17476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 259 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7552 (ptp-170) REVERT: A 87 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7073 (mm-40) REVERT: A 101 MET cc_start: 0.8718 (mmm) cc_final: 0.8502 (mmm) REVERT: B 152 ARG cc_start: 0.9130 (tmm-80) cc_final: 0.8794 (tmm-80) REVERT: C 123 MET cc_start: 0.7376 (tmm) cc_final: 0.6657 (tmm) REVERT: C 178 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8744 (mt-10) REVERT: C 194 LEU cc_start: 0.9433 (mt) cc_final: 0.9145 (tp) REVERT: D 101 MET cc_start: 0.9131 (tpp) cc_final: 0.8696 (tpp) REVERT: D 129 LYS cc_start: 0.8849 (mptt) cc_final: 0.8436 (pttt) REVERT: E 160 GLN cc_start: 0.8762 (pm20) cc_final: 0.8006 (pp30) REVERT: F 52 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8574 (mm) REVERT: F 127 ARG cc_start: 0.7942 (mtp85) cc_final: 0.7717 (mtp180) REVERT: F 210 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7811 (pt0) REVERT: F 229 MET cc_start: 0.9141 (tpp) cc_final: 0.8892 (tpp) REVERT: I 45 ASN cc_start: 0.6793 (OUTLIER) cc_final: 0.5727 (t0) REVERT: J 7 MET cc_start: 0.8866 (tpp) cc_final: 0.8322 (tpp) REVERT: J 14 MET cc_start: 0.7043 (mmt) cc_final: 0.6744 (ttm) REVERT: J 26 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9203 (mt) outliers start: 32 outliers final: 13 residues processed: 282 average time/residue: 0.2279 time to fit residues: 94.2601 Evaluate side-chains 254 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 45 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 52 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 122 optimal weight: 7.9990 chunk 63 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 146 optimal weight: 0.1980 chunk 132 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 76 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.077095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.061737 restraints weight = 48071.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063691 restraints weight = 26512.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.065014 restraints weight = 17839.945| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12820 Z= 0.143 Angle : 0.791 11.927 17476 Z= 0.376 Chirality : 0.044 0.184 2189 Planarity : 0.006 0.067 2130 Dihedral : 5.614 43.834 1695 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.52 % Favored : 92.42 % Rotamer: Outliers : 2.62 % Allowed : 19.62 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 (0.22), residues: 1609 helix: 0.61 (0.15), residues: 1241 sheet: None (None), residues: 0 loop : -3.39 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 232 HIS 0.005 0.001 HIS F 14 PHE 0.029 0.001 PHE B 64 TYR 0.022 0.002 TYR E 174 ARG 0.006 0.001 ARG F 96 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 788) hydrogen bonds : angle 4.11950 ( 2349) covalent geometry : bond 0.00321 (12820) covalent geometry : angle 0.79084 (17476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 268 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7466 (ptp-170) REVERT: A 87 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7058 (mm-40) REVERT: A 180 LYS cc_start: 0.8286 (mmtt) cc_final: 0.8025 (mmtt) REVERT: B 138 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8706 (mmt) REVERT: B 152 ARG cc_start: 0.9154 (tmm-80) cc_final: 0.8837 (tmm-80) REVERT: B 174 TYR cc_start: 0.8348 (t80) cc_final: 0.8111 (t80) REVERT: B 205 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8054 (mtp) REVERT: B 224 MET cc_start: 0.6882 (ttm) cc_final: 0.6662 (ttm) REVERT: C 95 PHE cc_start: 0.8994 (m-10) cc_final: 0.8754 (m-80) REVERT: C 123 MET cc_start: 0.7298 (tmm) cc_final: 0.6740 (tmm) REVERT: C 194 LEU cc_start: 0.9416 (mt) cc_final: 0.9128 (tp) REVERT: C 205 MET cc_start: 0.8920 (mmm) cc_final: 0.8594 (tpp) REVERT: C 210 MET cc_start: 0.8650 (ptp) cc_final: 0.7724 (pmm) REVERT: D 101 MET cc_start: 0.9126 (tpp) cc_final: 0.8701 (tpp) REVERT: D 129 LYS cc_start: 0.8862 (mptt) cc_final: 0.8611 (pttt) REVERT: E 160 GLN cc_start: 0.8750 (pm20) cc_final: 0.8411 (pp30) REVERT: F 52 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8564 (mm) REVERT: F 210 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7895 (pt0) REVERT: F 220 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8519 (tt) REVERT: J 7 MET cc_start: 0.8781 (tpp) cc_final: 0.8258 (tpp) REVERT: J 14 MET cc_start: 0.7016 (mmt) cc_final: 0.6667 (ttm) REVERT: J 26 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9217 (mm) REVERT: J 83 ASN cc_start: 0.9207 (t0) cc_final: 0.8946 (t0) outliers start: 36 outliers final: 12 residues processed: 296 average time/residue: 0.2381 time to fit residues: 103.2201 Evaluate side-chains 266 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 52 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 128 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN C 76 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.077234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.061833 restraints weight = 48514.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.063780 restraints weight = 26609.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.065110 restraints weight = 17923.019| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12820 Z= 0.143 Angle : 0.804 12.199 17476 Z= 0.380 Chirality : 0.044 0.196 2189 Planarity : 0.006 0.068 2130 Dihedral : 5.550 43.017 1695 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.71 % Favored : 92.23 % Rotamer: Outliers : 2.54 % Allowed : 20.93 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.27 (0.22), residues: 1609 helix: 0.74 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -3.41 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 232 HIS 0.003 0.001 HIS F 14 PHE 0.028 0.001 PHE B 64 TYR 0.020 0.002 TYR E 174 ARG 0.006 0.001 ARG F 96 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 788) hydrogen bonds : angle 4.06899 ( 2349) covalent geometry : bond 0.00319 (12820) covalent geometry : angle 0.80366 (17476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7579 (ptp-170) REVERT: A 87 GLN cc_start: 0.7335 (mm-40) cc_final: 0.7000 (mm-40) REVERT: A 101 MET cc_start: 0.8707 (mmm) cc_final: 0.8439 (mmm) REVERT: A 129 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8335 (tttm) REVERT: A 211 MET cc_start: 0.8489 (mtm) cc_final: 0.8268 (pmm) REVERT: B 138 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8718 (mmt) REVERT: B 152 ARG cc_start: 0.9191 (tmm-80) cc_final: 0.8861 (tmm-80) REVERT: B 174 TYR cc_start: 0.8377 (t80) cc_final: 0.7744 (t80) REVERT: B 178 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 224 MET cc_start: 0.6721 (ttm) cc_final: 0.6473 (ttm) REVERT: C 95 PHE cc_start: 0.9083 (m-10) cc_final: 0.8708 (m-80) REVERT: C 123 MET cc_start: 0.7313 (tmm) cc_final: 0.6739 (tmm) REVERT: C 194 LEU cc_start: 0.9415 (mt) cc_final: 0.9121 (tp) REVERT: C 210 MET cc_start: 0.8424 (ptp) cc_final: 0.7748 (pmm) REVERT: D 101 MET cc_start: 0.9108 (tpp) cc_final: 0.8747 (tpp) REVERT: D 123 MET cc_start: 0.8388 (pmm) cc_final: 0.6850 (ttt) REVERT: D 129 LYS cc_start: 0.8845 (mptt) cc_final: 0.8606 (pttt) REVERT: D 209 MET cc_start: 0.7776 (mmp) cc_final: 0.7095 (mmm) REVERT: E 66 ARG cc_start: 0.8197 (ttt180) cc_final: 0.7728 (ttm170) REVERT: E 160 GLN cc_start: 0.8794 (pm20) cc_final: 0.8442 (pp30) REVERT: F 100 GLU cc_start: 0.8032 (tt0) cc_final: 0.7724 (tt0) REVERT: F 210 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7748 (pt0) REVERT: F 258 MET cc_start: 0.8120 (tpp) cc_final: 0.7794 (ptp) REVERT: H 8 MET cc_start: 0.8772 (ttp) cc_final: 0.8450 (ptm) REVERT: I 59 PHE cc_start: 0.8084 (t80) cc_final: 0.6645 (t80) REVERT: J 7 MET cc_start: 0.8740 (tpp) cc_final: 0.8222 (tpp) REVERT: J 14 MET cc_start: 0.6952 (mmt) cc_final: 0.6633 (ttm) REVERT: J 26 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9223 (mm) REVERT: J 83 ASN cc_start: 0.9222 (t0) cc_final: 0.8916 (t0) outliers start: 35 outliers final: 15 residues processed: 282 average time/residue: 0.2288 time to fit residues: 94.2931 Evaluate side-chains 266 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 52 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 70 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 42 optimal weight: 0.2980 chunk 90 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN C 76 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.075872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.060595 restraints weight = 48536.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.062480 restraints weight = 27004.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063755 restraints weight = 18339.340| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12820 Z= 0.178 Angle : 0.842 12.381 17476 Z= 0.400 Chirality : 0.046 0.183 2189 Planarity : 0.007 0.110 2130 Dihedral : 5.588 42.831 1695 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.02 % Favored : 91.92 % Rotamer: Outliers : 2.47 % Allowed : 21.58 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.19 (0.22), residues: 1609 helix: 0.78 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -3.32 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 232 HIS 0.005 0.001 HIS F 14 PHE 0.029 0.002 PHE B 64 TYR 0.018 0.002 TYR C 174 ARG 0.007 0.001 ARG F 96 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 788) hydrogen bonds : angle 4.18892 ( 2349) covalent geometry : bond 0.00414 (12820) covalent geometry : angle 0.84173 (17476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 250 time to evaluate : 1.353 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 66 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7687 (ptp-170) REVERT: A 129 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8326 (tttm) REVERT: A 210 MET cc_start: 0.8363 (mtm) cc_final: 0.8117 (ttm) REVERT: B 138 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8682 (mmt) REVERT: B 152 ARG cc_start: 0.9181 (tmm-80) cc_final: 0.8872 (tmm-80) REVERT: B 210 MET cc_start: 0.8757 (mpp) cc_final: 0.8413 (mtt) REVERT: B 211 MET cc_start: 0.8741 (mmm) cc_final: 0.8188 (mmp) REVERT: B 224 MET cc_start: 0.6645 (ttm) cc_final: 0.6410 (ttm) REVERT: C 95 PHE cc_start: 0.8995 (m-10) cc_final: 0.8748 (m-80) REVERT: C 101 MET cc_start: 0.8647 (mpp) cc_final: 0.8011 (mpp) REVERT: C 123 MET cc_start: 0.7316 (tmm) cc_final: 0.7055 (tmm) REVERT: C 138 MET cc_start: 0.9161 (mpp) cc_final: 0.8949 (mtm) REVERT: C 194 LEU cc_start: 0.9431 (mt) cc_final: 0.9141 (tp) REVERT: C 210 MET cc_start: 0.8375 (ptp) cc_final: 0.7755 (pmm) REVERT: D 101 MET cc_start: 0.9028 (tpp) cc_final: 0.8744 (tpp) REVERT: D 123 MET cc_start: 0.8344 (pmm) cc_final: 0.6856 (ttt) REVERT: D 129 LYS cc_start: 0.8812 (mptt) cc_final: 0.8576 (pttt) REVERT: D 209 MET cc_start: 0.7850 (mmp) cc_final: 0.7117 (mmm) REVERT: E 160 GLN cc_start: 0.8796 (pm20) cc_final: 0.8406 (pp30) REVERT: E 205 MET cc_start: 0.8705 (tpt) cc_final: 0.8435 (tpt) REVERT: F 100 GLU cc_start: 0.7985 (tt0) cc_final: 0.7716 (tt0) REVERT: F 210 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: I 59 PHE cc_start: 0.7935 (t80) cc_final: 0.6480 (t80) REVERT: J 7 MET cc_start: 0.8748 (tpp) cc_final: 0.8235 (tpp) REVERT: J 14 MET cc_start: 0.6963 (mmt) cc_final: 0.6680 (ttm) REVERT: J 26 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9211 (mm) REVERT: J 83 ASN cc_start: 0.9226 (t0) cc_final: 0.8905 (t0) outliers start: 34 outliers final: 14 residues processed: 277 average time/residue: 0.2289 time to fit residues: 94.0440 Evaluate side-chains 257 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 52 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.076915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061871 restraints weight = 48277.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.063790 restraints weight = 26389.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065108 restraints weight = 17696.483| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12820 Z= 0.144 Angle : 0.824 12.647 17476 Z= 0.389 Chirality : 0.045 0.199 2189 Planarity : 0.006 0.068 2130 Dihedral : 5.497 42.786 1695 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.67 % Allowed : 22.02 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.03 (0.22), residues: 1609 helix: 0.87 (0.15), residues: 1259 sheet: None (None), residues: 0 loop : -3.30 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 232 HIS 0.007 0.001 HIS F 14 PHE 0.026 0.001 PHE B 64 TYR 0.018 0.002 TYR C 174 ARG 0.008 0.000 ARG F 96 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 788) hydrogen bonds : angle 4.08694 ( 2349) covalent geometry : bond 0.00325 (12820) covalent geometry : angle 0.82372 (17476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 256 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7628 (ptp-170) REVERT: A 101 MET cc_start: 0.8708 (mmm) cc_final: 0.8467 (mmm) REVERT: A 123 MET cc_start: 0.8039 (tpt) cc_final: 0.7495 (mpp) REVERT: A 129 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8298 (tttm) REVERT: B 138 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8580 (mmt) REVERT: B 152 ARG cc_start: 0.9183 (tmm-80) cc_final: 0.8878 (tmm-80) REVERT: B 178 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 224 MET cc_start: 0.6640 (ttm) cc_final: 0.6375 (ttm) REVERT: C 95 PHE cc_start: 0.9030 (m-10) cc_final: 0.8660 (m-80) REVERT: C 101 MET cc_start: 0.8660 (mpp) cc_final: 0.8202 (mpp) REVERT: C 123 MET cc_start: 0.7318 (tmm) cc_final: 0.6810 (tmm) REVERT: C 194 LEU cc_start: 0.9416 (mt) cc_final: 0.9108 (tp) REVERT: C 210 MET cc_start: 0.8279 (ptp) cc_final: 0.7500 (pmm) REVERT: C 224 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8527 (tmm) REVERT: D 101 MET cc_start: 0.8981 (tpp) cc_final: 0.8728 (tpp) REVERT: D 123 MET cc_start: 0.8407 (pmm) cc_final: 0.6973 (ttt) REVERT: D 129 LYS cc_start: 0.8843 (mptt) cc_final: 0.8618 (pttt) REVERT: D 209 MET cc_start: 0.7844 (mmp) cc_final: 0.7127 (mmm) REVERT: E 160 GLN cc_start: 0.8805 (pm20) cc_final: 0.8405 (pp30) REVERT: F 210 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: H 8 MET cc_start: 0.8714 (ttp) cc_final: 0.8508 (ptm) REVERT: I 59 PHE cc_start: 0.7837 (t80) cc_final: 0.7551 (t80) REVERT: J 7 MET cc_start: 0.8727 (tpp) cc_final: 0.8257 (tpp) REVERT: J 26 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9191 (mm) REVERT: J 83 ASN cc_start: 0.9232 (t0) cc_final: 0.8882 (t0) outliers start: 23 outliers final: 9 residues processed: 270 average time/residue: 0.2185 time to fit residues: 87.2648 Evaluate side-chains 266 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 52 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 121 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.077482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.062476 restraints weight = 47531.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.064419 restraints weight = 26082.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.065749 restraints weight = 17495.618| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12820 Z= 0.144 Angle : 0.855 13.041 17476 Z= 0.401 Chirality : 0.046 0.258 2189 Planarity : 0.006 0.068 2130 Dihedral : 5.463 42.406 1695 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.40 % Favored : 92.54 % Rotamer: Outliers : 1.74 % Allowed : 22.53 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1609 helix: 0.91 (0.15), residues: 1259 sheet: None (None), residues: 0 loop : -3.30 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 232 HIS 0.006 0.001 HIS F 14 PHE 0.026 0.001 PHE B 64 TYR 0.019 0.001 TYR D 174 ARG 0.008 0.000 ARG F 96 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 788) hydrogen bonds : angle 4.09165 ( 2349) covalent geometry : bond 0.00320 (12820) covalent geometry : angle 0.85529 (17476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 1.138 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 66 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7666 (ptp-170) REVERT: A 101 MET cc_start: 0.8711 (mmm) cc_final: 0.8493 (mmm) REVERT: A 123 MET cc_start: 0.8016 (tpt) cc_final: 0.7591 (mpp) REVERT: A 129 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8536 (tttm) REVERT: B 138 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8580 (mmt) REVERT: B 152 ARG cc_start: 0.9199 (tmm-80) cc_final: 0.8888 (tmm-80) REVERT: B 178 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8110 (mt-10) REVERT: B 224 MET cc_start: 0.6617 (ttm) cc_final: 0.6339 (ttm) REVERT: C 60 MET cc_start: 0.9203 (mmt) cc_final: 0.8876 (mmm) REVERT: C 95 PHE cc_start: 0.9002 (m-10) cc_final: 0.8744 (m-80) REVERT: C 101 MET cc_start: 0.8683 (mpp) cc_final: 0.8311 (mpp) REVERT: C 123 MET cc_start: 0.7326 (tmm) cc_final: 0.6847 (tmm) REVERT: C 194 LEU cc_start: 0.9407 (mt) cc_final: 0.9105 (tp) REVERT: C 224 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8530 (tmm) REVERT: D 94 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9018 (mt) REVERT: D 95 PHE cc_start: 0.8848 (m-10) cc_final: 0.8581 (m-80) REVERT: D 123 MET cc_start: 0.8470 (pmm) cc_final: 0.6956 (ttt) REVERT: D 129 LYS cc_start: 0.8863 (mptt) cc_final: 0.8658 (pttt) REVERT: E 160 GLN cc_start: 0.8794 (pm20) cc_final: 0.8357 (pp30) REVERT: F 105 GLN cc_start: 0.8456 (mt0) cc_final: 0.8081 (mt0) REVERT: F 210 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7834 (pt0) REVERT: I 59 PHE cc_start: 0.7839 (t80) cc_final: 0.6621 (t80) REVERT: J 7 MET cc_start: 0.8754 (tpp) cc_final: 0.8522 (tpp) REVERT: J 14 MET cc_start: 0.7000 (mmt) cc_final: 0.6583 (ttm) REVERT: J 26 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9206 (mm) REVERT: J 83 ASN cc_start: 0.9224 (t0) cc_final: 0.8855 (t0) outliers start: 24 outliers final: 12 residues processed: 280 average time/residue: 0.2200 time to fit residues: 91.5139 Evaluate side-chains 268 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 249 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 52 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 83 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.077811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.062536 restraints weight = 48070.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064430 restraints weight = 26419.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.065785 restraints weight = 17931.117| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12820 Z= 0.150 Angle : 0.871 15.202 17476 Z= 0.409 Chirality : 0.046 0.229 2189 Planarity : 0.006 0.068 2130 Dihedral : 5.378 42.169 1695 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 1.67 % Allowed : 23.18 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1609 helix: 0.90 (0.15), residues: 1262 sheet: None (None), residues: 0 loop : -3.35 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 72 HIS 0.005 0.001 HIS F 14 PHE 0.026 0.001 PHE B 64 TYR 0.031 0.002 TYR A 174 ARG 0.007 0.000 ARG F 96 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 788) hydrogen bonds : angle 4.11573 ( 2349) covalent geometry : bond 0.00344 (12820) covalent geometry : angle 0.87090 (17476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7681 (ptp-170) REVERT: A 76 ASN cc_start: 0.8516 (m-40) cc_final: 0.7669 (m-40) REVERT: A 123 MET cc_start: 0.8018 (tpt) cc_final: 0.7666 (mpp) REVERT: A 129 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8501 (tttt) REVERT: B 138 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8582 (mmt) REVERT: B 178 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8089 (mt-10) REVERT: B 224 MET cc_start: 0.6605 (ttm) cc_final: 0.6328 (ttm) REVERT: C 95 PHE cc_start: 0.9028 (m-10) cc_final: 0.8655 (m-80) REVERT: C 101 MET cc_start: 0.8672 (mpp) cc_final: 0.8322 (mpp) REVERT: C 123 MET cc_start: 0.7310 (tmm) cc_final: 0.6839 (tmm) REVERT: C 194 LEU cc_start: 0.9410 (mt) cc_final: 0.9105 (tp) REVERT: C 210 MET cc_start: 0.7891 (pmm) cc_final: 0.7348 (pmm) REVERT: C 224 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8529 (tmm) REVERT: D 94 LEU cc_start: 0.9219 (tt) cc_final: 0.9005 (mt) REVERT: D 95 PHE cc_start: 0.8813 (m-10) cc_final: 0.8566 (m-80) REVERT: D 123 MET cc_start: 0.8499 (pmm) cc_final: 0.7068 (ttt) REVERT: D 129 LYS cc_start: 0.8888 (mptt) cc_final: 0.8675 (pttt) REVERT: F 105 GLN cc_start: 0.8372 (mt0) cc_final: 0.7969 (mt0) REVERT: F 210 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: I 59 PHE cc_start: 0.7744 (t80) cc_final: 0.6489 (t80) REVERT: J 7 MET cc_start: 0.8765 (tpp) cc_final: 0.8496 (tpp) REVERT: J 14 MET cc_start: 0.7148 (mmt) cc_final: 0.6736 (ttm) REVERT: J 26 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9205 (mm) REVERT: J 83 ASN cc_start: 0.9209 (t0) cc_final: 0.8837 (t0) outliers start: 23 outliers final: 13 residues processed: 269 average time/residue: 0.2193 time to fit residues: 89.4209 Evaluate side-chains 262 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 52 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 114 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 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 76 ASN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.077668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062470 restraints weight = 48294.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.064410 restraints weight = 26576.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.065640 restraints weight = 17923.143| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12820 Z= 0.155 Angle : 0.884 14.012 17476 Z= 0.416 Chirality : 0.046 0.333 2189 Planarity : 0.006 0.069 2130 Dihedral : 5.396 41.724 1695 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.89 % Allowed : 23.33 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1609 helix: 0.91 (0.15), residues: 1269 sheet: None (None), residues: 0 loop : -3.32 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 72 HIS 0.004 0.001 HIS F 14 PHE 0.032 0.001 PHE B 64 TYR 0.022 0.002 TYR D 244 ARG 0.007 0.001 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 788) hydrogen bonds : angle 4.14859 ( 2349) covalent geometry : bond 0.00359 (12820) covalent geometry : angle 0.88394 (17476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3882.14 seconds wall clock time: 68 minutes 9.03 seconds (4089.03 seconds total)