Starting phenix.real_space_refine on Fri Aug 7 15:12:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fs6_29415/08_2026/8fs6_29415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fs6_29415/08_2026/8fs6_29415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fs6_29415/08_2026/8fs6_29415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fs6_29415/08_2026/8fs6_29415.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fs6_29415/08_2026/8fs6_29415.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fs6_29415/08_2026/8fs6_29415.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fs6_29415/08_2026/8fs6_29415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fs6_29415/08_2026/8fs6_29415.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 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: 6 Type Number sf(0) Gaussians P 71 5.49 5 Mg 4 5.21 5 S 115 5.16 5 C 13899 2.51 5 N 3821 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22246 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3559 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2743 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Chain: "F" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2238 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 9, 'TRANS': 267} Chain breaks: 6 Chain: "G" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2366 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain breaks: 1 Chain: "H" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2314 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 4 Chain: "I" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "J" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 313 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.52, per 1000 atoms: 0.20 Number of scatterers: 22246 At special positions: 0 Unit cell: (115.092, 127.512, 138.276, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 115 16.00 P 71 15.00 Mg 4 11.99 O 4336 8.00 N 3821 7.00 C 13899 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: 1.84 Conformation dependent library (CDL) restraints added in 920.9 milliseconds 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5016 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 16 sheets defined 50.7% alpha, 16.6% beta 22 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 118 through 131 removed outlier: 4.299A pdb=" N LYS A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 194 through 210 removed outlier: 3.846A pdb=" N ARG A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 271 through 284 removed outlier: 3.518A pdb=" N LYS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 280 " --> pdb=" O HIS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 297 through 308 removed outlier: 3.768A pdb=" N TYR A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.743A pdb=" N ILE A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 393 through 409 removed outlier: 3.895A pdb=" N CYS A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.919A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 removed outlier: 3.604A pdb=" N ARG A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 470 removed outlier: 3.569A pdb=" N LYS A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 removed outlier: 3.704A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.682A pdb=" N VAL B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.990A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.841A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.813A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 244 through 257 removed outlier: 3.786A pdb=" N GLN B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 251 " --> pdb=" O ASP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.519A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.693A pdb=" N LEU C 13 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.676A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 44 removed outlier: 3.844A pdb=" N LYS C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 removed outlier: 3.526A pdb=" N VAL C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 96 through 103 Processing helix chain 'C' and resid 119 through 122 Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 129 through 137 removed outlier: 4.012A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.738A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.572A pdb=" N CYS C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.715A pdb=" N LYS C 195 " --> pdb=" O PRO C 191 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.597A pdb=" N SER C 214 " --> pdb=" O ASN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 242 through 254 removed outlier: 3.707A pdb=" N VAL C 247 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 removed outlier: 3.810A pdb=" N TYR C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.575A pdb=" N LYS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.844A pdb=" N ASP C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 335 removed outlier: 3.527A pdb=" N SER C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 331 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 45 through 55 removed outlier: 3.716A pdb=" N LEU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.768A pdb=" N ALA D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.077A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.948A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 152 removed outlier: 3.732A pdb=" N ALA D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 removed outlier: 3.671A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.568A pdb=" N ARG D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.510A pdb=" N TYR D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 removed outlier: 3.792A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 277 removed outlier: 3.799A pdb=" N SER D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.569A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.542A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.756A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.535A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.243A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 97 through 104 removed outlier: 6.277A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN E 104 " --> pdb=" O MET E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 110 Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.906A pdb=" N LEU E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 151 through 161 removed outlier: 4.621A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.725A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.336A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 30 removed outlier: 3.596A pdb=" N TYR F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR F 25 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 96 through 113 removed outlier: 3.976A pdb=" N LEU F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 218 Processing helix chain 'F' and resid 242 through 253 removed outlier: 4.393A pdb=" N VAL F 253 " --> pdb=" O PHE F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 412 through 424 removed outlier: 3.632A pdb=" N ALA F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 27 removed outlier: 3.584A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 86 through 93 Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 244 through 246 No H-bonds generated for 'chain 'G' and resid 244 through 246' Processing helix chain 'G' and resid 247 through 251 removed outlier: 3.681A pdb=" N ILE G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 330 removed outlier: 3.852A pdb=" N THR G 322 " --> pdb=" O GLU G 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 27 removed outlier: 3.586A pdb=" N VAL H 22 " --> pdb=" O ARG H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 98 through 103 Processing helix chain 'H' and resid 161 through 166 Processing helix chain 'H' and resid 234 through 244 Processing helix chain 'H' and resid 326 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 3.693A pdb=" N GLY A 109 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA3, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.206A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.168A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.398A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 69 through 75 removed outlier: 3.523A pdb=" N PHE E 75 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE E 140 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 212 through 213 removed outlier: 7.582A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 79 through 82 removed outlier: 5.058A pdb=" N LEU F 3 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS F 122 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL F 207 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR F 92 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS F 70 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER F 46 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU F 68 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET F 231 " --> pdb=" O ILE F 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 408 through 411 removed outlier: 7.568A pdb=" N HIS F 261 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASN F 286 " --> pdb=" O HIS F 261 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG G 129 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER G 127 " --> pdb=" O CYS F 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 62 through 63 removed outlier: 5.819A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 62 through 63 removed outlier: 3.515A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP G 260 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 232 through 238 removed outlier: 3.765A pdb=" N ALA G 193 " --> pdb=" O TYR G 181 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE G 202 " --> pdb=" O CYS H 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 232 through 238 removed outlier: 4.131A pdb=" N PHE G 202 " --> pdb=" O CYS H 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 78 through 79 Processing sheet with id=AB6, first strand: chain 'H' and resid 78 through 79 removed outlier: 7.209A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN H 365 " --> pdb=" O ASN H 348 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN H 348 " --> pdb=" O GLN H 365 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN H 233 " --> pdb=" O LEU H 293 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU H 293 " --> pdb=" O ASN H 233 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 284 through 288 removed outlier: 3.624A pdb=" N GLU H 251 " --> pdb=" O PHE H 266 " (cutoff:3.500A) 1085 hydrogen bonds defined for protein. 3087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7201 1.36 - 1.51: 6039 1.51 - 1.65: 9331 1.65 - 1.80: 70 1.80 - 1.95: 101 Bond restraints: 22742 Sorted by residual: bond pdb=" C SER E 175 " pdb=" N PRO E 176 " ideal model delta sigma weight residual 1.334 1.365 -0.031 8.40e-03 1.42e+04 1.39e+01 bond pdb=" N ILE F 410 " pdb=" CA ILE F 410 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.18e+01 bond pdb=" N VAL F 267 " pdb=" CA VAL F 267 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N VAL A 148 " pdb=" CA VAL A 148 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N ILE E 96 " pdb=" CA ILE E 96 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.14e-02 7.69e+03 9.39e+00 ... (remaining 22737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 30341 2.28 - 4.56: 573 4.56 - 6.83: 51 6.83 - 9.11: 15 9.11 - 11.39: 4 Bond angle restraints: 30984 Sorted by residual: angle pdb=" N MET F 231 " pdb=" CA MET F 231 " pdb=" C MET F 231 " ideal model delta sigma weight residual 107.61 115.83 -8.22 1.74e+00 3.30e-01 2.23e+01 angle pdb=" N HIS E 18 " pdb=" CA HIS E 18 " pdb=" CB HIS E 18 " ideal model delta sigma weight residual 110.49 118.30 -7.81 1.69e+00 3.50e-01 2.14e+01 angle pdb=" N3 DT K 7 " pdb=" C4 DT K 7 " pdb=" O4 DT K 7 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" CA SER E 17 " pdb=" C SER E 17 " pdb=" O SER E 17 " ideal model delta sigma weight residual 121.39 116.30 5.09 1.12e+00 7.97e-01 2.06e+01 angle pdb=" N3 DT K 3 " pdb=" C4 DT K 3 " pdb=" O4 DT K 3 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 ... (remaining 30979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 12454 26.14 - 52.28: 1064 52.28 - 78.42: 177 78.42 - 104.56: 11 104.56 - 130.70: 3 Dihedral angle restraints: 13709 sinusoidal: 6015 harmonic: 7694 Sorted by residual: dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 70.70 -130.70 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 65.75 -125.75 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 58.13 -118.13 1 2.00e+01 2.50e-03 3.53e+01 ... (remaining 13706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3187 0.075 - 0.151: 363 0.151 - 0.226: 30 0.226 - 0.301: 1 0.301 - 0.377: 1 Chirality restraints: 3582 Sorted by residual: chirality pdb=" CG LEU G 327 " pdb=" CB LEU G 327 " pdb=" CD1 LEU G 327 " pdb=" CD2 LEU G 327 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CG LEU F 5 " pdb=" CB LEU F 5 " pdb=" CD1 LEU F 5 " pdb=" CD2 LEU F 5 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU B 319 " pdb=" CB LEU B 319 " pdb=" CD1 LEU B 319 " pdb=" CD2 LEU B 319 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3579 not shown) Planarity restraints: 3707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 541 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO A 542 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 542 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 542 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 333 " 0.016 2.00e-02 2.50e+03 3.03e-02 9.19e+00 pdb=" C ILE H 333 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE H 333 " 0.019 2.00e-02 2.50e+03 pdb=" N THR H 334 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 185 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C CYS E 185 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS E 185 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU E 186 " -0.015 2.00e-02 2.50e+03 ... (remaining 3704 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 245 2.62 - 3.19: 18448 3.19 - 3.76: 35593 3.76 - 4.33: 49813 4.33 - 4.90: 81554 Nonbonded interactions: 185653 Sorted by model distance: nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.045 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.054 2.170 nonbonded pdb=" OG1 THR D 72 " pdb="MG MG D 402 " model vdw 2.097 2.170 nonbonded pdb=" OE2 GLU A 187 " pdb="MG MG A 602 " model vdw 2.102 2.170 nonbonded pdb=" O3A AGS A 601 " pdb="MG MG A 602 " model vdw 2.103 2.170 ... (remaining 185648 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.450 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.340 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.004 0.076 22742 Z= 0.290 Angle : 0.697 11.391 30984 Z= 0.451 Chirality : 0.047 0.377 3582 Planarity : 0.004 0.102 3707 Dihedral : 18.341 130.697 8693 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.53 % Allowed : 23.86 % Favored : 73.61 % 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: -0.78 (0.17), residues: 2577 helix: -0.24 (0.15), residues: 1213 sheet: -0.34 (0.23), residues: 542 loop : -0.75 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 272 TYR 0.031 0.001 TYR F 466 PHE 0.030 0.001 PHE E 124 TRP 0.007 0.001 TRP H 352 HIS 0.016 0.001 HIS F 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.29 (22742) covalent geometry : angle 0.69720 / 0.45 (30984) hydrogen bonds : bond 0.19169 / 12.29 ( 1107) hydrogen bonds : angle 7.36545 / 5.27 ( 3197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 332 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7001 (mt-10) REVERT: F 79 LEU cc_start: 0.1740 (OUTLIER) cc_final: 0.1391 (mt) REVERT: H 55 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6846 (mtm-85) outliers start: 60 outliers final: 50 residues processed: 326 average time/residue: 0.6081 time to fit residues: 228.2896 Evaluate side-chains 313 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 262 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 268 ASN Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 256 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS C 140 ASN D 352 GLN E 86 ASN E 292 HIS F 226 ASN F 247 HIS H 122 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.180364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128329 restraints weight = 25271.468| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.05 r_work: 0.3251 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 22742 Z= 0.252 Angle : 0.629 8.262 30984 Z= 0.335 Chirality : 0.046 0.158 3582 Planarity : 0.005 0.073 3707 Dihedral : 15.990 145.502 3543 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.40 % Allowed : 20.40 % Favored : 74.20 % 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: -0.58 (0.16), residues: 2577 helix: -0.01 (0.15), residues: 1199 sheet: -0.36 (0.22), residues: 554 loop : -0.68 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 175 TYR 0.019 0.002 TYR H 166 PHE 0.022 0.002 PHE F 37 TRP 0.017 0.002 TRP F 69 HIS 0.012 0.002 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.25 (22742) covalent geometry : angle 0.62923 / 0.33 (30984) hydrogen bonds : bond 0.05291 / 3.48 ( 1107) hydrogen bonds : angle 5.28563 / 3.77 ( 3197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 274 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8465 (tt) REVERT: A 241 ASP cc_start: 0.7240 (m-30) cc_final: 0.6944 (m-30) REVERT: A 351 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7312 (m170) REVERT: A 372 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.7938 (p) REVERT: A 418 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8438 (mt-10) REVERT: C 199 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: C 332 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6996 (mt-10) REVERT: E 112 LEU cc_start: 0.7600 (mt) cc_final: 0.7348 (mt) REVERT: E 119 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.5852 (mpp) REVERT: E 134 ARG cc_start: 0.4384 (OUTLIER) cc_final: 0.2881 (mmt90) REVERT: E 197 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6408 (mt-10) REVERT: F 119 MET cc_start: 0.0202 (mmm) cc_final: -0.0158 (mmm) REVERT: G 128 GLU cc_start: 0.6087 (pp20) cc_final: 0.5759 (pp20) REVERT: H 55 ARG cc_start: 0.7552 (mtt180) cc_final: 0.6887 (mtm-85) REVERT: H 139 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: H 227 ILE cc_start: 0.5629 (OUTLIER) cc_final: 0.4751 (pp) REVERT: H 277 LEU cc_start: 0.6999 (tp) cc_final: 0.6616 (tp) REVERT: H 358 ASP cc_start: 0.7475 (m-30) cc_final: 0.6325 (p0) outliers start: 128 outliers final: 56 residues processed: 370 average time/residue: 0.5823 time to fit residues: 249.0540 Evaluate side-chains 326 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 261 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 32 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 3 optimal weight: 0.0000 chunk 36 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 102 HIS B 244 ASN E 292 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.182377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130923 restraints weight = 25215.231| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.81 r_work: 0.3287 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22742 Z= 0.136 Angle : 0.531 10.058 30984 Z= 0.282 Chirality : 0.042 0.172 3582 Planarity : 0.004 0.054 3707 Dihedral : 15.767 140.096 3499 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.68 % Allowed : 21.12 % Favored : 74.20 % 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: -0.26 (0.17), residues: 2577 helix: 0.38 (0.15), residues: 1195 sheet: -0.43 (0.21), residues: 558 loop : -0.55 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 50 TYR 0.016 0.001 TYR G 181 PHE 0.027 0.001 PHE G 202 TRP 0.012 0.001 TRP F 69 HIS 0.007 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (22742) covalent geometry : angle 0.53134 / 0.28 (30984) hydrogen bonds : bond 0.04314 / 2.85 ( 1107) hydrogen bonds : angle 4.89109 / 3.49 ( 3197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 279 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 241 ASP cc_start: 0.7123 (m-30) cc_final: 0.6823 (m-30) REVERT: A 245 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7854 (t) REVERT: A 351 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7213 (m170) REVERT: A 355 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7899 (t0) REVERT: A 418 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8417 (mt-10) REVERT: B 28 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8336 (mm-30) REVERT: B 100 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7914 (ttmm) REVERT: B 183 ASP cc_start: 0.8116 (t0) cc_final: 0.7897 (t0) REVERT: C 172 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6706 (pp20) REVERT: C 332 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6870 (mt-10) REVERT: E 94 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8268 (tp) REVERT: E 112 LEU cc_start: 0.7490 (mt) cc_final: 0.7196 (mt) REVERT: E 197 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6370 (mt-10) REVERT: F 79 LEU cc_start: 0.1183 (OUTLIER) cc_final: 0.0966 (mt) REVERT: F 413 LYS cc_start: 0.5424 (OUTLIER) cc_final: 0.4923 (ttpp) REVERT: G 128 GLU cc_start: 0.6050 (pp20) cc_final: 0.5817 (pp20) REVERT: G 202 PHE cc_start: 0.7285 (m-80) cc_final: 0.5652 (t80) REVERT: G 323 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6327 (tm-30) REVERT: H 55 ARG cc_start: 0.7495 (mtt180) cc_final: 0.6893 (mtm-85) REVERT: H 63 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: H 103 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.7445 (p) REVERT: H 139 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6904 (mm-30) REVERT: H 227 ILE cc_start: 0.5474 (OUTLIER) cc_final: 0.4643 (pp) REVERT: H 277 LEU cc_start: 0.6968 (tp) cc_final: 0.6585 (tp) REVERT: H 358 ASP cc_start: 0.7385 (m-30) cc_final: 0.6239 (p0) outliers start: 111 outliers final: 51 residues processed: 364 average time/residue: 0.6311 time to fit residues: 263.6008 Evaluate side-chains 323 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 256 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 372 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 245 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 173 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 203 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS E 224 GLN G 17 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.177907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123819 restraints weight = 25310.198| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.99 r_work: 0.3215 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 22742 Z= 0.238 Angle : 0.607 10.962 30984 Z= 0.318 Chirality : 0.045 0.160 3582 Planarity : 0.004 0.060 3707 Dihedral : 15.884 152.629 3494 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.90 % Allowed : 20.87 % Favored : 73.23 % 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: -0.37 (0.16), residues: 2577 helix: 0.26 (0.15), residues: 1200 sheet: -0.42 (0.21), residues: 566 loop : -0.60 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 166 TYR 0.014 0.002 TYR H 166 PHE 0.019 0.002 PHE A 376 TRP 0.012 0.002 TRP F 69 HIS 0.011 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 (22742) covalent geometry : angle 0.60729 / 0.32 (30984) hydrogen bonds : bond 0.04816 / 3.17 ( 1107) hydrogen bonds : angle 4.86583 / 3.48 ( 3197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 266 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8469 (tt) REVERT: A 241 ASP cc_start: 0.7109 (m-30) cc_final: 0.6811 (m-30) REVERT: A 245 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8005 (t) REVERT: A 301 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8222 (mp) REVERT: A 351 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7336 (m170) REVERT: A 355 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7926 (t0) REVERT: A 372 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.7805 (p) REVERT: A 418 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8479 (mt-10) REVERT: B 28 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8319 (mm-30) REVERT: B 100 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8073 (ttmm) REVERT: C 172 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6833 (pp20) REVERT: C 199 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: C 332 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6867 (mt-10) REVERT: D 38 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8261 (mt-10) REVERT: E 119 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6021 (mpp) REVERT: E 134 ARG cc_start: 0.4434 (OUTLIER) cc_final: 0.2952 (mmt90) REVERT: E 197 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6445 (mt-10) REVERT: E 204 ASP cc_start: 0.6957 (m-30) cc_final: 0.6577 (t0) REVERT: E 220 LYS cc_start: 0.6877 (tmmt) cc_final: 0.6054 (tppt) REVERT: F 100 LEU cc_start: 0.1745 (OUTLIER) cc_final: 0.1338 (tt) REVERT: F 119 MET cc_start: 0.2934 (tpp) cc_final: 0.1687 (mmm) REVERT: G 50 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7454 (ttt90) REVERT: H 55 ARG cc_start: 0.7517 (mtt180) cc_final: 0.7040 (mtm-85) REVERT: H 103 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7408 (p) REVERT: H 139 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: H 227 ILE cc_start: 0.5616 (OUTLIER) cc_final: 0.4847 (pp) REVERT: H 277 LEU cc_start: 0.6986 (tp) cc_final: 0.6596 (tp) REVERT: H 358 ASP cc_start: 0.7503 (m-30) cc_final: 0.6276 (p0) outliers start: 140 outliers final: 68 residues processed: 371 average time/residue: 0.6062 time to fit residues: 259.5847 Evaluate side-chains 339 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 253 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 381 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 242 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 237 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 173 optimal weight: 20.0000 chunk 209 optimal weight: 0.0980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 203 GLN A 298 GLN A 388 ASN A 411 ASN A 436 HIS B 8 GLN B 102 HIS C 184 HIS E 224 GLN G 17 HIS ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.180884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129887 restraints weight = 24982.685| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.78 r_work: 0.3269 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22742 Z= 0.122 Angle : 0.531 9.884 30984 Z= 0.280 Chirality : 0.042 0.165 3582 Planarity : 0.004 0.060 3707 Dihedral : 15.808 144.826 3491 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.72 % Allowed : 22.47 % Favored : 72.81 % 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 (0.17), residues: 2577 helix: 0.53 (0.15), residues: 1202 sheet: -0.39 (0.21), residues: 565 loop : -0.48 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 165 TYR 0.017 0.001 TYR B 186 PHE 0.015 0.001 PHE G 154 TRP 0.009 0.001 TRP E 259 HIS 0.007 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (22742) covalent geometry : angle 0.53106 / 0.28 (30984) hydrogen bonds : bond 0.03869 / 2.56 ( 1107) hydrogen bonds : angle 4.65220 / 3.33 ( 3197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 267 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8393 (tt) REVERT: A 187 GLU cc_start: 0.8364 (tt0) cc_final: 0.7921 (tp30) REVERT: A 245 SER cc_start: 0.8337 (p) cc_final: 0.7972 (t) REVERT: A 301 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8217 (mp) REVERT: A 351 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.7314 (m170) REVERT: A 418 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8401 (mt-10) REVERT: B 28 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8317 (mm-30) REVERT: B 100 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8008 (ttmm) REVERT: C 172 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6675 (pp20) REVERT: C 332 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6829 (mt-10) REVERT: D 38 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8263 (mt-10) REVERT: E 197 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6385 (mt-10) REVERT: E 204 ASP cc_start: 0.6878 (m-30) cc_final: 0.6526 (t0) REVERT: F 100 LEU cc_start: 0.1603 (OUTLIER) cc_final: 0.1230 (tt) REVERT: F 119 MET cc_start: 0.3071 (tpp) cc_final: 0.1765 (mmm) REVERT: F 413 LYS cc_start: 0.5503 (OUTLIER) cc_final: 0.5045 (ttpp) REVERT: G 20 HIS cc_start: 0.5142 (OUTLIER) cc_final: 0.4917 (t-170) REVERT: G 155 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7742 (pp20) REVERT: G 323 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: H 55 ARG cc_start: 0.7526 (mtt180) cc_final: 0.7075 (mtm-85) REVERT: H 103 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7475 (p) REVERT: H 139 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6960 (mm-30) REVERT: H 227 ILE cc_start: 0.5667 (OUTLIER) cc_final: 0.4886 (pp) REVERT: H 277 LEU cc_start: 0.6998 (tp) cc_final: 0.6621 (tp) REVERT: H 358 ASP cc_start: 0.7475 (m-30) cc_final: 0.6319 (OUTLIER) outliers start: 112 outliers final: 61 residues processed: 356 average time/residue: 0.6320 time to fit residues: 257.8231 Evaluate side-chains 335 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 260 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 20 HIS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 151 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 102 HIS E 103 ASN G 17 HIS ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.178080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124880 restraints weight = 25207.664| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.86 r_work: 0.3239 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22742 Z= 0.208 Angle : 0.581 10.977 30984 Z= 0.304 Chirality : 0.044 0.182 3582 Planarity : 0.004 0.060 3707 Dihedral : 15.858 152.817 3488 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.23 % Allowed : 22.26 % 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 (0.17), residues: 2577 helix: 0.39 (0.15), residues: 1213 sheet: -0.35 (0.21), residues: 566 loop : -0.57 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 129 TYR 0.023 0.002 TYR B 186 PHE 0.023 0.002 PHE A 279 TRP 0.010 0.002 TRP F 296 HIS 0.008 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (22742) covalent geometry : angle 0.58087 / 0.30 (30984) hydrogen bonds : bond 0.04383 / 2.89 ( 1107) hydrogen bonds : angle 4.67033 / 3.34 ( 3197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 259 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 187 GLU cc_start: 0.8364 (tt0) cc_final: 0.7912 (tp30) REVERT: A 245 SER cc_start: 0.8385 (p) cc_final: 0.8018 (t) REVERT: A 301 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8150 (mp) REVERT: A 351 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7351 (m170) REVERT: A 372 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.7848 (p) REVERT: A 418 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8323 (mt-10) REVERT: B 28 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8275 (mm-30) REVERT: B 100 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8079 (ttmm) REVERT: C 172 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6763 (pp20) REVERT: C 332 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6799 (mt-10) REVERT: E 119 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6016 (mpp) REVERT: E 197 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6445 (mt-10) REVERT: E 204 ASP cc_start: 0.6865 (m-30) cc_final: 0.6509 (t0) REVERT: F 100 LEU cc_start: 0.1304 (OUTLIER) cc_final: 0.1043 (tt) REVERT: F 119 MET cc_start: 0.3267 (tpp) cc_final: 0.2070 (mmm) REVERT: F 413 LYS cc_start: 0.5470 (OUTLIER) cc_final: 0.4991 (ttpp) REVERT: G 155 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7677 (pp20) REVERT: H 55 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7067 (mtm-85) REVERT: H 103 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7383 (p) REVERT: H 139 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6920 (mm-30) REVERT: H 227 ILE cc_start: 0.5657 (OUTLIER) cc_final: 0.4924 (pp) REVERT: H 277 LEU cc_start: 0.6964 (tp) cc_final: 0.6588 (tp) REVERT: H 358 ASP cc_start: 0.7479 (m-30) cc_final: 0.6315 (p0) outliers start: 124 outliers final: 73 residues processed: 353 average time/residue: 0.6274 time to fit residues: 253.5021 Evaluate side-chains 335 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 247 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 129 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS E 74 GLN E 224 GLN G 17 HIS ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN H 53 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.174657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.121409 restraints weight = 25321.976| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.89 r_work: 0.3180 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 22742 Z= 0.301 Angle : 0.673 12.358 30984 Z= 0.349 Chirality : 0.048 0.193 3582 Planarity : 0.005 0.063 3707 Dihedral : 16.093 169.147 3486 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.56 % Allowed : 22.18 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2577 helix: 0.10 (0.15), residues: 1206 sheet: -0.37 (0.21), residues: 559 loop : -0.82 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 16 TYR 0.026 0.002 TYR B 186 PHE 0.024 0.002 PHE G 154 TRP 0.014 0.002 TRP F 296 HIS 0.011 0.002 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.30 (22742) covalent geometry : angle 0.67349 / 0.35 (30984) hydrogen bonds : bond 0.05209 / 3.44 ( 1107) hydrogen bonds : angle 4.84265 / 3.47 ( 3197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 260 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8483 (tt) REVERT: A 189 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8926 (mt) REVERT: A 241 ASP cc_start: 0.7320 (m-30) cc_final: 0.6895 (m-30) REVERT: A 245 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8095 (t) REVERT: A 301 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8262 (mp) REVERT: A 351 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7558 (m170) REVERT: A 372 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.7774 (p) REVERT: A 418 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8334 (mt-10) REVERT: B 87 ASP cc_start: 0.7998 (t70) cc_final: 0.7185 (p0) REVERT: B 100 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8180 (ttmm) REVERT: C 199 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: C 332 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6903 (mt-10) REVERT: D 38 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8348 (mt-10) REVERT: E 119 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.5899 (mpp) REVERT: E 134 ARG cc_start: 0.4644 (OUTLIER) cc_final: 0.3173 (mmt90) REVERT: E 156 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7391 (tpt-90) REVERT: E 197 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6510 (mt-10) REVERT: E 204 ASP cc_start: 0.6940 (m-30) cc_final: 0.6580 (t0) REVERT: E 220 LYS cc_start: 0.7123 (tmmt) cc_final: 0.6325 (tppt) REVERT: F 100 LEU cc_start: 0.1205 (OUTLIER) cc_final: 0.0980 (tt) REVERT: F 119 MET cc_start: 0.3293 (tpp) cc_final: 0.2098 (mmm) REVERT: G 155 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7626 (pp20) REVERT: H 9 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7036 (tm-30) REVERT: H 55 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7085 (mtm-85) REVERT: H 103 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7362 (p) REVERT: H 139 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6961 (mm-30) REVERT: H 227 ILE cc_start: 0.5847 (OUTLIER) cc_final: 0.5142 (pp) REVERT: H 277 LEU cc_start: 0.7011 (tp) cc_final: 0.6728 (tp) REVERT: H 358 ASP cc_start: 0.7596 (m-30) cc_final: 0.6465 (p0) outliers start: 132 outliers final: 79 residues processed: 361 average time/residue: 0.5126 time to fit residues: 213.1332 Evaluate side-chains 344 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 248 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 26 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 411 ASN A 436 HIS B 8 GLN B 102 HIS C 74 ASN E 224 GLN E 292 HIS G 17 HIS ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN H 53 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.178968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126054 restraints weight = 24972.941| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.90 r_work: 0.3246 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22742 Z= 0.128 Angle : 0.557 9.921 30984 Z= 0.291 Chirality : 0.042 0.175 3582 Planarity : 0.004 0.081 3707 Dihedral : 15.961 162.197 3486 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.17 % Allowed : 23.48 % Favored : 72.34 % 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: -0.17 (0.17), residues: 2577 helix: 0.45 (0.15), residues: 1205 sheet: -0.32 (0.21), residues: 558 loop : -0.56 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 165 TYR 0.020 0.001 TYR B 186 PHE 0.026 0.001 PHE G 154 TRP 0.013 0.001 TRP E 259 HIS 0.007 0.001 HIS G 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (22742) covalent geometry : angle 0.55666 / 0.29 (30984) hydrogen bonds : bond 0.03857 / 2.57 ( 1107) hydrogen bonds : angle 4.59041 / 3.28 ( 3197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 261 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8379 (tt0) cc_final: 0.7898 (tp30) REVERT: A 245 SER cc_start: 0.8254 (p) cc_final: 0.7991 (t) REVERT: A 301 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8139 (mp) REVERT: A 307 GLU cc_start: 0.8195 (tp30) cc_final: 0.7843 (tp30) REVERT: A 351 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.7518 (m170) REVERT: A 418 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8272 (mt-10) REVERT: B 100 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8071 (ttmm) REVERT: C 172 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6783 (pp20) REVERT: C 332 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6738 (mt-10) REVERT: D 38 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8312 (mt-10) REVERT: E 197 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6411 (mt-10) REVERT: E 204 ASP cc_start: 0.6873 (m-30) cc_final: 0.6525 (t0) REVERT: F 19 LEU cc_start: 0.4025 (OUTLIER) cc_final: 0.3784 (mm) REVERT: F 100 LEU cc_start: 0.1177 (OUTLIER) cc_final: 0.0954 (tt) REVERT: F 119 MET cc_start: 0.3216 (tpp) cc_final: 0.2128 (mmm) REVERT: G 155 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7729 (pp20) REVERT: G 197 LYS cc_start: 0.6684 (mmmt) cc_final: 0.6380 (mmtt) REVERT: G 202 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6457 (t80) REVERT: G 323 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: H 9 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6945 (tm-30) REVERT: H 55 ARG cc_start: 0.7597 (mtt180) cc_final: 0.7111 (mtm-85) REVERT: H 63 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: H 103 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7376 (p) REVERT: H 139 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: H 227 ILE cc_start: 0.5809 (OUTLIER) cc_final: 0.5120 (pp) REVERT: H 277 LEU cc_start: 0.7025 (tp) cc_final: 0.6742 (tp) REVERT: H 358 ASP cc_start: 0.7543 (m-30) cc_final: 0.6373 (p0) outliers start: 99 outliers final: 62 residues processed: 336 average time/residue: 0.6355 time to fit residues: 244.2957 Evaluate side-chains 330 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 254 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 240 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 195 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 0.0060 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 411 ASN A 436 HIS B 102 HIS C 74 ASN E 103 ASN E 224 GLN G 17 HIS ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN G 218 GLN H 53 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.179890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127817 restraints weight = 25124.892| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.02 r_work: 0.3264 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22742 Z= 0.125 Angle : 0.544 10.664 30984 Z= 0.283 Chirality : 0.042 0.194 3582 Planarity : 0.004 0.067 3707 Dihedral : 15.841 157.138 3486 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.63 % Allowed : 24.16 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2577 helix: 0.62 (0.15), residues: 1218 sheet: -0.20 (0.21), residues: 557 loop : -0.44 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 175 TYR 0.021 0.001 TYR B 186 PHE 0.032 0.001 PHE A 279 TRP 0.011 0.001 TRP E 259 HIS 0.007 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (22742) covalent geometry : angle 0.54399 / 0.28 (30984) hydrogen bonds : bond 0.03659 / 2.44 ( 1107) hydrogen bonds : angle 4.46318 / 3.19 ( 3197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 268 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8385 (tt) REVERT: A 187 GLU cc_start: 0.8392 (tt0) cc_final: 0.7953 (tp30) REVERT: A 241 ASP cc_start: 0.7342 (m-30) cc_final: 0.6972 (m-30) REVERT: A 245 SER cc_start: 0.8329 (p) cc_final: 0.8062 (t) REVERT: A 307 GLU cc_start: 0.8184 (tp30) cc_final: 0.7846 (tp30) REVERT: A 351 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7523 (m170) REVERT: A 418 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8294 (mt-10) REVERT: B 100 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7869 (tptm) REVERT: C 332 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6777 (mt-10) REVERT: D 88 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7758 (mtm) REVERT: D 89 LYS cc_start: 0.8473 (ptpt) cc_final: 0.8262 (mptp) REVERT: F 100 LEU cc_start: 0.1138 (OUTLIER) cc_final: 0.0926 (tt) REVERT: F 119 MET cc_start: 0.3412 (tpp) cc_final: 0.2211 (mmm) REVERT: G 155 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7780 (pp20) REVERT: G 323 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: H 55 ARG cc_start: 0.7575 (mtt180) cc_final: 0.7157 (mtm-85) REVERT: H 63 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: H 103 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7433 (p) REVERT: H 139 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6973 (mm-30) REVERT: H 227 ILE cc_start: 0.5910 (OUTLIER) cc_final: 0.5230 (pp) REVERT: H 277 LEU cc_start: 0.6894 (tp) cc_final: 0.6604 (tp) REVERT: H 358 ASP cc_start: 0.7547 (m-30) cc_final: 0.6372 (p0) outliers start: 86 outliers final: 55 residues processed: 333 average time/residue: 0.6345 time to fit residues: 242.6080 Evaluate side-chains 317 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 251 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 211 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 chunk 70 optimal weight: 0.9980 chunk 233 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 411 ASN A 436 HIS B 8 GLN B 102 HIS C 74 ASN E 224 GLN G 17 HIS ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN H 53 GLN H 365 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.180274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128474 restraints weight = 25042.634| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.92 r_work: 0.3264 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22742 Z= 0.122 Angle : 0.536 10.049 30984 Z= 0.280 Chirality : 0.042 0.177 3582 Planarity : 0.004 0.068 3707 Dihedral : 15.807 153.335 3486 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.20 % Allowed : 24.58 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2577 helix: 0.72 (0.15), residues: 1212 sheet: -0.16 (0.22), residues: 557 loop : -0.34 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 184 TYR 0.021 0.001 TYR B 186 PHE 0.017 0.001 PHE G 154 TRP 0.011 0.001 TRP E 259 HIS 0.006 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (22742) covalent geometry : angle 0.53600 / 0.28 (30984) hydrogen bonds : bond 0.03586 / 2.39 ( 1107) hydrogen bonds : angle 4.40680 / 3.15 ( 3197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 261 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8335 (tt) REVERT: A 187 GLU cc_start: 0.8419 (tt0) cc_final: 0.7974 (tp30) REVERT: A 241 ASP cc_start: 0.7291 (m-30) cc_final: 0.6910 (m-30) REVERT: A 245 SER cc_start: 0.8213 (p) cc_final: 0.7989 (t) REVERT: A 307 GLU cc_start: 0.8187 (tp30) cc_final: 0.7849 (tp30) REVERT: A 351 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7501 (m170) REVERT: A 372 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.7906 (p) REVERT: A 418 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8254 (mt-10) REVERT: B 100 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7836 (tptm) REVERT: C 245 LYS cc_start: 0.7906 (mppt) cc_final: 0.7262 (mttt) REVERT: C 332 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6663 (mt-10) REVERT: D 38 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8280 (mt-10) REVERT: D 88 MET cc_start: 0.7913 (mtp) cc_final: 0.7690 (mtm) REVERT: D 89 LYS cc_start: 0.8464 (ptpt) cc_final: 0.8233 (mptp) REVERT: E 204 ASP cc_start: 0.6874 (m-30) cc_final: 0.6522 (t0) REVERT: F 19 LEU cc_start: 0.3285 (mm) cc_final: 0.2868 (pt) REVERT: F 100 LEU cc_start: 0.1243 (OUTLIER) cc_final: 0.1038 (tt) REVERT: F 119 MET cc_start: 0.3413 (tpp) cc_final: 0.2213 (mmm) REVERT: G 155 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7753 (pp20) REVERT: G 176 LYS cc_start: 0.8185 (tptm) cc_final: 0.7161 (pttm) REVERT: G 177 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6882 (mt-10) REVERT: H 55 ARG cc_start: 0.7542 (mtt180) cc_final: 0.7117 (mtm-85) REVERT: H 63 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: H 103 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7371 (p) REVERT: H 139 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6956 (mm-30) REVERT: H 227 ILE cc_start: 0.5827 (OUTLIER) cc_final: 0.5172 (pp) REVERT: H 277 LEU cc_start: 0.6980 (tp) cc_final: 0.6699 (tp) REVERT: H 358 ASP cc_start: 0.7536 (m-30) cc_final: 0.6330 (p0) outliers start: 76 outliers final: 55 residues processed: 321 average time/residue: 0.6272 time to fit residues: 231.6366 Evaluate side-chains 314 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 249 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 250 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS E 103 ASN E 224 GLN G 17 HIS ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.179804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126515 restraints weight = 24974.716| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.92 r_work: 0.3256 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22742 Z= 0.137 Angle : 0.548 10.521 30984 Z= 0.286 Chirality : 0.042 0.176 3582 Planarity : 0.004 0.065 3707 Dihedral : 15.779 151.604 3484 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.46 % Allowed : 24.45 % Favored : 72.09 % 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: 0.18 (0.17), residues: 2577 helix: 0.72 (0.15), residues: 1211 sheet: -0.10 (0.22), residues: 558 loop : -0.42 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 184 TYR 0.022 0.001 TYR B 186 PHE 0.031 0.001 PHE A 279 TRP 0.010 0.001 TRP E 259 HIS 0.007 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (22742) covalent geometry : angle 0.54807 / 0.29 (30984) hydrogen bonds : bond 0.03680 / 2.46 ( 1107) hydrogen bonds : angle 4.40328 / 3.15 ( 3197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8951.67 seconds wall clock time: 153 minutes 28.46 seconds (9208.46 seconds total)