Starting phenix.real_space_refine on Thu Mar 5 14:45:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjv_25933/03_2026/7tjv_25933.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjv_25933/03_2026/7tjv_25933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tjv_25933/03_2026/7tjv_25933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjv_25933/03_2026/7tjv_25933.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjv_25933/03_2026/7tjv_25933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjv_25933/03_2026/7tjv_25933.cif" } resolution = 3.6 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= 0.037 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 14 5.49 5 Mg 5 5.21 5 S 35 5.16 5 C 14649 2.51 5 N 4084 2.21 5 O 4383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s 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: 23170 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3585 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 459} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 3584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3584 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 456} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 3577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3577 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 85 Chain: "D" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3468 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 443} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "E" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3389 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 16, 'GLN:plan1': 4, 'ASP:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 106 Chain: "F" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3488 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "G" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1923 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 3, 'ASP:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.97, per 1000 atoms: 0.21 Number of scatterers: 23170 At special positions: 0 Unit cell: (125.317, 128.012, 156.31, 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 35 16.00 P 14 15.00 Mg 5 11.99 O 4383 8.00 N 4084 7.00 C 14649 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: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5650 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 17 sheets defined 51.0% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.546A pdb=" N LEU A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.929A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.717A pdb=" N VAL A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 229 removed outlier: 3.582A pdb=" N LYS A 229 " --> pdb=" O ASP A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 241 through 262 Proline residue: A 249 - end of helix removed outlier: 3.844A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.568A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 298 No H-bonds generated for 'chain 'A' and resid 297 through 298' Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 382 through 403 removed outlier: 4.086A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 412 removed outlier: 4.290A pdb=" N GLN A 407 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N SER A 410 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.560A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.981A pdb=" N GLY A 457 " --> pdb=" O HIS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 478 removed outlier: 4.486A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 489 removed outlier: 3.660A pdb=" N GLU A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 4.046A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 removed outlier: 3.663A pdb=" N ASN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 241 through 262 Proline residue: B 249 - end of helix removed outlier: 3.609A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 297 through 298 No H-bonds generated for 'chain 'B' and resid 297 through 298' Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.688A pdb=" N HIS B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 391 through 404 removed outlier: 3.611A pdb=" N ALA B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 Processing helix chain 'B' and resid 439 through 452 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 477 removed outlier: 3.650A pdb=" N SER B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'B' and resid 492 through 508 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.748A pdb=" N LEU C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.820A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 187 Processing helix chain 'C' and resid 188 through 193 removed outlier: 3.783A pdb=" N ASN C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 removed outlier: 3.654A pdb=" N VAL C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.706A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.633A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 297 through 298 No H-bonds generated for 'chain 'C' and resid 297 through 298' Processing helix chain 'C' and resid 299 through 309 removed outlier: 3.716A pdb=" N HIS C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 331 through 335 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.575A pdb=" N TYR C 360 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 removed outlier: 4.098A pdb=" N ALA C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 391 through 408 removed outlier: 3.602A pdb=" N GLU C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 4.012A pdb=" N LYS C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 453 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 478 removed outlier: 3.742A pdb=" N LEU C 471 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 488 removed outlier: 3.646A pdb=" N LEU C 482 " --> pdb=" O HIS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 508 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 246 removed outlier: 4.937A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 272 removed outlier: 3.560A pdb=" N ALA D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 319 through 326 Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 392 removed outlier: 4.575A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 Processing helix chain 'D' and resid 397 through 414 Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 447 removed outlier: 3.519A pdb=" N ALA D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 462 through 475 removed outlier: 4.003A pdb=" N ALA D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 178 removed outlier: 3.811A pdb=" N ALA E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 225 through 248 removed outlier: 5.141A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 284 through 294 removed outlier: 3.797A pdb=" N LEU E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 327 Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 392 removed outlier: 4.014A pdb=" N VAL E 370 " --> pdb=" O GLU E 366 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 396 Processing helix chain 'E' and resid 397 through 414 removed outlier: 4.180A pdb=" N ARG E 406 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 removed outlier: 3.605A pdb=" N PHE E 441 " --> pdb=" O THR E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 457 Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 178 removed outlier: 5.043A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 246 removed outlier: 4.896A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 removed outlier: 3.766A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 282 through 283 No H-bonds generated for 'chain 'F' and resid 282 through 283' Processing helix chain 'F' and resid 284 through 294 Processing helix chain 'F' and resid 295 through 297 No H-bonds generated for 'chain 'F' and resid 295 through 297' Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 326 Processing helix chain 'F' and resid 327 through 329 No H-bonds generated for 'chain 'F' and resid 327 through 329' Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 364 through 384 Processing helix chain 'F' and resid 384 through 392 Processing helix chain 'F' and resid 393 through 396 Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 474 Processing helix chain 'G' and resid 2 through 49 removed outlier: 3.791A pdb=" N ARG G 9 " --> pdb=" O GLU G 5 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 56 removed outlier: 3.571A pdb=" N ASN G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 102 removed outlier: 3.858A pdb=" N LEU G 91 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA G 92 " --> pdb=" O HIS G 88 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 119 removed outlier: 3.917A pdb=" N LYS G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 136 removed outlier: 4.234A pdb=" N LYS G 135 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP G 136 " --> pdb=" O ILE G 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 132 through 136' Processing helix chain 'G' and resid 139 through 154 Processing helix chain 'G' and resid 155 through 159 Processing helix chain 'G' and resid 184 through 191 removed outlier: 3.521A pdb=" N ILE G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 275 removed outlier: 4.013A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP G 269 " --> pdb=" O ASN G 265 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE G 270 " --> pdb=" O GLU G 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.936A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 40 through 45 current: chain 'A' and resid 62 through 68 removed outlier: 6.677A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 73 through 77 current: chain 'C' and resid 40 through 45 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 40 through 45 current: chain 'C' and resid 62 through 69 removed outlier: 5.554A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 72 through 77 current: chain 'D' and resid 20 through 24 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 20 through 24 current: chain 'D' and resid 46 through 55 removed outlier: 6.671A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 58 through 63 current: chain 'E' and resid 20 through 24 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 20 through 24 current: chain 'E' and resid 46 through 53 removed outlier: 6.594A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.568A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 331 removed outlier: 8.105A pdb=" N ILE A 329 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 169 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR A 331 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY A 171 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU A 354 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 170 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 69 removed outlier: 4.167A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA F 36 " --> pdb=" O THR F 79 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN F 35 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 111 removed outlier: 6.513A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 111 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 108 through 111 current: chain 'C' and resid 231 through 236 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 231 through 236 current: chain 'C' and resid 322 through 329 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 84 through 87 removed outlier: 4.908A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.698A pdb=" N SER D 182 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL D 218 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE D 184 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLY D 220 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY D 186 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA D 331 " --> pdb=" O LYS D 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.539A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.618A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS E 152 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N THR E 333 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY E 154 " --> pdb=" O THR E 333 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.649A pdb=" N VAL F 87 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 95 through 96 removed outlier: 3.533A pdb=" N PHE F 219 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 129 through 130 removed outlier: 8.502A pdb=" N ILE G 130 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR G 109 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE G 164 " --> pdb=" O LYS G 180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS G 180 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) 1129 hydrogen bonds defined for protein. 3162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4617 1.33 - 1.45: 5008 1.45 - 1.57: 13812 1.57 - 1.69: 24 1.69 - 1.81: 66 Bond restraints: 23527 Sorted by residual: bond pdb=" N PRO C 297 " pdb=" CD PRO C 297 " ideal model delta sigma weight residual 1.473 1.435 0.038 1.40e-02 5.10e+03 7.28e+00 bond pdb=" CZ ARG C 306 " pdb=" NH2 ARG C 306 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.23e+00 bond pdb=" C LEU A 308 " pdb=" O LEU A 308 " ideal model delta sigma weight residual 1.237 1.208 0.028 1.19e-02 7.06e+03 5.71e+00 bond pdb=" CZ ARG A 306 " pdb=" NH2 ARG A 306 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.30e-02 5.92e+03 5.42e+00 bond pdb=" N PRO A 297 " pdb=" CD PRO A 297 " ideal model delta sigma weight residual 1.473 1.443 0.030 1.40e-02 5.10e+03 4.63e+00 ... (remaining 23522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 30528 1.38 - 2.77: 1122 2.77 - 4.15: 244 4.15 - 5.53: 40 5.53 - 6.91: 25 Bond angle restraints: 31959 Sorted by residual: angle pdb=" CA ASP A 299 " pdb=" C ASP A 299 " pdb=" N VAL A 300 " ideal model delta sigma weight residual 116.84 123.47 -6.63 1.71e+00 3.42e-01 1.51e+01 angle pdb=" CB HIS C 304 " pdb=" CG HIS C 304 " pdb=" CD2 HIS C 304 " ideal model delta sigma weight residual 131.20 126.28 4.92 1.30e+00 5.92e-01 1.43e+01 angle pdb=" CA LEU A 308 " pdb=" C LEU A 308 " pdb=" N GLU A 309 " ideal model delta sigma weight residual 117.39 121.98 -4.59 1.24e+00 6.50e-01 1.37e+01 angle pdb=" CB HIS A 304 " pdb=" CG HIS A 304 " pdb=" CD2 HIS A 304 " ideal model delta sigma weight residual 131.20 126.42 4.78 1.30e+00 5.92e-01 1.35e+01 angle pdb=" N LEU C 303 " pdb=" CA LEU C 303 " pdb=" CB LEU C 303 " ideal model delta sigma weight residual 110.01 105.16 4.85 1.45e+00 4.76e-01 1.12e+01 ... (remaining 31954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.47: 13987 31.47 - 62.95: 274 62.95 - 94.42: 34 94.42 - 125.90: 0 125.90 - 157.37: 2 Dihedral angle restraints: 14297 sinusoidal: 5467 harmonic: 8830 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual 300.00 142.63 157.37 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual 300.00 170.02 129.98 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" CA GLN E 282 " pdb=" C GLN E 282 " pdb=" N PRO E 283 " pdb=" CA PRO E 283 " ideal model delta harmonic sigma weight residual 180.00 152.29 27.71 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 14294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3228 0.061 - 0.122: 496 0.122 - 0.183: 68 0.183 - 0.243: 7 0.243 - 0.304: 10 Chirality restraints: 3809 Sorted by residual: chirality pdb=" C3' ATP F 600 " pdb=" C2' ATP F 600 " pdb=" C4' ATP F 600 " pdb=" O3' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.94 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C3' ATP A 600 " pdb=" C2' ATP A 600 " pdb=" C4' ATP A 600 " pdb=" O3' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 3806 not shown) Planarity restraints: 4113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 302 " -0.049 2.00e-02 2.50e+03 3.49e-02 2.43e+01 pdb=" CG TYR C 302 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR C 302 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR C 302 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR C 302 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR C 302 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR C 302 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 302 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 301 " -0.039 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE C 301 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 301 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE C 301 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE C 301 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE C 301 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 301 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 304 " -0.035 2.00e-02 2.50e+03 2.58e-02 1.00e+01 pdb=" CG HIS C 304 " 0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS C 304 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS C 304 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS C 304 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS C 304 " -0.018 2.00e-02 2.50e+03 ... (remaining 4110 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 33 2.45 - 3.06: 16458 3.06 - 3.67: 33268 3.67 - 4.29: 52272 4.29 - 4.90: 86785 Nonbonded interactions: 188816 Sorted by model distance: nonbonded pdb=" O1G ATP F 600 " pdb="MG MG F 601 " model vdw 1.836 2.170 nonbonded pdb=" O3G ATP B 600 " pdb="MG MG B 601 " model vdw 1.933 2.170 nonbonded pdb=" O1B ATP C 600 " pdb="MG MG C 601 " model vdw 1.933 2.170 nonbonded pdb=" O3B ADP D 600 " pdb="MG MG D 601 " model vdw 1.936 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.941 2.170 ... (remaining 188811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 68 or (resid 69 and (name N or nam \ e CA or name C or name O or name CB )) or resid 70 through 145 or (resid 146 and \ (name N or name CA or name C or name O or name CB )) or resid 147 through 155 o \ r (resid 156 through 157 and (name N or name CA or name C or name O or name CB ) \ ) or resid 158 through 166 or (resid 167 and (name N or name CA or name C or nam \ e O or name CB )) or resid 168 through 171 or (resid 172 and (name N or name CA \ or name C or name O or name CB )) or resid 173 through 239 or (resid 240 through \ 242 and (name N or name CA or name C or name O or name CB )) or resid 243 throu \ gh 293 or (resid 294 through 295 and (name N or name CA or name C or name O or n \ ame CB )) or resid 296 through 393 or (resid 394 and (name N or name CA or name \ C or name O or name CB )) or resid 395 through 404 or (resid 405 and (name N or \ name CA or name C or name O or name CB )) or (resid 412 through 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throug \ h 430 or (resid 431 and (name N or name CA or name C or name O or name CB )) or \ resid 432 through 453 or (resid 454 through 456 and (name N or name CA or name C \ or name O or name CB )) or resid 457 or (resid 458 through 459 and (name N or n \ ame CA or name C or name O or name CB )) or resid 460 through 464 or (resid 465 \ and (name N or name CA or name C or name O or name CB )) or resid 466 through 47 \ 6 or (resid 477 and (name N or name CA or name C or name O or name CB )) or resi \ d 478 through 601)) selection = (chain 'B' and (resid 30 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 55 or (resid 56 and (name N or nam \ e CA or name C or name O or name CB )) or resid 57 through 87 or (resid 88 and ( \ name N or name CA or name C or name O or name CB )) or resid 89 through 119 or ( \ resid 120 and (name N or name CA or name C or name O or name CB )) or resid 121 \ through 155 or (resid 156 through 157 and (name N or name CA or name C or name O \ or name CB )) or resid 158 through 166 or (resid 167 and (name N or name CA or \ name C or name O or name CB )) or resid 168 through 171 or (resid 172 and (name \ N or name CA or name C or name O or name CB )) or resid 173 through 256 or (resi \ d 257 and (name N or name CA or name C or name O or name CB )) or resid 258 thro \ ugh 271 or (resid 272 and (name N or name CA or name C or name O or name CB )) o \ r resid 273 through 293 or (resid 294 through 295 and (name N or name CA or name \ C or name O or name CB )) or resid 296 through 298 or (resid 299 and (name N or \ name CA or name C or name O or name CB )) or resid 300 through 315 or (resid 31 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 317 through \ 354 or (resid 355 through 356 and (name N or name CA or name C or name O or name \ CB )) or resid 357 through 404 or (resid 405 through 414 and (name N or name CA \ or name C or name O or name CB )) or resid 415 through 416 or (resid 417 and (n \ ame N or name CA or name C or name O or name CB )) or resid 418 through 430 or ( \ resid 431 and (name N or name CA or name C or name O or name CB )) or resid 432 \ through 453 or (resid 454 through 456 and (name N or name CA or name C or name O \ or name CB )) or resid 457 or (resid 458 through 459 and (name N or name CA or \ name C or name O or name CB )) or resid 460 through 464 or (resid 465 and (name \ N or name CA or name C or name O or name CB )) or resid 466 through 479 or (resi \ d 480 and (name N or name CA or name C or name O or name CB )) or resid 481 thro \ ugh 601)) selection = (chain 'C' and (resid 30 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 68 or (resid 69 and (name N or nam \ e CA or name C or name O or name CB )) or resid 70 through 119 or (resid 120 and \ (name N or name CA or name C or name O or name CB )) or resid 121 through 145 o \ r (resid 146 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 47 through 239 or (resid 240 through 242 and (name N or name CA or name C or nam \ e O or name CB )) or resid 243 through 256 or (resid 257 and (name N or name CA \ or name C or name O or name CB )) or resid 258 through 271 or (resid 272 and (na \ me N or name CA or name C or name O or name CB )) or resid 273 through 298 or (r \ esid 299 and (name N or name CA or name C or name O or name CB )) or resid 300 t \ hrough 315 or (resid 316 and (name N or name CA or name C or name O or name CB ) \ ) or resid 317 through 393 or (resid 394 and (name N or name CA or name C or nam \ e O or name CB )) or resid 395 through 400 or (resid 401 and (name N or name CA \ or name C or name O or name CB )) or resid 402 through 405 or resid 412 through \ 476 or (resid 477 and (name N or name CA or name C or name O or name CB )) or re \ sid 478 through 601)) } ncs_group { reference = (chain 'D' and (resid 9 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 55 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 67 or (resid 68 and (n \ ame N or name CA or name C or name O or name CB )) or resid 69 through 111 or (r \ esid 112 and (name N or name CA or name C or name O or name CB )) or resid 113 t \ hrough 168 or (resid 169 and (name N or name CA or name C or name O or name CB ) \ ) or resid 170 through 188 or (resid 189 and (name N or name CA or name C or nam \ e O or name CB )) or resid 190 through 192 or (resid 193 and (name N or name CA \ or name C or name O or name CB )) or resid 194 through 202 or (resid 203 and (na \ me N or name CA or name C or name O or name CB )) or resid 204 through 240 or (r \ esid 241 and (name N or name CA or name C or name O or name CB )) or resid 242 t \ hrough 244 or (resid 245 through 246 and (name N or name CA or name C or name O \ or name CB )) or resid 247 through 266 or (resid 267 and (name N or name CA or n \ ame C or name O or name CB )) or resid 268 through 287 or (resid 288 and (name N \ or name CA or name C or name O or name CB )) or resid 289 through 314 or (resid \ 315 and (name N or name CA or name C or name O or name CB )) or resid 316 throu \ gh 336 or (resid 337 and (name N or name CA or name C or name O or name CB )) or \ resid 338 through 341 or (resid 342 and (name N or name CA or name C or name O \ or name CB )) or resid 343 through 358 or (resid 359 through 361 and (name N or \ name CA or name C or name O or name CB )) or resid 362 through 381 or (resid 382 \ and (name N or name CA or name C or name O or name CB )) or resid 383 or (resid \ 384 through 391 and (name N or name CA or name C or name O or name CB )) or res \ id 392 or (resid 393 through 402 and (name N or name CA or name C or name O or n \ ame CB )) or resid 403 through 408 or (resid 409 and (name N or name CA or name \ C or name O or name CB )) or resid 410 through 421 or (resid 422 and (name N or \ name CA or name C or name O or name CB )) or resid 423 through 429 or (resid 430 \ and (name N or name CA or name C or name O or name CB )) or resid 431 through 4 \ 75)) selection = (chain 'E' and (resid 9 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 67 or (resid 68 and (name N or name \ CA or name C or name O or name CB )) or resid 69 through 111 or (resid 112 and \ (name N or name CA or name C or name O or name CB )) or resid 113 through 188 or \ (resid 189 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 0 through 192 or (resid 193 and (name N or name CA or name C or name O or name C \ B )) or resid 194 through 195 or (resid 196 and (name N or name CA or name C or \ name O or name CB )) or resid 197 through 209 or (resid 210 and (name N or name \ CA or name C or name O or name CB )) or resid 211 or (resid 212 and (name N or n \ ame CA or name C or name O or name CB )) or resid 213 through 266 or (resid 267 \ and (name N or name CA or name C or name O or name CB )) or resid 268 through 29 \ 9 or (resid 300 and (name N or name CA or name C or name O or name CB )) or resi \ d 301 through 358 or (resid 359 through 361 and (name N or name CA or name C or \ name O or name CB )) or resid 362 through 429 or (resid 430 and (name N or name \ CA or name C or name O or name CB )) or resid 431 through 471 or (resid 472 and \ (name N or name CA or name C or name O or name CB )) or resid 473 through 475)) selection = (chain 'F' and (resid 9 through 25 or (resid 26 through 27 and (name N or name C \ A or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 42 or (resid 43 and (n \ ame N or name CA or name C or name O or name CB )) or resid 44 through 64 or (re \ sid 65 and (name N or name CA or name C or name O or name CB )) or resid 66 thro \ ugh 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) o \ r resid 170 through 195 or (resid 196 and (name N or name CA or name C or name O \ or name CB )) or resid 197 through 202 or (resid 203 and (name N or name CA or \ name C or name O or name CB )) or resid 204 through 211 or (resid 212 and (name \ N or name CA or name C or name O or name CB )) or resid 213 through 240 or (resi \ d 241 and (name N or name CA or name C or name O or name CB )) or resid 242 thro \ ugh 244 or (resid 245 through 246 and (name N or name CA or name C or name O or \ name CB )) or resid 247 through 287 or (resid 288 and (name N or name CA or name \ C or name O or name CB )) or resid 289 through 299 or (resid 300 and (name N or \ name CA or name C or name O or name CB )) or resid 301 through 314 or (resid 31 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 316 through \ 336 or (resid 337 and (name N or name CA or name C or name O or name CB )) or re \ sid 338 through 340 or (resid 341 through 342 and (name N or name CA or name C o \ r name O or name CB )) or resid 343 through 375 or (resid 376 and (name N or nam \ e CA or name C or name O or name CB )) or resid 377 through 381 or (resid 382 an \ d (name N or name CA or name C or name O or name CB )) or resid 383 or (resid 38 \ 4 through 391 and (name N or name CA or name C or name O or name CB )) or resid \ 392 or (resid 393 through 402 and (name N or name CA or name C or name O or name \ CB )) or resid 403 through 404 or (resid 405 and (name N or name CA or name C o \ r name O or name CB )) or resid 406 through 408 or (resid 409 and (name N or nam \ e CA or name C or name O or name CB )) or resid 410 through 421 or (resid 422 an \ d (name N or name CA or name C or name O or name CB )) or resid 423 through 445 \ or (resid 446 and (name N or name CA or name C or name O or name CB )) or resid \ 447 through 463 or (resid 464 through 465 and (name N or name CA or name C or na \ me O or name CB )) or resid 466 through 470 or (resid 471 through 472 and (name \ N or name CA or name C or name O or name CB )) or resid 473 through 475)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 20.790 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 0.078 23527 Z= 0.164 Angle : 0.663 6.914 31959 Z= 0.371 Chirality : 0.047 0.304 3809 Planarity : 0.005 0.076 4113 Dihedral : 12.839 157.371 8647 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % 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: 0.21 (0.15), residues: 3092 helix: 0.32 (0.14), residues: 1254 sheet: 0.03 (0.23), residues: 471 loop : 0.22 (0.18), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 306 TYR 0.062 0.002 TYR C 302 PHE 0.039 0.002 PHE C 301 TRP 0.012 0.001 TRP A 191 HIS 0.006 0.001 HIS D 367 Details of bonding type rmsd covalent geometry : bond 0.00312 (23527) covalent geometry : angle 0.66330 (31959) hydrogen bonds : bond 0.15826 ( 1129) hydrogen bonds : angle 7.14694 ( 3162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 955 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8011 (mp0) cc_final: 0.7713 (mp0) REVERT: A 62 LYS cc_start: 0.8666 (mttp) cc_final: 0.8205 (mtmm) REVERT: A 228 MET cc_start: 0.8159 (tpt) cc_final: 0.7529 (tpt) REVERT: A 302 TYR cc_start: 0.8934 (t80) cc_final: 0.8521 (t80) REVERT: A 342 THR cc_start: 0.8926 (m) cc_final: 0.8460 (p) REVERT: A 436 SER cc_start: 0.8368 (m) cc_final: 0.7926 (t) REVERT: A 462 ARG cc_start: 0.8036 (ttm170) cc_final: 0.6060 (ttt180) REVERT: B 56 GLU cc_start: 0.7391 (tt0) cc_final: 0.7124 (tt0) REVERT: B 124 ASP cc_start: 0.7000 (t0) cc_final: 0.6795 (t70) REVERT: B 165 GLN cc_start: 0.8086 (tt0) cc_final: 0.7824 (tt0) REVERT: B 189 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8089 (pttm) REVERT: B 226 ASP cc_start: 0.9008 (t0) cc_final: 0.8646 (t70) REVERT: B 247 LEU cc_start: 0.8860 (tp) cc_final: 0.8486 (tp) REVERT: B 257 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7270 (mt-10) REVERT: B 337 SER cc_start: 0.8760 (m) cc_final: 0.8528 (p) REVERT: B 486 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7140 (ttm-80) REVERT: C 64 MET cc_start: 0.8711 (ttt) cc_final: 0.8216 (ttm) REVERT: C 91 LYS cc_start: 0.8665 (mttt) cc_final: 0.8445 (mttm) REVERT: C 113 LEU cc_start: 0.9198 (mt) cc_final: 0.8845 (tp) REVERT: C 493 LYS cc_start: 0.7775 (mttt) cc_final: 0.7424 (mmmt) REVERT: D 38 GLU cc_start: 0.7650 (pt0) cc_final: 0.7327 (mt-10) REVERT: D 167 ILE cc_start: 0.9186 (mt) cc_final: 0.8822 (mt) REVERT: D 169 GLU cc_start: 0.7653 (tp30) cc_final: 0.7323 (tp30) REVERT: D 369 ASP cc_start: 0.7578 (m-30) cc_final: 0.7315 (m-30) REVERT: D 386 ASP cc_start: 0.7874 (m-30) cc_final: 0.7623 (m-30) REVERT: E 65 ASP cc_start: 0.8403 (t0) cc_final: 0.8124 (t0) REVERT: E 75 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7605 (ttpp) REVERT: E 101 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7539 (mm-30) REVERT: E 113 LEU cc_start: 0.7895 (mp) cc_final: 0.7611 (mt) REVERT: E 224 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8262 (mm-30) REVERT: E 262 THR cc_start: 0.8908 (m) cc_final: 0.8524 (m) REVERT: E 266 SER cc_start: 0.9340 (t) cc_final: 0.9099 (t) REVERT: E 282 GLN cc_start: 0.8927 (pt0) cc_final: 0.8614 (pt0) REVERT: E 354 LYS cc_start: 0.7861 (tttt) cc_final: 0.7265 (ttmm) REVERT: E 373 LYS cc_start: 0.8321 (mttm) cc_final: 0.7996 (mtpt) REVERT: F 84 SER cc_start: 0.8941 (m) cc_final: 0.8687 (p) REVERT: F 123 SER cc_start: 0.8727 (p) cc_final: 0.8225 (t) REVERT: F 126 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7454 (mm-30) REVERT: F 161 VAL cc_start: 0.9376 (m) cc_final: 0.9155 (p) REVERT: F 235 THR cc_start: 0.8658 (m) cc_final: 0.8445 (m) REVERT: F 237 LEU cc_start: 0.8277 (mp) cc_final: 0.8066 (mp) REVERT: F 241 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7687 (tt0) REVERT: F 336 SER cc_start: 0.9163 (t) cc_final: 0.8652 (p) REVERT: G 101 ASP cc_start: 0.7427 (m-30) cc_final: 0.6794 (m-30) REVERT: G 218 MET cc_start: 0.8163 (ttp) cc_final: 0.7882 (ttp) outliers start: 0 outliers final: 0 residues processed: 955 average time/residue: 0.1519 time to fit residues: 225.1603 Evaluate side-chains 727 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 727 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.0570 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.0570 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 174 GLN B 381 GLN B 478 HIS C 282 GLN D 127 GLN D 263 GLN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN F 178 HIS G 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.126693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.107503 restraints weight = 32731.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.110707 restraints weight = 17051.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.112818 restraints weight = 10597.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.114246 restraints weight = 7441.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.115148 restraints weight = 5749.170| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23527 Z= 0.184 Angle : 0.633 9.940 31959 Z= 0.329 Chirality : 0.046 0.166 3809 Planarity : 0.005 0.051 4113 Dihedral : 8.223 171.407 3486 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.46 % Allowed : 11.20 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % 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: 0.52 (0.15), residues: 3092 helix: 0.89 (0.15), residues: 1261 sheet: -0.11 (0.22), residues: 496 loop : 0.18 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 306 TYR 0.018 0.002 TYR E 458 PHE 0.019 0.002 PHE B 506 TRP 0.006 0.001 TRP C 258 HIS 0.007 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00424 (23527) covalent geometry : angle 0.63290 (31959) hydrogen bonds : bond 0.04981 ( 1129) hydrogen bonds : angle 5.46923 ( 3162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 742 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8098 (mp0) cc_final: 0.7671 (mp0) REVERT: A 62 LYS cc_start: 0.8757 (mttp) cc_final: 0.8275 (mtmm) REVERT: A 210 GLN cc_start: 0.8455 (mt0) cc_final: 0.8250 (mt0) REVERT: A 228 MET cc_start: 0.8127 (tpt) cc_final: 0.7538 (tpt) REVERT: A 342 THR cc_start: 0.9016 (m) cc_final: 0.8702 (p) REVERT: A 436 SER cc_start: 0.8501 (m) cc_final: 0.7986 (t) REVERT: A 448 TYR cc_start: 0.8865 (t80) cc_final: 0.8632 (t80) REVERT: B 29 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7050 (mm-30) REVERT: B 91 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8099 (mmtt) REVERT: B 124 ASP cc_start: 0.7114 (t0) cc_final: 0.6882 (t70) REVERT: B 165 GLN cc_start: 0.8063 (tt0) cc_final: 0.7723 (tt0) REVERT: B 189 LYS cc_start: 0.8424 (ttpp) cc_final: 0.7838 (pttm) REVERT: B 226 ASP cc_start: 0.9031 (t0) cc_final: 0.8658 (t70) REVERT: B 247 LEU cc_start: 0.8739 (tp) cc_final: 0.8354 (tp) REVERT: B 257 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7304 (mt-10) REVERT: B 313 LYS cc_start: 0.8426 (tttt) cc_final: 0.8163 (tttt) REVERT: B 337 SER cc_start: 0.9071 (m) cc_final: 0.8684 (p) REVERT: B 486 ARG cc_start: 0.8024 (ttm170) cc_final: 0.7371 (ttm-80) REVERT: C 64 MET cc_start: 0.8779 (ttt) cc_final: 0.8363 (ttt) REVERT: C 91 LYS cc_start: 0.8663 (mttt) cc_final: 0.8450 (mttm) REVERT: C 197 GLU cc_start: 0.7191 (tt0) cc_final: 0.6980 (mp0) REVERT: C 276 GLN cc_start: 0.8651 (tt0) cc_final: 0.8322 (tt0) REVERT: C 493 LYS cc_start: 0.7835 (mttt) cc_final: 0.7382 (mmmt) REVERT: D 38 GLU cc_start: 0.7677 (pt0) cc_final: 0.7260 (mt-10) REVERT: D 156 PHE cc_start: 0.8609 (m-80) cc_final: 0.8327 (m-80) REVERT: D 200 GLU cc_start: 0.8348 (tp30) cc_final: 0.8008 (tp30) REVERT: D 282 GLN cc_start: 0.8579 (pm20) cc_final: 0.8200 (pm20) REVERT: D 369 ASP cc_start: 0.7734 (m-30) cc_final: 0.7288 (m-30) REVERT: E 75 LYS cc_start: 0.7957 (ttpt) cc_final: 0.7608 (ttpp) REVERT: E 101 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7622 (mm-30) REVERT: E 136 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8885 (t) REVERT: E 196 ASP cc_start: 0.8155 (t70) cc_final: 0.7945 (t0) REVERT: E 282 GLN cc_start: 0.8939 (pt0) cc_final: 0.8610 (pt0) REVERT: E 354 LYS cc_start: 0.7844 (tttt) cc_final: 0.7539 (mtpp) REVERT: E 356 ARG cc_start: 0.8446 (tpp80) cc_final: 0.7872 (ttm170) REVERT: E 373 LYS cc_start: 0.8311 (mttm) cc_final: 0.7941 (mtpt) REVERT: F 38 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7829 (mt-10) REVERT: F 65 ASP cc_start: 0.8442 (t0) cc_final: 0.8228 (t0) REVERT: F 84 SER cc_start: 0.8850 (m) cc_final: 0.8448 (p) REVERT: F 126 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7551 (mm-30) REVERT: F 161 VAL cc_start: 0.9289 (m) cc_final: 0.8999 (p) REVERT: F 241 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7768 (tt0) REVERT: F 245 ASP cc_start: 0.8366 (m-30) cc_final: 0.8100 (m-30) REVERT: F 379 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8966 (tp40) REVERT: G 18 LYS cc_start: 0.7963 (ttmm) cc_final: 0.7600 (ttpp) REVERT: G 45 ASP cc_start: 0.8724 (t0) cc_final: 0.8511 (t0) REVERT: G 242 LYS cc_start: 0.8600 (tppt) cc_final: 0.8069 (tppt) outliers start: 58 outliers final: 39 residues processed: 769 average time/residue: 0.1462 time to fit residues: 175.8482 Evaluate side-chains 704 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 664 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 70 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 214 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 254 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 222 optimal weight: 0.0370 overall best weight: 1.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 ASN B 443 GLN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 HIS G 90 GLN G 217 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.126773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.106584 restraints weight = 32775.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.109968 restraints weight = 16716.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.112252 restraints weight = 10318.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.113661 restraints weight = 7215.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.114758 restraints weight = 5595.549| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23527 Z= 0.170 Angle : 0.591 10.351 31959 Z= 0.304 Chirality : 0.045 0.245 3809 Planarity : 0.004 0.040 4113 Dihedral : 7.935 174.072 3486 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.97 % Allowed : 14.97 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3092 helix: 1.01 (0.15), residues: 1273 sheet: -0.16 (0.23), residues: 490 loop : 0.04 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 142 TYR 0.021 0.001 TYR A 473 PHE 0.014 0.001 PHE B 506 TRP 0.004 0.001 TRP C 191 HIS 0.005 0.001 HIS G 88 Details of bonding type rmsd covalent geometry : bond 0.00390 (23527) covalent geometry : angle 0.59141 (31959) hydrogen bonds : bond 0.04394 ( 1129) hydrogen bonds : angle 5.13850 ( 3162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 717 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8120 (mp0) cc_final: 0.7663 (mp0) REVERT: A 228 MET cc_start: 0.8170 (tpt) cc_final: 0.7633 (tpt) REVERT: A 342 THR cc_start: 0.8968 (m) cc_final: 0.8667 (p) REVERT: A 372 SER cc_start: 0.8690 (m) cc_final: 0.8481 (m) REVERT: A 421 VAL cc_start: 0.8158 (t) cc_final: 0.7882 (p) REVERT: A 436 SER cc_start: 0.8498 (m) cc_final: 0.8028 (t) REVERT: B 29 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7111 (mm-30) REVERT: B 165 GLN cc_start: 0.8048 (tt0) cc_final: 0.7800 (tt0) REVERT: B 189 LYS cc_start: 0.8554 (ttpp) cc_final: 0.7925 (pttm) REVERT: B 205 TYR cc_start: 0.8767 (t80) cc_final: 0.8473 (t80) REVERT: B 226 ASP cc_start: 0.9007 (t0) cc_final: 0.8633 (t70) REVERT: B 247 LEU cc_start: 0.8514 (tp) cc_final: 0.8097 (tp) REVERT: B 337 SER cc_start: 0.9195 (m) cc_final: 0.8710 (p) REVERT: C 64 MET cc_start: 0.8806 (ttt) cc_final: 0.8374 (ttt) REVERT: C 91 LYS cc_start: 0.8663 (mttt) cc_final: 0.8435 (mttm) REVERT: C 197 GLU cc_start: 0.7217 (tt0) cc_final: 0.6956 (mp0) REVERT: C 208 VAL cc_start: 0.9085 (t) cc_final: 0.8797 (m) REVERT: C 257 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8376 (mt-10) REVERT: C 486 ARG cc_start: 0.6950 (ttp80) cc_final: 0.6724 (ttp-110) REVERT: C 493 LYS cc_start: 0.7496 (mttt) cc_final: 0.7242 (mmmt) REVERT: D 35 ASN cc_start: 0.8808 (m-40) cc_final: 0.8269 (t0) REVERT: D 38 GLU cc_start: 0.7679 (pt0) cc_final: 0.7305 (mt-10) REVERT: D 169 GLU cc_start: 0.7796 (tp30) cc_final: 0.7527 (tt0) REVERT: D 282 GLN cc_start: 0.8501 (pm20) cc_final: 0.8068 (pm20) REVERT: D 348 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8448 (p) REVERT: D 406 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7000 (mtm-85) REVERT: E 75 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7535 (ttpp) REVERT: E 101 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7646 (mm-30) REVERT: E 136 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8821 (t) REVERT: E 196 ASP cc_start: 0.8176 (t70) cc_final: 0.7886 (t0) REVERT: E 282 GLN cc_start: 0.8828 (pt0) cc_final: 0.8611 (pt0) REVERT: E 373 LYS cc_start: 0.8345 (mttm) cc_final: 0.7977 (mtpt) REVERT: F 65 ASP cc_start: 0.8530 (t0) cc_final: 0.8220 (t0) REVERT: F 126 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7473 (mm-30) REVERT: F 161 VAL cc_start: 0.9258 (m) cc_final: 0.8936 (p) REVERT: F 237 LEU cc_start: 0.8563 (mp) cc_final: 0.8235 (mp) REVERT: F 241 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7650 (tt0) REVERT: F 243 PHE cc_start: 0.8344 (m-10) cc_final: 0.7861 (m-80) REVERT: F 300 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7893 (mtmp) REVERT: F 324 THR cc_start: 0.9085 (m) cc_final: 0.8878 (p) REVERT: G 18 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7520 (ttpp) REVERT: G 218 MET cc_start: 0.7831 (ttm) cc_final: 0.7329 (ttm) REVERT: G 242 LYS cc_start: 0.8569 (tppt) cc_final: 0.8039 (tppt) outliers start: 70 outliers final: 52 residues processed: 752 average time/residue: 0.1431 time to fit residues: 170.0184 Evaluate side-chains 728 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 674 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 11 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 268 optimal weight: 0.0060 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 57 optimal weight: 0.0010 chunk 121 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 overall best weight: 0.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN D 178 HIS D 263 GLN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN F 118 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.129362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.109733 restraints weight = 32386.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.113171 restraints weight = 16469.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.115327 restraints weight = 10053.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.116913 restraints weight = 7015.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.117857 restraints weight = 5334.731| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23527 Z= 0.124 Angle : 0.550 9.477 31959 Z= 0.282 Chirality : 0.044 0.265 3809 Planarity : 0.004 0.039 4113 Dihedral : 7.520 179.909 3486 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.01 % Allowed : 17.56 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % 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: 0.66 (0.15), residues: 3092 helix: 1.17 (0.15), residues: 1284 sheet: -0.07 (0.23), residues: 515 loop : 0.05 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 425 TYR 0.019 0.001 TYR A 473 PHE 0.014 0.001 PHE B 395 TRP 0.003 0.001 TRP A 258 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00275 (23527) covalent geometry : angle 0.54982 (31959) hydrogen bonds : bond 0.03850 ( 1129) hydrogen bonds : angle 4.92424 ( 3162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 721 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8144 (mp0) cc_final: 0.7675 (mp0) REVERT: A 95 ASN cc_start: 0.7677 (m-40) cc_final: 0.7472 (m-40) REVERT: A 142 ARG cc_start: 0.7369 (ttt90) cc_final: 0.6890 (ttt90) REVERT: A 228 MET cc_start: 0.8153 (tpt) cc_final: 0.7601 (tpt) REVERT: A 342 THR cc_start: 0.8920 (m) cc_final: 0.8692 (p) REVERT: A 372 SER cc_start: 0.8700 (m) cc_final: 0.8479 (m) REVERT: A 436 SER cc_start: 0.8465 (m) cc_final: 0.8013 (t) REVERT: B 29 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7198 (mm-30) REVERT: B 189 LYS cc_start: 0.8458 (ttpp) cc_final: 0.7858 (pttm) REVERT: B 205 TYR cc_start: 0.8701 (t80) cc_final: 0.8477 (t80) REVERT: B 226 ASP cc_start: 0.8905 (t0) cc_final: 0.8422 (t0) REVERT: B 247 LEU cc_start: 0.8504 (tp) cc_final: 0.8065 (tp) REVERT: B 257 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7141 (mt-10) REVERT: B 336 VAL cc_start: 0.9154 (m) cc_final: 0.8776 (t) REVERT: B 337 SER cc_start: 0.9011 (m) cc_final: 0.8532 (p) REVERT: B 418 GLN cc_start: 0.5776 (OUTLIER) cc_final: 0.5567 (mp10) REVERT: B 480 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8469 (mp0) REVERT: C 64 MET cc_start: 0.8751 (ttt) cc_final: 0.8332 (ttt) REVERT: C 91 LYS cc_start: 0.8695 (mttt) cc_final: 0.8454 (mtpp) REVERT: C 141 ARG cc_start: 0.8009 (mtt-85) cc_final: 0.7557 (mtt90) REVERT: C 197 GLU cc_start: 0.6979 (tt0) cc_final: 0.6746 (mp0) REVERT: C 208 VAL cc_start: 0.9060 (t) cc_final: 0.8789 (m) REVERT: C 257 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8315 (mt-10) REVERT: C 493 LYS cc_start: 0.7477 (mttt) cc_final: 0.7218 (mmmt) REVERT: D 35 ASN cc_start: 0.8770 (m-40) cc_final: 0.8257 (t0) REVERT: D 38 GLU cc_start: 0.7617 (pt0) cc_final: 0.7290 (mt-10) REVERT: D 90 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7166 (mm-30) REVERT: D 246 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: D 282 GLN cc_start: 0.8414 (pm20) cc_final: 0.8008 (pm20) REVERT: D 401 LYS cc_start: 0.7519 (mtpp) cc_final: 0.7170 (mtmm) REVERT: D 406 ARG cc_start: 0.7540 (mtt180) cc_final: 0.6780 (mtt90) REVERT: E 75 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7579 (ttpp) REVERT: E 135 GLU cc_start: 0.8468 (mp0) cc_final: 0.8057 (mp0) REVERT: E 136 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8781 (t) REVERT: E 373 LYS cc_start: 0.8337 (mttm) cc_final: 0.7870 (mtpt) REVERT: F 65 ASP cc_start: 0.8376 (t0) cc_final: 0.7488 (m-30) REVERT: F 126 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7408 (mm-30) REVERT: F 163 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8185 (mtmm) REVERT: F 241 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7559 (tt0) REVERT: F 245 ASP cc_start: 0.8119 (m-30) cc_final: 0.7916 (m-30) REVERT: F 300 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7829 (mtmp) REVERT: F 379 GLN cc_start: 0.9305 (tp-100) cc_final: 0.9045 (tp40) REVERT: G 18 LYS cc_start: 0.7907 (ttmm) cc_final: 0.7512 (ttpp) REVERT: G 180 LYS cc_start: 0.6012 (pttt) cc_final: 0.5747 (pttm) REVERT: G 218 MET cc_start: 0.7814 (ttm) cc_final: 0.7396 (ttm) REVERT: G 242 LYS cc_start: 0.8527 (tppt) cc_final: 0.7996 (ttpt) outliers start: 71 outliers final: 48 residues processed: 756 average time/residue: 0.1403 time to fit residues: 167.0505 Evaluate side-chains 726 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 675 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 88 optimal weight: 0.0970 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 97 optimal weight: 0.0030 chunk 167 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 256 optimal weight: 0.6980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN C 192 ASN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.128791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.108689 restraints weight = 32544.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.112102 restraints weight = 16725.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.114388 restraints weight = 10351.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.115849 restraints weight = 7212.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.116917 restraints weight = 5574.677| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23527 Z= 0.138 Angle : 0.558 9.466 31959 Z= 0.286 Chirality : 0.044 0.285 3809 Planarity : 0.004 0.039 4113 Dihedral : 7.361 174.034 3486 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.31 % Allowed : 18.70 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % 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: 0.69 (0.15), residues: 3092 helix: 1.23 (0.15), residues: 1285 sheet: -0.05 (0.23), residues: 510 loop : 0.02 (0.18), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 190 TYR 0.025 0.001 TYR E 458 PHE 0.018 0.001 PHE B 506 TRP 0.003 0.001 TRP B 191 HIS 0.006 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00316 (23527) covalent geometry : angle 0.55787 (31959) hydrogen bonds : bond 0.03872 ( 1129) hydrogen bonds : angle 4.86993 ( 3162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 689 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7376 (ttt90) cc_final: 0.6897 (ttt90) REVERT: A 228 MET cc_start: 0.8160 (tpt) cc_final: 0.7612 (tpt) REVERT: A 342 THR cc_start: 0.8913 (m) cc_final: 0.8696 (p) REVERT: A 372 SER cc_start: 0.8780 (m) cc_final: 0.8548 (m) REVERT: A 436 SER cc_start: 0.8491 (m) cc_final: 0.8050 (t) REVERT: B 29 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7220 (mp0) REVERT: B 189 LYS cc_start: 0.8515 (ttpp) cc_final: 0.7847 (pttm) REVERT: B 226 ASP cc_start: 0.8891 (t0) cc_final: 0.8441 (t0) REVERT: B 247 LEU cc_start: 0.8476 (tp) cc_final: 0.8076 (tp) REVERT: B 257 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7016 (mt-10) REVERT: B 336 VAL cc_start: 0.9185 (m) cc_final: 0.8837 (t) REVERT: B 337 SER cc_start: 0.9028 (m) cc_final: 0.8549 (p) REVERT: B 418 GLN cc_start: 0.5933 (OUTLIER) cc_final: 0.5701 (mp10) REVERT: B 480 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8428 (mp0) REVERT: C 64 MET cc_start: 0.8755 (ttt) cc_final: 0.8366 (ttt) REVERT: C 91 LYS cc_start: 0.8730 (mttt) cc_final: 0.8501 (mtpp) REVERT: C 141 ARG cc_start: 0.7971 (mtt-85) cc_final: 0.7653 (mtt90) REVERT: C 493 LYS cc_start: 0.7609 (mttt) cc_final: 0.7301 (mmmt) REVERT: D 35 ASN cc_start: 0.8806 (m-40) cc_final: 0.8245 (t0) REVERT: D 38 GLU cc_start: 0.7618 (pt0) cc_final: 0.7277 (mt-10) REVERT: D 90 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7172 (mm-30) REVERT: D 169 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6368 (tp30) REVERT: D 282 GLN cc_start: 0.8449 (pm20) cc_final: 0.8039 (pm20) REVERT: D 393 MET cc_start: 0.8067 (mmm) cc_final: 0.7578 (mmm) REVERT: D 401 LYS cc_start: 0.7539 (mtpp) cc_final: 0.7176 (mtmm) REVERT: E 75 LYS cc_start: 0.7974 (ttpt) cc_final: 0.7586 (ttpp) REVERT: E 135 GLU cc_start: 0.8494 (mp0) cc_final: 0.8161 (mp0) REVERT: E 136 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8805 (t) REVERT: E 373 LYS cc_start: 0.8453 (mttm) cc_final: 0.8078 (mtpt) REVERT: F 65 ASP cc_start: 0.8386 (t0) cc_final: 0.7509 (m-30) REVERT: F 126 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7431 (mm-30) REVERT: F 163 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8193 (mtmm) REVERT: F 241 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7586 (tt0) REVERT: F 379 GLN cc_start: 0.9274 (tp40) cc_final: 0.9021 (tp40) REVERT: F 424 PHE cc_start: 0.8162 (m-80) cc_final: 0.7945 (m-10) REVERT: G 18 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7446 (ttpp) REVERT: G 180 LYS cc_start: 0.6098 (pttt) cc_final: 0.5872 (pttm) REVERT: G 218 MET cc_start: 0.7804 (ttm) cc_final: 0.7375 (ttm) REVERT: G 242 LYS cc_start: 0.8547 (tppt) cc_final: 0.8049 (ttpt) outliers start: 78 outliers final: 61 residues processed: 725 average time/residue: 0.1442 time to fit residues: 164.7800 Evaluate side-chains 729 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 665 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 258 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 343 ASN D 308 GLN E 127 GLN F 221 GLN F 293 GLN G 125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.124906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.104855 restraints weight = 33190.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.108234 restraints weight = 17090.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.110452 restraints weight = 10558.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.111964 restraints weight = 7404.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.112961 restraints weight = 5689.422| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23527 Z= 0.232 Angle : 0.630 11.191 31959 Z= 0.320 Chirality : 0.046 0.297 3809 Planarity : 0.004 0.046 4113 Dihedral : 7.583 169.407 3486 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.28 % Allowed : 18.74 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % 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: 0.41 (0.15), residues: 3092 helix: 1.06 (0.15), residues: 1277 sheet: -0.34 (0.23), residues: 512 loop : -0.13 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 425 TYR 0.030 0.002 TYR A 473 PHE 0.018 0.002 PHE B 506 TRP 0.005 0.001 TRP A 258 HIS 0.007 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00540 (23527) covalent geometry : angle 0.62971 (31959) hydrogen bonds : bond 0.04442 ( 1129) hydrogen bonds : angle 5.03056 ( 3162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 676 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8232 (tpt) cc_final: 0.7709 (tpt) REVERT: A 342 THR cc_start: 0.8928 (m) cc_final: 0.8627 (p) REVERT: A 436 SER cc_start: 0.8587 (m) cc_final: 0.8105 (t) REVERT: B 29 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7213 (mp0) REVERT: B 189 LYS cc_start: 0.8549 (ttpp) cc_final: 0.7971 (pttm) REVERT: B 226 ASP cc_start: 0.8964 (t0) cc_final: 0.8446 (t0) REVERT: B 257 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7088 (mt-10) REVERT: B 336 VAL cc_start: 0.9229 (m) cc_final: 0.8866 (t) REVERT: B 337 SER cc_start: 0.9278 (m) cc_final: 0.8777 (p) REVERT: B 418 GLN cc_start: 0.5941 (OUTLIER) cc_final: 0.5713 (mp10) REVERT: B 480 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8309 (mp0) REVERT: C 64 MET cc_start: 0.8795 (ttt) cc_final: 0.8413 (ttt) REVERT: C 141 ARG cc_start: 0.8032 (mtt-85) cc_final: 0.7550 (mtt90) REVERT: C 257 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 310 ARG cc_start: 0.8908 (mmm-85) cc_final: 0.8537 (mtp-110) REVERT: C 493 LYS cc_start: 0.7486 (mttt) cc_final: 0.7251 (mmmt) REVERT: D 35 ASN cc_start: 0.8831 (m-40) cc_final: 0.8438 (m-40) REVERT: D 38 GLU cc_start: 0.7658 (pt0) cc_final: 0.7294 (mt-10) REVERT: D 90 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7213 (mm-30) REVERT: D 105 GLU cc_start: 0.7791 (mp0) cc_final: 0.6952 (mp0) REVERT: D 169 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7020 (tp30) REVERT: D 282 GLN cc_start: 0.8554 (pm20) cc_final: 0.7679 (pm20) REVERT: D 352 ASP cc_start: 0.8710 (t0) cc_final: 0.8200 (t0) REVERT: D 393 MET cc_start: 0.7984 (mmm) cc_final: 0.7575 (mmm) REVERT: D 401 LYS cc_start: 0.7621 (mtpp) cc_final: 0.7244 (mtmm) REVERT: E 75 LYS cc_start: 0.8019 (ttpt) cc_final: 0.7683 (ttpp) REVERT: E 135 GLU cc_start: 0.8603 (mp0) cc_final: 0.8028 (mp0) REVERT: E 136 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8833 (t) REVERT: E 196 ASP cc_start: 0.8260 (t70) cc_final: 0.7730 (t0) REVERT: E 373 LYS cc_start: 0.8389 (mttm) cc_final: 0.7976 (mtpt) REVERT: F 65 ASP cc_start: 0.8206 (t0) cc_final: 0.7471 (m-30) REVERT: F 126 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7408 (mm-30) REVERT: F 130 SER cc_start: 0.7700 (OUTLIER) cc_final: 0.7446 (m) REVERT: F 163 LYS cc_start: 0.8669 (mtmm) cc_final: 0.8291 (mtmm) REVERT: F 237 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8148 (mp) REVERT: F 241 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7543 (tt0) REVERT: F 316 ASP cc_start: 0.9067 (t0) cc_final: 0.8818 (t70) REVERT: G 18 LYS cc_start: 0.7943 (ttmm) cc_final: 0.7549 (ttpp) REVERT: G 218 MET cc_start: 0.7931 (ttm) cc_final: 0.7508 (ttm) REVERT: G 242 LYS cc_start: 0.8496 (tppt) cc_final: 0.8009 (ttpt) outliers start: 101 outliers final: 83 residues processed: 719 average time/residue: 0.1401 time to fit residues: 161.1620 Evaluate side-chains 743 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 655 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 248 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 223 optimal weight: 5.9990 chunk 4 optimal weight: 0.0270 chunk 56 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN E 127 GLN F 379 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.127043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.107282 restraints weight = 32867.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.110655 restraints weight = 16892.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.112882 restraints weight = 10406.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.114393 restraints weight = 7277.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.115338 restraints weight = 5578.365| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23527 Z= 0.154 Angle : 0.584 9.717 31959 Z= 0.297 Chirality : 0.045 0.319 3809 Planarity : 0.004 0.041 4113 Dihedral : 7.373 171.331 3486 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.90 % Allowed : 20.14 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % 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: 0.50 (0.15), residues: 3092 helix: 1.18 (0.15), residues: 1283 sheet: -0.33 (0.23), residues: 512 loop : -0.11 (0.18), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 425 TYR 0.029 0.001 TYR E 458 PHE 0.014 0.001 PHE E 441 TRP 0.003 0.001 TRP A 258 HIS 0.005 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00356 (23527) covalent geometry : angle 0.58390 (31959) hydrogen bonds : bond 0.04026 ( 1129) hydrogen bonds : angle 4.91121 ( 3162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 662 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8188 (tpt) cc_final: 0.7680 (tpt) REVERT: A 240 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: A 342 THR cc_start: 0.8900 (m) cc_final: 0.8617 (p) REVERT: A 436 SER cc_start: 0.8532 (m) cc_final: 0.8068 (t) REVERT: A 487 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 29 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7235 (mp0) REVERT: B 189 LYS cc_start: 0.8563 (ttpp) cc_final: 0.7847 (pttp) REVERT: B 226 ASP cc_start: 0.8910 (t0) cc_final: 0.8431 (t0) REVERT: B 257 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 336 VAL cc_start: 0.9226 (m) cc_final: 0.8896 (t) REVERT: B 337 SER cc_start: 0.9099 (m) cc_final: 0.8591 (p) REVERT: B 418 GLN cc_start: 0.5938 (OUTLIER) cc_final: 0.5696 (mp10) REVERT: B 480 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8325 (mp0) REVERT: C 64 MET cc_start: 0.8758 (ttt) cc_final: 0.8372 (ttt) REVERT: C 141 ARG cc_start: 0.8009 (mtt-85) cc_final: 0.7628 (mtt90) REVERT: C 310 ARG cc_start: 0.8865 (mmm-85) cc_final: 0.8548 (mmm-85) REVERT: C 493 LYS cc_start: 0.7547 (mttt) cc_final: 0.7265 (mmmt) REVERT: D 35 ASN cc_start: 0.8805 (m-40) cc_final: 0.8265 (t0) REVERT: D 38 GLU cc_start: 0.7631 (pt0) cc_final: 0.7287 (mt-10) REVERT: D 90 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7188 (mm-30) REVERT: D 105 GLU cc_start: 0.7628 (mp0) cc_final: 0.6911 (mp0) REVERT: D 169 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6947 (tp30) REVERT: D 218 VAL cc_start: 0.9126 (p) cc_final: 0.8757 (m) REVERT: D 221 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: D 282 GLN cc_start: 0.8464 (pm20) cc_final: 0.8014 (pm20) REVERT: D 352 ASP cc_start: 0.8697 (t0) cc_final: 0.8165 (t0) REVERT: D 401 LYS cc_start: 0.7537 (mtpp) cc_final: 0.7178 (mtmm) REVERT: D 406 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7389 (mtt90) REVERT: E 75 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7655 (ttpp) REVERT: E 90 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7711 (mm-30) REVERT: E 135 GLU cc_start: 0.8570 (mp0) cc_final: 0.8025 (mp0) REVERT: E 136 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8795 (t) REVERT: E 196 ASP cc_start: 0.8180 (t70) cc_final: 0.7722 (t0) REVERT: E 260 ARG cc_start: 0.8290 (ttp-110) cc_final: 0.7766 (ttp-110) REVERT: E 326 PHE cc_start: 0.8103 (m-10) cc_final: 0.7844 (m-80) REVERT: E 373 LYS cc_start: 0.8469 (mttm) cc_final: 0.8109 (mtpt) REVERT: F 65 ASP cc_start: 0.8221 (t0) cc_final: 0.7577 (m-30) REVERT: F 130 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.7432 (m) REVERT: F 163 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8275 (mtmm) REVERT: F 237 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8183 (mp) REVERT: F 241 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7481 (tt0) REVERT: G 18 LYS cc_start: 0.7943 (ttmm) cc_final: 0.7541 (ttpp) REVERT: G 159 TYR cc_start: 0.7228 (m-80) cc_final: 0.6773 (m-80) REVERT: G 218 MET cc_start: 0.7847 (ttm) cc_final: 0.7398 (ttm) REVERT: G 254 LEU cc_start: 0.8777 (tp) cc_final: 0.8534 (tp) outliers start: 92 outliers final: 72 residues processed: 707 average time/residue: 0.1404 time to fit residues: 157.8741 Evaluate side-chains 729 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 650 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 276 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 282 optimal weight: 0.4980 chunk 37 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.128368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.108579 restraints weight = 32410.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.111988 restraints weight = 16620.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.114207 restraints weight = 10203.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.115736 restraints weight = 7104.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.116620 restraints weight = 5444.145| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23527 Z= 0.132 Angle : 0.569 9.015 31959 Z= 0.289 Chirality : 0.044 0.328 3809 Planarity : 0.004 0.040 4113 Dihedral : 7.065 170.461 3486 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.86 % Allowed : 20.53 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % 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: 0.62 (0.15), residues: 3092 helix: 1.29 (0.15), residues: 1289 sheet: -0.23 (0.23), residues: 508 loop : -0.08 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 425 TYR 0.027 0.001 TYR A 473 PHE 0.013 0.001 PHE E 441 TRP 0.002 0.001 TRP B 191 HIS 0.005 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00303 (23527) covalent geometry : angle 0.56890 (31959) hydrogen bonds : bond 0.03791 ( 1129) hydrogen bonds : angle 4.83808 ( 3162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 678 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8093 (tpt) cc_final: 0.7644 (tpt) REVERT: A 240 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: A 342 THR cc_start: 0.8853 (m) cc_final: 0.8619 (p) REVERT: A 436 SER cc_start: 0.8579 (m) cc_final: 0.7980 (t) REVERT: A 455 LEU cc_start: 0.8871 (mp) cc_final: 0.8670 (tp) REVERT: B 29 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7276 (mp0) REVERT: B 189 LYS cc_start: 0.8518 (ttpp) cc_final: 0.7853 (pttm) REVERT: B 226 ASP cc_start: 0.8856 (t0) cc_final: 0.8384 (t0) REVERT: B 257 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7111 (mt-10) REVERT: B 336 VAL cc_start: 0.9219 (m) cc_final: 0.8911 (t) REVERT: B 337 SER cc_start: 0.9084 (m) cc_final: 0.8569 (p) REVERT: B 418 GLN cc_start: 0.5932 (OUTLIER) cc_final: 0.5692 (mp10) REVERT: B 480 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8330 (mp0) REVERT: C 64 MET cc_start: 0.8754 (ttt) cc_final: 0.8383 (ttt) REVERT: C 141 ARG cc_start: 0.7985 (mtt-85) cc_final: 0.7692 (mtt90) REVERT: C 197 GLU cc_start: 0.8042 (mp0) cc_final: 0.7565 (tp30) REVERT: C 493 LYS cc_start: 0.7549 (mttt) cc_final: 0.7271 (mmmt) REVERT: D 35 ASN cc_start: 0.8773 (m-40) cc_final: 0.8330 (m-40) REVERT: D 38 GLU cc_start: 0.7619 (pt0) cc_final: 0.7273 (mt-10) REVERT: D 90 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7191 (mm-30) REVERT: D 105 GLU cc_start: 0.7726 (mp0) cc_final: 0.7094 (mp0) REVERT: D 156 PHE cc_start: 0.8271 (m-80) cc_final: 0.7932 (m-80) REVERT: D 169 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6972 (tp30) REVERT: D 218 VAL cc_start: 0.9116 (p) cc_final: 0.8784 (m) REVERT: D 221 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7954 (mp10) REVERT: D 282 GLN cc_start: 0.8403 (pm20) cc_final: 0.7979 (pm20) REVERT: D 352 ASP cc_start: 0.8687 (t0) cc_final: 0.8190 (t0) REVERT: D 393 MET cc_start: 0.7995 (mmm) cc_final: 0.7773 (mmm) REVERT: D 401 LYS cc_start: 0.7520 (mtpp) cc_final: 0.7150 (mtmm) REVERT: D 406 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7341 (mtt90) REVERT: E 75 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7662 (ttpp) REVERT: E 90 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7692 (mm-30) REVERT: E 135 GLU cc_start: 0.8579 (mp0) cc_final: 0.8042 (mp0) REVERT: E 136 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8793 (t) REVERT: E 260 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.7676 (ttp-110) REVERT: E 326 PHE cc_start: 0.8340 (m-10) cc_final: 0.8084 (m-80) REVERT: E 373 LYS cc_start: 0.8460 (mttm) cc_final: 0.8086 (mtpt) REVERT: F 65 ASP cc_start: 0.8131 (t0) cc_final: 0.7409 (m-30) REVERT: F 163 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8271 (mtmm) REVERT: F 190 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.6971 (mtp85) REVERT: F 237 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8190 (mp) REVERT: F 241 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7417 (tt0) REVERT: G 18 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7550 (ttpp) REVERT: G 33 LYS cc_start: 0.8149 (mttm) cc_final: 0.7568 (tttp) REVERT: G 159 TYR cc_start: 0.7319 (m-80) cc_final: 0.6896 (m-80) REVERT: G 218 MET cc_start: 0.8006 (ttm) cc_final: 0.7544 (ttm) REVERT: G 254 LEU cc_start: 0.8783 (tp) cc_final: 0.8541 (tp) outliers start: 91 outliers final: 74 residues processed: 722 average time/residue: 0.1398 time to fit residues: 159.6027 Evaluate side-chains 735 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 654 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 144 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 286 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 131 optimal weight: 0.2980 chunk 280 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS D 416 GLN E 127 GLN F 379 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.129889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.109963 restraints weight = 32644.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.113417 restraints weight = 16677.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.115720 restraints weight = 10230.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.117175 restraints weight = 7084.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.118263 restraints weight = 5442.592| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23527 Z= 0.115 Angle : 0.559 9.373 31959 Z= 0.285 Chirality : 0.044 0.339 3809 Planarity : 0.004 0.041 4113 Dihedral : 6.773 168.600 3486 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.10 % Allowed : 21.71 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % 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: 0.74 (0.15), residues: 3092 helix: 1.42 (0.15), residues: 1288 sheet: -0.08 (0.24), residues: 494 loop : -0.10 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 425 TYR 0.026 0.001 TYR B 399 PHE 0.012 0.001 PHE E 441 TRP 0.003 0.001 TRP B 191 HIS 0.005 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00259 (23527) covalent geometry : angle 0.55883 (31959) hydrogen bonds : bond 0.03571 ( 1129) hydrogen bonds : angle 4.77278 ( 3162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 672 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8134 (tpt) cc_final: 0.7718 (tpt) REVERT: A 240 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: A 436 SER cc_start: 0.8559 (m) cc_final: 0.7988 (t) REVERT: B 29 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7275 (mp0) REVERT: B 189 LYS cc_start: 0.8435 (ttpp) cc_final: 0.7745 (pttm) REVERT: B 226 ASP cc_start: 0.8792 (t0) cc_final: 0.8337 (t0) REVERT: B 257 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7081 (mt-10) REVERT: B 328 VAL cc_start: 0.8825 (t) cc_final: 0.8591 (m) REVERT: B 336 VAL cc_start: 0.9207 (m) cc_final: 0.8944 (t) REVERT: B 337 SER cc_start: 0.9068 (m) cc_final: 0.8544 (p) REVERT: B 480 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8024 (mp0) REVERT: C 64 MET cc_start: 0.8733 (ttt) cc_final: 0.8380 (ttt) REVERT: C 141 ARG cc_start: 0.7992 (mtt-85) cc_final: 0.7749 (mtt90) REVERT: C 197 GLU cc_start: 0.8039 (mp0) cc_final: 0.7582 (tp30) REVERT: C 493 LYS cc_start: 0.7510 (mttt) cc_final: 0.7245 (mmmt) REVERT: D 35 ASN cc_start: 0.8743 (m-40) cc_final: 0.8346 (m-40) REVERT: D 38 GLU cc_start: 0.7592 (pt0) cc_final: 0.7300 (mt-10) REVERT: D 90 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7196 (mm-30) REVERT: D 105 GLU cc_start: 0.7724 (mp0) cc_final: 0.7124 (mp0) REVERT: D 169 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7037 (tp30) REVERT: D 221 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: D 246 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: D 266 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8347 (p) REVERT: D 352 ASP cc_start: 0.8675 (t0) cc_final: 0.8160 (t0) REVERT: D 401 LYS cc_start: 0.7496 (mtpp) cc_final: 0.7117 (mtmm) REVERT: D 406 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7359 (mtt90) REVERT: E 75 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7655 (ttpp) REVERT: E 90 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7672 (mm-30) REVERT: E 135 GLU cc_start: 0.8599 (mp0) cc_final: 0.8080 (mp0) REVERT: E 136 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8791 (t) REVERT: E 196 ASP cc_start: 0.8243 (t70) cc_final: 0.7787 (t0) REVERT: E 326 PHE cc_start: 0.8445 (m-10) cc_final: 0.8128 (m-80) REVERT: E 373 LYS cc_start: 0.8463 (mttm) cc_final: 0.8080 (mtpt) REVERT: F 65 ASP cc_start: 0.7991 (t0) cc_final: 0.7391 (m-30) REVERT: F 163 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8233 (mtmm) REVERT: F 190 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.6943 (mtp85) REVERT: F 237 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8169 (mp) REVERT: F 241 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7393 (tt0) REVERT: G 18 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7544 (ttpp) REVERT: G 33 LYS cc_start: 0.8112 (mttm) cc_final: 0.7534 (tttm) REVERT: G 218 MET cc_start: 0.7958 (ttm) cc_final: 0.7526 (ttm) REVERT: G 254 LEU cc_start: 0.8744 (tp) cc_final: 0.8517 (tp) outliers start: 73 outliers final: 57 residues processed: 705 average time/residue: 0.1419 time to fit residues: 159.4399 Evaluate side-chains 712 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 647 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 19 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN D 308 GLN D 416 GLN E 127 GLN F 379 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.128349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.108398 restraints weight = 32698.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.111837 restraints weight = 16805.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.114092 restraints weight = 10316.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.115602 restraints weight = 7190.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.116615 restraints weight = 5492.901| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23527 Z= 0.152 Angle : 0.589 9.848 31959 Z= 0.299 Chirality : 0.045 0.353 3809 Planarity : 0.004 0.041 4113 Dihedral : 6.734 167.337 3486 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.10 % Allowed : 22.48 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % 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: 0.67 (0.15), residues: 3092 helix: 1.37 (0.15), residues: 1286 sheet: -0.15 (0.23), residues: 506 loop : -0.13 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 425 TYR 0.040 0.002 TYR D 147 PHE 0.012 0.001 PHE B 506 TRP 0.003 0.001 TRP B 191 HIS 0.006 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00351 (23527) covalent geometry : angle 0.58932 (31959) hydrogen bonds : bond 0.03824 ( 1129) hydrogen bonds : angle 4.81970 ( 3162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 654 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8167 (tpt) cc_final: 0.7789 (tpt) REVERT: A 436 SER cc_start: 0.8597 (m) cc_final: 0.7989 (t) REVERT: B 29 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7302 (mp0) REVERT: B 189 LYS cc_start: 0.8482 (ttpp) cc_final: 0.7773 (pttm) REVERT: B 226 ASP cc_start: 0.8831 (t0) cc_final: 0.8354 (t0) REVERT: B 257 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7080 (mt-10) REVERT: B 328 VAL cc_start: 0.8883 (t) cc_final: 0.8647 (m) REVERT: B 336 VAL cc_start: 0.9223 (m) cc_final: 0.8952 (t) REVERT: B 337 SER cc_start: 0.9086 (m) cc_final: 0.8570 (p) REVERT: B 480 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8318 (mp0) REVERT: C 64 MET cc_start: 0.8769 (ttt) cc_final: 0.8393 (ttt) REVERT: C 197 GLU cc_start: 0.8078 (mp0) cc_final: 0.7681 (tp30) REVERT: C 293 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8011 (ttp80) REVERT: D 35 ASN cc_start: 0.8756 (m-40) cc_final: 0.8298 (m-40) REVERT: D 38 GLU cc_start: 0.7730 (pt0) cc_final: 0.7388 (mt-10) REVERT: D 90 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7208 (mt-10) REVERT: D 105 GLU cc_start: 0.7754 (mp0) cc_final: 0.7087 (mp0) REVERT: D 169 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: D 221 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: D 282 GLN cc_start: 0.8308 (pm20) cc_final: 0.8012 (pm20) REVERT: D 352 ASP cc_start: 0.8676 (t0) cc_final: 0.8157 (t0) REVERT: D 401 LYS cc_start: 0.7605 (mtpp) cc_final: 0.7204 (mtmm) REVERT: D 406 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7369 (mtt90) REVERT: E 75 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7683 (ttpp) REVERT: E 90 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7688 (mm-30) REVERT: E 135 GLU cc_start: 0.8620 (mp0) cc_final: 0.8086 (mp0) REVERT: E 136 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8792 (t) REVERT: E 196 ASP cc_start: 0.8274 (t70) cc_final: 0.7799 (t0) REVERT: E 260 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7503 (ttp-110) REVERT: E 326 PHE cc_start: 0.8505 (m-10) cc_final: 0.8198 (m-10) REVERT: E 373 LYS cc_start: 0.8464 (mttm) cc_final: 0.8080 (mtpt) REVERT: F 65 ASP cc_start: 0.7906 (t0) cc_final: 0.7325 (m-30) REVERT: F 163 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8347 (mtmm) REVERT: F 190 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.6981 (mtp85) REVERT: F 237 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8191 (mp) REVERT: F 241 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7424 (tt0) REVERT: G 18 LYS cc_start: 0.7883 (ttmm) cc_final: 0.7481 (ttpp) REVERT: G 33 LYS cc_start: 0.8151 (mttm) cc_final: 0.7574 (tttp) REVERT: G 218 MET cc_start: 0.7984 (ttm) cc_final: 0.7532 (ttm) REVERT: G 254 LEU cc_start: 0.8812 (tp) cc_final: 0.8567 (tp) outliers start: 73 outliers final: 65 residues processed: 689 average time/residue: 0.1374 time to fit residues: 150.9967 Evaluate side-chains 714 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 644 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 287 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 221 optimal weight: 0.0470 chunk 226 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 276 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 236 optimal weight: 0.5980 chunk 303 optimal weight: 7.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN D 308 GLN D 416 GLN F 379 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.128584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.108596 restraints weight = 32906.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.112027 restraints weight = 16849.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.114293 restraints weight = 10351.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.115793 restraints weight = 7194.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.116822 restraints weight = 5515.660| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.273 23527 Z= 0.176 Angle : 0.743 59.176 31959 Z= 0.411 Chirality : 0.045 0.521 3809 Planarity : 0.005 0.150 4113 Dihedral : 6.728 166.792 3486 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.88 % Allowed : 23.03 % Favored : 74.09 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % 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: 0.68 (0.15), residues: 3092 helix: 1.38 (0.15), residues: 1286 sheet: -0.15 (0.23), residues: 506 loop : -0.12 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 310 TYR 0.027 0.001 TYR D 147 PHE 0.025 0.001 PHE D 156 TRP 0.003 0.001 TRP B 191 HIS 0.005 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00400 (23527) covalent geometry : angle 0.74260 (31959) hydrogen bonds : bond 0.03840 ( 1129) hydrogen bonds : angle 4.82990 ( 3162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4244.11 seconds wall clock time: 73 minutes 39.21 seconds (4419.21 seconds total)