Starting phenix.real_space_refine on Wed Mar 4 05:09:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k3x_62031/03_2026/9k3x_62031_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k3x_62031/03_2026/9k3x_62031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k3x_62031/03_2026/9k3x_62031_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k3x_62031/03_2026/9k3x_62031_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k3x_62031/03_2026/9k3x_62031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k3x_62031/03_2026/9k3x_62031.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.063 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 53 5.16 5 C 6989 2.51 5 N 1768 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10769 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2153 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 268} Chain breaks: 1 Chain: "B" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2265 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 15, 'TRANS': 284} Chain: "C" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1957 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "D" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1957 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "E" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2432 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.51, per 1000 atoms: 0.23 Number of scatterers: 10769 At special positions: 0 Unit cell: (72.36, 108.54, 148.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 1 15.00 O 1958 8.00 N 1768 7.00 C 6989 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: 0.77 Conformation dependent library (CDL) restraints added in 574.7 milliseconds 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2564 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 8 sheets defined 63.8% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 12 through 57 removed outlier: 3.839A pdb=" N TRP A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 79 through 111 Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.965A pdb=" N ASP A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.855A pdb=" N VAL A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 152 through 177 removed outlier: 3.844A pdb=" N GLY A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) Proline residue: A 166 - end of helix Processing helix chain 'A' and resid 180 through 190 removed outlier: 3.727A pdb=" N ARG A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 206 through 223 removed outlier: 4.081A pdb=" N GLY A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 4.388A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.682A pdb=" N MET A 258 " --> pdb=" O PHE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 289 Processing helix chain 'B' and resid 15 through 45 removed outlier: 3.569A pdb=" N ALA B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.995A pdb=" N THR B 59 " --> pdb=" O PHE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 103 Proline residue: B 91 - end of helix Processing helix chain 'B' and resid 105 through 118 removed outlier: 4.522A pdb=" N ARG B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 134 through 143 removed outlier: 4.138A pdb=" N LEU B 138 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 153 removed outlier: 4.684A pdb=" N ASN B 153 " --> pdb=" O ASN B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 removed outlier: 3.970A pdb=" N SER B 162 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 195 removed outlier: 3.572A pdb=" N ILE B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 3.526A pdb=" N ALA B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 207 removed outlier: 3.616A pdb=" N LYS B 201 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 223 through 240 removed outlier: 3.509A pdb=" N GLY B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.551A pdb=" N PHE B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 275 Processing helix chain 'B' and resid 281 through 311 removed outlier: 3.536A pdb=" N ALA B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.747A pdb=" N THR C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 Processing helix chain 'C' and resid 85 through 92 removed outlier: 3.809A pdb=" N LEU C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 119 removed outlier: 4.412A pdb=" N GLY C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL C 115 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 117 " --> pdb=" O PHE C 113 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 removed outlier: 3.575A pdb=" N LYS C 136 " --> pdb=" O TRP C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.596A pdb=" N LEU C 154 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 169 removed outlier: 3.648A pdb=" N ARG C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 184 removed outlier: 4.238A pdb=" N ALA C 183 " --> pdb=" O PRO C 180 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 184 " --> pdb=" O CYS C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 184' Processing helix chain 'C' and resid 185 through 203 removed outlier: 3.675A pdb=" N GLU C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLN C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'D' and resid 48 through 57 removed outlier: 3.532A pdb=" N LEU D 52 " --> pdb=" O GLY D 48 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR D 55 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.589A pdb=" N GLU D 61 " --> pdb=" O LYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 removed outlier: 3.590A pdb=" N LEU D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 117 removed outlier: 4.356A pdb=" N GLY D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 117 " --> pdb=" O PHE D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 removed outlier: 4.014A pdb=" N GLU D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 147 removed outlier: 4.554A pdb=" N LYS D 144 " --> pdb=" O ASN D 141 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP D 145 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 146 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU D 147 " --> pdb=" O LYS D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 180 through 184 Processing helix chain 'D' and resid 188 through 199 removed outlier: 4.029A pdb=" N ILE D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 236 through 242 Processing helix chain 'D' and resid 245 through 252 removed outlier: 4.002A pdb=" N GLU D 249 " --> pdb=" O LYS D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 28 Processing helix chain 'E' and resid 37 through 47 Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 113 through 120 removed outlier: 3.794A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 153 removed outlier: 3.632A pdb=" N PHE E 143 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS E 151 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 176 through 186 removed outlier: 3.614A pdb=" N ARG E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 201 removed outlier: 3.576A pdb=" N GLN E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 229 Processing helix chain 'E' and resid 266 through 284 removed outlier: 3.634A pdb=" N LYS E 282 " --> pdb=" O ASP E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 291 removed outlier: 3.516A pdb=" N LEU E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 312 removed outlier: 3.561A pdb=" N GLU E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR E 310 " --> pdb=" O ALA E 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 23 through 34 removed outlier: 6.282A pdb=" N ALA C 25 " --> pdb=" O TYR C 19 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C 19 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS C 27 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN C 17 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE C 29 " --> pdb=" O ASN C 15 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 11 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL C 13 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU C 73 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN C 15 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU C 71 " --> pdb=" O ASN C 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 93 through 96 removed outlier: 6.395A pdb=" N LEU C 175 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL C 208 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 177 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR C 222 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE C 233 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE C 224 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 24 through 34 removed outlier: 6.301A pdb=" N ALA D 25 " --> pdb=" O TYR D 19 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR D 19 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LYS D 27 " --> pdb=" O ASN D 17 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN D 17 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE D 29 " --> pdb=" O ASN D 15 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE D 11 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL D 13 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU D 73 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN D 15 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU D 71 " --> pdb=" O ASN D 15 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 67 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 93 through 96 removed outlier: 6.605A pdb=" N GLY D 94 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASP D 178 " --> pdb=" O GLY D 94 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 96 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR D 39 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D 232 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TYR D 226 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 30 through 35 removed outlier: 9.259A pdb=" N PHE E 52 " --> pdb=" O SER E 3 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR E 5 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ALA E 54 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA E 7 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER E 254 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE E 76 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR E 256 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA E 205 " --> pdb=" O VAL E 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 172 through 174 removed outlier: 6.904A pdb=" N VAL E 132 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLY E 174 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG E 134 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR E 193 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG E 135 " --> pdb=" O TYR E 193 " (cutoff:3.500A) removed outlier: 13.286A pdb=" N GLU E 195 " --> pdb=" O ARG E 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 94 through 95 Processing sheet with id=AA8, first strand: chain 'E' and resid 263 through 264 590 hydrogen bonds defined for protein. 1713 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: 1.61 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3405 1.34 - 1.46: 2391 1.46 - 1.58: 5112 1.58 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 11000 Sorted by residual: bond pdb=" N GLU E 1 " pdb=" CA GLU E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N LYS B 14 " pdb=" CA LYS B 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N LEU A 12 " pdb=" CA LEU A 12 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" CA GLU C 179 " pdb=" C GLU C 179 " ideal model delta sigma weight residual 1.532 1.525 0.007 6.50e-03 2.37e+04 1.25e+00 bond pdb=" C GLU C 179 " pdb=" O GLU C 179 " ideal model delta sigma weight residual 1.233 1.237 -0.004 4.80e-03 4.34e+04 8.42e-01 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 14415 1.19 - 2.38: 404 2.38 - 3.57: 93 3.57 - 4.76: 18 4.76 - 5.95: 3 Bond angle restraints: 14933 Sorted by residual: angle pdb=" N ILE C 170 " pdb=" CA ILE C 170 " pdb=" C ILE C 170 " ideal model delta sigma weight residual 111.91 109.55 2.36 8.90e-01 1.26e+00 7.00e+00 angle pdb=" CA GLY E 37 " pdb=" C GLY E 37 " pdb=" O GLY E 37 " ideal model delta sigma weight residual 122.29 120.51 1.78 8.10e-01 1.52e+00 4.82e+00 angle pdb=" CA GLY A 77 " pdb=" C GLY A 77 " pdb=" O GLY A 77 " ideal model delta sigma weight residual 122.57 120.64 1.93 9.20e-01 1.18e+00 4.39e+00 angle pdb=" N PHE E 11 " pdb=" CA PHE E 11 " pdb=" CB PHE E 11 " ideal model delta sigma weight residual 110.30 107.21 3.09 1.49e+00 4.50e-01 4.30e+00 angle pdb=" CA GLY E 176 " pdb=" C GLY E 176 " pdb=" O GLY E 176 " ideal model delta sigma weight residual 122.57 120.66 1.91 9.20e-01 1.18e+00 4.29e+00 ... (remaining 14928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5902 17.98 - 35.97: 472 35.97 - 53.95: 122 53.95 - 71.94: 28 71.94 - 89.92: 8 Dihedral angle restraints: 6532 sinusoidal: 2539 harmonic: 3993 Sorted by residual: dihedral pdb=" CG ARG B 217 " pdb=" CD ARG B 217 " pdb=" NE ARG B 217 " pdb=" CZ ARG B 217 " ideal model delta sinusoidal sigma weight residual 90.00 133.81 -43.81 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG C 116 " pdb=" CD ARG C 116 " pdb=" NE ARG C 116 " pdb=" CZ ARG C 116 " ideal model delta sinusoidal sigma weight residual 90.00 133.00 -43.00 2 1.50e+01 4.44e-03 9.92e+00 dihedral pdb=" CB GLU D 173 " pdb=" CG GLU D 173 " pdb=" CD GLU D 173 " pdb=" OE1 GLU D 173 " ideal model delta sinusoidal sigma weight residual 0.00 85.27 -85.27 1 3.00e+01 1.11e-03 9.79e+00 ... (remaining 6529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1157 0.029 - 0.059: 372 0.059 - 0.088: 121 0.088 - 0.118: 64 0.118 - 0.147: 14 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA ILE E 85 " pdb=" N ILE E 85 " pdb=" C ILE E 85 " pdb=" CB ILE E 85 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE B 122 " pdb=" N ILE B 122 " pdb=" C ILE B 122 " pdb=" CB ILE B 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE C 72 " pdb=" N ILE C 72 " pdb=" C ILE C 72 " pdb=" CB ILE C 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1725 not shown) Planarity restraints: 1874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 198 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C ILE A 198 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE A 198 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 199 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 141 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.36e+00 pdb=" C TYR A 141 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" N THR A 142 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 11 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO E 12 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 12 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 12 " 0.019 5.00e-02 4.00e+02 ... (remaining 1871 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2229 2.78 - 3.31: 10403 3.31 - 3.84: 16981 3.84 - 4.37: 20639 4.37 - 4.90: 36178 Nonbonded interactions: 86430 Sorted by model distance: nonbonded pdb=" OE2 GLU B 202 " pdb=" OH TYR D 63 " model vdw 2.245 3.040 nonbonded pdb=" O LYS A 114 " pdb=" OG SER A 115 " model vdw 2.262 3.040 nonbonded pdb=" O THR C 143 " pdb=" OG1 THR C 143 " model vdw 2.267 3.040 nonbonded pdb=" O ALA D 215 " pdb=" OG SER D 219 " model vdw 2.334 3.040 nonbonded pdb=" OE2 GLU C 179 " pdb=" NE2 HIS C 210 " model vdw 2.344 3.120 ... (remaining 86425 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 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.320 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.010 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11000 Z= 0.119 Angle : 0.519 5.953 14933 Z= 0.297 Chirality : 0.037 0.147 1728 Planarity : 0.004 0.034 1874 Dihedral : 14.638 89.919 3968 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.18 % Allowed : 14.89 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1383 helix: 0.64 (0.19), residues: 768 sheet: 0.00 (0.39), residues: 154 loop : -0.13 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 14 TYR 0.008 0.001 TYR E 293 PHE 0.012 0.001 PHE E 11 TRP 0.011 0.001 TRP A 154 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00253 (11000) covalent geometry : angle 0.51872 (14933) hydrogen bonds : bond 0.23159 ( 590) hydrogen bonds : angle 7.14262 ( 1713) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7590 (ttt90) cc_final: 0.7369 (ttp80) REVERT: A 177 LYS cc_start: 0.8116 (mttm) cc_final: 0.7895 (mtmm) REVERT: B 33 MET cc_start: 0.8470 (mtt) cc_final: 0.8200 (mtp) REVERT: C 67 ARG cc_start: 0.6943 (ttp80) cc_final: 0.6560 (ttp80) REVERT: C 116 ARG cc_start: 0.8595 (ttm110) cc_final: 0.8334 (mtm-85) REVERT: D 80 LEU cc_start: 0.7863 (mm) cc_final: 0.7548 (mm) REVERT: D 139 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5286 (tm) REVERT: D 173 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7652 (mm-30) REVERT: E 62 GLU cc_start: 0.7525 (mp0) cc_final: 0.7104 (mp0) REVERT: E 66 GLN cc_start: 0.7719 (tt0) cc_final: 0.7227 (tm130) REVERT: E 208 LYS cc_start: 0.8110 (mttt) cc_final: 0.7886 (mtpp) outliers start: 2 outliers final: 0 residues processed: 146 average time/residue: 0.7734 time to fit residues: 119.3335 Evaluate side-chains 128 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 overall best weight: 1.2070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN C 210 HIS D 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.193337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135092 restraints weight = 11354.980| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.62 r_work: 0.3086 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11000 Z= 0.155 Angle : 0.595 7.884 14933 Z= 0.314 Chirality : 0.042 0.178 1728 Planarity : 0.004 0.042 1874 Dihedral : 4.497 30.589 1478 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.71 % Allowed : 13.66 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.23), residues: 1383 helix: 1.18 (0.19), residues: 786 sheet: 0.50 (0.41), residues: 145 loop : -0.45 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 67 TYR 0.024 0.002 TYR D 251 PHE 0.022 0.001 PHE E 11 TRP 0.016 0.001 TRP C 132 HIS 0.005 0.001 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00359 (11000) covalent geometry : angle 0.59485 (14933) hydrogen bonds : bond 0.06441 ( 590) hydrogen bonds : angle 5.10356 ( 1713) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.5409 (OUTLIER) cc_final: 0.5176 (tt) REVERT: A 28 ARG cc_start: 0.7807 (ttt90) cc_final: 0.7581 (ttp80) REVERT: B 33 MET cc_start: 0.8412 (mtt) cc_final: 0.8203 (mtp) REVERT: B 213 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: B 217 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8018 (mmm160) REVERT: B 307 PHE cc_start: 0.8281 (t80) cc_final: 0.6991 (m-80) REVERT: B 308 MET cc_start: 0.9013 (mmm) cc_final: 0.8735 (mmp) REVERT: C 42 ILE cc_start: 0.8224 (mt) cc_final: 0.7690 (pt) REVERT: C 67 ARG cc_start: 0.6993 (ttp80) cc_final: 0.6572 (ttp80) REVERT: C 116 ARG cc_start: 0.8655 (ttm110) cc_final: 0.8351 (mtm-85) REVERT: C 121 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6593 (pp) REVERT: D 80 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7525 (mm) REVERT: D 139 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.5921 (tm) REVERT: D 173 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7684 (mm-30) REVERT: E 62 GLU cc_start: 0.7645 (mp0) cc_final: 0.7251 (mp0) REVERT: E 66 GLN cc_start: 0.7810 (tt0) cc_final: 0.7292 (tm130) outliers start: 31 outliers final: 9 residues processed: 161 average time/residue: 0.6604 time to fit residues: 113.2108 Evaluate side-chains 155 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 302 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 24 optimal weight: 0.0570 chunk 81 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN D 131 GLN D 214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.194538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.130604 restraints weight = 11573.465| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.66 r_work: 0.3115 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11000 Z= 0.119 Angle : 0.530 8.137 14933 Z= 0.276 Chirality : 0.040 0.156 1728 Planarity : 0.004 0.038 1874 Dihedral : 4.400 35.061 1478 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.15 % Allowed : 13.92 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.23), residues: 1383 helix: 1.54 (0.19), residues: 784 sheet: 0.48 (0.41), residues: 145 loop : -0.35 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 14 TYR 0.020 0.001 TYR D 251 PHE 0.018 0.001 PHE E 11 TRP 0.031 0.001 TRP C 132 HIS 0.004 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00257 (11000) covalent geometry : angle 0.52999 (14933) hydrogen bonds : bond 0.04928 ( 590) hydrogen bonds : angle 4.70170 ( 1713) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.5178 (OUTLIER) cc_final: 0.4937 (tt) REVERT: A 28 ARG cc_start: 0.7814 (ttt90) cc_final: 0.7609 (ttp80) REVERT: B 213 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: B 217 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7870 (mmm160) REVERT: B 307 PHE cc_start: 0.8216 (t80) cc_final: 0.6886 (m-80) REVERT: B 308 MET cc_start: 0.8947 (mmm) cc_final: 0.8597 (mmp) REVERT: C 42 ILE cc_start: 0.8044 (mt) cc_final: 0.7651 (pt) REVERT: C 67 ARG cc_start: 0.7009 (ttp80) cc_final: 0.6562 (ttp80) REVERT: C 116 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8364 (mtm-85) REVERT: C 121 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6550 (pp) REVERT: C 196 ILE cc_start: 0.7428 (pt) cc_final: 0.7199 (pp) REVERT: C 214 GLN cc_start: 0.5988 (tm-30) cc_final: 0.5482 (tm-30) REVERT: D 80 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7477 (mm) REVERT: E 62 GLU cc_start: 0.7677 (mp0) cc_final: 0.7304 (mp0) outliers start: 36 outliers final: 14 residues processed: 171 average time/residue: 0.6421 time to fit residues: 117.2224 Evaluate side-chains 152 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 183 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN D 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.194972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.137724 restraints weight = 11538.306| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.63 r_work: 0.3119 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11000 Z= 0.120 Angle : 0.527 7.339 14933 Z= 0.274 Chirality : 0.040 0.150 1728 Planarity : 0.004 0.044 1874 Dihedral : 4.312 32.669 1478 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.88 % Favored : 98.05 % Rotamer: Outliers : 3.42 % Allowed : 13.84 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1383 helix: 1.67 (0.19), residues: 773 sheet: 0.46 (0.41), residues: 145 loop : -0.45 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 67 TYR 0.011 0.001 TYR D 19 PHE 0.024 0.001 PHE C 23 TRP 0.022 0.001 TRP C 132 HIS 0.004 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00272 (11000) covalent geometry : angle 0.52722 (14933) hydrogen bonds : bond 0.04820 ( 590) hydrogen bonds : angle 4.57779 ( 1713) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.4998 (OUTLIER) cc_final: 0.4758 (tt) REVERT: A 28 ARG cc_start: 0.7728 (ttt90) cc_final: 0.7519 (ttp80) REVERT: B 217 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7787 (mmm160) REVERT: B 307 PHE cc_start: 0.8204 (t80) cc_final: 0.6832 (m-80) REVERT: B 308 MET cc_start: 0.8931 (mmm) cc_final: 0.8605 (mmp) REVERT: C 14 ARG cc_start: 0.6536 (mmt-90) cc_final: 0.6190 (mmm160) REVERT: C 42 ILE cc_start: 0.8110 (mt) cc_final: 0.7708 (pt) REVERT: C 67 ARG cc_start: 0.7065 (ttp80) cc_final: 0.6713 (ttp80) REVERT: C 121 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6533 (pp) REVERT: C 214 GLN cc_start: 0.6008 (tm-30) cc_final: 0.5642 (tm-30) REVERT: D 72 ILE cc_start: 0.6702 (OUTLIER) cc_final: 0.6394 (mt) REVERT: D 116 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7753 (ttp-110) REVERT: E 62 GLU cc_start: 0.7653 (mp0) cc_final: 0.7328 (mp0) REVERT: E 134 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8667 (ppt170) REVERT: E 167 CYS cc_start: 0.8244 (p) cc_final: 0.7243 (t) outliers start: 39 outliers final: 16 residues processed: 167 average time/residue: 0.6810 time to fit residues: 121.1002 Evaluate side-chains 151 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 183 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 131 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 13 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.196942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143881 restraints weight = 11478.950| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.62 r_work: 0.3142 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11000 Z= 0.102 Angle : 0.508 8.471 14933 Z= 0.262 Chirality : 0.039 0.149 1728 Planarity : 0.004 0.037 1874 Dihedral : 4.219 35.723 1478 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.02 % Favored : 97.90 % Rotamer: Outliers : 2.63 % Allowed : 15.15 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.23), residues: 1383 helix: 1.87 (0.20), residues: 767 sheet: 0.38 (0.43), residues: 129 loop : -0.38 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 116 TYR 0.012 0.001 TYR D 20 PHE 0.016 0.001 PHE E 11 TRP 0.022 0.001 TRP C 132 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00214 (11000) covalent geometry : angle 0.50838 (14933) hydrogen bonds : bond 0.04181 ( 590) hydrogen bonds : angle 4.43441 ( 1713) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.4884 (OUTLIER) cc_final: 0.4657 (tt) REVERT: A 177 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8096 (tptp) REVERT: B 23 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8579 (m) REVERT: B 217 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8364 (mmm160) REVERT: B 307 PHE cc_start: 0.8219 (t80) cc_final: 0.6846 (m-80) REVERT: B 308 MET cc_start: 0.8977 (mmm) cc_final: 0.8695 (mmp) REVERT: C 42 ILE cc_start: 0.8007 (mt) cc_final: 0.7639 (pt) REVERT: C 67 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6657 (ttp80) REVERT: C 121 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6541 (pp) REVERT: C 214 GLN cc_start: 0.6035 (tm-30) cc_final: 0.5698 (tm-30) REVERT: D 116 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7741 (ttp-110) REVERT: E 62 GLU cc_start: 0.7669 (mp0) cc_final: 0.7385 (mp0) REVERT: E 167 CYS cc_start: 0.8278 (p) cc_final: 0.7286 (t) REVERT: E 318 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7835 (ttmt) outliers start: 30 outliers final: 11 residues processed: 163 average time/residue: 0.6963 time to fit residues: 120.6380 Evaluate side-chains 146 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 318 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 110 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 102 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN D 78 ASN D 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.195572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141496 restraints weight = 11485.169| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.69 r_work: 0.3110 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11000 Z= 0.113 Angle : 0.505 6.160 14933 Z= 0.263 Chirality : 0.039 0.155 1728 Planarity : 0.004 0.036 1874 Dihedral : 4.207 38.521 1478 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.17 % Favored : 97.76 % Rotamer: Outliers : 3.15 % Allowed : 14.97 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.23), residues: 1383 helix: 1.81 (0.19), residues: 771 sheet: 0.38 (0.43), residues: 129 loop : -0.41 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 123 TYR 0.008 0.001 TYR E 293 PHE 0.025 0.001 PHE C 23 TRP 0.026 0.001 TRP C 132 HIS 0.003 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00258 (11000) covalent geometry : angle 0.50488 (14933) hydrogen bonds : bond 0.04517 ( 590) hydrogen bonds : angle 4.41932 ( 1713) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.4772 (OUTLIER) cc_final: 0.4533 (tt) REVERT: A 177 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8120 (tptp) REVERT: B 217 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7854 (mmm160) REVERT: B 307 PHE cc_start: 0.8323 (t80) cc_final: 0.6942 (m-80) REVERT: B 308 MET cc_start: 0.8987 (mmm) cc_final: 0.8746 (mmp) REVERT: C 14 ARG cc_start: 0.6587 (mmt-90) cc_final: 0.5990 (mmt180) REVERT: C 42 ILE cc_start: 0.7929 (mt) cc_final: 0.7599 (pt) REVERT: C 67 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6692 (ttp80) REVERT: C 116 ARG cc_start: 0.8850 (mtm-85) cc_final: 0.8638 (mtm-85) REVERT: C 121 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6573 (pp) REVERT: C 197 THR cc_start: 0.8019 (m) cc_final: 0.7712 (t) REVERT: C 224 PHE cc_start: 0.5672 (t80) cc_final: 0.5247 (t80) REVERT: C 225 MET cc_start: 0.7003 (mmt) cc_final: 0.6633 (mmt) REVERT: E 62 GLU cc_start: 0.7663 (mp0) cc_final: 0.7372 (mp0) REVERT: E 134 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8633 (ppt170) REVERT: E 167 CYS cc_start: 0.8314 (p) cc_final: 0.7315 (t) outliers start: 36 outliers final: 15 residues processed: 163 average time/residue: 0.6007 time to fit residues: 104.8688 Evaluate side-chains 155 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 201 GLN Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 183 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 10 optimal weight: 0.1980 chunk 57 optimal weight: 0.3980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN C 214 GLN D 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.192802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137867 restraints weight = 11422.283| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.54 r_work: 0.3091 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11000 Z= 0.167 Angle : 0.570 9.881 14933 Z= 0.296 Chirality : 0.042 0.186 1728 Planarity : 0.004 0.039 1874 Dihedral : 4.162 17.290 1476 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 3.59 % Allowed : 15.15 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.23), residues: 1383 helix: 1.58 (0.19), residues: 770 sheet: 0.30 (0.43), residues: 129 loop : -0.49 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 116 TYR 0.013 0.001 TYR E 293 PHE 0.026 0.002 PHE E 11 TRP 0.030 0.001 TRP C 132 HIS 0.004 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00416 (11000) covalent geometry : angle 0.56958 (14933) hydrogen bonds : bond 0.05608 ( 590) hydrogen bonds : angle 4.56136 ( 1713) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.4888 (OUTLIER) cc_final: 0.4637 (tt) REVERT: B 217 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7835 (mmm160) REVERT: B 307 PHE cc_start: 0.8364 (t80) cc_final: 0.7010 (m-80) REVERT: B 308 MET cc_start: 0.8986 (mmm) cc_final: 0.8771 (mmp) REVERT: C 14 ARG cc_start: 0.6543 (mmt-90) cc_final: 0.6027 (mmt180) REVERT: C 42 ILE cc_start: 0.8020 (mt) cc_final: 0.7655 (pt) REVERT: C 67 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6795 (ttp80) REVERT: C 116 ARG cc_start: 0.8858 (mtm-85) cc_final: 0.8410 (mtt-85) REVERT: C 121 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6609 (pp) REVERT: C 197 THR cc_start: 0.8067 (m) cc_final: 0.7754 (t) REVERT: C 224 PHE cc_start: 0.5732 (t80) cc_final: 0.5403 (t80) REVERT: C 225 MET cc_start: 0.7016 (mmt) cc_final: 0.6655 (mmt) REVERT: D 16 LEU cc_start: 0.7412 (mt) cc_final: 0.7171 (mm) REVERT: D 35 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6840 (tmtm) REVERT: E 62 GLU cc_start: 0.7653 (mp0) cc_final: 0.7355 (mp0) REVERT: E 134 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8628 (ppt170) REVERT: E 167 CYS cc_start: 0.8324 (p) cc_final: 0.7343 (t) outliers start: 41 outliers final: 16 residues processed: 164 average time/residue: 0.6105 time to fit residues: 107.3766 Evaluate side-chains 157 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 201 GLN Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 57 optimal weight: 0.7980 chunk 69 optimal weight: 0.0980 chunk 126 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN D 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.196594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.143694 restraints weight = 11488.877| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.61 r_work: 0.3142 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11000 Z= 0.099 Angle : 0.502 6.727 14933 Z= 0.260 Chirality : 0.039 0.141 1728 Planarity : 0.004 0.035 1874 Dihedral : 3.977 17.713 1476 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 2.01 % Allowed : 17.16 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1383 helix: 1.82 (0.20), residues: 767 sheet: 0.50 (0.44), residues: 129 loop : -0.46 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 123 TYR 0.009 0.001 TYR C 108 PHE 0.027 0.001 PHE C 240 TRP 0.035 0.001 TRP C 132 HIS 0.003 0.001 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00205 (11000) covalent geometry : angle 0.50245 (14933) hydrogen bonds : bond 0.04033 ( 590) hydrogen bonds : angle 4.41500 ( 1713) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.4702 (OUTLIER) cc_final: 0.4476 (tt) REVERT: A 177 LYS cc_start: 0.8524 (mtpt) cc_final: 0.8068 (tptp) REVERT: B 307 PHE cc_start: 0.8262 (t80) cc_final: 0.6818 (m-80) REVERT: C 14 ARG cc_start: 0.6602 (mmt-90) cc_final: 0.6072 (mmt180) REVERT: C 42 ILE cc_start: 0.7851 (mt) cc_final: 0.7524 (pt) REVERT: C 67 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6735 (ttp80) REVERT: C 116 ARG cc_start: 0.8812 (mtm-85) cc_final: 0.8331 (mtt-85) REVERT: C 121 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6566 (pp) REVERT: C 197 THR cc_start: 0.8021 (m) cc_final: 0.7803 (t) REVERT: C 224 PHE cc_start: 0.5729 (t80) cc_final: 0.5357 (t80) REVERT: C 225 MET cc_start: 0.7270 (mmt) cc_final: 0.6908 (mmt) REVERT: D 35 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6863 (tmtm) REVERT: D 116 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7770 (ttp-110) REVERT: E 62 GLU cc_start: 0.7663 (mp0) cc_final: 0.7378 (mp0) REVERT: E 167 CYS cc_start: 0.8274 (p) cc_final: 0.7284 (t) outliers start: 23 outliers final: 11 residues processed: 160 average time/residue: 0.6727 time to fit residues: 114.7566 Evaluate side-chains 151 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain E residue 183 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 82 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.192712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139724 restraints weight = 11411.127| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.63 r_work: 0.3082 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11000 Z= 0.164 Angle : 0.579 8.312 14933 Z= 0.297 Chirality : 0.042 0.141 1728 Planarity : 0.004 0.038 1874 Dihedral : 4.097 17.556 1476 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.02 % Favored : 97.90 % Rotamer: Outliers : 2.80 % Allowed : 17.25 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.23), residues: 1383 helix: 1.61 (0.19), residues: 765 sheet: 0.48 (0.44), residues: 129 loop : -0.53 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 116 TYR 0.013 0.002 TYR E 293 PHE 0.030 0.002 PHE C 240 TRP 0.037 0.001 TRP C 132 HIS 0.004 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00407 (11000) covalent geometry : angle 0.57899 (14933) hydrogen bonds : bond 0.05483 ( 590) hydrogen bonds : angle 4.53828 ( 1713) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.4620 (tt) REVERT: B 217 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7846 (mmm160) REVERT: B 307 PHE cc_start: 0.8413 (t80) cc_final: 0.6992 (m-80) REVERT: C 14 ARG cc_start: 0.6541 (mmt-90) cc_final: 0.6007 (mmt180) REVERT: C 42 ILE cc_start: 0.7987 (mt) cc_final: 0.7622 (pt) REVERT: C 67 ARG cc_start: 0.7093 (ttp80) cc_final: 0.6735 (ttp80) REVERT: C 116 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8362 (mtt-85) REVERT: C 121 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6600 (pp) REVERT: C 197 THR cc_start: 0.8050 (m) cc_final: 0.7814 (t) REVERT: C 224 PHE cc_start: 0.5811 (t80) cc_final: 0.5443 (t80) REVERT: C 225 MET cc_start: 0.7308 (mmt) cc_final: 0.6975 (mmt) REVERT: D 35 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6848 (tmtm) REVERT: D 52 LEU cc_start: 0.7382 (tp) cc_final: 0.7047 (pt) REVERT: D 116 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7821 (ttp-110) REVERT: E 62 GLU cc_start: 0.7736 (mp0) cc_final: 0.7429 (mp0) REVERT: E 134 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8699 (ppt170) REVERT: E 167 CYS cc_start: 0.8387 (p) cc_final: 0.7417 (t) outliers start: 32 outliers final: 15 residues processed: 159 average time/residue: 0.7280 time to fit residues: 122.9500 Evaluate side-chains 151 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain E residue 66 GLN Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 39 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.194888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.140606 restraints weight = 11438.866| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.56 r_work: 0.3128 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11000 Z= 0.113 Angle : 0.533 8.392 14933 Z= 0.272 Chirality : 0.040 0.133 1728 Planarity : 0.004 0.037 1874 Dihedral : 4.016 18.111 1476 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 1.75 % Allowed : 17.69 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1383 helix: 1.76 (0.20), residues: 766 sheet: 0.57 (0.44), residues: 129 loop : -0.47 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 123 TYR 0.009 0.001 TYR E 293 PHE 0.028 0.001 PHE C 240 TRP 0.047 0.001 TRP C 132 HIS 0.003 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00257 (11000) covalent geometry : angle 0.53306 (14933) hydrogen bonds : bond 0.04463 ( 590) hydrogen bonds : angle 4.42047 ( 1713) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.4825 (OUTLIER) cc_final: 0.4597 (tt) REVERT: A 177 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8133 (tptp) REVERT: B 217 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7795 (mmm160) REVERT: B 307 PHE cc_start: 0.8321 (t80) cc_final: 0.6916 (m-80) REVERT: C 14 ARG cc_start: 0.6537 (mmt-90) cc_final: 0.6024 (mmt180) REVERT: C 42 ILE cc_start: 0.7785 (mt) cc_final: 0.7475 (pt) REVERT: C 67 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6749 (ttp80) REVERT: C 116 ARG cc_start: 0.8833 (mtm-85) cc_final: 0.8360 (mtt-85) REVERT: C 197 THR cc_start: 0.8046 (m) cc_final: 0.7822 (t) REVERT: C 224 PHE cc_start: 0.5845 (t80) cc_final: 0.5521 (t80) REVERT: C 225 MET cc_start: 0.7263 (mmt) cc_final: 0.6988 (mmt) REVERT: D 35 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6817 (tmtm) REVERT: D 52 LEU cc_start: 0.7413 (tp) cc_final: 0.7081 (pt) REVERT: D 116 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7794 (ttp-110) REVERT: E 62 GLU cc_start: 0.7702 (mp0) cc_final: 0.7445 (mp0) REVERT: E 167 CYS cc_start: 0.8357 (p) cc_final: 0.7396 (t) outliers start: 20 outliers final: 12 residues processed: 149 average time/residue: 0.7203 time to fit residues: 114.1148 Evaluate side-chains 153 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.194492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.140166 restraints weight = 11469.049| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.62 r_work: 0.3081 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11000 Z= 0.122 Angle : 0.536 8.734 14933 Z= 0.274 Chirality : 0.040 0.135 1728 Planarity : 0.004 0.037 1874 Dihedral : 3.994 18.033 1476 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.17 % Favored : 97.76 % Rotamer: Outliers : 2.01 % Allowed : 17.51 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.23), residues: 1383 helix: 1.74 (0.19), residues: 766 sheet: 0.53 (0.44), residues: 129 loop : -0.46 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 116 TYR 0.009 0.001 TYR E 293 PHE 0.027 0.001 PHE C 240 TRP 0.048 0.001 TRP C 132 HIS 0.003 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00287 (11000) covalent geometry : angle 0.53575 (14933) hydrogen bonds : bond 0.04645 ( 590) hydrogen bonds : angle 4.42337 ( 1713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4280.28 seconds wall clock time: 73 minutes 21.11 seconds (4401.11 seconds total)