Starting phenix.real_space_refine on Thu Mar 5 12:20:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fs5_29414/03_2026/8fs5_29414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fs5_29414/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fs5_29414/03_2026/8fs5_29414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fs5_29414/03_2026/8fs5_29414.map" model { file = "/net/cci-nas-00/data/ceres_data/8fs5_29414/03_2026/8fs5_29414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fs5_29414/03_2026/8fs5_29414.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.42, per 1000 atoms: 0.20 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: 1.66 Conformation dependent library (CDL) restraints added in 952.4 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: 2.70 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: 4.18 Time building geometry restraints manager: 2.29 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=" 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 bond pdb=" N LEU G 28 " pdb=" CA LEU G 28 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.27e-02 6.20e+03 7.24e+00 ... (remaining 22700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 30112 1.84 - 3.68: 707 3.68 - 5.52: 91 5.52 - 7.36: 16 7.36 - 9.20: 5 Bond angle restraints: 30931 Sorted by residual: angle pdb=" N GLU E 21 " pdb=" CA GLU E 21 " pdb=" C GLU E 21 " ideal model delta sigma weight residual 112.54 107.31 5.23 1.22e+00 6.72e-01 1.84e+01 angle pdb=" N GLU A 68 " pdb=" CA GLU A 68 " pdb=" C GLU A 68 " ideal model delta sigma weight residual 113.88 108.85 5.03 1.23e+00 6.61e-01 1.67e+01 angle pdb=" CA GLY G 303 " pdb=" C GLY G 303 " pdb=" O GLY G 303 " ideal model delta sigma weight residual 122.78 117.99 4.79 1.20e+00 6.94e-01 1.59e+01 angle pdb=" CA GLN A 65 " pdb=" C GLN A 65 " pdb=" O GLN A 65 " ideal model delta sigma weight residual 121.47 117.10 4.37 1.15e+00 7.56e-01 1.44e+01 angle pdb=" N TYR A 67 " pdb=" CA TYR A 67 " pdb=" C TYR A 67 " ideal model delta sigma weight residual 113.16 108.51 4.65 1.24e+00 6.50e-01 1.41e+01 ... (remaining 30926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 13003 35.10 - 70.20: 699 70.20 - 105.30: 22 105.30 - 140.40: 2 140.40 - 175.50: 1 Dihedral angle restraints: 13727 sinusoidal: 6045 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 13724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2781 0.046 - 0.092: 609 0.092 - 0.138: 174 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: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.440 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22705 Z= 0.192 Angle : 0.687 9.200 30931 Z= 0.432 Chirality : 0.042 0.229 3574 Planarity : 0.005 0.121 3703 Dihedral : 18.408 175.496 8719 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 covalent geometry : bond 0.00318 (22705) covalent geometry : angle 0.68684 (30931) hydrogen bonds : bond 0.18282 ( 1137) hydrogen bonds : angle 7.06931 ( 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 : 0.870 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: 0.6612 time to fit residues: 243.5337 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 : 0.792 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: 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 14 ASN H 100 HIS H 151 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.175499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.127729 restraints weight = 23481.938| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.75 r_work: 0.3357 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22705 Z= 0.167 Angle : 0.561 7.730 30931 Z= 0.298 Chirality : 0.043 0.171 3574 Planarity : 0.005 0.078 3703 Dihedral : 16.173 145.156 3550 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.97 % Allowed : 20.72 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2575 helix: 0.53 (0.15), residues: 1218 sheet: -0.22 (0.22), residues: 553 loop : -0.56 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 165 TYR 0.020 0.001 TYR E 135 PHE 0.014 0.002 PHE G 154 TRP 0.011 0.001 TRP A 463 HIS 0.008 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00392 (22705) covalent geometry : angle 0.56083 (30931) hydrogen bonds : bond 0.04538 ( 1137) hydrogen bonds : angle 5.01504 ( 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 380 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 286 time to evaluate : 0.800 Fit side-chains REVERT: A 68 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: A 131 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7469 (ttm-80) REVERT: A 273 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7678 (mp) REVERT: D 175 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7573 (mmp80) REVERT: E 19 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.7119 (t0) REVERT: E 69 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6813 (ptmm) REVERT: E 230 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7695 (tt) REVERT: F 280 GLU cc_start: 0.7181 (tt0) cc_final: 0.6408 (pt0) REVERT: G 95 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.7426 (p) REVERT: G 146 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7009 (pp20) REVERT: G 215 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: G 216 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7718 (tmtm) REVERT: G 258 ARG cc_start: 0.8557 (mtm180) cc_final: 0.8299 (mtp180) REVERT: G 323 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.5574 (tm-30) REVERT: H 276 ASP cc_start: 0.6686 (t70) cc_final: 0.6313 (m-30) REVERT: H 363 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: H 365 GLN cc_start: 0.7359 (mm-40) cc_final: 0.6559 (mp-120) outliers start: 94 outliers final: 38 residues processed: 360 average time/residue: 0.6493 time to fit residues: 265.0980 Evaluate side-chains 323 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 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 175 ARG Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 94 LEU 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 253 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 95 VAL 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 252 VAL Chi-restraints excluded: chain H residue 256 ILE 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: 2.9990 chunk 98 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 162 GLN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 224 GLN G 218 GLN 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 = 0.3993 r_free = 0.3993 target = 0.174600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126702 restraints weight = 23421.630| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.74 r_work: 0.3340 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1558 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= 0.145 Angle : 0.522 7.329 30931 Z= 0.278 Chirality : 0.042 0.156 3574 Planarity : 0.004 0.075 3703 Dihedral : 16.051 130.976 3534 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.47 % Allowed : 20.46 % Favored : 75.06 % 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: 1223 sheet: -0.16 (0.22), residues: 545 loop : -0.54 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 67 TYR 0.019 0.001 TYR E 135 PHE 0.013 0.001 PHE E 328 TRP 0.008 0.001 TRP A 463 HIS 0.010 0.001 HIS H 89 Details of bonding type rmsd covalent geometry : bond 0.00339 (22705) covalent geometry : angle 0.52172 (30931) hydrogen bonds : bond 0.04141 ( 1137) hydrogen bonds : angle 4.69994 ( 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 391 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 285 time to evaluate : 0.832 Fit side-chains REVERT: A 68 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: A 131 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.7429 (ttm-80) REVERT: A 273 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7738 (mp) REVERT: D 148 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7720 (p0) REVERT: D 175 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7833 (mmp80) REVERT: E 19 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.7166 (t0) REVERT: E 69 LYS cc_start: 0.7340 (ptpt) cc_final: 0.6792 (ptmm) REVERT: E 230 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7697 (tt) REVERT: E 311 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: F 280 GLU cc_start: 0.7134 (tt0) cc_final: 0.6353 (pt0) REVERT: G 35 ASP cc_start: 0.6895 (t0) cc_final: 0.6694 (t0) REVERT: G 95 VAL cc_start: 0.7730 (OUTLIER) cc_final: 0.7426 (p) REVERT: G 215 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: G 216 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7414 (pptt) REVERT: G 258 ARG cc_start: 0.8570 (mtm180) cc_final: 0.8285 (mtp180) REVERT: H 276 ASP cc_start: 0.6676 (t70) cc_final: 0.6254 (m-30) outliers start: 106 outliers final: 40 residues processed: 369 average time/residue: 0.6497 time to fit residues: 271.0082 Evaluate side-chains 315 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 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 471 TYR 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 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 148 ASP 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 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 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 95 VAL 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 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 136 VAL Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 252 VAL 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: 9.9990 chunk 109 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 190 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.175332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127403 restraints weight = 23378.932| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.75 r_work: 0.3349 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22705 Z= 0.118 Angle : 0.497 7.142 30931 Z= 0.264 Chirality : 0.041 0.157 3574 Planarity : 0.004 0.073 3703 Dihedral : 15.964 135.404 3531 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.71 % Allowed : 21.73 % 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: 0.37 (0.17), residues: 2575 helix: 0.97 (0.15), residues: 1216 sheet: -0.09 (0.22), residues: 546 loop : -0.44 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 67 TYR 0.014 0.001 TYR E 135 PHE 0.013 0.001 PHE H 353 TRP 0.006 0.001 TRP A 463 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00267 (22705) covalent geometry : angle 0.49661 (30931) hydrogen bonds : bond 0.03617 ( 1137) hydrogen bonds : angle 4.50093 ( 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 370 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 282 time to evaluate : 0.847 Fit side-chains REVERT: A 68 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: A 131 ARG cc_start: 0.7703 (ttm-80) cc_final: 0.7387 (ttm-80) REVERT: A 227 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7073 (tp30) REVERT: A 273 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 457 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7426 (mptm) REVERT: C 38 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6557 (mtm180) REVERT: D 148 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7679 (p0) REVERT: D 175 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7854 (mmp80) REVERT: D 274 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.6947 (mptm) REVERT: E 69 LYS cc_start: 0.7279 (ptpt) cc_final: 0.6749 (ptmm) REVERT: E 208 ASN cc_start: 0.7532 (m-40) cc_final: 0.7322 (m-40) REVERT: E 230 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7694 (tt) REVERT: E 311 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: F 280 GLU cc_start: 0.7130 (tt0) cc_final: 0.6345 (pt0) REVERT: F 465 ILE cc_start: 0.6977 (mt) cc_final: 0.6684 (mp) REVERT: G 26 SER cc_start: 0.7714 (m) cc_final: 0.6886 (p) REVERT: G 35 ASP cc_start: 0.6890 (t0) cc_final: 0.6677 (t0) REVERT: G 95 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7521 (p) REVERT: G 215 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: G 216 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7426 (pptt) REVERT: G 258 ARG cc_start: 0.8574 (mtm180) cc_final: 0.8364 (mtp-110) REVERT: H 276 ASP cc_start: 0.6710 (t70) cc_final: 0.6290 (m-30) outliers start: 88 outliers final: 43 residues processed: 352 average time/residue: 0.6750 time to fit residues: 269.1041 Evaluate side-chains 326 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 270 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 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 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 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 E residue 94 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 311 GLU 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 95 VAL 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 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 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 99 optimal weight: 0.6980 chunk 260 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 230 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 224 GLN ** E 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3944 r_free = 0.3944 target = 0.170086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121900 restraints weight = 23390.406| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.73 r_work: 0.3276 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22705 Z= 0.240 Angle : 0.610 7.608 30931 Z= 0.319 Chirality : 0.046 0.163 3574 Planarity : 0.005 0.070 3703 Dihedral : 16.238 147.063 3528 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.73 % Allowed : 21.18 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2575 helix: 0.68 (0.15), residues: 1212 sheet: -0.20 (0.22), residues: 545 loop : -0.59 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 67 TYR 0.029 0.002 TYR E 135 PHE 0.018 0.002 PHE A 376 TRP 0.011 0.002 TRP A 463 HIS 0.011 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00583 (22705) covalent geometry : angle 0.60958 (30931) hydrogen bonds : bond 0.04722 ( 1137) hydrogen bonds : angle 4.72673 ( 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 397 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 285 time to evaluate : 0.789 Fit side-chains REVERT: A 227 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7057 (tp30) REVERT: C 38 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6478 (mtm180) REVERT: D 148 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7703 (p0) REVERT: D 175 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7885 (mmp80) REVERT: D 274 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.6988 (mptm) REVERT: D 353 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7579 (mp) REVERT: E 69 LYS cc_start: 0.7438 (ptpt) cc_final: 0.6804 (ptmm) REVERT: E 113 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7919 (tt) REVERT: E 208 ASN cc_start: 0.7712 (m-40) cc_final: 0.7490 (m-40) REVERT: E 230 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7805 (tt) REVERT: F 280 GLU cc_start: 0.7141 (tt0) cc_final: 0.6433 (pt0) REVERT: F 436 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6454 (tt0) REVERT: G 95 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7577 (p) REVERT: G 215 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: G 216 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7802 (tmtm) REVERT: G 258 ARG cc_start: 0.8618 (mtm180) cc_final: 0.8382 (mtp180) REVERT: H 55 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7393 (mtp180) REVERT: H 158 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.6272 (m-30) REVERT: H 353 PHE cc_start: 0.7365 (p90) cc_final: 0.7000 (p90) outliers start: 112 outliers final: 54 residues processed: 370 average time/residue: 0.6600 time to fit residues: 277.0926 Evaluate side-chains 342 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 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 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 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 C residue 38 ARG 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 148 ASP Chi-restraints excluded: chain D residue 163 VAL 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 6 ASP 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 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 436 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 95 VAL 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 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 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 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: 3.9990 chunk 128 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 209 optimal weight: 0.2980 chunk 245 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN ** E 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.171580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.123715 restraints weight = 23327.227| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.71 r_work: 0.3302 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22705 Z= 0.184 Angle : 0.558 7.426 30931 Z= 0.294 Chirality : 0.043 0.159 3574 Planarity : 0.004 0.072 3703 Dihedral : 16.232 164.905 3526 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.43 % Allowed : 21.86 % Favored : 73.71 % 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: 0.77 (0.15), residues: 1212 sheet: -0.18 (0.22), residues: 543 loop : -0.55 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.020 0.002 TYR E 135 PHE 0.014 0.002 PHE E 328 TRP 0.008 0.001 TRP E 259 HIS 0.009 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00443 (22705) covalent geometry : angle 0.55833 (30931) hydrogen bonds : bond 0.04130 ( 1137) hydrogen bonds : angle 4.59622 ( 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 383 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 278 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.6151 (pm20) REVERT: A 227 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6977 (tp30) REVERT: A 273 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7656 (mp) REVERT: A 298 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7154 (mm-40) REVERT: C 38 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6502 (mtm180) REVERT: C 334 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: D 148 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7697 (p0) REVERT: D 175 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7920 (mmp80) REVERT: D 274 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.6996 (mptm) REVERT: D 353 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7535 (mp) REVERT: E 69 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6780 (ptmm) REVERT: E 208 ASN cc_start: 0.7715 (m-40) cc_final: 0.7506 (m-40) REVERT: E 230 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7737 (tt) REVERT: F 280 GLU cc_start: 0.7202 (tt0) cc_final: 0.6496 (pt0) REVERT: F 427 GLU cc_start: 0.4451 (OUTLIER) cc_final: 0.4148 (tt0) REVERT: G 26 SER cc_start: 0.8129 (m) cc_final: 0.7346 (p) REVERT: G 73 ARG cc_start: 0.7127 (mtm180) cc_final: 0.6469 (mpp80) REVERT: G 215 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: G 216 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7849 (tmtm) REVERT: H 55 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7432 (mtp180) REVERT: H 276 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6654 (m-30) outliers start: 105 outliers final: 56 residues processed: 356 average time/residue: 0.6468 time to fit residues: 260.7098 Evaluate side-chains 338 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 266 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 298 GLN 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 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 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 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 6 ASP Chi-restraints excluded: chain E residue 69 LYS 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 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 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 224 MET Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 427 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 95 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 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 276 ASP Chi-restraints excluded: chain H residue 333 ILE Chi-restraints excluded: chain H residue 381 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 162 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 231 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 256 optimal weight: 30.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127379 restraints weight = 23297.657| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.67 r_work: 0.3325 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2190 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= 0.124 Angle : 0.519 9.896 30931 Z= 0.274 Chirality : 0.041 0.155 3574 Planarity : 0.004 0.071 3703 Dihedral : 16.163 179.000 3524 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.01 % Allowed : 22.41 % 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: 0.38 (0.17), residues: 2575 helix: 1.01 (0.15), residues: 1217 sheet: -0.12 (0.22), residues: 542 loop : -0.45 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 34 TYR 0.022 0.001 TYR C 75 PHE 0.026 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 covalent geometry : bond 0.00285 (22705) covalent geometry : angle 0.51853 (30931) hydrogen bonds : bond 0.03612 ( 1137) hydrogen bonds : angle 4.43510 ( 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 377 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 282 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6361 (mp0) REVERT: A 203 GLN cc_start: 0.7256 (pt0) cc_final: 0.6694 (mm110) REVERT: A 227 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6943 (tp30) REVERT: A 273 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7699 (mp) REVERT: C 38 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6401 (mtm180) REVERT: C 78 MET cc_start: 0.8510 (mmp) cc_final: 0.8174 (tpt) REVERT: C 332 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6328 (pt0) REVERT: C 334 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: D 148 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7683 (p0) REVERT: D 175 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7855 (mmp80) REVERT: D 274 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.6960 (mptm) REVERT: E 69 LYS cc_start: 0.7322 (ptpt) cc_final: 0.6681 (ptmm) REVERT: E 144 ASN cc_start: 0.7967 (m110) cc_final: 0.7752 (m110) REVERT: E 208 ASN cc_start: 0.7639 (m-40) cc_final: 0.7437 (m-40) REVERT: E 230 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7679 (tt) REVERT: F 280 GLU cc_start: 0.7226 (tt0) cc_final: 0.6577 (pt0) REVERT: F 427 GLU cc_start: 0.4273 (OUTLIER) cc_final: 0.4004 (tt0) REVERT: F 465 ILE cc_start: 0.7069 (mt) cc_final: 0.6764 (mp) REVERT: G 26 SER cc_start: 0.8060 (m) cc_final: 0.7285 (p) REVERT: G 42 ASP cc_start: 0.8007 (p0) cc_final: 0.7497 (p0) REVERT: G 44 ASP cc_start: 0.7853 (m-30) cc_final: 0.7375 (p0) REVERT: G 73 ARG cc_start: 0.7078 (mtm180) cc_final: 0.6415 (mpp80) REVERT: G 215 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: G 216 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7903 (tmtm) REVERT: H 55 ARG cc_start: 0.7827 (mtp180) cc_final: 0.7429 (mtp180) REVERT: H 276 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6642 (m-30) REVERT: H 365 GLN cc_start: 0.7467 (mm-40) cc_final: 0.6587 (mp10) outliers start: 95 outliers final: 56 residues processed: 353 average time/residue: 0.6560 time to fit residues: 262.4926 Evaluate side-chains 335 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 266 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 164 GLU 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 403 CYS 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 27 LYS 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 C residue 38 ARG 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 E residue 6 ASP 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 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 224 MET Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 427 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 95 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 H residue 35 THR Chi-restraints excluded: chain H residue 43 SER 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 276 ASP 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: 0.9990 chunk 173 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 228 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 112 optimal weight: 0.0070 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 19 ASN H 122 ASN H 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127963 restraints weight = 23160.123| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.66 r_work: 0.3335 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2231 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= 0.123 Angle : 0.517 9.480 30931 Z= 0.273 Chirality : 0.041 0.155 3574 Planarity : 0.004 0.070 3703 Dihedral : 16.030 162.097 3524 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.54 % Allowed : 23.00 % 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: 0.54 (0.17), residues: 2575 helix: 1.14 (0.15), residues: 1217 sheet: -0.04 (0.22), residues: 537 loop : -0.39 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.021 0.001 TYR B 186 PHE 0.013 0.001 PHE G 40 TRP 0.009 0.001 TRP E 259 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00284 (22705) covalent geometry : angle 0.51714 (30931) hydrogen bonds : bond 0.03523 ( 1137) hydrogen bonds : angle 4.35171 ( 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 366 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 282 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: A 131 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7333 (ttm-80) REVERT: A 203 GLN cc_start: 0.7258 (pt0) cc_final: 0.6736 (mm110) REVERT: A 227 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: A 273 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7725 (mp) REVERT: A 286 LYS cc_start: 0.7993 (tptt) cc_final: 0.7047 (tptt) REVERT: A 298 GLN cc_start: 0.7581 (tp40) cc_final: 0.7058 (mm-40) REVERT: A 461 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6178 (mm-30) REVERT: B 301 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7384 (mt-10) REVERT: C 38 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6607 (mtm180) REVERT: C 332 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6379 (pt0) REVERT: C 334 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: D 148 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7729 (p0) REVERT: D 175 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.7851 (mmp80) REVERT: D 274 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.6984 (mptm) REVERT: E 69 LYS cc_start: 0.7388 (ptpt) cc_final: 0.6750 (ptmm) REVERT: E 144 ASN cc_start: 0.7900 (m110) cc_final: 0.7671 (m110) REVERT: E 208 ASN cc_start: 0.7658 (m-40) cc_final: 0.7453 (m-40) REVERT: E 230 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7743 (tt) REVERT: F 280 GLU cc_start: 0.7155 (tt0) cc_final: 0.6493 (pt0) REVERT: F 427 GLU cc_start: 0.4226 (OUTLIER) cc_final: 0.3946 (tt0) REVERT: F 465 ILE cc_start: 0.7117 (mt) cc_final: 0.6807 (mp) REVERT: G 26 SER cc_start: 0.7997 (m) cc_final: 0.7222 (p) REVERT: G 42 ASP cc_start: 0.7936 (p0) cc_final: 0.7291 (p0) REVERT: G 44 ASP cc_start: 0.7829 (m-30) cc_final: 0.7372 (p0) REVERT: G 73 ARG cc_start: 0.7105 (mtm180) cc_final: 0.6760 (mpp80) REVERT: G 215 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: G 216 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7924 (tmtm) REVERT: H 55 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7470 (mtp180) REVERT: H 276 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6651 (m-30) REVERT: H 365 GLN cc_start: 0.7410 (mm-40) cc_final: 0.6629 (mp10) outliers start: 84 outliers final: 52 residues processed: 347 average time/residue: 0.6482 time to fit residues: 255.3646 Evaluate side-chains 331 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 266 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU 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 403 CYS 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 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 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 E residue 6 ASP 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 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 224 MET Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 427 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 95 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 H residue 35 THR Chi-restraints excluded: chain H residue 43 SER 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 136 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 276 ASP 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: 0.9990 chunk 156 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 250 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** D 24 GLN E 19 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.172542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124576 restraints weight = 23294.771| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.77 r_work: 0.3316 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2328 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= 0.166 Angle : 0.554 10.519 30931 Z= 0.291 Chirality : 0.043 0.152 3574 Planarity : 0.004 0.070 3703 Dihedral : 16.019 147.520 3522 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.46 % Allowed : 23.21 % Favored : 73.33 % 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: 0.43 (0.17), residues: 2575 helix: 1.01 (0.15), residues: 1217 sheet: -0.02 (0.22), residues: 538 loop : -0.43 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 67 TYR 0.021 0.002 TYR B 186 PHE 0.016 0.002 PHE H 353 TRP 0.008 0.001 TRP E 259 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00397 (22705) covalent geometry : angle 0.55427 (30931) hydrogen bonds : bond 0.03911 ( 1137) hydrogen bonds : angle 4.41901 ( 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 355 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 273 time to evaluate : 0.698 Fit side-chains REVERT: A 131 ARG cc_start: 0.7653 (ttm-80) cc_final: 0.7319 (ttm-80) REVERT: A 203 GLN cc_start: 0.7319 (pt0) cc_final: 0.6777 (mm110) REVERT: A 227 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6793 (tp30) REVERT: A 273 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7627 (mp) REVERT: A 290 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7074 (pt0) REVERT: A 293 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6009 (ptmt) REVERT: A 298 GLN cc_start: 0.7664 (tp40) cc_final: 0.7064 (mm-40) REVERT: A 461 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6249 (mm-30) REVERT: B 301 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7369 (mt-10) REVERT: C 38 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6741 (mtm180) REVERT: C 78 MET cc_start: 0.8539 (mmp) cc_final: 0.8183 (tpt) REVERT: C 332 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6387 (pt0) REVERT: D 148 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7699 (p0) REVERT: D 175 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7834 (mmp80) REVERT: D 274 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.6955 (mptm) REVERT: E 208 ASN cc_start: 0.7706 (m-40) cc_final: 0.7494 (m-40) REVERT: E 230 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7750 (tt) REVERT: F 40 GLU cc_start: 0.4386 (pp20) cc_final: 0.3390 (tp30) REVERT: F 280 GLU cc_start: 0.7128 (tt0) cc_final: 0.6506 (pt0) REVERT: F 427 GLU cc_start: 0.4300 (OUTLIER) cc_final: 0.3996 (tt0) REVERT: F 465 ILE cc_start: 0.7104 (mt) cc_final: 0.6787 (mp) REVERT: G 26 SER cc_start: 0.7899 (m) cc_final: 0.7139 (p) REVERT: G 42 ASP cc_start: 0.7949 (p0) cc_final: 0.7301 (p0) REVERT: G 44 ASP cc_start: 0.7829 (m-30) cc_final: 0.7366 (p0) REVERT: G 73 ARG cc_start: 0.7109 (mtm180) cc_final: 0.6457 (mpp80) REVERT: G 215 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: G 216 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7906 (tmtm) REVERT: H 55 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7443 (mtp180) REVERT: H 365 GLN cc_start: 0.7406 (mm-40) cc_final: 0.6621 (mp10) outliers start: 82 outliers final: 57 residues processed: 335 average time/residue: 0.6600 time to fit residues: 250.0413 Evaluate side-chains 338 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 270 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU 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 403 CYS 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 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 297 MET 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 274 LYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 6 ASP 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 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 G residue 37 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 95 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 43 SER 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 136 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 161 optimal weight: 1.9990 chunk 243 optimal weight: 0.0970 chunk 175 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 8 optimal weight: 0.0870 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 35 GLN B 146 GLN B 148 ASN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN G 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.174059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127721 restraints weight = 23314.496| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.66 r_work: 0.3332 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22705 Z= 0.126 Angle : 0.531 10.295 30931 Z= 0.279 Chirality : 0.041 0.191 3574 Planarity : 0.004 0.071 3703 Dihedral : 15.930 137.445 3522 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 3.04 % Allowed : 23.67 % Favored : 73.29 % 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: 0.57 (0.17), residues: 2575 helix: 1.15 (0.15), residues: 1217 sheet: 0.04 (0.22), residues: 537 loop : -0.37 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 67 TYR 0.021 0.001 TYR B 186 PHE 0.013 0.001 PHE G 202 TRP 0.012 0.001 TRP A 463 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00293 (22705) covalent geometry : angle 0.53059 (30931) hydrogen bonds : bond 0.03534 ( 1137) hydrogen bonds : angle 4.33307 ( 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 353 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 281 time to evaluate : 0.794 Fit side-chains REVERT: A 64 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.6035 (pm20) REVERT: A 131 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7301 (ttm-80) REVERT: A 203 GLN cc_start: 0.7246 (pt0) cc_final: 0.6663 (mm110) REVERT: A 227 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6741 (tp30) REVERT: A 273 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7628 (mp) REVERT: A 293 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.5811 (ptmt) REVERT: A 298 GLN cc_start: 0.7565 (tp40) cc_final: 0.7034 (mm-40) REVERT: A 372 SER cc_start: 0.8396 (m) cc_final: 0.8052 (p) REVERT: A 461 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6231 (mm-30) REVERT: B 301 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7376 (mt-10) REVERT: C 38 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6576 (mtm180) REVERT: C 78 MET cc_start: 0.8502 (mmp) cc_final: 0.8164 (tpt) REVERT: C 332 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6344 (pt0) REVERT: D 148 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7667 (p0) REVERT: D 175 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7821 (mmp80) REVERT: D 273 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7344 (mt-10) REVERT: D 274 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.6911 (mptm) REVERT: E 144 ASN cc_start: 0.7887 (m110) cc_final: 0.7672 (m110) REVERT: E 208 ASN cc_start: 0.7647 (m-40) cc_final: 0.7441 (m-40) REVERT: E 230 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7674 (tt) REVERT: F 40 GLU cc_start: 0.4438 (pp20) cc_final: 0.3451 (tp30) REVERT: F 52 LEU cc_start: 0.6951 (mm) cc_final: 0.6732 (mp) REVERT: F 280 GLU cc_start: 0.7106 (tt0) cc_final: 0.6478 (pt0) REVERT: F 427 GLU cc_start: 0.4188 (OUTLIER) cc_final: 0.3882 (tt0) REVERT: F 465 ILE cc_start: 0.6936 (mt) cc_final: 0.6617 (mp) REVERT: G 26 SER cc_start: 0.7830 (m) cc_final: 0.7068 (p) REVERT: G 215 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: G 216 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7880 (tmtm) REVERT: H 55 ARG cc_start: 0.7838 (mtp180) cc_final: 0.7424 (mtp180) REVERT: H 365 GLN cc_start: 0.7354 (mm-40) cc_final: 0.6598 (mp10) outliers start: 72 outliers final: 51 residues processed: 338 average time/residue: 0.6550 time to fit residues: 251.1302 Evaluate side-chains 341 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 278 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 403 CYS 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 133 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 146 GLN 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 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 274 LYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 6 ASP 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 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 G residue 37 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 95 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 H residue 35 THR Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 50 THR 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 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 224 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 35 GLN B 146 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.174038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126233 restraints weight = 23228.384| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.73 r_work: 0.3337 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 22705 Z= 0.180 Angle : 0.754 59.144 30931 Z= 0.419 Chirality : 0.042 0.482 3574 Planarity : 0.004 0.070 3703 Dihedral : 15.917 137.397 3519 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 3.08 % Allowed : 23.63 % Favored : 73.29 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.17), residues: 2575 helix: 1.15 (0.15), residues: 1217 sheet: 0.04 (0.22), residues: 537 loop : -0.37 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 67 TYR 0.019 0.001 TYR B 186 PHE 0.021 0.001 PHE G 202 TRP 0.009 0.001 TRP A 463 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00383 (22705) covalent geometry : angle 0.75430 (30931) hydrogen bonds : bond 0.03538 ( 1137) hydrogen bonds : angle 4.33338 ( 3212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8581.57 seconds wall clock time: 146 minutes 28.06 seconds (8788.06 seconds total)