Starting phenix.real_space_refine on Sun May 3 08:39:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9omz_70625/05_2026/9omz_70625.cif Found real_map, /net/cci-nas-00/data/ceres_data/9omz_70625/05_2026/9omz_70625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9omz_70625/05_2026/9omz_70625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9omz_70625/05_2026/9omz_70625.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9omz_70625/05_2026/9omz_70625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9omz_70625/05_2026/9omz_70625.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 12 5.49 5 S 67 5.16 5 C 7372 2.51 5 N 2068 2.21 5 O 2213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11732 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2523 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 307} Chain breaks: 2 Chain: "C" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2470 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 11, 'TRANS': 302} Chain breaks: 2 Chain: "D" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2288 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 7, 'TRANS': 295} Chain breaks: 2 Chain: "B" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2415 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain: "X" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1912 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 5, 'TRANS': 230} Chain breaks: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.40, per 1000 atoms: 0.20 Number of scatterers: 11732 At special positions: 0 Unit cell: (93.96, 101.79, 147.9, 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 67 16.00 P 12 15.00 O 2213 8.00 N 2068 7.00 C 7372 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: 0.66 Conformation dependent library (CDL) restraints added in 473.6 milliseconds 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 10 sheets defined 50.9% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.659A pdb=" N LEU A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1 through 6' Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 31 through 39 Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.843A pdb=" N HIS A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 147 through 157 removed outlier: 3.649A pdb=" N ALA A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 186 through 204 removed outlier: 4.635A pdb=" N VAL A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 215 through 223 removed outlier: 3.983A pdb=" N PHE A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 250 Processing helix chain 'A' and resid 284 through 291 removed outlier: 4.196A pdb=" N TRP A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 30 Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.602A pdb=" N LEU C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'C' and resid 130 through 143 removed outlier: 4.285A pdb=" N GLN C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 165 through 187 Processing helix chain 'C' and resid 189 through 199 Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 215 through 233 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 254 through 277 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 46 through 62 Processing helix chain 'D' and resid 68 through 79 removed outlier: 3.935A pdb=" N THR D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 142 through 154 Processing helix chain 'D' and resid 156 through 166 Processing helix chain 'D' and resid 174 through 192 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.517A pdb=" N VAL D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 239 Processing helix chain 'D' and resid 267 through 271 Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 34 through 45 removed outlier: 3.706A pdb=" N LYS B 40 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.544A pdb=" N VAL B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.695A pdb=" N ILE B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 Processing helix chain 'B' and resid 89 through 97 removed outlier: 4.518A pdb=" N HIS B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.687A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 196 through 214 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 237 through 260 Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.882A pdb=" N SER B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 23 through 28 Processing helix chain 'X' and resid 53 through 67 Processing helix chain 'X' and resid 88 through 100 Processing helix chain 'X' and resid 104 through 114 removed outlier: 3.885A pdb=" N ARG X 114 " --> pdb=" O TYR X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 140 removed outlier: 4.203A pdb=" N GLU X 134 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 162 Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 170 through 187 Processing helix chain 'X' and resid 228 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 339 removed outlier: 3.931A pdb=" N ARG A 313 " --> pdb=" O TYR A 330 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG A 295 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 102 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU A 296 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLU A 104 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 298 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA A 106 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ARG A 300 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR A 103 " --> pdb=" O CYS A 255 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASN A 257 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 105 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU A 254 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL A 210 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE A 256 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 212 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLY A 136 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 209 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR B 87 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.743A pdb=" N CYS C 85 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL D 132 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL D 170 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR D 134 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN D 131 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N VAL D 204 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU D 133 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LYS D 201 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL D 246 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL D 203 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR D 248 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL D 205 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N HIS D 250 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.743A pdb=" N CYS C 85 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL D 132 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL D 170 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR D 134 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN D 131 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N VAL D 204 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU D 133 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LYS D 201 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL D 246 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL D 203 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR D 248 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL D 205 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N HIS D 250 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE D 251 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL D 102 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE D 276 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU D 104 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU D 278 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL D 106 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR D 280 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ARG D 275 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 208 through 210 removed outlier: 6.694A pdb=" N GLU C 154 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE C 240 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C 156 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP C 242 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE C 158 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG C 237 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE C 281 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C 239 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR C 283 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL C 241 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N GLN C 285 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AA7, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.590A pdb=" N GLU X 77 " --> pdb=" O LEU X 145 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ILE X 147 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU X 79 " --> pdb=" O ILE X 147 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP X 149 " --> pdb=" O LEU X 79 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE X 81 " --> pdb=" O ASP X 149 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N CYS X 144 " --> pdb=" O VAL X 190 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE X 192 " --> pdb=" O CYS X 144 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU X 146 " --> pdb=" O PHE X 192 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N THR X 194 " --> pdb=" O LEU X 146 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU X 148 " --> pdb=" O THR X 194 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE X 43 " --> pdb=" O HIS X 237 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N MET X 239 " --> pdb=" O ILE X 43 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU X 45 " --> pdb=" O MET X 239 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE X 241 " --> pdb=" O GLU X 45 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N HIS X 47 " --> pdb=" O PHE X 241 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N LYS X 243 " --> pdb=" O HIS X 47 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE X 269 " --> pdb=" O CYS X 280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'B' and resid 189 through 193 removed outlier: 6.831A pdb=" N LYS B 156 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ILE B 220 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N MET B 158 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP B 222 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE B 160 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA B 262 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE B 220 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 264 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP B 222 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 189 through 193 removed outlier: 6.831A pdb=" N LYS B 156 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ILE B 220 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N MET B 158 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP B 222 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE B 160 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA B 262 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE B 220 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 264 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP B 222 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N SER B 121 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE B 265 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR B 123 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ASN B 267 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N MET B 125 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL B 269 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY B 127 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N ALA B 271 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE B 122 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU B 302 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE B 126 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N LYS B 304 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) 581 hydrogen bonds defined for protein. 1698 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: 1.71 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3902 1.34 - 1.46: 1949 1.46 - 1.58: 5952 1.58 - 1.70: 19 1.70 - 1.82: 98 Bond restraints: 11920 Sorted by residual: bond pdb=" O3A ANP A 401 " pdb=" PB ANP A 401 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.41e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3A ANP X 301 " pdb=" PB ANP X 301 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.562 0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" N3B ANP A 401 " pdb=" PG ANP A 401 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 11915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 15978 3.66 - 7.33: 129 7.33 - 10.99: 17 10.99 - 14.66: 1 14.66 - 18.32: 4 Bond angle restraints: 16129 Sorted by residual: angle pdb=" PB ANP A 401 " pdb=" N3B ANP A 401 " pdb=" PG ANP A 401 " ideal model delta sigma weight residual 126.95 108.63 18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" PB ANP X 301 " pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 126.95 108.83 18.12 3.00e+00 1.11e-01 3.65e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 109.01 17.94 3.00e+00 1.11e-01 3.58e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 110.22 16.73 3.00e+00 1.11e-01 3.11e+01 angle pdb=" CA PRO D 262 " pdb=" N PRO D 262 " pdb=" CD PRO D 262 " ideal model delta sigma weight residual 112.00 105.29 6.71 1.40e+00 5.10e-01 2.30e+01 ... (remaining 16124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 6576 24.77 - 49.54: 619 49.54 - 74.32: 87 74.32 - 99.09: 25 99.09 - 123.86: 3 Dihedral angle restraints: 7310 sinusoidal: 3013 harmonic: 4297 Sorted by residual: dihedral pdb=" CD ARG C 193 " pdb=" NE ARG C 193 " pdb=" CZ ARG C 193 " pdb=" NH1 ARG C 193 " ideal model delta sinusoidal sigma weight residual 0.00 -76.86 76.86 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CD ARG C 168 " pdb=" NE ARG C 168 " pdb=" CZ ARG C 168 " pdb=" NH1 ARG C 168 " ideal model delta sinusoidal sigma weight residual 0.00 -56.63 56.63 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CD ARG C 212 " pdb=" NE ARG C 212 " pdb=" CZ ARG C 212 " pdb=" NH1 ARG C 212 " ideal model delta sinusoidal sigma weight residual 0.00 55.25 -55.25 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 7307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1496 0.057 - 0.114: 306 0.114 - 0.171: 60 0.171 - 0.228: 13 0.228 - 0.285: 5 Chirality restraints: 1880 Sorted by residual: chirality pdb=" C3' ANP A 401 " pdb=" C2' ANP A 401 " pdb=" C4' ANP A 401 " pdb=" O3' ANP A 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C3' ANP X 301 " pdb=" C2' ANP X 301 " pdb=" C4' ANP X 301 " pdb=" O3' ANP X 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1877 not shown) Planarity restraints: 2047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 193 " -1.079 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARG C 193 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG C 193 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 193 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 193 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 168 " -0.936 9.50e-02 1.11e+02 4.20e-01 1.07e+02 pdb=" NE ARG C 168 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG C 168 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG C 168 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 168 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 212 " 0.889 9.50e-02 1.11e+02 3.98e-01 9.64e+01 pdb=" NE ARG C 212 " -0.054 2.00e-02 2.50e+03 pdb=" CZ ARG C 212 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 212 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 212 " 0.023 2.00e-02 2.50e+03 ... (remaining 2044 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 301 2.68 - 3.24: 11800 3.24 - 3.79: 20180 3.79 - 4.35: 26404 4.35 - 4.90: 42781 Nonbonded interactions: 101466 Sorted by model distance: nonbonded pdb=" O ASP C 13 " pdb=" OG SER C 16 " model vdw 2.126 3.040 nonbonded pdb=" O ARG A 108 " pdb=" NZ LYS A 113 " model vdw 2.196 3.120 nonbonded pdb=" O GLN X 196 " pdb=" OH TYR X 226 " model vdw 2.197 3.040 nonbonded pdb=" O ARG B 306 " pdb=" OG1 THR B 309 " model vdw 2.199 3.040 nonbonded pdb=" O LEU D 58 " pdb=" OG SER D 62 " model vdw 2.200 3.040 ... (remaining 101461 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.070 Find NCS groups from input model: 0.090 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 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 : 0.006 0.147 11920 Z= 0.357 Angle : 0.896 18.319 16129 Z= 0.482 Chirality : 0.052 0.285 1880 Planarity : 0.020 0.483 2047 Dihedral : 18.852 123.859 4526 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.49 % Favored : 95.17 % Rotamer: Outliers : 2.84 % Allowed : 23.14 % Favored : 74.01 % 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: -0.55 (0.22), residues: 1469 helix: 0.59 (0.20), residues: 677 sheet: -1.05 (0.28), residues: 274 loop : -1.11 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 24 TYR 0.022 0.002 TYR B 216 PHE 0.012 0.002 PHE X 192 TRP 0.054 0.003 TRP D 314 HIS 0.006 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00625 (11920) covalent geometry : angle 0.89596 (16129) hydrogen bonds : bond 0.13856 ( 575) hydrogen bonds : angle 6.45862 ( 1698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 212 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7624 (tpt90) REVERT: D 32 VAL cc_start: 0.8872 (p) cc_final: 0.8572 (m) REVERT: D 180 ASP cc_start: 0.6965 (t0) cc_final: 0.6741 (t0) REVERT: B 49 VAL cc_start: 0.6953 (t) cc_final: 0.6693 (t) REVERT: B 62 ASN cc_start: 0.5727 (p0) cc_final: 0.5437 (m-40) outliers start: 36 outliers final: 11 residues processed: 196 average time/residue: 0.0992 time to fit residues: 28.5493 Evaluate side-chains 169 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain X residue 256 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.0470 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.197919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.163313 restraints weight = 15609.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.165837 restraints weight = 10727.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.169937 restraints weight = 7410.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.170858 restraints weight = 5615.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.171022 restraints weight = 5291.451| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11920 Z= 0.137 Angle : 0.581 7.112 16129 Z= 0.290 Chirality : 0.042 0.203 1880 Planarity : 0.005 0.061 2047 Dihedral : 9.952 143.088 1758 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.19 % Allowed : 21.80 % Favored : 74.01 % 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: -0.04 (0.22), residues: 1469 helix: 1.05 (0.20), residues: 700 sheet: -0.92 (0.30), residues: 263 loop : -0.93 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 24 TYR 0.019 0.002 TYR X 155 PHE 0.016 0.002 PHE X 80 TRP 0.020 0.002 TRP D 314 HIS 0.007 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00310 (11920) covalent geometry : angle 0.58097 (16129) hydrogen bonds : bond 0.03458 ( 575) hydrogen bonds : angle 5.01328 ( 1698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8513 (tp) cc_final: 0.8292 (tp) REVERT: A 161 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8025 (tt) REVERT: C 187 HIS cc_start: 0.5239 (OUTLIER) cc_final: 0.4774 (p-80) REVERT: C 188 LYS cc_start: 0.6174 (OUTLIER) cc_final: 0.5384 (mttm) REVERT: C 225 LEU cc_start: 0.6712 (tp) cc_final: 0.6422 (tp) REVERT: D 180 ASP cc_start: 0.7632 (t0) cc_final: 0.7423 (t0) REVERT: B 49 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7490 (t) REVERT: B 251 MET cc_start: 0.6526 (mmm) cc_final: 0.6162 (mmm) REVERT: X 268 HIS cc_start: 0.6243 (OUTLIER) cc_final: 0.5912 (t-170) outliers start: 53 outliers final: 24 residues processed: 208 average time/residue: 0.0915 time to fit residues: 28.3972 Evaluate side-chains 182 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 198 ILE Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 259 CYS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 271 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 146 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.194805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.160962 restraints weight = 15956.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.164022 restraints weight = 10371.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.166893 restraints weight = 7755.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.168294 restraints weight = 5970.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.168885 restraints weight = 5574.343| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11920 Z= 0.142 Angle : 0.562 7.288 16129 Z= 0.278 Chirality : 0.042 0.291 1880 Planarity : 0.004 0.058 2047 Dihedral : 9.274 136.461 1748 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.87 % Allowed : 23.54 % Favored : 72.59 % 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: 0.03 (0.22), residues: 1469 helix: 1.14 (0.20), residues: 700 sheet: -1.01 (0.30), residues: 263 loop : -0.88 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 24 TYR 0.016 0.001 TYR X 155 PHE 0.015 0.001 PHE X 80 TRP 0.013 0.001 TRP D 314 HIS 0.008 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00339 (11920) covalent geometry : angle 0.56218 (16129) hydrogen bonds : bond 0.03197 ( 575) hydrogen bonds : angle 4.80826 ( 1698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8021 (tt) REVERT: C 187 HIS cc_start: 0.5670 (OUTLIER) cc_final: 0.5375 (p-80) REVERT: C 188 LYS cc_start: 0.6058 (mttm) cc_final: 0.5406 (mttm) REVERT: C 225 LEU cc_start: 0.6872 (tp) cc_final: 0.6546 (tp) REVERT: D 16 MET cc_start: 0.4514 (ptt) cc_final: 0.4131 (tmm) REVERT: D 180 ASP cc_start: 0.7653 (t0) cc_final: 0.7443 (t0) REVERT: D 227 MET cc_start: 0.8161 (tmm) cc_final: 0.7864 (ttp) REVERT: B 49 VAL cc_start: 0.7766 (OUTLIER) cc_final: 0.7498 (t) REVERT: B 62 ASN cc_start: 0.5982 (p0) cc_final: 0.5650 (m-40) REVERT: B 107 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8227 (mtmt) REVERT: X 268 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.5916 (t-170) outliers start: 49 outliers final: 32 residues processed: 214 average time/residue: 0.1061 time to fit residues: 33.0011 Evaluate side-chains 191 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 198 ILE Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 259 CYS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 271 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 18 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.190837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.156434 restraints weight = 15903.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.161055 restraints weight = 9508.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.164129 restraints weight = 6813.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.166215 restraints weight = 5479.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.167466 restraints weight = 4739.417| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11920 Z= 0.162 Angle : 0.575 6.675 16129 Z= 0.287 Chirality : 0.043 0.218 1880 Planarity : 0.004 0.055 2047 Dihedral : 9.093 132.540 1743 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.03 % Allowed : 22.27 % Favored : 73.70 % 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: -0.14 (0.22), residues: 1469 helix: 1.04 (0.20), residues: 702 sheet: -1.26 (0.30), residues: 262 loop : -0.93 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 24 TYR 0.014 0.002 TYR X 155 PHE 0.017 0.002 PHE X 80 TRP 0.012 0.001 TRP X 231 HIS 0.009 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00388 (11920) covalent geometry : angle 0.57459 (16129) hydrogen bonds : bond 0.03145 ( 575) hydrogen bonds : angle 4.74567 ( 1698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8074 (tt) REVERT: C 188 LYS cc_start: 0.5958 (mttm) cc_final: 0.5279 (mttm) REVERT: D 180 ASP cc_start: 0.7723 (t0) cc_final: 0.7471 (t0) REVERT: D 314 TRP cc_start: 0.4926 (OUTLIER) cc_final: 0.4472 (m-90) REVERT: B 49 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7517 (t) REVERT: B 114 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7380 (mm-40) REVERT: B 202 GLN cc_start: 0.6314 (mm-40) cc_final: 0.6105 (tm-30) REVERT: B 254 ARG cc_start: 0.6595 (mtp85) cc_final: 0.6327 (ttm-80) REVERT: X 268 HIS cc_start: 0.6532 (OUTLIER) cc_final: 0.6012 (t-170) outliers start: 51 outliers final: 32 residues processed: 206 average time/residue: 0.1052 time to fit residues: 32.0413 Evaluate side-chains 193 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 198 ILE Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 259 CYS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 271 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 102 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 0.0980 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.190577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.157336 restraints weight = 15765.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.161940 restraints weight = 9203.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.164964 restraints weight = 6499.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.167099 restraints weight = 5188.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.168260 restraints weight = 4443.882| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11920 Z= 0.131 Angle : 0.551 9.114 16129 Z= 0.273 Chirality : 0.042 0.194 1880 Planarity : 0.004 0.055 2047 Dihedral : 8.676 127.995 1742 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.74 % Allowed : 22.91 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.22), residues: 1469 helix: 1.14 (0.20), residues: 704 sheet: -1.26 (0.30), residues: 252 loop : -1.08 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 24 TYR 0.016 0.001 TYR X 155 PHE 0.023 0.001 PHE D 305 TRP 0.013 0.001 TRP X 231 HIS 0.009 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00312 (11920) covalent geometry : angle 0.55125 (16129) hydrogen bonds : bond 0.02911 ( 575) hydrogen bonds : angle 4.59423 ( 1698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 179 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8075 (tt) REVERT: C 188 LYS cc_start: 0.5843 (mttm) cc_final: 0.5138 (mttm) REVERT: D 35 ASP cc_start: 0.7646 (t0) cc_final: 0.6941 (p0) REVERT: D 57 LEU cc_start: 0.7863 (pp) cc_final: 0.7033 (tt) REVERT: D 58 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7495 (mm) REVERT: D 120 MET cc_start: 0.7721 (ttp) cc_final: 0.7359 (tmm) REVERT: D 180 ASP cc_start: 0.7561 (t0) cc_final: 0.7344 (t0) REVERT: B 251 MET cc_start: 0.6321 (mmm) cc_final: 0.6120 (tpt) REVERT: B 254 ARG cc_start: 0.6874 (mtp85) cc_final: 0.6608 (ttm-80) outliers start: 60 outliers final: 36 residues processed: 222 average time/residue: 0.1032 time to fit residues: 34.0716 Evaluate side-chains 204 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 198 ILE Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 259 CYS Chi-restraints excluded: chain X residue 271 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 65 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS D 60 GLN ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.200826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.167072 restraints weight = 15520.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.170496 restraints weight = 9889.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.174613 restraints weight = 7444.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.174860 restraints weight = 5524.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.175270 restraints weight = 5258.957| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11920 Z= 0.159 Angle : 0.586 9.061 16129 Z= 0.289 Chirality : 0.043 0.183 1880 Planarity : 0.004 0.055 2047 Dihedral : 8.682 127.649 1741 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.58 % Allowed : 22.91 % Favored : 72.51 % 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: -0.22 (0.22), residues: 1469 helix: 1.06 (0.20), residues: 704 sheet: -1.34 (0.30), residues: 246 loop : -1.11 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 24 TYR 0.016 0.001 TYR X 155 PHE 0.020 0.002 PHE D 305 TRP 0.014 0.001 TRP D 314 HIS 0.009 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00384 (11920) covalent geometry : angle 0.58610 (16129) hydrogen bonds : bond 0.02993 ( 575) hydrogen bonds : angle 4.60561 ( 1698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.5926 (tp) REVERT: C 188 LYS cc_start: 0.5868 (mttm) cc_final: 0.5165 (mttm) REVERT: C 220 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7523 (mt) REVERT: D 16 MET cc_start: 0.4639 (ptt) cc_final: 0.4416 (tmm) REVERT: D 35 ASP cc_start: 0.7832 (t0) cc_final: 0.7032 (p0) REVERT: D 120 MET cc_start: 0.7689 (ttp) cc_final: 0.7343 (tmm) REVERT: D 180 ASP cc_start: 0.7602 (t0) cc_final: 0.7394 (t0) REVERT: D 314 TRP cc_start: 0.4856 (OUTLIER) cc_final: 0.4400 (m-90) REVERT: B 144 CYS cc_start: 0.7924 (p) cc_final: 0.7486 (t) REVERT: B 202 GLN cc_start: 0.6670 (mm-40) cc_final: 0.6416 (tt0) REVERT: B 243 MET cc_start: 0.7500 (tpt) cc_final: 0.7225 (tpt) REVERT: B 254 ARG cc_start: 0.7119 (mtp85) cc_final: 0.6904 (ttm-80) REVERT: X 239 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.4962 (mtm) REVERT: X 268 HIS cc_start: 0.6417 (OUTLIER) cc_final: 0.6071 (t-170) outliers start: 58 outliers final: 38 residues processed: 207 average time/residue: 0.1014 time to fit residues: 31.3349 Evaluate side-chains 201 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain X residue 70 SER Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 198 ILE Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 259 CYS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 271 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 4 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 29 optimal weight: 0.0470 chunk 146 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 18 optimal weight: 0.0370 chunk 125 optimal weight: 1.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 HIS ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.203499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.170326 restraints weight = 15457.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.173703 restraints weight = 9736.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.177741 restraints weight = 7309.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.177899 restraints weight = 5459.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.178178 restraints weight = 5217.594| |-----------------------------------------------------------------------------| r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11920 Z= 0.123 Angle : 0.556 8.619 16129 Z= 0.273 Chirality : 0.042 0.277 1880 Planarity : 0.004 0.056 2047 Dihedral : 8.289 121.190 1739 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.79 % Allowed : 23.70 % Favored : 72.51 % 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: -0.05 (0.22), residues: 1469 helix: 1.19 (0.20), residues: 703 sheet: -1.20 (0.31), residues: 244 loop : -1.05 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 24 TYR 0.015 0.001 TYR X 155 PHE 0.021 0.001 PHE A 223 TRP 0.014 0.001 TRP X 231 HIS 0.009 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00293 (11920) covalent geometry : angle 0.55635 (16129) hydrogen bonds : bond 0.02766 ( 575) hydrogen bonds : angle 4.48660 ( 1698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 LEU cc_start: 0.6683 (mm) cc_final: 0.5937 (tp) REVERT: C 188 LYS cc_start: 0.5866 (mttm) cc_final: 0.5164 (mttm) REVERT: C 220 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7479 (mt) REVERT: D 35 ASP cc_start: 0.7862 (t0) cc_final: 0.7108 (p0) REVERT: D 57 LEU cc_start: 0.7912 (pp) cc_final: 0.7463 (tt) REVERT: D 120 MET cc_start: 0.7582 (ttp) cc_final: 0.7239 (tmm) REVERT: D 314 TRP cc_start: 0.4814 (OUTLIER) cc_final: 0.4580 (m-90) REVERT: B 243 MET cc_start: 0.7513 (tpt) cc_final: 0.7244 (tpt) REVERT: B 254 ARG cc_start: 0.7248 (mtp85) cc_final: 0.7030 (ttm-80) REVERT: B 326 MET cc_start: 0.5927 (mmm) cc_final: 0.5716 (mmm) REVERT: X 46 PHE cc_start: 0.7978 (m-10) cc_final: 0.7512 (m-80) REVERT: X 97 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6668 (tm-30) REVERT: X 239 MET cc_start: 0.5691 (OUTLIER) cc_final: 0.4837 (mtm) outliers start: 48 outliers final: 33 residues processed: 203 average time/residue: 0.1075 time to fit residues: 31.7357 Evaluate side-chains 188 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 70 SER Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 198 ILE Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 259 CYS Chi-restraints excluded: chain X residue 271 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 109 optimal weight: 0.0770 chunk 63 optimal weight: 0.0060 chunk 91 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS D 60 GLN ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 268 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.201562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.169293 restraints weight = 15395.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.172709 restraints weight = 9781.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.177632 restraints weight = 7147.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.177590 restraints weight = 5098.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.177731 restraints weight = 4724.435| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11920 Z= 0.124 Angle : 0.572 9.635 16129 Z= 0.279 Chirality : 0.042 0.258 1880 Planarity : 0.004 0.057 2047 Dihedral : 8.156 117.814 1738 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.79 % Allowed : 24.33 % Favored : 71.88 % 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: -0.07 (0.22), residues: 1469 helix: 1.19 (0.20), residues: 697 sheet: -1.26 (0.30), residues: 258 loop : -1.01 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 24 TYR 0.014 0.001 TYR B 178 PHE 0.021 0.002 PHE A 223 TRP 0.013 0.001 TRP X 231 HIS 0.010 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00297 (11920) covalent geometry : angle 0.57173 (16129) hydrogen bonds : bond 0.02780 ( 575) hydrogen bonds : angle 4.50626 ( 1698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.5943 (tp) REVERT: C 188 LYS cc_start: 0.5972 (mttm) cc_final: 0.5255 (mttm) REVERT: C 220 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7455 (mt) REVERT: C 274 ASN cc_start: 0.8598 (m-40) cc_final: 0.8343 (m110) REVERT: D 35 ASP cc_start: 0.7818 (t0) cc_final: 0.7121 (p0) REVERT: D 57 LEU cc_start: 0.7931 (pp) cc_final: 0.7566 (tt) REVERT: D 120 MET cc_start: 0.7563 (ttp) cc_final: 0.7243 (tmm) REVERT: D 279 ASP cc_start: 0.7366 (m-30) cc_final: 0.7100 (m-30) REVERT: D 314 TRP cc_start: 0.4770 (OUTLIER) cc_final: 0.4567 (m-90) REVERT: B 243 MET cc_start: 0.7495 (tpt) cc_final: 0.7214 (tpt) REVERT: X 56 GLU cc_start: 0.7569 (tp30) cc_final: 0.7321 (mm-30) REVERT: X 239 MET cc_start: 0.5719 (OUTLIER) cc_final: 0.4872 (mtm) outliers start: 48 outliers final: 35 residues processed: 191 average time/residue: 0.1058 time to fit residues: 29.9425 Evaluate side-chains 188 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 70 SER Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 198 ILE Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 259 CYS Chi-restraints excluded: chain X residue 271 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 54 optimal weight: 0.1980 chunk 112 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN C 233 HIS ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 268 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.202785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.170739 restraints weight = 15222.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.174350 restraints weight = 9683.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.177298 restraints weight = 7101.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.178731 restraints weight = 5319.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.179199 restraints weight = 5059.841| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11920 Z= 0.119 Angle : 0.588 11.390 16129 Z= 0.286 Chirality : 0.042 0.233 1880 Planarity : 0.004 0.066 2047 Dihedral : 8.025 113.412 1738 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.08 % Allowed : 24.88 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.22), residues: 1469 helix: 1.19 (0.20), residues: 697 sheet: -1.22 (0.30), residues: 258 loop : -0.98 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 24 TYR 0.013 0.001 TYR X 226 PHE 0.031 0.002 PHE C 246 TRP 0.013 0.001 TRP X 231 HIS 0.009 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00281 (11920) covalent geometry : angle 0.58814 (16129) hydrogen bonds : bond 0.02784 ( 575) hydrogen bonds : angle 4.50444 ( 1698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6174 (tp) REVERT: C 188 LYS cc_start: 0.5894 (mttm) cc_final: 0.5187 (mttm) REVERT: C 191 GLU cc_start: 0.6821 (pm20) cc_final: 0.6597 (pt0) REVERT: C 220 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7415 (mt) REVERT: C 274 ASN cc_start: 0.8601 (m-40) cc_final: 0.8351 (m110) REVERT: D 35 ASP cc_start: 0.7741 (t0) cc_final: 0.7091 (p0) REVERT: D 57 LEU cc_start: 0.7967 (pp) cc_final: 0.7498 (tt) REVERT: D 120 MET cc_start: 0.7545 (ttp) cc_final: 0.7224 (tmm) REVERT: D 279 ASP cc_start: 0.7363 (m-30) cc_final: 0.7129 (m-30) REVERT: B 243 MET cc_start: 0.7504 (tpt) cc_final: 0.7246 (tpt) REVERT: X 46 PHE cc_start: 0.8039 (m-10) cc_final: 0.7531 (m-80) REVERT: X 56 GLU cc_start: 0.7571 (tp30) cc_final: 0.7332 (mm-30) REVERT: X 239 MET cc_start: 0.5711 (OUTLIER) cc_final: 0.4874 (mtm) outliers start: 39 outliers final: 29 residues processed: 188 average time/residue: 0.1016 time to fit residues: 28.0322 Evaluate side-chains 176 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain X residue 34 ASP Chi-restraints excluded: chain X residue 70 SER Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 58 optimal weight: 0.0770 chunk 52 optimal weight: 0.0050 chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 106 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN C 233 HIS D 60 GLN D 126 HIS ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 268 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.203500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.170708 restraints weight = 15398.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.175714 restraints weight = 8881.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.178928 restraints weight = 6237.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.181004 restraints weight = 4957.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.182262 restraints weight = 4273.150| |-----------------------------------------------------------------------------| r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11920 Z= 0.119 Angle : 0.600 9.859 16129 Z= 0.293 Chirality : 0.042 0.199 1880 Planarity : 0.004 0.067 2047 Dihedral : 7.831 108.788 1738 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.92 % Allowed : 25.51 % Favored : 71.56 % 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: -0.02 (0.22), residues: 1469 helix: 1.19 (0.20), residues: 695 sheet: -1.11 (0.31), residues: 255 loop : -1.00 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 24 TYR 0.012 0.001 TYR B 178 PHE 0.025 0.002 PHE A 223 TRP 0.024 0.002 TRP D 314 HIS 0.009 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00284 (11920) covalent geometry : angle 0.60030 (16129) hydrogen bonds : bond 0.02839 ( 575) hydrogen bonds : angle 4.48707 ( 1698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6337 (tp) REVERT: C 188 LYS cc_start: 0.5912 (mttm) cc_final: 0.5144 (mttm) REVERT: C 274 ASN cc_start: 0.8690 (m-40) cc_final: 0.8489 (m110) REVERT: D 35 ASP cc_start: 0.7557 (t0) cc_final: 0.7011 (p0) REVERT: D 57 LEU cc_start: 0.7925 (pp) cc_final: 0.7607 (tt) REVERT: D 120 MET cc_start: 0.7545 (ttp) cc_final: 0.7206 (tmm) REVERT: B 243 MET cc_start: 0.7469 (tpt) cc_final: 0.7200 (tpt) REVERT: X 46 PHE cc_start: 0.8020 (m-10) cc_final: 0.7423 (m-80) REVERT: X 56 GLU cc_start: 0.7569 (tp30) cc_final: 0.7335 (mm-30) REVERT: X 239 MET cc_start: 0.5636 (OUTLIER) cc_final: 0.4807 (mtm) outliers start: 37 outliers final: 31 residues processed: 180 average time/residue: 0.1078 time to fit residues: 28.3217 Evaluate side-chains 178 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain X residue 70 SER Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 234 LEU Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 144 optimal weight: 0.0370 chunk 9 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS D 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.202634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.170524 restraints weight = 15485.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.174578 restraints weight = 9686.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.176863 restraints weight = 6523.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.178059 restraints weight = 5637.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.178382 restraints weight = 5186.896| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11920 Z= 0.141 Angle : 0.613 10.387 16129 Z= 0.300 Chirality : 0.043 0.193 1880 Planarity : 0.005 0.086 2047 Dihedral : 7.851 109.131 1738 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 2.76 % Allowed : 25.36 % Favored : 71.88 % 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: -0.10 (0.22), residues: 1469 helix: 1.13 (0.20), residues: 695 sheet: -1.18 (0.31), residues: 255 loop : -1.01 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 24 TYR 0.011 0.001 TYR X 226 PHE 0.027 0.002 PHE A 223 TRP 0.029 0.002 TRP D 314 HIS 0.009 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00341 (11920) covalent geometry : angle 0.61253 (16129) hydrogen bonds : bond 0.02937 ( 575) hydrogen bonds : angle 4.53878 ( 1698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2023.12 seconds wall clock time: 35 minutes 55.83 seconds (2155.83 seconds total)