Starting phenix.real_space_refine on Fri Jun 20 02:07:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjv_25933/06_2025/7tjv_25933.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjv_25933/06_2025/7tjv_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_25933/06_2025/7tjv_25933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjv_25933/06_2025/7tjv_25933.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjv_25933/06_2025/7tjv_25933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjv_25933/06_2025/7tjv_25933.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 2, 'GLU:plan': 14, 'HIS:plan': 1, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 10, '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: {'GLN:plan1': 4, 'GLU:plan': 16, 'ARG:plan': 1, 'ASP:plan': 7} 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: {'ASP:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 11, '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: 15.16, per 1000 atoms: 0.65 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: 6.61 Conformation dependent library (CDL) restraints added in 3.4 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: 2.99 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: 8.62 Time building geometry restraints manager: 7.81 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 509 or resid 600 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 509 or resid 600 through 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 509 or resid 600 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 57.280 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP A 191 HIS 0.006 0.001 HIS D 367 PHE 0.039 0.002 PHE C 301 TYR 0.062 0.002 TYR C 302 ARG 0.007 0.001 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.15826 ( 1129) hydrogen bonds : angle 7.14694 ( 3162) covalent geometry : bond 0.00312 (23527) covalent geometry : angle 0.66330 (31959) *********************** 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 : 2.696 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: 0.8485 (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: 0.8686 (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: 0.8162 (ttp) cc_final: 0.7881 (ttp) outliers start: 0 outliers final: 0 residues processed: 955 average time/residue: 0.3389 time to fit residues: 496.1336 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 : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 0.8980 chunk 232 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 chunk 156 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 240 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 146 optimal weight: 0.2980 chunk 179 optimal weight: 0.7980 chunk 278 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN E 379 GLN F 178 HIS F 293 GLN G 90 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.129746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.110596 restraints weight = 32212.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.113825 restraints weight = 16791.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.115972 restraints weight = 10421.890| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23527 Z= 0.133 Angle : 0.600 10.564 31959 Z= 0.312 Chirality : 0.045 0.155 3809 Planarity : 0.004 0.050 4113 Dihedral : 7.982 168.521 3486 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.87 % Allowed : 11.32 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3092 helix: 1.03 (0.15), residues: 1266 sheet: 0.01 (0.22), residues: 500 loop : 0.31 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.007 0.001 HIS B 478 PHE 0.019 0.001 PHE B 506 TYR 0.020 0.001 TYR D 458 ARG 0.006 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 1129) hydrogen bonds : angle 5.34947 ( 3162) covalent geometry : bond 0.00285 (23527) covalent geometry : angle 0.59976 (31959) *********************** 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 813 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 769 time to evaluate : 2.664 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: 0.8050 (mp0) cc_final: 0.7703 (mp0) REVERT: A 62 LYS cc_start: 0.8696 (mttp) cc_final: 0.8235 (mtmm) REVERT: A 228 MET cc_start: 0.8130 (tpt) cc_final: 0.7533 (tpt) REVERT: A 342 THR cc_start: 0.9009 (m) cc_final: 0.8747 (p) REVERT: A 436 SER cc_start: 0.8442 (m) cc_final: 0.7892 (t) REVERT: B 29 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 64 MET cc_start: 0.8196 (ttp) cc_final: 0.7990 (ttp) REVERT: B 91 LYS cc_start: 0.8334 (mmmm) cc_final: 0.8069 (mmtt) REVERT: B 124 ASP cc_start: 0.7101 (t0) cc_final: 0.6833 (t70) REVERT: B 165 GLN cc_start: 0.7965 (tt0) cc_final: 0.7744 (tt0) REVERT: B 189 LYS cc_start: 0.8376 (ttpp) cc_final: 0.7796 (pttm) REVERT: B 226 ASP cc_start: 0.8979 (t0) cc_final: 0.8622 (t70) REVERT: B 247 LEU cc_start: 0.8715 (tp) cc_final: 0.8320 (tp) REVERT: B 257 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7138 (mt-10) REVERT: B 313 LYS cc_start: 0.8355 (tttt) cc_final: 0.8125 (tttt) REVERT: B 336 VAL cc_start: 0.8962 (m) cc_final: 0.8536 (t) REVERT: B 337 SER cc_start: 0.9020 (m) cc_final: 0.8613 (p) REVERT: B 400 ARG cc_start: 0.7555 (tpp-160) cc_final: 0.7337 (tpp-160) REVERT: B 431 LYS cc_start: 0.7327 (mttt) cc_final: 0.7067 (mtmt) REVERT: B 486 ARG cc_start: 0.7928 (ttm170) cc_final: 0.7299 (ttm-80) REVERT: C 64 MET cc_start: 0.8710 (ttt) cc_final: 0.8313 (ttt) REVERT: C 196 ASP cc_start: 0.7616 (t0) cc_final: 0.7386 (t0) REVERT: C 349 ASP cc_start: 0.8004 (m-30) cc_final: 0.7359 (m-30) REVERT: C 441 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7956 (pt0) REVERT: C 493 LYS cc_start: 0.7785 (mttt) cc_final: 0.7317 (mmmt) REVERT: D 38 GLU cc_start: 0.7647 (pt0) cc_final: 0.7243 (mt-10) REVERT: D 169 GLU cc_start: 0.7807 (tp30) cc_final: 0.7220 (tp30) REVERT: D 200 GLU cc_start: 0.8349 (tp30) cc_final: 0.8119 (tp30) REVERT: D 282 GLN cc_start: 0.8462 (pm20) cc_final: 0.8029 (pm20) REVERT: D 369 ASP cc_start: 0.7741 (m-30) cc_final: 0.7276 (m-30) REVERT: E 75 LYS cc_start: 0.7795 (ttpt) cc_final: 0.7475 (ttpp) REVERT: E 90 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7386 (mm-30) REVERT: E 101 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7630 (mm-30) REVERT: E 136 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8891 (t) REVERT: E 354 LYS cc_start: 0.7914 (tttt) cc_final: 0.7251 (mtmm) REVERT: E 373 LYS cc_start: 0.8320 (mttm) cc_final: 0.7960 (mtpt) REVERT: F 38 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7804 (mt-10) REVERT: F 65 ASP cc_start: 0.8413 (t0) cc_final: 0.8191 (t0) REVERT: F 84 SER cc_start: 0.8793 (m) cc_final: 0.8436 (p) REVERT: F 126 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7559 (mm-30) REVERT: F 218 VAL cc_start: 0.8968 (t) cc_final: 0.8766 (m) REVERT: F 241 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7640 (tt0) REVERT: F 243 PHE cc_start: 0.8380 (m-80) cc_final: 0.7717 (m-80) REVERT: F 245 ASP cc_start: 0.8269 (m-30) cc_final: 0.8026 (m-30) REVERT: F 379 GLN cc_start: 0.9190 (tp-100) cc_final: 0.8952 (tp40) REVERT: F 393 MET cc_start: 0.7647 (ttp) cc_final: 0.7258 (ttm) REVERT: G 15 ASN cc_start: 0.8572 (m-40) cc_final: 0.7948 (t0) REVERT: G 18 LYS cc_start: 0.7893 (ttmm) cc_final: 0.7496 (ttpp) REVERT: G 45 ASP cc_start: 0.8724 (t0) cc_final: 0.8467 (t0) REVERT: G 242 LYS cc_start: 0.8574 (tppt) cc_final: 0.8037 (tppt) outliers start: 44 outliers final: 24 residues processed: 785 average time/residue: 0.3402 time to fit residues: 413.6547 Evaluate side-chains 719 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 693 time to evaluate : 2.561 ------------------------------------------------------------------------------- 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 444 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 123 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 297 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 352 ASP Chi-restraints excluded: chain F residue 71 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 34 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 153 optimal weight: 0.0050 chunk 56 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 300 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 452 ASN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN B 443 GLN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN E 127 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.127945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.107561 restraints weight = 32356.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.111100 restraints weight = 16070.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.113431 restraints weight = 9761.438| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 23527 Z= 0.174 Angle : 0.591 10.180 31959 Z= 0.304 Chirality : 0.045 0.239 3809 Planarity : 0.004 0.040 4113 Dihedral : 7.891 175.116 3486 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.01 % Allowed : 14.80 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3092 helix: 1.06 (0.15), residues: 1280 sheet: 0.01 (0.23), residues: 486 loop : 0.14 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 258 HIS 0.005 0.001 HIS G 88 PHE 0.014 0.001 PHE E 441 TYR 0.021 0.001 TYR A 473 ARG 0.006 0.001 ARG D 190 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 1129) hydrogen bonds : angle 5.11784 ( 3162) covalent geometry : bond 0.00405 (23527) covalent geometry : angle 0.59119 (31959) *********************** 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 796 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 725 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7555 (ttt90) cc_final: 0.6994 (ttt90) REVERT: A 228 MET cc_start: 0.8152 (tpt) cc_final: 0.7602 (tpt) REVERT: A 342 THR cc_start: 0.8963 (m) cc_final: 0.8686 (p) REVERT: A 421 VAL cc_start: 0.8123 (t) cc_final: 0.7845 (p) REVERT: A 436 SER cc_start: 0.8514 (m) cc_final: 0.8027 (t) REVERT: A 442 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7887 (mp0) REVERT: B 29 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7151 (mm-30) REVERT: B 165 GLN cc_start: 0.8054 (tt0) cc_final: 0.7787 (tt0) REVERT: B 189 LYS cc_start: 0.8485 (ttpp) cc_final: 0.7923 (pttm) REVERT: B 226 ASP cc_start: 0.8998 (t0) cc_final: 0.8624 (t70) REVERT: B 247 LEU cc_start: 0.8736 (tp) cc_final: 0.8251 (tp) REVERT: B 257 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7068 (mt-10) REVERT: B 336 VAL cc_start: 0.9101 (m) cc_final: 0.8692 (t) REVERT: B 337 SER cc_start: 0.9194 (m) cc_final: 0.8715 (p) REVERT: B 400 ARG cc_start: 0.7621 (tpp-160) cc_final: 0.7412 (tpp-160) REVERT: B 474 LEU cc_start: 0.8328 (mt) cc_final: 0.8013 (mt) REVERT: C 56 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6913 (tm-30) REVERT: C 64 MET cc_start: 0.8835 (ttt) cc_final: 0.8434 (ttt) REVERT: C 141 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7503 (mtt90) REVERT: C 197 GLU cc_start: 0.7207 (tt0) cc_final: 0.6947 (mp0) REVERT: C 257 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8281 (mt-10) REVERT: C 276 GLN cc_start: 0.8640 (tt0) cc_final: 0.8322 (tt0) REVERT: C 493 LYS cc_start: 0.7466 (mttt) cc_final: 0.7192 (mmmt) REVERT: D 35 ASN cc_start: 0.8799 (m-40) cc_final: 0.8400 (t0) REVERT: D 38 GLU cc_start: 0.7685 (pt0) cc_final: 0.7293 (mt-10) REVERT: D 156 PHE cc_start: 0.8491 (m-80) cc_final: 0.8242 (m-80) REVERT: D 282 GLN cc_start: 0.8515 (pm20) cc_final: 0.8068 (pm20) REVERT: D 406 ARG cc_start: 0.7571 (mtt180) cc_final: 0.6971 (mtm-85) REVERT: E 75 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7630 (ttpp) REVERT: E 101 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7654 (mm-30) REVERT: E 135 GLU cc_start: 0.8393 (mp0) cc_final: 0.8070 (mp0) REVERT: E 136 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8827 (t) REVERT: E 354 LYS cc_start: 0.7830 (tttt) cc_final: 0.7326 (mtmm) REVERT: E 373 LYS cc_start: 0.8367 (mttm) cc_final: 0.8012 (mtpt) REVERT: F 65 ASP cc_start: 0.8496 (t0) cc_final: 0.8182 (t0) REVERT: F 126 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7532 (mm-30) REVERT: F 163 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8191 (mtmm) REVERT: F 237 LEU cc_start: 0.8566 (mp) cc_final: 0.8119 (mp) REVERT: F 241 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7406 (tt0) REVERT: F 243 PHE cc_start: 0.8380 (m-80) cc_final: 0.7912 (m-80) REVERT: F 245 ASP cc_start: 0.8363 (m-30) cc_final: 0.8024 (m-30) REVERT: G 18 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7485 (ttpp) REVERT: G 242 LYS cc_start: 0.8542 (tppt) cc_final: 0.8028 (tppt) outliers start: 71 outliers final: 52 residues processed: 756 average time/residue: 0.3375 time to fit residues: 402.1440 Evaluate side-chains 734 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 681 time to evaluate : 2.543 ------------------------------------------------------------------------------- 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 335 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 76 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 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 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 197 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 297 THR 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 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 161 VAL Chi-restraints excluded: chain F residue 268 VAL 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 271 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 193 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 235 optimal weight: 0.0050 chunk 233 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 187 optimal weight: 0.4980 chunk 178 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 227 optimal weight: 20.0000 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 GLN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 HIS ** 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 = 0.3268 r_free = 0.3268 target = 0.127095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.106905 restraints weight = 33043.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.110388 restraints weight = 16779.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.112639 restraints weight = 10268.065| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23527 Z= 0.163 Angle : 0.572 10.504 31959 Z= 0.293 Chirality : 0.045 0.276 3809 Planarity : 0.004 0.039 4113 Dihedral : 7.624 179.756 3486 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.56 % Allowed : 16.50 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3092 helix: 1.14 (0.15), residues: 1278 sheet: -0.11 (0.23), residues: 499 loop : 0.03 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.004 0.001 HIS G 98 PHE 0.013 0.001 PHE E 441 TYR 0.021 0.001 TYR A 473 ARG 0.006 0.000 ARG A 425 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 1129) hydrogen bonds : angle 4.98780 ( 3162) covalent geometry : bond 0.00374 (23527) covalent geometry : angle 0.57177 (31959) *********************** 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 797 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 713 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ASN cc_start: 0.7710 (m-40) cc_final: 0.7505 (m-40) REVERT: A 228 MET cc_start: 0.8186 (tpt) cc_final: 0.7648 (tpt) REVERT: A 342 THR cc_start: 0.8890 (m) cc_final: 0.8643 (p) REVERT: A 372 SER cc_start: 0.8759 (m) cc_final: 0.8554 (m) REVERT: A 421 VAL cc_start: 0.8055 (t) cc_final: 0.7799 (p) REVERT: A 436 SER cc_start: 0.8506 (m) cc_final: 0.8026 (t) REVERT: A 442 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7893 (mp0) REVERT: B 29 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 165 GLN cc_start: 0.8010 (tt0) cc_final: 0.7808 (tt0) REVERT: B 189 LYS cc_start: 0.8557 (ttpp) cc_final: 0.7982 (pttm) REVERT: B 226 ASP cc_start: 0.8990 (t0) cc_final: 0.8514 (t0) REVERT: B 247 LEU cc_start: 0.8513 (tp) cc_final: 0.8101 (tp) REVERT: B 257 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7086 (mt-10) REVERT: B 337 SER cc_start: 0.9173 (m) cc_final: 0.8692 (p) REVERT: B 418 GLN cc_start: 0.5798 (mp10) cc_final: 0.5457 (mp10) REVERT: C 56 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6965 (tm-30) REVERT: C 64 MET cc_start: 0.8804 (ttt) cc_final: 0.8399 (ttt) REVERT: C 141 ARG cc_start: 0.8006 (mtt-85) cc_final: 0.7531 (mtt90) REVERT: C 197 GLU cc_start: 0.7239 (tt0) cc_final: 0.6874 (mp0) REVERT: C 208 VAL cc_start: 0.9108 (t) cc_final: 0.8822 (m) REVERT: C 276 GLN cc_start: 0.8664 (tt0) cc_final: 0.8329 (tt0) REVERT: C 441 GLU cc_start: 0.8254 (pt0) cc_final: 0.7924 (pt0) REVERT: C 486 ARG cc_start: 0.6857 (ttp80) cc_final: 0.6645 (ttp-110) REVERT: C 493 LYS cc_start: 0.7539 (mttt) cc_final: 0.7247 (mmmt) REVERT: D 35 ASN cc_start: 0.8804 (m-40) cc_final: 0.8255 (t0) REVERT: D 38 GLU cc_start: 0.7669 (pt0) cc_final: 0.7282 (mt-10) REVERT: D 90 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7165 (mm-30) REVERT: D 156 PHE cc_start: 0.8469 (m-80) cc_final: 0.8186 (m-80) REVERT: D 169 GLU cc_start: 0.7741 (tp30) cc_final: 0.7516 (tt0) REVERT: D 218 VAL cc_start: 0.9098 (p) cc_final: 0.8722 (m) REVERT: D 282 GLN cc_start: 0.8458 (pm20) cc_final: 0.8049 (pm20) REVERT: D 401 LYS cc_start: 0.7442 (mtpp) cc_final: 0.7075 (mtmm) REVERT: D 406 ARG cc_start: 0.7525 (mtt180) cc_final: 0.6774 (mtt90) REVERT: E 75 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7584 (ttpp) REVERT: E 90 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7694 (mm-30) REVERT: E 135 GLU cc_start: 0.8494 (mp0) cc_final: 0.8047 (mp0) REVERT: E 136 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8784 (t) REVERT: E 373 LYS cc_start: 0.8360 (mttm) cc_final: 0.7896 (mtpt) REVERT: E 459 MET cc_start: 0.7989 (mmm) cc_final: 0.7769 (mmm) REVERT: F 65 ASP cc_start: 0.8368 (t0) cc_final: 0.7508 (m-30) REVERT: F 126 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7436 (mm-30) REVERT: F 163 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8258 (mtmm) REVERT: F 241 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7420 (tt0) REVERT: F 243 PHE cc_start: 0.8370 (m-80) cc_final: 0.8089 (m-80) REVERT: F 245 ASP cc_start: 0.8329 (m-30) cc_final: 0.8007 (m-30) REVERT: G 18 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7479 (ttpp) REVERT: G 180 LYS cc_start: 0.6269 (pttt) cc_final: 0.6052 (pttm) REVERT: G 242 LYS cc_start: 0.8501 (tppt) cc_final: 0.7969 (ttpt) outliers start: 84 outliers final: 63 residues processed: 754 average time/residue: 0.3328 time to fit residues: 393.6510 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 : 2.405 ------------------------------------------------------------------------------- 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 B residue 76 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 431 LYS 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 170 ILE Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 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 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 272 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 299 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 99 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 132 GLU 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 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 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 109 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 178 SER 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 57 optimal weight: 0.0370 chunk 260 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 227 optimal weight: 30.0000 chunk 292 optimal weight: 9.9990 chunk 303 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 443 GLN B 210 GLN C 343 ASN D 178 HIS D 263 GLN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 GLN G 125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.124374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.104251 restraints weight = 33271.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.107636 restraints weight = 16997.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.109889 restraints weight = 10492.271| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 23527 Z= 0.252 Angle : 0.640 11.701 31959 Z= 0.327 Chirality : 0.047 0.287 3809 Planarity : 0.004 0.043 4113 Dihedral : 7.715 175.063 3486 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.05 % Allowed : 17.05 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3092 helix: 0.99 (0.15), residues: 1279 sheet: -0.28 (0.23), residues: 508 loop : -0.18 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.005 0.001 HIS C 478 PHE 0.020 0.002 PHE D 457 TYR 0.025 0.002 TYR E 458 ARG 0.008 0.001 ARG A 425 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 1129) hydrogen bonds : angle 5.09099 ( 3162) covalent geometry : bond 0.00587 (23527) covalent geometry : angle 0.64007 (31959) *********************** 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 804 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 685 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8252 (tpt) cc_final: 0.7692 (tpt) REVERT: A 342 THR cc_start: 0.9009 (m) cc_final: 0.8684 (p) REVERT: A 421 VAL cc_start: 0.8086 (t) cc_final: 0.7826 (p) REVERT: A 436 SER cc_start: 0.8536 (m) cc_final: 0.8086 (t) REVERT: A 442 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7932 (mp0) REVERT: A 465 GLU cc_start: 0.7860 (pt0) cc_final: 0.7640 (pm20) REVERT: A 473 TYR cc_start: 0.8378 (t80) cc_final: 0.8100 (t80) REVERT: B 29 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7104 (mp0) REVERT: B 189 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8052 (pttm) REVERT: B 226 ASP cc_start: 0.9015 (t0) cc_final: 0.8455 (t0) REVERT: B 257 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7115 (mt-10) REVERT: B 337 SER cc_start: 0.9255 (m) cc_final: 0.8785 (p) REVERT: B 349 ASP cc_start: 0.8543 (m-30) cc_final: 0.8296 (m-30) REVERT: B 418 GLN cc_start: 0.6300 (mt0) cc_final: 0.5968 (mp10) REVERT: C 56 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6904 (tm-30) REVERT: C 64 MET cc_start: 0.8819 (ttt) cc_final: 0.8465 (ttt) REVERT: C 141 ARG cc_start: 0.8050 (mtt-85) cc_final: 0.7597 (mtt90) REVERT: C 208 VAL cc_start: 0.9130 (t) cc_final: 0.8890 (m) REVERT: C 276 GLN cc_start: 0.8731 (tt0) cc_final: 0.8367 (tt0) REVERT: C 493 LYS cc_start: 0.7500 (mttt) cc_final: 0.7269 (mmmt) REVERT: D 35 ASN cc_start: 0.8876 (m-40) cc_final: 0.8388 (t0) REVERT: D 38 GLU cc_start: 0.7706 (pt0) cc_final: 0.7293 (mt-10) REVERT: D 90 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7201 (mm-30) REVERT: D 169 GLU cc_start: 0.7873 (tp30) cc_final: 0.7621 (tt0) REVERT: D 282 GLN cc_start: 0.8499 (pm20) cc_final: 0.7529 (pm20) REVERT: D 401 LYS cc_start: 0.7562 (mtpp) cc_final: 0.7180 (mtmm) REVERT: D 406 ARG cc_start: 0.7569 (mtt180) cc_final: 0.7048 (mtm-85) REVERT: E 75 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7784 (ttpp) REVERT: E 90 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7716 (mm-30) REVERT: E 136 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8848 (t) REVERT: E 196 ASP cc_start: 0.8211 (t70) cc_final: 0.7854 (t0) REVERT: E 326 PHE cc_start: 0.8297 (m-10) cc_final: 0.7981 (m-80) REVERT: E 373 LYS cc_start: 0.8362 (mttm) cc_final: 0.7932 (mtpt) REVERT: F 65 ASP cc_start: 0.8357 (t0) cc_final: 0.7493 (m-30) REVERT: F 163 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8356 (mtmm) REVERT: F 237 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8243 (mp) REVERT: F 241 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7364 (tt0) REVERT: F 243 PHE cc_start: 0.8482 (m-80) cc_final: 0.8169 (m-80) REVERT: F 245 ASP cc_start: 0.8349 (m-30) cc_final: 0.8057 (m-30) REVERT: F 424 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7913 (m-10) REVERT: G 18 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7458 (ttpp) REVERT: G 242 LYS cc_start: 0.8485 (tppt) cc_final: 0.8009 (tppt) outliers start: 119 outliers final: 96 residues processed: 736 average time/residue: 0.3312 time to fit residues: 384.4600 Evaluate side-chains 764 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 665 time to evaluate : 2.611 ------------------------------------------------------------------------------- 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 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 B residue 55 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 ILE 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 C residue 30 THR 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 170 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 345 ILE 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 133 ILE Chi-restraints excluded: chain D residue 136 THR 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 201 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 223 ASN 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 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 170 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 298 THR 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 388 ILE Chi-restraints excluded: chain F residue 393 MET Chi-restraints excluded: chain F residue 424 PHE Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 213 THR Chi-restraints excluded: chain G residue 248 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 99 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 252 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS A 443 GLN B 165 GLN F 221 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 = 0.3274 r_free = 0.3274 target = 0.127554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.107783 restraints weight = 32757.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.111157 restraints weight = 16734.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.113403 restraints weight = 10308.839| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23527 Z= 0.130 Angle : 0.564 10.080 31959 Z= 0.287 Chirality : 0.044 0.303 3809 Planarity : 0.004 0.041 4113 Dihedral : 7.358 175.481 3486 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.01 % Allowed : 20.36 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3092 helix: 1.26 (0.15), residues: 1279 sheet: -0.28 (0.23), residues: 497 loop : -0.08 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.009 0.001 HIS A 145 PHE 0.012 0.001 PHE E 441 TYR 0.021 0.001 TYR C 399 ARG 0.007 0.000 ARG A 425 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 1129) hydrogen bonds : angle 4.87711 ( 3162) covalent geometry : bond 0.00291 (23527) covalent geometry : angle 0.56405 (31959) *********************** 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 758 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 687 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8207 (tpt) cc_final: 0.7658 (tpt) REVERT: A 342 THR cc_start: 0.8884 (m) cc_final: 0.8629 (p) REVERT: A 436 SER cc_start: 0.8542 (m) cc_final: 0.7968 (t) REVERT: B 29 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7197 (mp0) REVERT: B 189 LYS cc_start: 0.8538 (ttpp) cc_final: 0.7813 (pttp) REVERT: B 205 TYR cc_start: 0.8755 (t80) cc_final: 0.8392 (t80) REVERT: B 226 ASP cc_start: 0.8914 (t0) cc_final: 0.8417 (t0) REVERT: B 257 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7130 (mt-10) REVERT: B 336 VAL cc_start: 0.9203 (m) cc_final: 0.8853 (t) REVERT: B 337 SER cc_start: 0.9089 (m) cc_final: 0.8586 (p) REVERT: B 349 ASP cc_start: 0.8490 (m-30) cc_final: 0.8222 (m-30) REVERT: C 56 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6889 (tm-30) REVERT: C 64 MET cc_start: 0.8806 (ttt) cc_final: 0.8430 (ttt) REVERT: C 141 ARG cc_start: 0.7986 (mtt-85) cc_final: 0.7622 (mtt90) REVERT: C 208 VAL cc_start: 0.9114 (t) cc_final: 0.8868 (m) REVERT: C 310 ARG cc_start: 0.8714 (mmm-85) cc_final: 0.8281 (mtp180) REVERT: C 493 LYS cc_start: 0.7529 (mttt) cc_final: 0.7252 (mmmt) REVERT: D 35 ASN cc_start: 0.8841 (m-40) cc_final: 0.8256 (t0) REVERT: D 38 GLU cc_start: 0.7653 (pt0) cc_final: 0.7266 (mt-10) REVERT: D 90 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7156 (mm-30) REVERT: D 169 GLU cc_start: 0.7853 (tp30) cc_final: 0.7588 (tt0) REVERT: D 282 GLN cc_start: 0.8441 (pm20) cc_final: 0.8022 (pm20) REVERT: D 393 MET cc_start: 0.8070 (mmm) cc_final: 0.7702 (mmm) REVERT: D 401 LYS cc_start: 0.7529 (mtpp) cc_final: 0.7127 (mtmm) REVERT: E 75 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7692 (ttpp) REVERT: E 90 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7661 (mm-30) REVERT: E 260 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7636 (ttp-110) REVERT: E 373 LYS cc_start: 0.8531 (mttm) cc_final: 0.8054 (mtpt) REVERT: F 65 ASP cc_start: 0.8339 (t0) cc_final: 0.7507 (m-30) REVERT: F 163 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8354 (mtmm) REVERT: F 237 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8119 (mp) REVERT: F 241 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7344 (tt0) REVERT: F 356 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8218 (ttp80) REVERT: G 18 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7498 (ttpp) REVERT: G 242 LYS cc_start: 0.8505 (tppt) cc_final: 0.8294 (ttmm) REVERT: G 254 LEU cc_start: 0.8743 (tp) cc_final: 0.8507 (tp) outliers start: 71 outliers final: 53 residues processed: 721 average time/residue: 0.4003 time to fit residues: 461.2997 Evaluate side-chains 711 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 657 time to evaluate : 2.955 ------------------------------------------------------------------------------- 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 330 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 480 GLU 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 262 ASN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 496 LEU 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 201 MET Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain E residue 113 LEU 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 445 LEU 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 237 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 223 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 225 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** C 192 ASN F 379 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.127261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.107549 restraints weight = 32987.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.110967 restraints weight = 16809.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.113152 restraints weight = 10258.436| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23527 Z= 0.150 Angle : 0.581 9.916 31959 Z= 0.295 Chirality : 0.045 0.315 3809 Planarity : 0.004 0.040 4113 Dihedral : 7.243 171.626 3486 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.39 % Allowed : 20.70 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3092 helix: 1.29 (0.15), residues: 1279 sheet: -0.27 (0.23), residues: 508 loop : -0.10 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.007 0.001 HIS A 145 PHE 0.015 0.001 PHE F 261 TYR 0.032 0.001 TYR E 458 ARG 0.009 0.000 ARG A 425 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 1129) hydrogen bonds : angle 4.86506 ( 3162) covalent geometry : bond 0.00346 (23527) covalent geometry : angle 0.58090 (31959) *********************** 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 743 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 663 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8234 (tpt) cc_final: 0.7722 (tpt) REVERT: A 342 THR cc_start: 0.8884 (m) cc_final: 0.8649 (p) REVERT: A 436 SER cc_start: 0.8535 (m) cc_final: 0.7946 (t) REVERT: A 455 LEU cc_start: 0.8882 (mp) cc_final: 0.8655 (tp) REVERT: A 465 GLU cc_start: 0.7727 (pm20) cc_final: 0.7361 (pm20) REVERT: B 29 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7246 (mp0) REVERT: B 189 LYS cc_start: 0.8534 (ttpp) cc_final: 0.7835 (pttp) REVERT: B 226 ASP cc_start: 0.8903 (t0) cc_final: 0.8434 (t0) REVERT: B 257 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7075 (mt-10) REVERT: B 336 VAL cc_start: 0.9238 (m) cc_final: 0.8905 (t) REVERT: B 337 SER cc_start: 0.9081 (m) cc_final: 0.8597 (p) REVERT: B 349 ASP cc_start: 0.8516 (m-30) cc_final: 0.8241 (m-30) REVERT: C 56 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6779 (tm-30) REVERT: C 64 MET cc_start: 0.8794 (ttt) cc_final: 0.8430 (ttt) REVERT: C 141 ARG cc_start: 0.8015 (mtt-85) cc_final: 0.7762 (mtt90) REVERT: C 208 VAL cc_start: 0.9123 (t) cc_final: 0.8897 (m) REVERT: C 257 GLU cc_start: 0.8582 (mt-10) cc_final: 0.7606 (mt-10) REVERT: C 310 ARG cc_start: 0.8780 (mmm-85) cc_final: 0.8346 (mtp180) REVERT: C 493 LYS cc_start: 0.7551 (mttt) cc_final: 0.7271 (mmmt) REVERT: D 35 ASN cc_start: 0.8810 (m-40) cc_final: 0.8278 (t0) REVERT: D 38 GLU cc_start: 0.7626 (pt0) cc_final: 0.7269 (mt-10) REVERT: D 90 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7161 (mm-30) REVERT: D 167 ILE cc_start: 0.9026 (mp) cc_final: 0.8714 (mp) REVERT: D 221 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8070 (mp10) REVERT: D 282 GLN cc_start: 0.8414 (pm20) cc_final: 0.8002 (pm20) REVERT: D 352 ASP cc_start: 0.8749 (t0) cc_final: 0.8123 (t0) REVERT: D 401 LYS cc_start: 0.7425 (mtpp) cc_final: 0.7052 (mtmm) REVERT: E 75 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7672 (ttpp) REVERT: E 90 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7645 (mm-30) REVERT: E 136 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8849 (t) REVERT: E 260 ARG cc_start: 0.8152 (ttp-110) cc_final: 0.7580 (ttp-170) REVERT: E 326 PHE cc_start: 0.8376 (m-10) cc_final: 0.8083 (m-80) REVERT: E 373 LYS cc_start: 0.8511 (mttm) cc_final: 0.8168 (mtpt) REVERT: E 454 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.5961 (mm-30) REVERT: F 65 ASP cc_start: 0.8196 (t0) cc_final: 0.7557 (m-30) REVERT: F 130 SER cc_start: 0.7661 (OUTLIER) cc_final: 0.7427 (m) REVERT: F 163 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8360 (mtmm) REVERT: F 237 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8279 (mp) REVERT: F 356 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8293 (ttp80) REVERT: F 455 HIS cc_start: 0.6804 (t70) cc_final: 0.6406 (t70) REVERT: G 18 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7580 (ttpp) REVERT: G 159 TYR cc_start: 0.7194 (m-80) cc_final: 0.6929 (m-80) REVERT: G 254 LEU cc_start: 0.8790 (tp) cc_final: 0.8539 (tp) outliers start: 80 outliers final: 64 residues processed: 700 average time/residue: 0.3605 time to fit residues: 398.2806 Evaluate side-chains 720 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 651 time to evaluate : 2.554 ------------------------------------------------------------------------------- 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 330 GLU Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 480 GLU 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 262 ASN 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 496 LEU 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 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 272 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 LEU 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 445 LEU Chi-restraints excluded: chain E residue 454 GLU 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 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 237 LEU 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 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 178 SER Chi-restraints excluded: chain G residue 213 THR 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 76 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 245 optimal weight: 0.0670 chunk 174 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 249 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 GLN F 379 GLN G 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.129706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.109871 restraints weight = 32651.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.113289 restraints weight = 16837.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.115546 restraints weight = 10372.090| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23527 Z= 0.115 Angle : 0.558 9.899 31959 Z= 0.284 Chirality : 0.044 0.326 3809 Planarity : 0.004 0.048 4113 Dihedral : 6.997 172.824 3486 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.31 % Allowed : 21.46 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3092 helix: 1.42 (0.15), residues: 1288 sheet: -0.17 (0.23), residues: 501 loop : -0.07 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 191 HIS 0.007 0.001 HIS A 145 PHE 0.015 0.001 PHE B 506 TYR 0.032 0.001 TYR B 399 ARG 0.009 0.000 ARG A 425 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 1129) hydrogen bonds : angle 4.76337 ( 3162) covalent geometry : bond 0.00257 (23527) covalent geometry : angle 0.55817 (31959) *********************** 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 752 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 674 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8071 (tpt) cc_final: 0.7625 (tpt) REVERT: A 436 SER cc_start: 0.8509 (m) cc_final: 0.7949 (t) REVERT: A 465 GLU cc_start: 0.7769 (pm20) cc_final: 0.7397 (pm20) REVERT: B 29 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7263 (mp0) REVERT: B 189 LYS cc_start: 0.8533 (ttpp) cc_final: 0.7789 (pttm) REVERT: B 226 ASP cc_start: 0.8789 (t0) cc_final: 0.8366 (t0) REVERT: B 257 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7112 (mt-10) REVERT: B 328 VAL cc_start: 0.8859 (t) cc_final: 0.8652 (m) REVERT: B 336 VAL cc_start: 0.9212 (m) cc_final: 0.8936 (t) REVERT: B 337 SER cc_start: 0.9061 (m) cc_final: 0.8557 (p) REVERT: B 349 ASP cc_start: 0.8454 (m-30) cc_final: 0.8235 (m-30) REVERT: C 56 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6683 (tm-30) REVERT: C 64 MET cc_start: 0.8808 (ttt) cc_final: 0.8450 (ttt) REVERT: C 208 VAL cc_start: 0.9134 (t) cc_final: 0.8906 (m) REVERT: C 257 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8026 (mt-10) REVERT: C 310 ARG cc_start: 0.8731 (mmm-85) cc_final: 0.8514 (mmm-85) REVERT: C 493 LYS cc_start: 0.7534 (mttt) cc_final: 0.7261 (mmmt) REVERT: D 22 ASP cc_start: 0.7305 (m-30) cc_final: 0.6986 (m-30) REVERT: D 35 ASN cc_start: 0.8784 (m-40) cc_final: 0.8213 (t0) REVERT: D 38 GLU cc_start: 0.7602 (pt0) cc_final: 0.7287 (mt-10) REVERT: D 90 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7139 (mm-30) REVERT: D 135 GLU cc_start: 0.8032 (tt0) cc_final: 0.7728 (tp30) REVERT: D 156 PHE cc_start: 0.8178 (m-80) cc_final: 0.7950 (m-10) REVERT: D 167 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8698 (mp) REVERT: D 169 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6193 (tp30) REVERT: D 218 VAL cc_start: 0.9114 (p) cc_final: 0.8829 (m) REVERT: D 221 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: D 266 SER cc_start: 0.9014 (OUTLIER) cc_final: 0.8429 (p) REVERT: D 393 MET cc_start: 0.7959 (mmm) cc_final: 0.7753 (mmm) REVERT: D 401 LYS cc_start: 0.7618 (mtpp) cc_final: 0.7233 (mtmm) REVERT: E 75 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7663 (ttpp) REVERT: E 90 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7659 (mm-30) REVERT: E 135 GLU cc_start: 0.8506 (mp0) cc_final: 0.8058 (mp0) REVERT: E 136 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8786 (t) REVERT: E 196 ASP cc_start: 0.8135 (t70) cc_final: 0.7878 (t0) REVERT: E 326 PHE cc_start: 0.8469 (m-10) cc_final: 0.8109 (m-80) REVERT: E 373 LYS cc_start: 0.8504 (mttm) cc_final: 0.8134 (mtpt) REVERT: E 454 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6026 (mm-30) REVERT: F 65 ASP cc_start: 0.8117 (t0) cc_final: 0.7495 (m-30) REVERT: F 163 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8357 (mtmm) REVERT: F 190 ARG cc_start: 0.8519 (ptp90) cc_final: 0.8208 (ptp90) REVERT: F 237 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8258 (mp) REVERT: G 18 LYS cc_start: 0.7891 (ttmm) cc_final: 0.7438 (ttpp) REVERT: G 33 LYS cc_start: 0.8172 (mttm) cc_final: 0.7561 (tttp) REVERT: G 254 LEU cc_start: 0.8733 (tp) cc_final: 0.8500 (tp) outliers start: 78 outliers final: 57 residues processed: 715 average time/residue: 0.4146 time to fit residues: 473.7585 Evaluate side-chains 718 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 654 time to evaluate : 3.076 ------------------------------------------------------------------------------- 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 156 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 480 GLU 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 240 GLU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 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 167 ILE 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 272 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 LEU 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 312 VAL 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 E residue 454 GLU 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 237 LEU 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 F residue 437 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 139 THR 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 165 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** A 477 ASN D 308 GLN D 416 GLN E 52 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 = 0.3274 r_free = 0.3274 target = 0.127534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.107760 restraints weight = 32922.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.111070 restraints weight = 16819.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.113367 restraints weight = 10382.351| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23527 Z= 0.159 Angle : 0.586 9.380 31959 Z= 0.298 Chirality : 0.045 0.349 3809 Planarity : 0.004 0.051 4113 Dihedral : 7.046 169.467 3486 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.10 % Allowed : 22.22 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3092 helix: 1.37 (0.15), residues: 1283 sheet: -0.13 (0.23), residues: 499 loop : -0.15 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 191 HIS 0.007 0.001 HIS A 145 PHE 0.014 0.001 PHE F 261 TYR 0.026 0.001 TYR B 399 ARG 0.011 0.000 ARG A 425 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 1129) hydrogen bonds : angle 4.82384 ( 3162) covalent geometry : bond 0.00366 (23527) covalent geometry : angle 0.58556 (31959) *********************** 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 737 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 664 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8104 (tpt) cc_final: 0.7652 (tpt) REVERT: A 436 SER cc_start: 0.8487 (m) cc_final: 0.8035 (t) REVERT: B 29 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7283 (mp0) REVERT: B 189 LYS cc_start: 0.8527 (ttpp) cc_final: 0.7736 (pttm) REVERT: B 226 ASP cc_start: 0.8864 (t0) cc_final: 0.8374 (t0) REVERT: B 257 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7064 (mt-10) REVERT: B 336 VAL cc_start: 0.9231 (m) cc_final: 0.8897 (t) REVERT: B 337 SER cc_start: 0.9096 (m) cc_final: 0.8575 (p) REVERT: B 349 ASP cc_start: 0.8464 (m-30) cc_final: 0.8199 (m-30) REVERT: C 56 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6667 (tm-30) REVERT: C 64 MET cc_start: 0.8776 (ttt) cc_final: 0.8417 (ttt) REVERT: C 141 ARG cc_start: 0.8284 (mtt90) cc_final: 0.7128 (mtt90) REVERT: C 208 VAL cc_start: 0.9147 (t) cc_final: 0.8922 (m) REVERT: C 257 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8356 (mt-10) REVERT: D 22 ASP cc_start: 0.7364 (m-30) cc_final: 0.7021 (m-30) REVERT: D 35 ASN cc_start: 0.8815 (m-40) cc_final: 0.8371 (m-40) REVERT: D 38 GLU cc_start: 0.7769 (pt0) cc_final: 0.7395 (mt-10) REVERT: D 90 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7155 (mm-30) REVERT: D 105 GLU cc_start: 0.7651 (mp0) cc_final: 0.6948 (mp0) REVERT: D 135 GLU cc_start: 0.8055 (tt0) cc_final: 0.7768 (tp30) REVERT: D 156 PHE cc_start: 0.8214 (m-80) cc_final: 0.7976 (m-10) REVERT: D 167 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8712 (mp) REVERT: D 169 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6910 (tp30) REVERT: D 221 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: D 282 GLN cc_start: 0.8317 (pm20) cc_final: 0.7981 (pm20) REVERT: D 401 LYS cc_start: 0.7306 (mtpp) cc_final: 0.6933 (mtmm) REVERT: D 406 ARG cc_start: 0.7472 (mtt180) cc_final: 0.6923 (mtt90) REVERT: E 75 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7692 (ttpp) REVERT: E 90 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7712 (mm-30) REVERT: E 136 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8841 (t) REVERT: E 196 ASP cc_start: 0.8208 (t70) cc_final: 0.7903 (t0) REVERT: E 260 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7610 (ttp-170) REVERT: E 326 PHE cc_start: 0.8543 (m-10) cc_final: 0.8179 (m-80) REVERT: E 373 LYS cc_start: 0.8483 (mttm) cc_final: 0.8107 (mtpt) REVERT: F 65 ASP cc_start: 0.7950 (t0) cc_final: 0.7393 (m-30) REVERT: F 163 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8361 (mtmm) REVERT: F 237 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8252 (mp) REVERT: G 18 LYS cc_start: 0.7922 (ttmm) cc_final: 0.7496 (ttpp) REVERT: G 33 LYS cc_start: 0.8144 (mttm) cc_final: 0.7593 (tttp) REVERT: G 159 TYR cc_start: 0.7201 (m-80) cc_final: 0.6851 (m-80) REVERT: G 254 LEU cc_start: 0.8770 (tp) cc_final: 0.8522 (tp) outliers start: 73 outliers final: 62 residues processed: 696 average time/residue: 0.3231 time to fit residues: 357.1279 Evaluate side-chains 722 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 655 time to evaluate : 2.708 ------------------------------------------------------------------------------- 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 156 ASP 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 443 GLN Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 480 GLU 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 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 337 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 167 ILE 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 272 LEU Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 LEU 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 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 237 LEU 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 119 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 276 optimal weight: 0.5980 chunk 25 optimal weight: 0.0030 chunk 59 optimal weight: 0.9980 chunk 267 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- 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 D 416 GLN E 52 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 = 0.3264 r_free = 0.3264 target = 0.126839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.106935 restraints weight = 33005.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.110337 restraints weight = 16959.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.112583 restraints weight = 10406.726| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23527 Z= 0.185 Angle : 0.608 11.571 31959 Z= 0.309 Chirality : 0.046 0.360 3809 Planarity : 0.004 0.055 4113 Dihedral : 7.149 168.593 3486 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.01 % Allowed : 22.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3092 helix: 1.30 (0.15), residues: 1287 sheet: -0.19 (0.24), residues: 484 loop : -0.18 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.007 0.001 HIS A 145 PHE 0.016 0.001 PHE F 261 TYR 0.032 0.002 TYR B 399 ARG 0.011 0.000 ARG B 173 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 1129) hydrogen bonds : angle 4.88457 ( 3162) covalent geometry : bond 0.00429 (23527) covalent geometry : angle 0.60755 (31959) ********************** 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 731 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 660 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLN cc_start: 0.8410 (tt0) cc_final: 0.8190 (tt0) REVERT: A 228 MET cc_start: 0.8115 (tpt) cc_final: 0.7662 (tpt) REVERT: A 436 SER cc_start: 0.8514 (m) cc_final: 0.8056 (t) REVERT: B 29 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7303 (mp0) REVERT: B 189 LYS cc_start: 0.8623 (ttpp) cc_final: 0.7860 (pttm) REVERT: B 205 TYR cc_start: 0.8764 (t80) cc_final: 0.8383 (t80) REVERT: B 226 ASP cc_start: 0.8894 (t0) cc_final: 0.8430 (t0) REVERT: B 257 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7076 (mt-10) REVERT: B 336 VAL cc_start: 0.9194 (m) cc_final: 0.8927 (t) REVERT: B 337 SER cc_start: 0.9029 (m) cc_final: 0.8590 (p) REVERT: B 349 ASP cc_start: 0.8554 (m-30) cc_final: 0.8298 (m-30) REVERT: C 56 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6709 (tm-30) REVERT: C 64 MET cc_start: 0.8789 (ttt) cc_final: 0.8418 (ttt) REVERT: C 141 ARG cc_start: 0.8281 (mtt90) cc_final: 0.7177 (mtt90) REVERT: C 257 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8362 (mt-10) REVERT: C 441 GLU cc_start: 0.8244 (pt0) cc_final: 0.7809 (pt0) REVERT: D 22 ASP cc_start: 0.7344 (m-30) cc_final: 0.6989 (m-30) REVERT: D 35 ASN cc_start: 0.8832 (m-40) cc_final: 0.8384 (m-40) REVERT: D 38 GLU cc_start: 0.7736 (pt0) cc_final: 0.7369 (mt-10) REVERT: D 90 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7193 (mm-30) REVERT: D 105 GLU cc_start: 0.7790 (mp0) cc_final: 0.7035 (mp0) REVERT: D 135 GLU cc_start: 0.8064 (tt0) cc_final: 0.7783 (tp30) REVERT: D 156 PHE cc_start: 0.8255 (m-80) cc_final: 0.8012 (m-10) REVERT: D 167 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8732 (mp) REVERT: D 169 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6673 (tp30) REVERT: D 221 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: D 282 GLN cc_start: 0.8363 (pm20) cc_final: 0.7967 (pm20) REVERT: D 352 ASP cc_start: 0.8695 (t0) cc_final: 0.8148 (t0) REVERT: D 401 LYS cc_start: 0.7353 (mtpp) cc_final: 0.6969 (mtmm) REVERT: D 406 ARG cc_start: 0.7465 (mtt180) cc_final: 0.7140 (mtt90) REVERT: E 75 LYS cc_start: 0.8065 (ttpt) cc_final: 0.7722 (ttpp) REVERT: E 90 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7726 (mm-30) REVERT: E 136 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8831 (t) REVERT: E 192 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7563 (ptt90) REVERT: E 196 ASP cc_start: 0.8212 (t70) cc_final: 0.7920 (t0) REVERT: E 260 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7607 (ttp-170) REVERT: E 373 LYS cc_start: 0.8472 (mttm) cc_final: 0.8109 (mtpp) REVERT: F 65 ASP cc_start: 0.7963 (t0) cc_final: 0.7278 (m-30) REVERT: F 163 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8427 (mtmm) REVERT: F 237 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8264 (mp) REVERT: F 241 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7313 (tt0) REVERT: F 356 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8169 (ttp80) REVERT: G 18 LYS cc_start: 0.7941 (ttmm) cc_final: 0.7534 (ttpp) REVERT: G 33 LYS cc_start: 0.8174 (mttm) cc_final: 0.7596 (tttp) REVERT: G 159 TYR cc_start: 0.7193 (m-80) cc_final: 0.6885 (m-80) REVERT: G 254 LEU cc_start: 0.8746 (tp) cc_final: 0.8493 (tp) outliers start: 71 outliers final: 64 residues processed: 694 average time/residue: 0.3238 time to fit residues: 357.1823 Evaluate side-chains 731 residues out of total 2522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 662 time to evaluate : 2.616 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 156 ASP 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 443 GLN Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 76 VAL 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 346 SER Chi-restraints excluded: chain B residue 480 GLU 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 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 337 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 167 ILE 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 272 LEU Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 LEU 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 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 237 LEU 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 119 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 139 THR 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 98 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 288 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 242 optimal weight: 0.5980 chunk 235 optimal weight: 2.9990 chunk 217 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 416 GLN E 52 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 = 0.3291 r_free = 0.3291 target = 0.129024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.109225 restraints weight = 32721.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.112647 restraints weight = 16720.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.114922 restraints weight = 10246.008| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3485 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= 0.123 Angle : 0.572 12.830 31959 Z= 0.292 Chirality : 0.045 0.350 3809 Planarity : 0.004 0.051 4113 Dihedral : 7.030 169.793 3486 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.93 % Allowed : 22.86 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3092 helix: 1.44 (0.15), residues: 1285 sheet: -0.06 (0.24), residues: 499 loop : -0.16 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 191 HIS 0.007 0.001 HIS A 145 PHE 0.016 0.001 PHE D 156 TYR 0.043 0.001 TYR E 458 ARG 0.010 0.000 ARG B 173 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 1129) hydrogen bonds : angle 4.77952 ( 3162) covalent geometry : bond 0.00277 (23527) covalent geometry : angle 0.57231 (31959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9448.04 seconds wall clock time: 167 minutes 23.80 seconds (10043.80 seconds total)