Starting phenix.real_space_refine on Fri Aug 7 14:52:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fs5_29414/08_2026/8fs5_29414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fs5_29414/08_2026/8fs5_29414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8fs5_29414/08_2026/8fs5_29414.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fs5_29414/08_2026/8fs5_29414.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fs5_29414/08_2026/8fs5_29414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fs5_29414/08_2026/8fs5_29414.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fs5_29414/08_2026/8fs5_29414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fs5_29414/08_2026/8fs5_29414.map" } resolution = 2.76 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= 0.047 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 13862 2.51 5 N 3821 2.21 5 O 4338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s 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: 22211 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3559 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 2 Chain: "B" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2490 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 9, 'TRANS': 307} 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: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2787 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain: "F" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2337 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 5 Chain: "G" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2322 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 4, 'TRANS': 288} Chain breaks: 1 Chain: "H" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2193 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 6 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: 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: "C" 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: "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: 4.24, per 1000 atoms: 0.19 Number of scatterers: 22211 At special positions: 0 Unit cell: (116.748, 137.448, 139.104, 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 4338 8.00 N 3821 7.00 C 13862 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: 1.86 Conformation dependent library (CDL) restraints added in 857.1 milliseconds 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5008 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 18 sheets defined 52.7% alpha, 15.3% beta 22 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.508A pdb=" N GLN A 77 " --> pdb=" O CYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 114 through 131 removed outlier: 3.631A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.937A 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 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 194 through 210 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.575A pdb=" N VAL A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 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 373 through 384 removed outlier: 3.959A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) 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 408 Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.950A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 470 removed outlier: 4.356A pdb=" N TYR A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.502A pdb=" N LEU A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 497 removed outlier: 3.973A pdb=" N CYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.854A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.591A 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: 3.938A 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: 3.909A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 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 228 removed outlier: 3.622A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.770A pdb=" N SER B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.538A pdb=" N ARG B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.717A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.576A pdb=" N ASN C 12 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 13 " --> pdb=" O LYS C 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 9 through 13' Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.559A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.763A pdb=" N ILE C 34 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.909A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.739A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.783A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 253 removed outlier: 3.764A pdb=" N LYS C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 271 removed outlier: 3.596A pdb=" N HIS C 260 " --> pdb=" O TRP C 256 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.031A pdb=" N LEU C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.901A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 335 removed outlier: 3.949A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR C 335 " --> pdb=" O PHE C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.710A pdb=" N VAL D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.257A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.935A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.797A 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 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.522A 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: 3.505A 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 218 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.540A pdb=" N GLY D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.552A pdb=" N GLY D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 removed outlier: 3.629A pdb=" N GLY D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.764A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.585A pdb=" N ASN D 311 " --> pdb=" O TYR D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.603A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.538A 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 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.783A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.601A pdb=" N THR E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 4.376A 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 98 through 103 removed outlier: 7.372A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.806A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.716A 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: 3.873A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.583A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 243 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: 4.645A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 30 removed outlier: 3.502A pdb=" N THR F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 removed outlier: 3.903A pdb=" N LEU F 61 " --> pdb=" O ASN F 57 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 57 through 62' Processing helix chain 'F' and resid 75 through 77 No H-bonds generated for 'chain 'F' and resid 75 through 77' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 96 through 113 removed outlier: 4.086A pdb=" N LEU F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 removed outlier: 3.537A pdb=" N ARG F 219 " --> pdb=" O ALA F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 252 removed outlier: 4.254A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 256 removed outlier: 4.003A pdb=" N TYR F 256 " --> pdb=" O VAL F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 253 through 256' Processing helix chain 'F' and resid 412 through 424 removed outlier: 3.625A pdb=" N CYS F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 27 removed outlier: 4.067A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 86 through 97 removed outlier: 4.136A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 245 through 250 removed outlier: 3.533A pdb=" N LYS G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 330 Processing helix chain 'H' and resid 10 through 27 removed outlier: 3.542A pdb=" N TRP H 16 " --> pdb=" O LYS H 12 " (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 105 removed outlier: 3.983A pdb=" N THR H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE H 104 " --> pdb=" O HIS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 243 removed outlier: 3.726A pdb=" N LEU H 237 " --> pdb=" O ASN H 233 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 336 removed outlier: 4.115A pdb=" N ASN H 331 " --> pdb=" O LYS H 327 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.268A pdb=" N LEU A 105 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE A 223 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A 107 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 263 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 106 " --> pdb=" O ILE A 263 " (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 75 through 78 removed outlier: 6.213A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 186 removed outlier: 7.584A pdb=" N LYS B 185 " --> pdb=" O VAL B 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.061A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.057A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.241A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.643A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 79 through 83 removed outlier: 3.973A pdb=" N LEU F 79 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE F 6 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR F 81 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS F 4 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 72 through 73 removed outlier: 3.594A pdb=" N LEU F 35 " --> pdb=" O MET F 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 72 through 73 removed outlier: 4.115A pdb=" N ILE F 44 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE F 432 " --> pdb=" O MET F 231 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET F 231 " --> pdb=" O ILE F 432 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 405 through 411 removed outlier: 4.568A pdb=" N LEU F 281 " --> pdb=" O TRP F 296 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU G 122 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER G 69 " --> pdb=" O SER G 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 80 through 85 removed outlier: 7.207A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 270 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE G 154 " --> pdb=" O MET G 259 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 232 through 238 removed outlier: 4.671A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR H 148 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL H 136 " --> pdb=" O TYR H 148 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU H 63 " --> pdb=" O THR H 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 78 through 79 Processing sheet with id=AB7, first strand: chain 'H' and resid 78 through 79 removed outlier: 7.275A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 283 through 289 Processing sheet with id=AB9, first strand: chain 'H' and resid 270 through 271 removed outlier: 6.266A pdb=" N VAL H 270 " --> pdb=" O LEU H 278 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 2.48 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: 7206 1.36 - 1.51: 5995 1.51 - 1.65: 9333 1.65 - 1.80: 74 1.80 - 1.95: 97 Bond restraints: 22705 Sorted by residual: bond pdb=" C SER E 175 " pdb=" N PRO E 176 " ideal model delta sigma weight residual 1.334 1.366 -0.032 8.40e-03 1.42e+04 1.47e+01 bond pdb=" CA SER F 51 " pdb=" CB SER F 51 " ideal model delta sigma weight residual 1.539 1.494 0.045 1.20e-02 6.94e+03 1.40e+01 bond pdb=" C3' DG I 33 " pdb=" C2' DG I 33 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.83e+00 bond pdb=" N HIS E 18 " pdb=" CA HIS E 18 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.31e-02 5.83e+03 8.30e+00 bond pdb=" N ILE F 468 " pdb=" CA ILE F 468 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.24e+00 ... (remaining 22700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 30016 1.84 - 3.68: 803 3.68 - 5.52: 91 5.52 - 7.36: 16 7.36 - 9.20: 5 Bond angle restraints: 30931 Sorted by residual: angle pdb=" N3 DT J 8 " pdb=" C4 DT J 8 " pdb=" O4 DT J 8 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+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 1.97e+01 angle pdb=" N3 DT K 7 " pdb=" C4 DT K 7 " pdb=" O4 DT K 7 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT K 4 " pdb=" C4 DT K 4 " pdb=" O4 DT K 4 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" O4 DT J 8 " pdb=" C4 DT J 8 " pdb=" C5 DT J 8 " ideal model delta sigma weight residual 124.90 121.86 3.04 7.00e-01 2.04e+00 1.89e+01 ... (remaining 30926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 12980 35.10 - 70.20: 678 70.20 - 105.30: 22 105.30 - 140.40: 2 140.40 - 175.50: 1 Dihedral angle restraints: 13683 sinusoidal: 6001 harmonic: 7682 Sorted by residual: 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 -60.00 115.50 -175.50 1 2.00e+01 2.50e-03 4.79e+01 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 80.07 -140.07 1 2.00e+01 2.50e-03 4.24e+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 62.73 -122.73 1 2.00e+01 2.50e-03 3.70e+01 ... (remaining 13680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2713 0.046 - 0.092: 659 0.092 - 0.138: 192 0.138 - 0.183: 7 0.183 - 0.229: 3 Chirality restraints: 3574 Sorted by residual: chirality pdb=" CA ILE F 468 " pdb=" N ILE F 468 " pdb=" C ILE F 468 " pdb=" CB ILE F 468 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE E 211 " pdb=" CA ILE E 211 " pdb=" CG1 ILE E 211 " pdb=" CG2 ILE E 211 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL C 133 " pdb=" N VAL C 133 " pdb=" C VAL C 133 " pdb=" CB VAL C 133 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.31e-01 ... (remaining 3571 not shown) Planarity restraints: 3703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.080 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO E 63 " -0.208 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 336 " -0.054 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO H 337 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO H 337 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 337 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 235 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.67e+00 pdb=" N PRO F 236 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO F 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 236 " 0.030 5.00e-02 4.00e+02 ... (remaining 3700 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 262 2.63 - 3.19: 18785 3.19 - 3.76: 35597 3.76 - 4.33: 50262 4.33 - 4.90: 82510 Nonbonded interactions: 187416 Sorted by model distance: nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.057 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.066 2.170 nonbonded pdb=" OE2 GLU A 187 " pdb="MG MG A 602 " model vdw 2.087 2.170 nonbonded pdb=" OG1 THR D 72 " pdb="MG MG D 402 " model vdw 2.095 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.122 2.170 ... (remaining 187411 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: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 22.070 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 0.060 22705 Z= 0.254 Angle : 0.708 9.200 30931 Z= 0.479 Chirality : 0.043 0.229 3574 Planarity : 0.005 0.121 3703 Dihedral : 18.260 175.496 8675 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.77 % Allowed : 23.84 % Favored : 74.39 % 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: -0.31 (0.17), residues: 2575 helix: 0.33 (0.15), residues: 1216 sheet: -0.31 (0.23), residues: 542 loop : -0.71 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.013 0.001 TYR A 67 PHE 0.012 0.001 PHE G 140 TRP 0.015 0.001 TRP A 463 HIS 0.009 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.25 (22705) covalent geometry : angle 0.70836 / 0.48 (30931) hydrogen bonds : bond 0.18282 / 11.77 ( 1137) hydrogen bonds : angle 7.06931 / 5.05 ( 3212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 0.849 Fit side-chains REVERT: A 131 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7500 (ttm-80) REVERT: B 183 ASP cc_start: 0.7421 (m-30) cc_final: 0.7172 (m-30) REVERT: C 78 MET cc_start: 0.8343 (mmp) cc_final: 0.7865 (tpt) REVERT: C 199 GLU cc_start: 0.7383 (mp0) cc_final: 0.7002 (mp0) REVERT: D 80 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7662 (mmmt) REVERT: E 67 ARG cc_start: 0.7310 (ttm-80) cc_final: 0.7063 (tpp80) REVERT: E 104 ASN cc_start: 0.7054 (m-40) cc_final: 0.6631 (m110) REVERT: E 142 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7558 (mm-30) REVERT: E 221 ARG cc_start: 0.6979 (mtp-110) cc_final: 0.6691 (mtm110) REVERT: G 35 ASP cc_start: 0.6732 (t0) cc_final: 0.6442 (t0) REVERT: G 146 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6974 (pp20) REVERT: G 314 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6894 (mm-30) REVERT: H 133 ARG cc_start: 0.6594 (mtt90) cc_final: 0.6358 (mtt90) outliers start: 42 outliers final: 31 residues processed: 325 average time/residue: 0.6033 time to fit residues: 224.6657 Evaluate side-chains 301 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 264 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN B 35 GLN C 184 HIS D 128 ASN E 19 ASN E 243 ASN F 57 ASN G 52 ASN G 53 ASN G 87 ASN G 218 GLN H 100 HIS H 151 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.176329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128576 restraints weight = 23486.805| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.76 r_work: 0.3370 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22705 Z= 0.166 Angle : 0.571 8.477 30931 Z= 0.306 Chirality : 0.043 0.172 3574 Planarity : 0.005 0.080 3703 Dihedral : 16.115 151.714 3506 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.14 % Allowed : 20.46 % Favored : 75.40 % 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: -0.08 (0.17), residues: 2575 helix: 0.49 (0.15), residues: 1221 sheet: -0.17 (0.23), residues: 546 loop : -0.57 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 152 TYR 0.016 0.001 TYR E 135 PHE 0.015 0.002 PHE A 376 TRP 0.011 0.001 TRP A 463 HIS 0.009 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (22705) covalent geometry : angle 0.57107 / 0.31 (30931) hydrogen bonds : bond 0.04786 / 3.14 ( 1137) hydrogen bonds : angle 5.08965 / 3.64 ( 3212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 287 time to evaluate : 1.010 Fit side-chains REVERT: A 68 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: A 273 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7642 (mp) REVERT: D 100 GLU cc_start: 0.7499 (pm20) cc_final: 0.7299 (tm-30) REVERT: D 126 LEU cc_start: 0.8575 (mt) cc_final: 0.8372 (mt) REVERT: D 175 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7883 (mmp80) REVERT: D 270 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7693 (mt-10) REVERT: D 274 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.6952 (mptm) REVERT: E 19 ASN cc_start: 0.7329 (OUTLIER) cc_final: 0.7105 (t0) REVERT: E 69 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6836 (ptmm) REVERT: E 230 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7673 (tt) REVERT: G 95 VAL cc_start: 0.7703 (OUTLIER) cc_final: 0.7413 (p) REVERT: G 122 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6164 (pm20) REVERT: G 146 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7017 (pp20) REVERT: G 215 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: G 216 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7733 (tmtm) REVERT: G 258 ARG cc_start: 0.8561 (mtm180) cc_final: 0.8325 (mtp180) REVERT: G 323 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6527 (tm-30) REVERT: H 276 ASP cc_start: 0.6675 (t70) cc_final: 0.6311 (m-30) REVERT: H 363 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: H 365 GLN cc_start: 0.7370 (mm-40) cc_final: 0.6590 (mp-120) outliers start: 98 outliers final: 39 residues processed: 362 average time/residue: 0.5983 time to fit residues: 247.7801 Evaluate side-chains 324 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 272 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 363 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 240 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 219 optimal weight: 0.4980 chunk 149 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 120 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 224 GLN G 87 ASN G 218 GLN H 14 ASN H 151 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.176133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.128683 restraints weight = 23405.229| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.76 r_work: 0.3355 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22705 Z= 0.132 Angle : 0.514 8.002 30931 Z= 0.277 Chirality : 0.041 0.196 3574 Planarity : 0.004 0.075 3703 Dihedral : 16.004 133.831 3491 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.54 % Allowed : 21.56 % Favored : 74.89 % 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: 0.15 (0.17), residues: 2575 helix: 0.76 (0.15), residues: 1223 sheet: -0.14 (0.22), residues: 547 loop : -0.52 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 55 TYR 0.016 0.001 TYR E 135 PHE 0.012 0.001 PHE E 328 TRP 0.008 0.001 TRP A 463 HIS 0.007 0.001 HIS H 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (22705) covalent geometry : angle 0.51420 / 0.28 (30931) hydrogen bonds : bond 0.04219 / 2.77 ( 1137) hydrogen bonds : angle 4.75616 / 3.41 ( 3212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 285 time to evaluate : 0.920 Fit side-chains REVERT: A 68 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: A 227 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7268 (tp30) REVERT: A 273 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7705 (mp) REVERT: A 293 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.6060 (ptpt) REVERT: D 100 GLU cc_start: 0.7601 (pm20) cc_final: 0.7385 (tm-30) REVERT: D 126 LEU cc_start: 0.8561 (mt) cc_final: 0.8357 (mt) REVERT: D 175 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7845 (mmp80) REVERT: E 19 ASN cc_start: 0.7350 (OUTLIER) cc_final: 0.7103 (t0) REVERT: E 69 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6756 (ptmm) REVERT: E 230 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7651 (tt) REVERT: E 311 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: F 280 GLU cc_start: 0.7165 (tt0) cc_final: 0.6372 (pt0) REVERT: G 95 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7415 (p) REVERT: G 202 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.6993 (t80) REVERT: G 215 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: G 216 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7362 (pptt) REVERT: G 258 ARG cc_start: 0.8537 (mtm180) cc_final: 0.8271 (mtp180) REVERT: G 323 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: H 276 ASP cc_start: 0.6652 (t70) cc_final: 0.6261 (m-30) outliers start: 84 outliers final: 42 residues processed: 352 average time/residue: 0.6411 time to fit residues: 257.5831 Evaluate side-chains 328 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 272 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 181 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 218 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 259 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 chunk 190 optimal weight: 0.0670 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 298 GLN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN E 224 GLN G 218 GLN H 151 GLN H 228 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.175010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127886 restraints weight = 23412.743| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.84 r_work: 0.3326 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22705 Z= 0.134 Angle : 0.509 7.300 30931 Z= 0.272 Chirality : 0.042 0.161 3574 Planarity : 0.004 0.074 3703 Dihedral : 16.008 132.863 3488 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.97 % Allowed : 21.48 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2575 helix: 0.87 (0.15), residues: 1223 sheet: -0.10 (0.22), residues: 546 loop : -0.47 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 183 TYR 0.018 0.001 TYR E 135 PHE 0.012 0.001 PHE E 328 TRP 0.008 0.001 TRP A 463 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (22705) covalent geometry : angle 0.50942 / 0.27 (30931) hydrogen bonds : bond 0.03948 / 2.60 ( 1137) hydrogen bonds : angle 4.57878 / 3.28 ( 3212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 284 time to evaluate : 0.906 Fit side-chains REVERT: A 68 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: A 227 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7280 (tp30) REVERT: A 273 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7686 (mp) REVERT: C 38 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6660 (mtm180) REVERT: D 148 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7625 (p0) REVERT: D 175 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.7836 (mmp80) REVERT: E 19 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.7075 (t0) REVERT: E 58 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7617 (tm-30) REVERT: E 69 LYS cc_start: 0.7263 (ptpt) cc_final: 0.6707 (ptmm) REVERT: E 230 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7668 (tt) REVERT: F 280 GLU cc_start: 0.7111 (tt0) cc_final: 0.6260 (pt0) REVERT: F 289 ASP cc_start: 0.7294 (m-30) cc_final: 0.7057 (m-30) REVERT: G 122 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6116 (pm20) REVERT: G 215 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: G 216 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7395 (pptt) REVERT: G 258 ARG cc_start: 0.8537 (mtm180) cc_final: 0.8253 (mtp180) REVERT: G 260 ASP cc_start: 0.7919 (p0) cc_final: 0.7695 (p0) REVERT: H 276 ASP cc_start: 0.6684 (t70) cc_final: 0.6275 (m-30) REVERT: H 298 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.5118 (mt) outliers start: 94 outliers final: 42 residues processed: 361 average time/residue: 0.6570 time to fit residues: 270.7205 Evaluate side-chains 328 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 274 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 298 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 99 optimal weight: 0.9990 chunk 260 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 230 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 67 optimal weight: 0.3980 chunk 64 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN G 218 GLN H 45 ASN H 151 GLN H 228 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.172189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123944 restraints weight = 23339.852| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.75 r_work: 0.3305 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22705 Z= 0.198 Angle : 0.563 7.449 30931 Z= 0.298 Chirality : 0.044 0.177 3574 Planarity : 0.004 0.072 3703 Dihedral : 16.086 138.288 3486 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.22 % Allowed : 21.65 % Favored : 74.14 % 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: 0.13 (0.17), residues: 2575 helix: 0.74 (0.15), residues: 1225 sheet: -0.15 (0.22), residues: 547 loop : -0.57 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 183 TYR 0.023 0.002 TYR E 135 PHE 0.034 0.002 PHE H 353 TRP 0.009 0.001 TRP A 463 HIS 0.010 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (22705) covalent geometry : angle 0.56302 / 0.30 (30931) hydrogen bonds : bond 0.04386 / 2.91 ( 1137) hydrogen bonds : angle 4.63830 / 3.32 ( 3212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 284 time to evaluate : 0.885 Fit side-chains REVERT: A 227 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7319 (tp30) REVERT: A 273 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7713 (mp) REVERT: A 538 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.3612 (ttt90) REVERT: B 250 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: B 301 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7360 (mt-10) REVERT: C 38 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6547 (mtm180) REVERT: D 148 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7709 (p0) REVERT: D 175 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7797 (mmp80) REVERT: D 274 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.6966 (mptm) REVERT: D 353 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7537 (mp) REVERT: E 69 LYS cc_start: 0.7374 (ptpt) cc_final: 0.6756 (ptmm) REVERT: E 113 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7891 (tt) REVERT: F 280 GLU cc_start: 0.7146 (tt0) cc_final: 0.6360 (pt0) REVERT: G 42 ASP cc_start: 0.7899 (p0) cc_final: 0.7450 (p0) REVERT: G 44 ASP cc_start: 0.7859 (m-30) cc_final: 0.7386 (p0) REVERT: G 215 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: G 216 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7779 (tmtm) REVERT: G 227 VAL cc_start: 0.8368 (t) cc_final: 0.8131 (p) REVERT: G 258 ARG cc_start: 0.8576 (mtm180) cc_final: 0.8356 (mtp180) REVERT: H 276 ASP cc_start: 0.6704 (t70) cc_final: 0.6212 (m-30) REVERT: H 298 LEU cc_start: 0.5269 (OUTLIER) cc_final: 0.5057 (mt) outliers start: 100 outliers final: 57 residues processed: 367 average time/residue: 0.6587 time to fit residues: 275.7554 Evaluate side-chains 343 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 273 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 126 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 298 GLN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 121 GLN F 56 ASN G 218 GLN H 45 ASN H 228 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.172206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124112 restraints weight = 23342.478| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.84 r_work: 0.3303 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22705 Z= 0.169 Angle : 0.544 7.333 30931 Z= 0.289 Chirality : 0.043 0.235 3574 Planarity : 0.004 0.072 3703 Dihedral : 16.137 148.159 3484 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.77 % Allowed : 21.35 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2575 helix: 0.81 (0.15), residues: 1225 sheet: -0.15 (0.22), residues: 545 loop : -0.54 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 67 TYR 0.022 0.002 TYR E 135 PHE 0.014 0.002 PHE E 328 TRP 0.008 0.001 TRP A 463 HIS 0.009 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (22705) covalent geometry : angle 0.54409 / 0.29 (30931) hydrogen bonds : bond 0.04102 / 2.72 ( 1137) hydrogen bonds : angle 4.56959 / 3.27 ( 3212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 282 time to evaluate : 0.864 Fit side-chains REVERT: A 227 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7327 (tp30) REVERT: A 273 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7651 (mp) REVERT: A 298 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6946 (mm-40) REVERT: B 243 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8175 (t) REVERT: C 38 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6554 (mtm180) REVERT: D 135 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8703 (pttm) REVERT: D 148 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7667 (p0) REVERT: D 175 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7837 (mmp80) REVERT: D 274 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.6925 (mptm) REVERT: D 353 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7499 (mp) REVERT: E 58 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7654 (tm-30) REVERT: E 69 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6740 (ptmm) REVERT: E 208 ASN cc_start: 0.7601 (m-40) cc_final: 0.7352 (m-40) REVERT: E 230 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7479 (tt) REVERT: F 280 GLU cc_start: 0.7134 (tt0) cc_final: 0.6400 (pt0) REVERT: F 436 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6319 (tt0) REVERT: G 42 ASP cc_start: 0.7933 (p0) cc_final: 0.7398 (p0) REVERT: G 44 ASP cc_start: 0.7887 (m-30) cc_final: 0.7348 (p0) REVERT: G 73 ARG cc_start: 0.7085 (mtm180) cc_final: 0.6268 (mpp80) REVERT: G 75 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7012 (pm20) REVERT: G 122 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6226 (pm20) REVERT: G 215 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: G 216 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7809 (tmtm) REVERT: G 227 VAL cc_start: 0.8365 (t) cc_final: 0.8148 (p) REVERT: G 228 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7558 (pt) REVERT: H 276 ASP cc_start: 0.6599 (t70) cc_final: 0.6054 (m-30) outliers start: 113 outliers final: 54 residues processed: 375 average time/residue: 0.6502 time to fit residues: 277.8972 Evaluate side-chains 343 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 271 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 162 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 256 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 121 GLN ** E 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.171412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123585 restraints weight = 23344.606| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.77 r_work: 0.3308 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22705 Z= 0.193 Angle : 0.570 8.647 30931 Z= 0.301 Chirality : 0.044 0.196 3574 Planarity : 0.004 0.071 3703 Dihedral : 16.179 153.608 3483 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.35 % Allowed : 22.03 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2575 helix: 0.77 (0.15), residues: 1226 sheet: -0.16 (0.22), residues: 546 loop : -0.54 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 538 TYR 0.021 0.002 TYR E 135 PHE 0.021 0.002 PHE G 202 TRP 0.008 0.001 TRP A 463 HIS 0.009 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (22705) covalent geometry : angle 0.56980 / 0.30 (30931) hydrogen bonds : bond 0.04270 / 2.84 ( 1137) hydrogen bonds : angle 4.59032 / 3.29 ( 3212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 273 time to evaluate : 0.826 Fit side-chains REVERT: A 227 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: A 273 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7650 (mp) REVERT: A 298 GLN cc_start: 0.7547 (tp-100) cc_final: 0.7081 (mm-40) REVERT: C 38 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6616 (mtm180) REVERT: D 148 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7668 (p0) REVERT: D 175 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7813 (mmp80) REVERT: D 274 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.6941 (mptm) REVERT: D 353 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7521 (mp) REVERT: E 58 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7678 (tm-30) REVERT: E 69 LYS cc_start: 0.7418 (ptpt) cc_final: 0.6754 (ptmm) REVERT: E 208 ASN cc_start: 0.7646 (m-40) cc_final: 0.7414 (m-40) REVERT: E 230 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7511 (tt) REVERT: F 232 MET cc_start: 0.7332 (mpt) cc_final: 0.7056 (mpp) REVERT: F 280 GLU cc_start: 0.7112 (tt0) cc_final: 0.6386 (pt0) REVERT: F 427 GLU cc_start: 0.4423 (OUTLIER) cc_final: 0.4157 (tt0) REVERT: F 436 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6328 (tt0) REVERT: G 26 SER cc_start: 0.8085 (m) cc_final: 0.7284 (p) REVERT: G 42 ASP cc_start: 0.7959 (p0) cc_final: 0.7356 (p0) REVERT: G 44 ASP cc_start: 0.7888 (m-30) cc_final: 0.7367 (p0) REVERT: G 73 ARG cc_start: 0.7103 (mtm180) cc_final: 0.6279 (mpp80) REVERT: G 75 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: G 215 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: G 216 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7819 (tmtm) REVERT: G 227 VAL cc_start: 0.8358 (t) cc_final: 0.8144 (p) REVERT: H 276 ASP cc_start: 0.6676 (t70) cc_final: 0.6101 (m-30) outliers start: 103 outliers final: 58 residues processed: 352 average time/residue: 0.6782 time to fit residues: 271.4324 Evaluate side-chains 337 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 266 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 427 GLU Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 381 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 30 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 223 optimal weight: 0.0670 chunk 100 optimal weight: 0.7980 chunk 112 optimal weight: 0.2980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.174913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128523 restraints weight = 23142.289| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.68 r_work: 0.3342 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22705 Z= 0.113 Angle : 0.513 9.529 30931 Z= 0.273 Chirality : 0.041 0.169 3574 Planarity : 0.004 0.070 3703 Dihedral : 16.108 160.805 3482 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.08 % Allowed : 23.50 % Favored : 73.42 % 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: 0.46 (0.17), residues: 2575 helix: 1.08 (0.15), residues: 1219 sheet: -0.10 (0.22), residues: 544 loop : -0.42 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 67 TYR 0.020 0.001 TYR C 75 PHE 0.018 0.001 PHE H 353 TRP 0.009 0.001 TRP E 259 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (22705) covalent geometry : angle 0.51320 / 0.27 (30931) hydrogen bonds : bond 0.03548 / 2.35 ( 1137) hydrogen bonds : angle 4.39668 / 3.14 ( 3212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 279 time to evaluate : 0.861 Fit side-chains REVERT: A 203 GLN cc_start: 0.7217 (pt0) cc_final: 0.6656 (mm110) REVERT: A 227 GLU cc_start: 0.7790 (tt0) cc_final: 0.7236 (tp30) REVERT: A 273 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7753 (mp) REVERT: A 298 GLN cc_start: 0.7531 (tp-100) cc_final: 0.7070 (mm-40) REVERT: B 301 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: C 38 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6628 (mtm180) REVERT: C 42 ASP cc_start: 0.6769 (m-30) cc_final: 0.6485 (m-30) REVERT: D 148 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7663 (p0) REVERT: D 175 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7825 (mmp80) REVERT: E 58 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7660 (tm-30) REVERT: E 69 LYS cc_start: 0.7266 (ptpt) cc_final: 0.6691 (ptmm) REVERT: E 208 ASN cc_start: 0.7580 (m-40) cc_final: 0.7359 (m-40) REVERT: E 230 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7423 (tt) REVERT: F 232 MET cc_start: 0.7229 (mpt) cc_final: 0.6927 (mpp) REVERT: F 280 GLU cc_start: 0.7190 (tt0) cc_final: 0.6436 (pt0) REVERT: F 465 ILE cc_start: 0.7061 (mt) cc_final: 0.6760 (mp) REVERT: G 26 SER cc_start: 0.8051 (m) cc_final: 0.7241 (p) REVERT: G 42 ASP cc_start: 0.7920 (p0) cc_final: 0.7325 (p0) REVERT: G 44 ASP cc_start: 0.7836 (m-30) cc_final: 0.7347 (p0) REVERT: G 73 ARG cc_start: 0.7085 (mtm180) cc_final: 0.6477 (mpp80) REVERT: G 215 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: G 216 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7815 (tmtm) REVERT: G 227 VAL cc_start: 0.8305 (t) cc_final: 0.8081 (p) REVERT: H 276 ASP cc_start: 0.6665 (t70) cc_final: 0.6107 (m-30) outliers start: 73 outliers final: 41 residues processed: 338 average time/residue: 0.6828 time to fit residues: 262.8731 Evaluate side-chains 325 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 276 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 381 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 239 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 258 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 223 optimal weight: 0.3980 chunk 187 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 121 GLN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.172403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124472 restraints weight = 23374.691| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.74 r_work: 0.3315 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22705 Z= 0.171 Angle : 0.558 9.774 30931 Z= 0.293 Chirality : 0.043 0.173 3574 Planarity : 0.004 0.069 3703 Dihedral : 16.160 169.660 3479 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 3.00 % Allowed : 23.76 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2575 helix: 0.96 (0.15), residues: 1220 sheet: -0.09 (0.22), residues: 544 loop : -0.46 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 67 TYR 0.020 0.001 TYR E 135 PHE 0.015 0.002 PHE A 376 TRP 0.009 0.001 TRP A 463 HIS 0.008 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (22705) covalent geometry : angle 0.55836 / 0.29 (30931) hydrogen bonds : bond 0.04084 / 2.71 ( 1137) hydrogen bonds : angle 4.46727 / 3.20 ( 3212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 281 time to evaluate : 0.880 Fit side-chains REVERT: A 203 GLN cc_start: 0.7310 (pt0) cc_final: 0.6760 (mm110) REVERT: A 227 GLU cc_start: 0.7803 (tt0) cc_final: 0.7257 (tp30) REVERT: A 273 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7677 (mp) REVERT: A 298 GLN cc_start: 0.7583 (tp-100) cc_final: 0.7133 (mm-40) REVERT: A 461 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6162 (mm-30) REVERT: B 301 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.6980 (mt-10) REVERT: C 38 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6721 (mtm180) REVERT: C 334 GLU cc_start: 0.7466 (tt0) cc_final: 0.7213 (mt-10) REVERT: D 148 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7707 (p0) REVERT: D 175 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7834 (mmp80) REVERT: D 353 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7539 (mp) REVERT: E 58 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7739 (tm-30) REVERT: E 69 LYS cc_start: 0.7387 (ptpt) cc_final: 0.6738 (ptmm) REVERT: E 208 ASN cc_start: 0.7650 (m-40) cc_final: 0.7363 (m-40) REVERT: E 230 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7555 (tt) REVERT: F 232 MET cc_start: 0.7306 (mpt) cc_final: 0.6976 (mpp) REVERT: F 280 GLU cc_start: 0.7214 (tt0) cc_final: 0.6501 (pt0) REVERT: F 465 ILE cc_start: 0.7128 (mt) cc_final: 0.6820 (mp) REVERT: G 26 SER cc_start: 0.8080 (m) cc_final: 0.7290 (p) REVERT: G 42 ASP cc_start: 0.7983 (p0) cc_final: 0.7396 (p0) REVERT: G 44 ASP cc_start: 0.7875 (m-30) cc_final: 0.7379 (p0) REVERT: G 73 ARG cc_start: 0.7118 (mtm180) cc_final: 0.6462 (mpp80) REVERT: G 215 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: G 216 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7853 (tmtm) REVERT: G 227 VAL cc_start: 0.8339 (t) cc_final: 0.8117 (p) REVERT: H 55 ARG cc_start: 0.7828 (mtp180) cc_final: 0.7451 (mtp180) REVERT: H 276 ASP cc_start: 0.6695 (t70) cc_final: 0.6114 (m-30) REVERT: H 365 GLN cc_start: 0.7437 (mm-40) cc_final: 0.6599 (mp10) outliers start: 71 outliers final: 44 residues processed: 338 average time/residue: 0.6788 time to fit residues: 261.0816 Evaluate side-chains 321 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 314 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 381 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 161 optimal weight: 6.9990 chunk 243 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 8 optimal weight: 0.0370 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 411 ASN B 35 GLN B 146 GLN B 148 ASN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN E 19 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.174134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125982 restraints weight = 23332.798| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.74 r_work: 0.3337 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22705 Z= 0.118 Angle : 0.525 9.782 30931 Z= 0.278 Chirality : 0.042 0.171 3574 Planarity : 0.004 0.070 3703 Dihedral : 16.145 176.434 3479 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 2.45 % Allowed : 24.09 % Favored : 73.46 % 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: 0.51 (0.17), residues: 2575 helix: 1.11 (0.15), residues: 1220 sheet: -0.07 (0.22), residues: 540 loop : -0.39 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.022 0.001 TYR C 75 PHE 0.034 0.001 PHE G 202 TRP 0.010 0.001 TRP E 259 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (22705) covalent geometry : angle 0.52482 / 0.28 (30931) hydrogen bonds : bond 0.03652 / 2.42 ( 1137) hydrogen bonds : angle 4.38309 / 3.14 ( 3212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 271 time to evaluate : 0.974 Fit side-chains REVERT: A 203 GLN cc_start: 0.7248 (pt0) cc_final: 0.6715 (mm110) REVERT: A 227 GLU cc_start: 0.7728 (tt0) cc_final: 0.7169 (tp30) REVERT: A 273 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7722 (mp) REVERT: A 298 GLN cc_start: 0.7559 (tp-100) cc_final: 0.7113 (mm-40) REVERT: A 461 GLU cc_start: 0.6654 (mm-30) cc_final: 0.6166 (mm-30) REVERT: B 301 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: C 38 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6736 (mtm180) REVERT: C 332 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6376 (pt0) REVERT: C 334 GLU cc_start: 0.7427 (tt0) cc_final: 0.7173 (mt-10) REVERT: D 148 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7706 (p0) REVERT: D 175 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7866 (mmp80) REVERT: D 353 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7510 (mp) REVERT: E 69 LYS cc_start: 0.7371 (ptpt) cc_final: 0.6728 (ptmm) REVERT: E 144 ASN cc_start: 0.7976 (m110) cc_final: 0.7763 (m110) REVERT: E 208 ASN cc_start: 0.7616 (m-40) cc_final: 0.7389 (m-40) REVERT: E 230 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7505 (tt) REVERT: F 232 MET cc_start: 0.7275 (mpt) cc_final: 0.6946 (mpp) REVERT: F 280 GLU cc_start: 0.7206 (tt0) cc_final: 0.6536 (pt0) REVERT: F 465 ILE cc_start: 0.7078 (mt) cc_final: 0.6764 (mp) REVERT: G 26 SER cc_start: 0.8068 (m) cc_final: 0.7276 (p) REVERT: G 42 ASP cc_start: 0.7978 (p0) cc_final: 0.7400 (p0) REVERT: G 44 ASP cc_start: 0.7837 (m-30) cc_final: 0.7365 (p0) REVERT: G 73 ARG cc_start: 0.7109 (mtm180) cc_final: 0.6455 (mpp80) REVERT: G 146 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7064 (pp20) REVERT: G 215 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: G 216 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7869 (tmtm) REVERT: G 227 VAL cc_start: 0.8317 (t) cc_final: 0.8084 (p) REVERT: H 55 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7420 (mtp180) REVERT: H 276 ASP cc_start: 0.6684 (t70) cc_final: 0.6114 (m-30) REVERT: H 365 GLN cc_start: 0.7398 (mm-40) cc_final: 0.6615 (mp10) outliers start: 58 outliers final: 40 residues processed: 316 average time/residue: 0.6453 time to fit residues: 232.7875 Evaluate side-chains 318 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 381 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 224 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 219 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 194 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.175042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127266 restraints weight = 23288.231| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.74 r_work: 0.3353 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22705 Z= 0.112 Angle : 0.515 10.937 30931 Z= 0.273 Chirality : 0.041 0.166 3574 Planarity : 0.004 0.070 3703 Dihedral : 16.082 173.644 3477 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.41 % Allowed : 24.01 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2575 helix: 1.22 (0.15), residues: 1219 sheet: 0.04 (0.23), residues: 535 loop : -0.36 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.022 0.001 TYR C 75 PHE 0.022 0.001 PHE G 67 TRP 0.009 0.001 TRP E 259 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (22705) covalent geometry : angle 0.51535 / 0.27 (30931) hydrogen bonds : bond 0.03481 / 2.30 ( 1137) hydrogen bonds : angle 4.31125 / 3.08 ( 3212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8825.52 seconds wall clock time: 150 minutes 56.79 seconds (9056.79 seconds total)