Starting phenix.real_space_refine on Sat Jul 4 15:44:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tjx_25939/07_2026/7tjx_25939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjx_25939/07_2026/7tjx_25939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7tjx_25939/07_2026/7tjx_25939.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tjx_25939/07_2026/7tjx_25939.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tjx_25939/07_2026/7tjx_25939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjx_25939/07_2026/7tjx_25939.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjx_25939/07_2026/7tjx_25939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjx_25939/07_2026/7tjx_25939.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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 15 5.49 5 Mg 5 5.21 5 S 25 5.16 5 C 13686 2.51 5 N 3896 2.21 5 O 4036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21663 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3384 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 450} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 21, 'ASP:plan': 8, 'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3375 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 23, 'ASP:plan': 10, 'GLN:plan1': 4, 'ARG:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 171 Chain: "C" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3523 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 17, 'GLN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 130 Chain: "D" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3206 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 430} Chain breaks: 1 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 14, 'GLN:plan1': 6, 'GLU:plan': 17, 'ASN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 157 Chain: "E" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3105 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 433} Chain breaks: 2 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 430 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 28, 'GLN:plan1': 8, 'ASN:plan1': 1, 'TYR:plan': 2, 'ARG:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 243 Chain: "F" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3349 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 443} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 23, 'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "G" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1560 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 513 Unresolved non-hydrogen angles: 640 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 7, 'PHE:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 14, 'ASP:plan': 10, 'HIS:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 247 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.84, per 1000 atoms: 0.22 Number of scatterers: 21663 At special positions: 0 Unit cell: (126.665, 126.665, 154.962, 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 25 16.00 P 15 15.00 Mg 5 11.99 O 4036 8.00 N 3896 7.00 C 13686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 1.0 seconds 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 23 sheets defined 49.9% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.515A pdb=" N LEU A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 111 through 115 removed outlier: 4.319A pdb=" N ASN A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.673A pdb=" N VAL A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.763A pdb=" N ASN A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 226 through 229 removed outlier: 3.875A 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 removed outlier: 3.583A pdb=" N GLN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.637A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.633A 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 362 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.801A pdb=" N GLN A 381 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 402 removed outlier: 3.596A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 439 through 453 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 459 through 478 removed outlier: 3.891A pdb=" N ILE A 463 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 489 Processing helix chain 'A' and resid 492 through 508 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.723A pdb=" N LEU B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.546A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.728A pdb=" N VAL B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 196 through 200 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 removed outlier: 3.639A pdb=" N GLN B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Proline residue: B 249 - end of helix removed outlier: 3.530A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 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: 3.646A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 335 removed outlier: 3.802A pdb=" N ASP B 335 " --> pdb=" O GLN B 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 332 through 335' Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.696A pdb=" N VAL B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.641A pdb=" N PHE B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.620A pdb=" N VAL B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 removed outlier: 3.655A pdb=" N GLN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 4.152A pdb=" N GLY B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 476 removed outlier: 3.530A pdb=" N SER B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 4.460A pdb=" N GLU B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY B 489 " --> pdb=" O ILE B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 508 removed outlier: 3.686A pdb=" N GLU B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.652A pdb=" N LEU C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.830A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 211 through 225 removed outlier: 3.512A pdb=" N VAL C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 241 through 262 removed outlier: 3.509A pdb=" N GLN C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Proline residue: C 249 - end of helix removed outlier: 3.657A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.599A 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 299 through 309 removed outlier: 3.635A pdb=" N ARG C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 319 removed outlier: 3.622A pdb=" N GLY C 319 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 380 Processing helix chain 'C' and resid 382 through 407 removed outlier: 5.587A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 430 removed outlier: 4.237A pdb=" N THR C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 453 Proline residue: C 445 - end of helix removed outlier: 3.578A pdb=" N GLY C 453 " --> pdb=" O ALA C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 removed outlier: 4.243A pdb=" N GLY C 457 " --> pdb=" O HIS C 454 " (cutoff:3.500A) 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: 4.039A pdb=" N LEU C 471 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 489 removed outlier: 3.938A pdb=" N LEU C 482 " --> pdb=" O HIS C 478 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 509 removed outlier: 3.510A pdb=" N ALA C 497 " --> pdb=" O LYS C 493 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) 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 178 removed outlier: 3.830A pdb=" N LYS D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 177 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.645A pdb=" N LYS D 202 " --> pdb=" O TYR D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 246 removed outlier: 5.007A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 273 removed outlier: 3.549A pdb=" N PHE D 261 " --> pdb=" O ASN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 294 removed outlier: 3.671A pdb=" N LEU D 291 " --> pdb=" O THR D 287 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) 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 removed outlier: 3.507A pdb=" N SER D 340 " --> pdb=" O SER D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 385 removed outlier: 3.606A pdb=" N LYS D 373 " --> pdb=" O ASP D 369 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER D 383 " --> pdb=" O GLN D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 404 through 414 removed outlier: 3.743A pdb=" N LYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 462 through 475 removed outlier: 3.887A 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 138 through 145 Processing helix chain 'E' and resid 162 through 178 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 246 removed outlier: 5.148A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 273 removed outlier: 3.567A pdb=" N THR E 262 " --> pdb=" O ILE E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 284 through 294 removed outlier: 3.756A pdb=" N GLY E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 removed outlier: 4.052A pdb=" N ASP E 315 " --> pdb=" O VAL E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.871A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 341 removed outlier: 4.131A pdb=" N SER E 340 " --> pdb=" O SER E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 385 removed outlier: 3.677A pdb=" N GLN E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 removed outlier: 3.619A pdb=" N THR E 437 " --> pdb=" O ARG E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 474 removed outlier: 3.997A pdb=" N ASP E 465 " --> pdb=" O GLY E 461 " (cutoff:3.500A) 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 175 Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 190 through 204 removed outlier: 3.598A pdb=" N LYS F 202 " --> pdb=" O TYR F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 246 removed outlier: 4.891A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 239 " --> pdb=" O THR F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 removed outlier: 3.963A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.629A 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 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 341 Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 364 through 392 removed outlier: 3.897A pdb=" N VAL F 370 " --> pdb=" O GLU F 366 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 396 removed outlier: 3.924A pdb=" N LEU F 396 " --> pdb=" O MET F 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 393 through 396' Processing helix chain 'F' and resid 397 through 414 removed outlier: 3.603A pdb=" N ARG F 412 " --> pdb=" O ARG F 408 " (cutoff:3.500A) 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 475 Processing helix chain 'G' and resid 3 through 54 removed outlier: 4.351A pdb=" N SER G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 101 removed outlier: 3.758A pdb=" N ALA G 92 " --> pdb=" O HIS G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 120 Processing helix chain 'G' and resid 139 through 153 removed outlier: 4.077A pdb=" N VAL G 153 " --> pdb=" O LYS G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 Processing helix chain 'G' and resid 184 through 190 Processing helix chain 'G' and resid 204 through 276 removed outlier: 3.602A pdb=" N SER G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 37 removed outlier: 6.703A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU A 68 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 93 " --> pdb=" O LEU A 54 " (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 110 removed outlier: 6.208A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR A 202 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL A 269 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 204 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASP A 271 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL A 206 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.208A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR A 202 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL A 269 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 204 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASP A 271 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL A 206 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A 172 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 77 through 78 removed outlier: 6.773A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS F 24 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL F 13 " --> pdb=" O HIS F 24 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 31 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (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 110 removed outlier: 6.593A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA B 266 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LEU B 326 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 268 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 328 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR B 270 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLU B 330 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.593A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA B 266 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LEU B 326 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 268 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 328 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR B 270 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLU B 330 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 62 through 68 removed outlier: 6.627A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN C 67 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LYS D 75 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS D 40 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA D 36 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN D 35 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 110 removed outlier: 6.279A pdb=" N ARG C 108 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA C 235 " --> pdb=" O ARG C 108 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 110 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR C 202 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL C 269 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 204 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASP C 271 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 206 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR C 270 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 108 through 110 removed outlier: 6.279A pdb=" N ARG C 108 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA C 235 " --> pdb=" O ARG C 108 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 110 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR C 202 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL C 269 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 204 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASP C 271 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 206 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR C 270 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.921A pdb=" N SER D 182 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL D 218 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE D 184 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLY D 220 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY D 186 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE D 153 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL D 310 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU D 155 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.449A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 17 removed outlier: 6.834A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.722A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.722A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE E 153 " --> pdb=" O GLN E 308 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS E 152 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N THR E 333 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY E 154 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU E 335 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE E 156 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC3, first strand: chain 'F' and resid 95 through 96 removed outlier: 3.717A pdb=" N PHE F 219 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS F 152 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N THR F 333 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY F 154 " --> pdb=" O THR F 333 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU F 335 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE F 156 " --> pdb=" O LEU F 335 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL F 334 " --> pdb=" O ASP F 352 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP F 352 " --> pdb=" O VAL F 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.322A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 105 through 109 removed outlier: 5.954A pdb=" N GLU G 72 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL G 108 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.61 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7304 1.34 - 1.46: 3262 1.46 - 1.58: 11347 1.58 - 1.69: 18 1.69 - 1.81: 47 Bond restraints: 21978 Sorted by residual: bond pdb=" O3 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.68e+00 bond pdb=" O4 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" O2 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.567 1.510 0.057 2.00e-02 2.50e+03 8.10e+00 bond pdb=" O1 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.565 1.509 0.056 2.00e-02 2.50e+03 7.92e+00 bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.46e+00 ... (remaining 21973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 28828 1.35 - 2.70: 913 2.70 - 4.04: 190 4.04 - 5.39: 32 5.39 - 6.74: 20 Bond angle restraints: 29983 Sorted by residual: angle pdb=" N ILE F 103 " pdb=" CA ILE F 103 " pdb=" C ILE F 103 " ideal model delta sigma weight residual 113.20 109.78 3.42 9.60e-01 1.09e+00 1.27e+01 angle pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 121.70 127.90 -6.20 1.80e+00 3.09e-01 1.19e+01 angle pdb=" C ASP F 256 " pdb=" N ASN F 257 " pdb=" CA ASN F 257 " ideal model delta sigma weight residual 121.70 127.34 -5.64 1.80e+00 3.09e-01 9.83e+00 angle pdb=" C3' ATP A 600 " pdb=" C4' ATP A 600 " pdb=" O4' ATP A 600 " ideal model delta sigma weight residual 105.22 101.23 3.99 1.30e+00 5.94e-01 9.43e+00 angle pdb=" C3' ATP F 600 " pdb=" C4' ATP F 600 " pdb=" O4' ATP F 600 " ideal model delta sigma weight residual 105.22 101.51 3.71 1.30e+00 5.94e-01 8.15e+00 ... (remaining 29978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 12678 21.80 - 43.61: 339 43.61 - 65.41: 57 65.41 - 87.22: 16 87.22 - 109.02: 2 Dihedral angle restraints: 13092 sinusoidal: 4381 harmonic: 8711 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 -60.00 -169.02 109.02 1 2.00e+01 2.50e-03 3.18e+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 -60.00 43.60 -103.60 1 2.00e+01 2.50e-03 2.96e+01 dihedral pdb=" CA GLY E 157 " pdb=" C GLY E 157 " pdb=" N GLY E 158 " pdb=" CA GLY E 158 " ideal model delta harmonic sigma weight residual -180.00 -153.63 -26.37 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 13089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3130 0.059 - 0.117: 455 0.117 - 0.176: 83 0.176 - 0.234: 3 0.234 - 0.293: 10 Chirality restraints: 3681 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 -2.93 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP F 600 " pdb=" C1' ATP F 600 " pdb=" C3' ATP F 600 " pdb=" O2' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3678 not shown) Planarity restraints: 3859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 41 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO D 42 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 42 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 42 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 102 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 103 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 146 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 147 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 147 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 147 " -0.023 5.00e-02 4.00e+02 ... (remaining 3856 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 49 2.47 - 3.07: 15989 3.07 - 3.68: 31349 3.68 - 4.29: 46312 4.29 - 4.90: 76933 Nonbonded interactions: 170632 Sorted by model distance: nonbonded pdb="MG MG D 601 " pdb=" O2 PO4 D 602 " model vdw 1.858 2.170 nonbonded pdb=" O1G ATP F 600 " pdb="MG MG F 601 " model vdw 1.886 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.911 2.170 nonbonded pdb=" O1G ATP B 600 " pdb="MG MG B 601 " model vdw 1.936 2.170 nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 1.983 2.170 ... (remaining 170627 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 29 through 51 or (resid 52 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 55 or (resid 56 and (na \ me N or name CA or name C or name O or name CB )) or resid 57 through 80 or (res \ id 81 and (name N or name CA or name C or name O or name CB )) or resid 82 throu \ gh 155 or (resid 156 through 157 and (name N or name CA or name C or name O or n \ ame CB )) or resid 158 through 164 or (resid 165 and (name N or name CA or name \ C or name O or name CB )) or resid 166 through 167 or (resid 168 and (name N or \ name CA or name C or name O or name CB )) or resid 169 through 171 or (resid 172 \ and (name N or name CA or name C or name O or name CB )) or resid 173 through 1 \ 87 or (resid 188 and (name N or name CA or name C or name O or name CB )) or res \ id 189 through 192 or (resid 193 and (name N or name CA or name C or name O or n \ ame CB )) or resid 194 through 195 or (resid 196 through 197 and (name N or name \ CA or name C or name O or name CB )) or resid 198 through 239 or (resid 240 thr \ ough 242 and (name N or name CA or name C or name O or name CB )) or resid 243 t \ hrough 306 or (resid 307 through 309 and (name N or name CA or name C or name O \ or name CB )) or resid 310 through 325 or (resid 326 and (name N or name CA or n \ ame C or name O or name CB )) or resid 327 through 382 or (resid 383 through 384 \ and (name N or name CA or name C or name O or name CB )) or resid 385 or (resid \ 386 and (name N or name CA or name C or name O or name CB )) or resid 387 throu \ gh 417 or (resid 418 and (name N or name CA or name C or name O or name CB )) or \ resid 419 through 420 or (resid 421 through 422 and (name N or name CA or name \ C or name O or name CB )) or resid 423 through 428 or (resid 429 and (name N or \ name CA or name C or name O or name CB )) or resid 430 through 431 or (resid 432 \ and (name N or name CA or name C or name O or name CB )) or resid 433 through 4 \ 42 or (resid 443 through 444 and (name N or name CA or name C or name O or name \ CB )) or resid 445 through 453 or (resid 454 and (name N or name CA or name C or \ name O or name CB )) or resid 455 through 464 or (resid 465 through 467 and (na \ me N or name CA or name C or name O or name CB )) or resid 468 through 474 or (r \ esid 475 through 477 and (name N or name CA or name C or name O or name CB )) or \ (resid 480 through 481 and (name N or name CA or name C or name O or name CB )) \ or resid 482 through 491 or (resid 492 through 508 and (name N or name CA or na \ me C or name O or name CB )) or resid 600 through 601)) selection = (chain 'B' and (resid 29 through 51 or (resid 52 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 65 or (resid 66 and (na \ me N or name CA or name C or name O or name CB )) or resid 67 through 145 or (re \ sid 146 and (name N or name CA or name C or name O or name CB )) or resid 147 th \ rough 164 or (resid 165 and (name N or name CA or name C or name O or name CB )) \ or resid 166 through 173 or (resid 174 and (name N or name CA or name C or name \ O or name CB )) or resid 175 through 187 or (resid 188 and (name N or name CA o \ r name C or name O or name CB )) or resid 189 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 throug \ h 306 or (resid 307 through 309 and (name N or name CA or name C or name O or na \ me CB )) or resid 310 through 316 or (resid 317 through 318 and (name N or name \ CA or name C or name O or name CB )) or resid 319 through 325 or (resid 326 and \ (name N or name CA or name C or name O or name CB )) or resid 327 through 334 or \ (resid 335 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 6 through 352 or (resid 353 and (name N or name CA or name C or name O or name C \ B )) or resid 354 through 356 or (resid 357 through 358 and (name N or name CA o \ r name C or name O or name CB )) or resid 359 through 392 or (resid 393 through \ 395 and (name N or name CA or name C or name O or name CB )) or resid 396 throug \ h 399 or (resid 400 through 402 and (name N or name CA or name C or name O or na \ me CB )) or (resid 413 through 418 and (name N or name CA or name C or name O or \ name CB )) or resid 419 through 425 or (resid 426 and (name N or name CA or nam \ e C or name O or name CB )) or resid 427 through 450 or (resid 451 and (name N o \ r name CA or name C or name O or name CB )) or resid 452 through 461 or (resid 4 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 463 through \ 476 or (resid 479 through 481 and (name N or name CA or name C or name O or nam \ e CB )) or resid 482 through 601)) selection = (chain 'C' and (resid 29 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 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 65 or (resid 66 and ( \ name N or name CA or name C or name O or name CB )) or resid 67 through 68 or (r \ esid 69 and (name N or name CA or name C or name O or name CB )) or resid 70 thr \ ough 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) or \ resid 82 through 85 or (resid 86 and (name N or name CA or name C or name O or \ name CB )) or resid 87 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 or (resid 156 through 157 and \ (name N or name CA or name C or name O or name CB )) or resid 158 through 167 o \ r (resid 168 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 69 through 173 or (resid 174 and (name N or name CA or name C or name O or name \ CB )) or resid 175 through 192 or (resid 193 and (name N or name CA or name C or \ name O or name CB )) or resid 194 through 195 or (resid 196 through 197 and (na \ me N or name CA or name C or name O or name CB )) or resid 198 through 239 or (r \ esid 240 through 242 and (name N or name CA or name C or name O or name CB )) or \ resid 243 through 270 or (resid 271 through 272 and (name N or name CA or name \ C or name O or name CB )) or 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 315 o \ r (resid 316 through 318 and (name N or name CA or name C or name O or name CB ) \ ) or resid 319 through 352 or (resid 353 and (name N or name CA or name C or nam \ e O or name CB )) or resid 354 through 357 or (resid 358 and (name N or name CA \ or name C or name O or name CB )) or resid 359 through 382 or (resid 383 through \ 384 and (name N or name CA or name C or name O or name CB )) or resid 385 or (r \ esid 386 and (name N or name CA or name C or name O or name CB )) or resid 387 t \ hrough 392 or (resid 393 through 395 and (name N or name CA or name C or name O \ or name CB )) or resid 396 through 399 or (resid 400 through 402 and (name N or \ name CA or name C or name O or name CB )) or (resid 413 through 418 and (name N \ or name CA or name C or name O or name CB )) or resid 419 through 420 or (resid \ 421 through 422 and (name N or name CA or name C or name O or name CB )) or resi \ d 423 or (resid 424 through 426 and (name N or name CA or name C or name O or na \ me CB )) or resid 427 through 428 or (resid 429 and (name N or name CA or name C \ or name O or name CB )) or resid 430 through 431 or (resid 432 and (name N or n \ ame CA or name C or name O or name CB )) or resid 433 or (resid 434 and (name N \ or name CA or name C or name O or name CB )) or resid 435 through 441 or (resid \ 442 through 444 and (name N or name CA or name C or name O or name CB )) or resi \ d 445 through 450 or (resid 451 and (name N or name CA or name C or name O or na \ me CB )) or resid 452 through 453 or (resid 454 and (name N or name CA or name C \ or name O or name CB )) or resid 455 through 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 465 or \ (resid 466 through 467 and (name N or name CA or name C or name O or name CB )) \ or resid 468 through 470 or (resid 471 and (name N or name CA or name C or name \ O or name CB )) or resid 472 through 474 or (resid 475 through 477 and (name N \ or name CA or name C or name O or name CB )) or (resid 480 through 481 and (name \ N or name CA or name C or name O or name CB )) or resid 482 through 487 or (res \ id 488 and (name N or name CA or name C or name O or name CB )) or resid 489 or \ (resid 490 and (name N or name CA or name C or name O or name CB )) or resid 491 \ or (resid 492 through 508 and (name N or name CA or name C or name O or name CB \ )) or resid 600 through 601)) } ncs_group { reference = (chain 'D' 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 through 34 or (resid 35 through \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 or (resi \ d 38 and (name N or name CA or name C or name O or name CB )) or resid 39 throug \ h 48 or (resid 49 and (name N or name CA or name C or name O or name CB )) or re \ sid 50 through 67 or (resid 68 and (name N or name CA or name C or name O or nam \ e CB )) or resid 69 through 77 or (resid 78 and (name N or name CA or name C or \ name O or name CB )) or resid 79 through 89 or (resid 90 and (name N or name CA \ or name C or name O or name CB )) or resid 91 or (resid 92 and (name N or name C \ A or name C or name O or name CB )) or resid 93 through 100 or (resid 101 and (n \ ame N or name CA or name C or name O or name CB )) or resid 102 through 103 or ( \ resid 104 through 105 and (name N or name CA or name C or name O or name CB )) o \ r resid 106 through 109 or (resid 110 and (name N or name CA or name C or name O \ or name CB )) or resid 111 through 131 or (resid 132 and (name N or name CA or \ name C or name O or name CB )) or resid 133 through 134 or (resid 135 and (name \ N or name CA or name C or name O or name CB )) or resid 136 through 142 or (resi \ d 143 and (name N or name CA or name C or name O or name CB )) or resid 144 thro \ ugh 162 or (resid 163 through 164 and (name N or name CA or name C or name O or \ name CB )) or resid 165 through 167 or (resid 168 through 169 and (name N or nam \ e CA or name C or name O or name CB )) or resid 170 through 175 or (resid 176 th \ rough 177 and (name N or name CA or name C or name O or name CB )) or resid 178 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 208 or (resid 209 through 210 and (name N or name CA or \ name C or name O or name CB )) or resid 211 through 213 or (resid 214 and (name \ N or name CA or name C or name O or name CB )) or resid 215 through 220 or (resi \ d 221 through 222 and (name N or name CA or name C or name O or name CB )) or re \ sid 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) o \ r resid 225 through 240 or (resid 241 and (name N or name CA or name C or name O \ or name CB )) or resid 242 through 255 or (resid 256 through 257 and (name N or \ name CA or name C or name O or name CB )) or resid 258 through 266 or (resid 26 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 268 through \ 281 or (resid 282 and (name N or name CA or name C or name O or name CB )) or re \ sid 283 through 293 or (resid 294 and (name N or name CA or name C or name O or \ name CB )) or resid 295 through 299 or (resid 300 through 301 and (name N or nam \ e CA or name C or name O or name CB )) or resid 302 through 307 or (resid 308 th \ rough 309 and (name N or name CA or name C or name O or name CB )) or resid 310 \ or (resid 311 and (name N or name CA or name C or name O or name CB )) or resid \ 312 through 314 or (resid 315 through 316 and (name N or name CA or name C or na \ me O or name CB )) or resid 317 through 328 or (resid 329 and (name N or name CA \ or name C or name O or name CB )) or resid 330 through 336 or (resid 337 and (n \ ame N or name CA or name C or name O or name CB )) or resid 338 through 340 or ( \ resid 341 through 342 and (name N or name CA or name C or name O or name CB )) o \ r resid 343 through 353 or (resid 354 and (name N or name CA or name C or name O \ or name CB )) or resid 355 through 372 or (resid 373 and (name N or name CA or \ name C or name O or name CB )) or resid 374 through 380 or (resid 381 through 38 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 383 through \ 386 or (resid 387 and (name N or name CA or name C or name O or name CB )) or re \ sid 403 through 407 or (resid 408 through 410 and (name N or name CA or name C o \ r name O or name CB )) or resid 411 or (resid 412 and (name N or name CA or name \ C or name O or name CB )) or resid 413 through 423 or (resid 424 and (name N or \ name CA or name C or name O or name CB )) or resid 425 through 426 or (resid 42 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 428 through \ 430 or (resid 431 and (name N or name CA or name C or name O or name CB )) or re \ sid 432 through 434 or (resid 435 through 436 and (name N or name CA or name C o \ r name O or name CB )) or resid 437 through 444 or (resid 445 through 446 and (n \ ame N or name CA or name C or name O or name CB )) or resid 447 or (resid 448 th \ rough 449 and (name N or name CA or name C or name O or name CB )) or resid 450 \ or (resid 455 through 457 and (name N or name CA or name C or name O or name CB \ )) or resid 458 through 466 or (resid 467 through 474 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'E' and ((resid 9 and (name N or name CA or name C or name O or name CB ) \ ) or resid 10 through 28 or (resid 29 and (name N or name CA or name C or name O \ or name CB )) or resid 30 through 74 or (resid 75 and (name N or name CA or nam \ e C or name O or name CB )) or resid 76 through 100 or (resid 101 and (name N or \ name CA or name C or name O or name CB )) or resid 102 through 111 or (resid 11 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 113 through \ 126 or (resid 127 and (name N or name CA or name C or name O or name CB )) or re \ sid 128 through 131 or (resid 132 and (name N or name CA or name C or name O or \ name CB )) or resid 133 through 141 or (resid 142 through 143 and (name N or nam \ e CA or name C or name O or name CB )) or resid 144 through 162 or (resid 163 th \ rough 164 and (name N or name CA or name C or name O or name CB )) or resid 165 \ through 199 or (resid 200 and (name N or name CA or name C or name O or name CB \ )) or resid 201 through 207 or (resid 208 through 210 and (name N or name CA or \ name C or name O or name CB )) or resid 211 through 221 or (resid 222 and (name \ N or name CA or name C or name O or name CB )) or resid 223 or (resid 224 and (n \ ame N or name CA or name C or name O or name CB )) or resid 225 through 255 or ( \ resid 256 through 257 and (name N or name CA or name C or name O or name CB )) o \ r resid 258 through 287 or (resid 288 and (name N or name CA or name C or name O \ or name CB )) or resid 289 through 307 or (resid 308 through 309 and (name N or \ name CA or name C or name O or name CB )) or resid 310 through 328 or (resid 32 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 330 through \ 341 or (resid 342 and (name N or name CA or name C or name O or name CB )) or re \ sid 343 through 348 or (resid 349 and (name N or name CA or name C or name O or \ name CB )) or resid 350 or (resid 351 through 352 and (name N or name CA or name \ C or name O or name CB )) or resid 353 or (resid 354 and (name N or name CA or \ name C or name O or name CB )) or resid 355 through 368 or (resid 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 through 387 or resid \ 403 through 409 or (resid 410 and (name N or name CA or name C or name O or nam \ e CB )) or resid 411 through 415 or (resid 416 and (name N or name CA or name C \ or name O or name CB )) or resid 417 through 430 or (resid 431 and (name N or na \ me CA or name C or name O or name CB )) or resid 432 through 437 or (resid 438 t \ hrough 439 and (name N or name CA or name C or name O or name CB )) or resid 440 \ through 448 or (resid 449 and (name N or name CA or name C or name O or name CB \ )) or resid 450 through 474)) selection = (chain 'F' and (resid 9 through 21 or (resid 22 and (name N or name CA or name C \ or name O or name CB )) or resid 23 through 26 or (resid 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 through 34 or (resid 35 throug \ h 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or re \ sid 57 through 64 or (resid 65 and (name N or name CA or name C or name O or nam \ e CB )) or resid 66 through 77 or (resid 78 and (name N or name CA or name C or \ name O or name CB )) or resid 79 through 91 or (resid 92 and (name N or name CA \ or name C or name O or name CB )) or resid 93 through 103 or (resid 104 through \ 105 and (name N or name CA or name C or name O or name CB )) or resid 106 throug \ h 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 or (resid 112 and (name N or name CA or name C or name O or name CB )) \ or resid 113 through 119 or (resid 120 and (name N or name CA or name C or name \ O or name CB )) or resid 121 through 126 or (resid 127 and (name N or name CA o \ r name C or name O or name CB )) or resid 128 through 134 or (resid 135 and (nam \ e N or name CA or name C or name O or name CB )) or resid 136 through 141 or (re \ sid 142 through 143 and (name N or name CA or name C or name O or name CB )) or \ resid 144 through 163 or (resid 164 and (name N or name CA or name C or name O o \ r name CB )) or resid 165 through 167 or (resid 168 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 175 or (resid 176 \ through 177 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 8 through 199 or (resid 200 and (name N or name CA or name C or name O or name C \ B )) or resid 201 or (resid 202 and (name N or name CA or name C or name O or na \ me CB )) or resid 203 through 207 or (resid 208 through 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 or (resid 214 and (name N \ or name CA or name C or name O or name CB )) or resid 215 through 240 or (resid \ 241 and (name N or name CA or name C or name O or name CB )) or resid 242 throug \ h 244 or (resid 245 through 247 and (name N or name CA or name C or name O or na \ me CB )) or resid 248 or (resid 249 through 250 and (name N or name CA or name C \ or name O or name CB )) or resid 251 through 266 or (resid 267 and (name N or n \ ame CA or name C or name O or name CB )) or resid 268 through 281 or (resid 282 \ and (name N or name CA or name C or name O or name CB )) or resid 283 through 28 \ 7 or (resid 288 and (name N or name CA or name C or name O or name CB )) or resi \ d 289 through 300 or (resid 301 and (name N or name CA or name C or name O or na \ me CB )) or resid 302 through 310 or (resid 311 and (name N or name CA or name C \ or name O or name CB )) or resid 312 through 314 or (resid 315 through 316 and \ (name N or name CA or name C or name O or name CB )) or resid 317 through 336 or \ (resid 337 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 8 through 340 or (resid 341 through 342 and (name N or name CA or name C or name \ O or name CB )) or resid 343 through 348 or (resid 349 and (name N or name CA o \ r name C or name O or name CB )) or resid 350 or (resid 351 through 352 and (nam \ e N or name CA or name C or name O or name CB )) or resid 353 through 358 or (re \ sid 359 through 361 and (name N or name CA or name C or name O or name CB )) or \ resid 362 through 365 or (resid 366 and (name N or name CA or name C or name O o \ r name CB )) or resid 367 through 368 or (resid 369 and (name N or name CA or na \ me C or name O or name CB )) or resid 370 through 372 or (resid 373 and (name N \ or name CA or name C or name O or name CB )) or resid 374 through 375 or (resid \ 376 and (name N or name CA or name C or name O or name CB )) or resid 377 throug \ h 380 or (resid 381 through 382 and (name N or name CA or name C or name O or na \ me CB )) or resid 383 or (resid 384 through 387 and (name N or name CA or name C \ or name O or name CB )) or resid 403 through 405 or (resid 406 through 410 and \ (name N or name CA or name C or name O or name CB )) or resid 411 or (resid 412 \ and (name N or name CA or name C or name O or name CB )) or resid 413 through 41 \ 5 or (resid 416 and (name N or name CA or name C or name O or name CB )) or resi \ d 417 through 423 or (resid 424 and (name N or name CA or name C or name O or na \ me CB )) or resid 425 through 426 or (resid 427 and (name N or name CA or name C \ or name O or name CB )) or resid 428 through 429 or (resid 430 through 431 and \ (name N or name CA or name C or name O or name CB )) or resid 432 through 434 or \ (resid 435 through 436 and (name N or name CA or name C or name O or name CB )) \ or resid 437 or (resid 438 through 439 and (name N or name CA or name C or name \ O or name CB )) or resid 440 through 444 or (resid 445 through 446 and (name N \ or name CA or name C or name O or name CB )) or resid 447 or (resid 448 through \ 449 and (name N or name CA or name C or name O or name CB )) or resid 450 or (re \ sid 455 through 457 and (name N or name CA or name C or name O or name CB )) or \ resid 458 or (resid 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 or (resid 467 through 474 and (name N or name CA o \ r name C or name O or name CB )))) } 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.320 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 0.059 21978 Z= 0.138 Angle : 0.619 6.741 29983 Z= 0.341 Chirality : 0.046 0.293 3681 Planarity : 0.004 0.047 3859 Dihedral : 11.433 109.023 7512 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3044 helix: 0.41 (0.14), residues: 1204 sheet: -0.04 (0.23), residues: 487 loop : -0.04 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 462 TYR 0.021 0.002 TYR G 255 PHE 0.020 0.001 PHE E 326 TRP 0.020 0.001 TRP C 258 HIS 0.010 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (21978) covalent geometry : angle 0.61945 / 0.34 (29983) hydrogen bonds : bond 0.14670 / 10.04 ( 1099) hydrogen bonds : angle 6.83134 / 4.93 ( 3159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 932 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 SER cc_start: 0.8135 (m) cc_final: 0.7486 (t) REVERT: A 199 LYS cc_start: 0.8227 (mttt) cc_final: 0.8015 (mttt) REVERT: A 246 TYR cc_start: 0.8430 (t80) cc_final: 0.8216 (t80) REVERT: A 308 LEU cc_start: 0.8225 (mt) cc_final: 0.8006 (mt) REVERT: A 466 PHE cc_start: 0.8507 (t80) cc_final: 0.8202 (t80) REVERT: A 477 ASN cc_start: 0.7900 (m-40) cc_final: 0.7417 (t0) REVERT: B 44 PHE cc_start: 0.8880 (t80) cc_final: 0.8676 (t80) REVERT: B 84 VAL cc_start: 0.9030 (t) cc_final: 0.8820 (p) REVERT: B 91 LYS cc_start: 0.8322 (mttt) cc_final: 0.8109 (mtpp) REVERT: B 146 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 150 THR cc_start: 0.8241 (p) cc_final: 0.7996 (p) REVERT: B 187 ASN cc_start: 0.9155 (t0) cc_final: 0.8849 (t0) REVERT: B 228 MET cc_start: 0.8885 (tpt) cc_final: 0.8436 (tpp) REVERT: B 251 THR cc_start: 0.9275 (p) cc_final: 0.9061 (p) REVERT: B 262 ASN cc_start: 0.8614 (m-40) cc_final: 0.8401 (m-40) REVERT: B 448 TYR cc_start: 0.7986 (t80) cc_final: 0.7267 (t80) REVERT: B 480 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8296 (tm-30) REVERT: B 486 ARG cc_start: 0.8639 (ttt180) cc_final: 0.8398 (mtp85) REVERT: C 72 GLN cc_start: 0.7238 (pt0) cc_final: 0.6767 (pt0) REVERT: C 115 ASN cc_start: 0.8774 (m-40) cc_final: 0.8548 (m-40) REVERT: C 130 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7461 (ttp80) REVERT: C 152 LEU cc_start: 0.9388 (mt) cc_final: 0.9173 (mt) REVERT: C 178 THR cc_start: 0.8418 (m) cc_final: 0.8213 (m) REVERT: C 294 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8719 (mt-10) REVERT: C 364 ARG cc_start: 0.8862 (mtt180) cc_final: 0.8112 (mtt180) REVERT: C 368 ASN cc_start: 0.8266 (t0) cc_final: 0.7826 (t0) REVERT: C 369 VAL cc_start: 0.8931 (t) cc_final: 0.8564 (p) REVERT: C 383 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7914 (mmmt) REVERT: C 398 GLN cc_start: 0.8867 (mt0) cc_final: 0.8350 (mt0) REVERT: C 425 ARG cc_start: 0.8592 (mtt90) cc_final: 0.8331 (mtt90) REVERT: C 455 LEU cc_start: 0.8316 (tp) cc_final: 0.7990 (tp) REVERT: C 478 HIS cc_start: 0.7669 (m-70) cc_final: 0.7326 (m-70) REVERT: D 12 LYS cc_start: 0.8633 (mptt) cc_final: 0.8142 (mtpp) REVERT: D 77 LEU cc_start: 0.8134 (tp) cc_final: 0.7909 (tt) REVERT: D 90 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7323 (mm-30) REVERT: D 110 LYS cc_start: 0.8187 (mttt) cc_final: 0.7920 (mttt) REVERT: D 176 LYS cc_start: 0.8498 (tttt) cc_final: 0.8173 (tppt) REVERT: D 198 TYR cc_start: 0.8910 (t80) cc_final: 0.8704 (t80) REVERT: D 203 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8258 (mt-10) REVERT: D 332 THR cc_start: 0.8562 (p) cc_final: 0.8322 (m) REVERT: D 356 ARG cc_start: 0.7799 (ttt90) cc_final: 0.7418 (ttm-80) REVERT: D 375 GLN cc_start: 0.7918 (mt0) cc_final: 0.7392 (tm-30) REVERT: D 412 ARG cc_start: 0.7794 (mtt90) cc_final: 0.7296 (mtt-85) REVERT: D 440 SER cc_start: 0.9096 (m) cc_final: 0.8888 (t) REVERT: E 128 SER cc_start: 0.9125 (t) cc_final: 0.8891 (p) REVERT: E 196 ASP cc_start: 0.8218 (t0) cc_final: 0.7830 (t0) REVERT: E 207 ILE cc_start: 0.9180 (mt) cc_final: 0.8863 (tt) REVERT: E 277 SER cc_start: 0.8320 (t) cc_final: 0.8097 (m) REVERT: E 308 GLN cc_start: 0.8923 (mt0) cc_final: 0.8696 (mt0) REVERT: E 352 ASP cc_start: 0.7559 (m-30) cc_final: 0.7280 (m-30) REVERT: E 353 SER cc_start: 0.8538 (m) cc_final: 0.8308 (p) REVERT: E 441 PHE cc_start: 0.8718 (m-80) cc_final: 0.8469 (m-80) REVERT: F 35 ASN cc_start: 0.9145 (m-40) cc_final: 0.8752 (m-40) REVERT: F 128 SER cc_start: 0.9222 (t) cc_final: 0.8997 (m) REVERT: F 201 MET cc_start: 0.8546 (mmt) cc_final: 0.8221 (mmt) REVERT: F 202 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8199 (mtmm) REVERT: F 237 LEU cc_start: 0.8781 (mp) cc_final: 0.8519 (mp) REVERT: F 259 PHE cc_start: 0.7704 (t80) cc_final: 0.7400 (t80) REVERT: F 262 THR cc_start: 0.8989 (m) cc_final: 0.8695 (p) REVERT: F 281 TYR cc_start: 0.8866 (m-80) cc_final: 0.8362 (m-80) REVERT: F 285 LEU cc_start: 0.8474 (tt) cc_final: 0.8043 (tp) REVERT: F 288 ASP cc_start: 0.7783 (m-30) cc_final: 0.7093 (m-30) REVERT: F 293 GLN cc_start: 0.8727 (tt0) cc_final: 0.8195 (tt0) REVERT: F 349 ASP cc_start: 0.8479 (t0) cc_final: 0.8104 (t0) REVERT: F 351 LEU cc_start: 0.9363 (mt) cc_final: 0.9095 (mt) REVERT: F 356 ARG cc_start: 0.8273 (tpt170) cc_final: 0.7985 (ttp-170) REVERT: F 369 ASP cc_start: 0.8180 (t0) cc_final: 0.7939 (t70) REVERT: F 375 GLN cc_start: 0.9037 (mt0) cc_final: 0.8540 (mm-40) REVERT: F 449 TYR cc_start: 0.8735 (m-80) cc_final: 0.8473 (m-80) REVERT: F 463 ILE cc_start: 0.7868 (tp) cc_final: 0.7566 (tp) REVERT: F 464 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8138 (mt-10) REVERT: G 3 LEU cc_start: 0.6845 (tt) cc_final: 0.6538 (tp) REVERT: G 4 LYS cc_start: 0.8312 (tptt) cc_final: 0.7969 (tppp) REVERT: G 24 LYS cc_start: 0.4822 (tmtt) cc_final: 0.4323 (mtmt) REVERT: G 214 LEU cc_start: 0.8397 (tp) cc_final: 0.8126 (tp) REVERT: G 247 MET cc_start: 0.7066 (tpt) cc_final: 0.6599 (tpp) outliers start: 1 outliers final: 0 residues processed: 933 average time/residue: 0.1451 time to fit residues: 209.5347 Evaluate side-chains 747 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 747 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 GLN A 387 GLN A 398 GLN B 381 GLN B 452 ASN C 145 HIS C 387 GLN D 52 GLN D 168 GLN E 24 HIS E 308 GLN ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN F 379 GLN G 217 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.131306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.113459 restraints weight = 36232.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.116920 restraints weight = 18721.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.119229 restraints weight = 11185.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.120711 restraints weight = 7437.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.121726 restraints weight = 5404.837| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21978 Z= 0.194 Angle : 0.642 8.004 29983 Z= 0.337 Chirality : 0.047 0.164 3681 Planarity : 0.005 0.054 3859 Dihedral : 5.880 94.597 3299 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.44 % Allowed : 15.02 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 3044 helix: 1.03 (0.15), residues: 1204 sheet: -0.07 (0.23), residues: 476 loop : 0.06 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 166 TYR 0.020 0.002 TYR B 399 PHE 0.029 0.002 PHE D 441 TRP 0.016 0.002 TRP B 191 HIS 0.005 0.001 HIS C 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (21978) covalent geometry : angle 0.64170 / 0.34 (29983) hydrogen bonds : bond 0.04826 / 3.29 ( 1099) hydrogen bonds : angle 5.37020 / 3.92 ( 3159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 780 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 SER cc_start: 0.8520 (m) cc_final: 0.7978 (t) REVERT: A 159 VAL cc_start: 0.9171 (t) cc_final: 0.8789 (m) REVERT: A 246 TYR cc_start: 0.8554 (t80) cc_final: 0.8203 (t80) REVERT: A 308 LEU cc_start: 0.8186 (mt) cc_final: 0.7958 (mt) REVERT: A 309 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7147 (mm-30) REVERT: A 399 TYR cc_start: 0.7662 (t80) cc_final: 0.7228 (t80) REVERT: A 477 ASN cc_start: 0.7869 (m-40) cc_final: 0.7437 (t0) REVERT: B 84 VAL cc_start: 0.8906 (t) cc_final: 0.8600 (p) REVERT: B 91 LYS cc_start: 0.8355 (mttt) cc_final: 0.8116 (mtpp) REVERT: B 228 MET cc_start: 0.8867 (tpt) cc_final: 0.8406 (tpp) REVERT: B 299 ASP cc_start: 0.8896 (p0) cc_final: 0.8650 (p0) REVERT: B 309 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7497 (mm-30) REVERT: B 317 LYS cc_start: 0.8437 (ttpt) cc_final: 0.8175 (ptmm) REVERT: B 342 THR cc_start: 0.9405 (p) cc_final: 0.9160 (t) REVERT: B 349 ASP cc_start: 0.8043 (m-30) cc_final: 0.6744 (m-30) REVERT: B 448 TYR cc_start: 0.8113 (t80) cc_final: 0.7258 (t80) REVERT: B 480 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8348 (tm-30) REVERT: B 486 ARG cc_start: 0.8511 (ttt180) cc_final: 0.8177 (mtp85) REVERT: C 78 PHE cc_start: 0.9002 (m-80) cc_final: 0.8759 (m-10) REVERT: C 93 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7813 (t) REVERT: C 142 ARG cc_start: 0.8639 (tmm-80) cc_final: 0.8305 (tmm-80) REVERT: C 223 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8709 (mm-30) REVERT: C 364 ARG cc_start: 0.8883 (mtt180) cc_final: 0.8488 (mtt180) REVERT: C 383 LYS cc_start: 0.8410 (mmtm) cc_final: 0.8126 (mmmt) REVERT: C 398 GLN cc_start: 0.8698 (mt0) cc_final: 0.8490 (mt0) REVERT: C 425 ARG cc_start: 0.8685 (mtt90) cc_final: 0.8033 (mtt90) REVERT: C 428 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8649 (mm110) REVERT: C 434 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: C 440 THR cc_start: 0.8860 (p) cc_final: 0.8615 (t) REVERT: C 478 HIS cc_start: 0.7932 (m-70) cc_final: 0.7709 (m90) REVERT: D 12 LYS cc_start: 0.8641 (mptt) cc_final: 0.8256 (mtpp) REVERT: D 89 ARG cc_start: 0.8373 (mmt-90) cc_final: 0.7213 (ttp80) REVERT: D 90 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7272 (mm-30) REVERT: D 110 LYS cc_start: 0.7920 (mttt) cc_final: 0.7689 (mttt) REVERT: D 190 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8253 (mtm-85) REVERT: D 267 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7924 (mt-10) REVERT: D 277 SER cc_start: 0.8718 (t) cc_final: 0.8350 (m) REVERT: D 282 GLN cc_start: 0.9302 (pm20) cc_final: 0.8743 (pm20) REVERT: D 329 LEU cc_start: 0.8877 (mt) cc_final: 0.8497 (mt) REVERT: D 332 THR cc_start: 0.8514 (p) cc_final: 0.8258 (m) REVERT: D 356 ARG cc_start: 0.7635 (ttt90) cc_final: 0.7386 (ttm-80) REVERT: D 375 GLN cc_start: 0.7952 (mt0) cc_final: 0.7516 (tm-30) REVERT: E 103 ILE cc_start: 0.9127 (pt) cc_final: 0.8902 (pt) REVERT: E 128 SER cc_start: 0.9081 (t) cc_final: 0.8802 (p) REVERT: E 201 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8186 (mpp) REVERT: E 207 ILE cc_start: 0.9063 (mt) cc_final: 0.8649 (tt) REVERT: E 353 SER cc_start: 0.8858 (m) cc_final: 0.8535 (p) REVERT: E 354 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7694 (mtpp) REVERT: F 35 ASN cc_start: 0.9173 (m-40) cc_final: 0.8796 (m-40) REVERT: F 61 THR cc_start: 0.8435 (p) cc_final: 0.8222 (t) REVERT: F 192 ARG cc_start: 0.9058 (ttp-110) cc_final: 0.8549 (ttp80) REVERT: F 201 MET cc_start: 0.8631 (mmt) cc_final: 0.8232 (mmt) REVERT: F 202 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8173 (mtmm) REVERT: F 237 LEU cc_start: 0.8771 (mp) cc_final: 0.8459 (mp) REVERT: F 262 THR cc_start: 0.8947 (m) cc_final: 0.8534 (p) REVERT: F 281 TYR cc_start: 0.9003 (m-80) cc_final: 0.8706 (m-80) REVERT: F 282 GLN cc_start: 0.9279 (pm20) cc_final: 0.8215 (pm20) REVERT: F 288 ASP cc_start: 0.8118 (m-30) cc_final: 0.7598 (m-30) REVERT: F 293 GLN cc_start: 0.8565 (tt0) cc_final: 0.8340 (tt0) REVERT: F 349 ASP cc_start: 0.8519 (t0) cc_final: 0.8196 (t0) REVERT: F 351 LEU cc_start: 0.9353 (mt) cc_final: 0.8694 (mt) REVERT: F 356 ARG cc_start: 0.8493 (tpt170) cc_final: 0.8214 (ttp-170) REVERT: F 375 GLN cc_start: 0.9005 (mt0) cc_final: 0.8588 (mm-40) REVERT: F 449 TYR cc_start: 0.8867 (m-80) cc_final: 0.8640 (m-80) REVERT: F 463 ILE cc_start: 0.7883 (tp) cc_final: 0.7574 (tp) REVERT: F 464 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7920 (mt-10) REVERT: G 4 LYS cc_start: 0.8376 (tptt) cc_final: 0.8037 (tppp) REVERT: G 24 LYS cc_start: 0.5198 (tmtt) cc_final: 0.4638 (mtpt) REVERT: G 214 LEU cc_start: 0.8455 (tp) cc_final: 0.8220 (tp) REVERT: G 247 MET cc_start: 0.7256 (tpt) cc_final: 0.6760 (tpp) REVERT: G 250 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.7770 (mtm180) outliers start: 68 outliers final: 41 residues processed: 806 average time/residue: 0.1374 time to fit residues: 174.0513 Evaluate side-chains 758 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 714 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain G residue 29 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 207 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 276 optimal weight: 0.0170 chunk 273 optimal weight: 1.9990 chunk 270 optimal weight: 0.0030 chunk 4 optimal weight: 1.9990 overall best weight: 0.5028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 ASN C 387 GLN E 24 HIS E 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.135390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.117369 restraints weight = 35936.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.120944 restraints weight = 18395.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.123276 restraints weight = 10916.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.124748 restraints weight = 7230.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.125840 restraints weight = 5262.685| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21978 Z= 0.113 Angle : 0.562 8.411 29983 Z= 0.290 Chirality : 0.044 0.155 3681 Planarity : 0.004 0.055 3859 Dihedral : 5.333 96.484 3299 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.88 % Allowed : 19.37 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.16), residues: 3044 helix: 1.30 (0.15), residues: 1216 sheet: -0.10 (0.23), residues: 469 loop : 0.21 (0.18), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 190 TYR 0.020 0.001 TYR C 246 PHE 0.020 0.002 PHE A 44 TRP 0.007 0.001 TRP A 258 HIS 0.006 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (21978) covalent geometry : angle 0.56159 / 0.29 (29983) hydrogen bonds : bond 0.03953 / 2.72 ( 1099) hydrogen bonds : angle 4.89495 / 3.56 ( 3159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 773 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 SER cc_start: 0.8497 (m) cc_final: 0.7931 (t) REVERT: A 159 VAL cc_start: 0.9272 (t) cc_final: 0.8924 (m) REVERT: A 187 ASN cc_start: 0.9037 (t0) cc_final: 0.8561 (t0) REVERT: A 196 ASP cc_start: 0.6997 (t0) cc_final: 0.6610 (t0) REVERT: A 199 LYS cc_start: 0.8173 (mttt) cc_final: 0.7882 (mmtp) REVERT: A 221 THR cc_start: 0.8546 (m) cc_final: 0.8289 (p) REVERT: A 246 TYR cc_start: 0.8323 (t80) cc_final: 0.8110 (t80) REVERT: A 308 LEU cc_start: 0.8236 (mt) cc_final: 0.7989 (mt) REVERT: A 309 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7289 (mm-30) REVERT: A 477 ASN cc_start: 0.7806 (m-40) cc_final: 0.7533 (t0) REVERT: B 84 VAL cc_start: 0.8704 (t) cc_final: 0.8446 (p) REVERT: B 91 LYS cc_start: 0.8416 (mttt) cc_final: 0.8161 (mtpp) REVERT: B 124 ASP cc_start: 0.6261 (p0) cc_final: 0.6013 (p0) REVERT: B 228 MET cc_start: 0.8780 (tpt) cc_final: 0.8259 (tpp) REVERT: B 309 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7376 (mm-30) REVERT: B 317 LYS cc_start: 0.8360 (ttpt) cc_final: 0.8110 (ptmm) REVERT: B 349 ASP cc_start: 0.7958 (m-30) cc_final: 0.6323 (m-30) REVERT: B 448 TYR cc_start: 0.7997 (t80) cc_final: 0.7350 (t80) REVERT: B 480 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8442 (tm-30) REVERT: B 486 ARG cc_start: 0.8575 (ttt180) cc_final: 0.8244 (mtp85) REVERT: C 44 PHE cc_start: 0.8158 (t80) cc_final: 0.7865 (t80) REVERT: C 78 PHE cc_start: 0.8789 (m-80) cc_final: 0.8553 (m-10) REVERT: C 155 VAL cc_start: 0.8545 (m) cc_final: 0.8015 (t) REVERT: C 223 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8629 (mm-30) REVERT: C 345 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8283 (mp) REVERT: C 349 ASP cc_start: 0.6984 (m-30) cc_final: 0.6700 (m-30) REVERT: C 425 ARG cc_start: 0.8637 (mtt90) cc_final: 0.8398 (mtt90) REVERT: C 428 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8636 (mm110) REVERT: C 471 LEU cc_start: 0.9107 (mt) cc_final: 0.8903 (mm) REVERT: C 478 HIS cc_start: 0.7816 (m-70) cc_final: 0.7549 (m-70) REVERT: D 77 LEU cc_start: 0.8319 (tp) cc_final: 0.8019 (tt) REVERT: D 89 ARG cc_start: 0.8223 (mmt-90) cc_final: 0.6904 (ttp80) REVERT: D 90 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7407 (mm-30) REVERT: D 110 LYS cc_start: 0.7885 (mttt) cc_final: 0.7605 (mttt) REVERT: D 149 ARG cc_start: 0.8170 (ttp-170) cc_final: 0.7863 (tmm-80) REVERT: D 267 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7919 (mt-10) REVERT: D 282 GLN cc_start: 0.9257 (pm20) cc_final: 0.8828 (pm20) REVERT: D 315 ASP cc_start: 0.7278 (t0) cc_final: 0.7037 (t0) REVERT: D 375 GLN cc_start: 0.8002 (mt0) cc_final: 0.7497 (tm-30) REVERT: E 101 GLU cc_start: 0.8199 (pm20) cc_final: 0.7847 (pm20) REVERT: E 128 SER cc_start: 0.9060 (t) cc_final: 0.8825 (p) REVERT: E 201 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8057 (mpp) REVERT: E 207 ILE cc_start: 0.8986 (mt) cc_final: 0.8714 (tt) REVERT: E 293 GLN cc_start: 0.8868 (mm110) cc_final: 0.8243 (mm110) REVERT: E 354 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7681 (mtpp) REVERT: F 35 ASN cc_start: 0.9121 (m-40) cc_final: 0.8768 (m110) REVERT: F 56 GLU cc_start: 0.8075 (pm20) cc_final: 0.7863 (pm20) REVERT: F 61 THR cc_start: 0.8433 (p) cc_final: 0.7990 (t) REVERT: F 168 GLN cc_start: 0.8180 (tt0) cc_final: 0.7799 (tp-100) REVERT: F 192 ARG cc_start: 0.9109 (ttp-110) cc_final: 0.8394 (ttp80) REVERT: F 201 MET cc_start: 0.8542 (mmt) cc_final: 0.8114 (mmt) REVERT: F 237 LEU cc_start: 0.8749 (mp) cc_final: 0.8461 (mp) REVERT: F 263 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8375 (tp-100) REVERT: F 281 TYR cc_start: 0.8964 (m-80) cc_final: 0.8691 (m-80) REVERT: F 282 GLN cc_start: 0.9115 (pm20) cc_final: 0.8912 (pm20) REVERT: F 288 ASP cc_start: 0.8046 (m-30) cc_final: 0.7457 (m-30) REVERT: F 349 ASP cc_start: 0.8539 (t0) cc_final: 0.8242 (t0) REVERT: F 352 ASP cc_start: 0.7684 (t0) cc_final: 0.7424 (t0) REVERT: F 356 ARG cc_start: 0.8442 (tpt170) cc_final: 0.8071 (ttp-170) REVERT: F 463 ILE cc_start: 0.7848 (tp) cc_final: 0.7559 (tp) REVERT: G 4 LYS cc_start: 0.8204 (tptt) cc_final: 0.7859 (tppp) REVERT: G 24 LYS cc_start: 0.5070 (tmtt) cc_final: 0.4627 (mtpt) REVERT: G 214 LEU cc_start: 0.8407 (tp) cc_final: 0.8178 (tp) REVERT: G 247 MET cc_start: 0.7129 (tpt) cc_final: 0.6466 (tpp) outliers start: 57 outliers final: 35 residues processed: 791 average time/residue: 0.1333 time to fit residues: 166.2306 Evaluate side-chains 763 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 725 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 450 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 14 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 283 optimal weight: 5.9990 chunk 288 optimal weight: 20.0000 chunk 199 optimal weight: 3.9990 chunk 184 optimal weight: 0.2980 chunk 270 optimal weight: 0.2980 chunk 129 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 GLN B 67 ASN B 115 ASN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN D 35 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 195 ASN E 223 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.135764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.117926 restraints weight = 36099.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.121362 restraints weight = 19001.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.123642 restraints weight = 11509.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.125163 restraints weight = 7702.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.126207 restraints weight = 5602.585| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21978 Z= 0.155 Angle : 0.576 7.526 29983 Z= 0.296 Chirality : 0.044 0.151 3681 Planarity : 0.004 0.054 3859 Dihedral : 5.252 98.865 3299 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.50 % Allowed : 21.80 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 3044 helix: 1.29 (0.15), residues: 1227 sheet: -0.16 (0.23), residues: 486 loop : 0.19 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 337 TYR 0.020 0.002 TYR E 242 PHE 0.051 0.002 PHE A 470 TRP 0.020 0.001 TRP B 191 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (21978) covalent geometry : angle 0.57552 / 0.30 (29983) hydrogen bonds : bond 0.03927 / 2.69 ( 1099) hydrogen bonds : angle 4.84653 / 3.51 ( 3159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 736 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7760 (mm-30) REVERT: A 85 LYS cc_start: 0.8745 (ptpt) cc_final: 0.8434 (ptpp) REVERT: A 129 SER cc_start: 0.8537 (m) cc_final: 0.7974 (t) REVERT: A 159 VAL cc_start: 0.9239 (t) cc_final: 0.8891 (m) REVERT: A 187 ASN cc_start: 0.9042 (t0) cc_final: 0.8591 (t0) REVERT: A 196 ASP cc_start: 0.7118 (t0) cc_final: 0.6660 (t0) REVERT: A 199 LYS cc_start: 0.8228 (mttt) cc_final: 0.7895 (mmtp) REVERT: A 221 THR cc_start: 0.8677 (m) cc_final: 0.8380 (p) REVERT: A 308 LEU cc_start: 0.8216 (mt) cc_final: 0.7985 (mt) REVERT: A 309 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7205 (mm-30) REVERT: A 399 TYR cc_start: 0.7609 (t80) cc_final: 0.7265 (t80) REVERT: A 480 GLU cc_start: 0.8296 (pm20) cc_final: 0.7985 (pm20) REVERT: B 84 VAL cc_start: 0.8743 (t) cc_final: 0.8510 (p) REVERT: B 91 LYS cc_start: 0.8425 (mttt) cc_final: 0.8168 (mtpp) REVERT: B 228 MET cc_start: 0.8809 (tpt) cc_final: 0.8314 (tpp) REVERT: B 309 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7191 (mm-30) REVERT: B 349 ASP cc_start: 0.7901 (m-30) cc_final: 0.6273 (m-30) REVERT: B 448 TYR cc_start: 0.7891 (t80) cc_final: 0.7125 (t80) REVERT: B 480 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8432 (tm-30) REVERT: B 486 ARG cc_start: 0.8571 (ttt180) cc_final: 0.8348 (mtp85) REVERT: C 44 PHE cc_start: 0.8097 (t80) cc_final: 0.7872 (t80) REVERT: C 78 PHE cc_start: 0.8907 (m-80) cc_final: 0.8655 (m-10) REVERT: C 155 VAL cc_start: 0.8628 (m) cc_final: 0.8070 (t) REVERT: C 196 ASP cc_start: 0.7543 (t0) cc_final: 0.7044 (p0) REVERT: C 223 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8693 (mm-30) REVERT: C 345 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8430 (mp) REVERT: C 349 ASP cc_start: 0.6935 (m-30) cc_final: 0.6715 (m-30) REVERT: C 364 ARG cc_start: 0.8715 (mtt180) cc_final: 0.8430 (mtt180) REVERT: C 398 GLN cc_start: 0.8779 (mt0) cc_final: 0.8452 (mm-40) REVERT: C 428 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8774 (mm110) REVERT: D 77 LEU cc_start: 0.8461 (tp) cc_final: 0.8165 (tt) REVERT: D 89 ARG cc_start: 0.8221 (mmt-90) cc_final: 0.6817 (tmt170) REVERT: D 90 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7359 (mm-30) REVERT: D 267 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8025 (mt-10) REVERT: D 282 GLN cc_start: 0.9287 (pm20) cc_final: 0.8766 (pm20) REVERT: D 315 ASP cc_start: 0.7120 (t0) cc_final: 0.6849 (t70) REVERT: D 356 ARG cc_start: 0.7895 (ttm-80) cc_final: 0.7493 (ttm-80) REVERT: D 375 GLN cc_start: 0.8193 (mt0) cc_final: 0.7700 (tm-30) REVERT: E 128 SER cc_start: 0.9093 (t) cc_final: 0.8818 (p) REVERT: E 147 TYR cc_start: 0.8970 (m-10) cc_final: 0.8750 (m-10) REVERT: E 293 GLN cc_start: 0.8836 (mm110) cc_final: 0.8294 (mm110) REVERT: E 353 SER cc_start: 0.8770 (m) cc_final: 0.8495 (p) REVERT: E 354 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7735 (tttm) REVERT: F 35 ASN cc_start: 0.9101 (m-40) cc_final: 0.8764 (m110) REVERT: F 56 GLU cc_start: 0.8289 (pm20) cc_final: 0.8077 (pm20) REVERT: F 72 ARG cc_start: 0.8885 (mtm-85) cc_final: 0.8437 (ttm110) REVERT: F 192 ARG cc_start: 0.9135 (ttp-110) cc_final: 0.8284 (ttp80) REVERT: F 201 MET cc_start: 0.8610 (mmt) cc_final: 0.8161 (mmt) REVERT: F 237 LEU cc_start: 0.8676 (mp) cc_final: 0.8438 (mp) REVERT: F 263 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8276 (tp-100) REVERT: F 281 TYR cc_start: 0.9021 (m-80) cc_final: 0.8695 (m-80) REVERT: F 282 GLN cc_start: 0.9056 (pm20) cc_final: 0.7962 (pm20) REVERT: F 288 ASP cc_start: 0.7996 (m-30) cc_final: 0.7494 (m-30) REVERT: F 349 ASP cc_start: 0.8576 (t0) cc_final: 0.8338 (t0) REVERT: F 356 ARG cc_start: 0.8419 (tpt170) cc_final: 0.8041 (ttp-170) REVERT: F 391 LEU cc_start: 0.7676 (mp) cc_final: 0.7406 (mp) REVERT: G 4 LYS cc_start: 0.8133 (tptt) cc_final: 0.7894 (tppp) REVERT: G 24 LYS cc_start: 0.4920 (tmtt) cc_final: 0.4403 (mtpt) REVERT: G 211 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6069 (mt-10) REVERT: G 214 LEU cc_start: 0.8426 (tp) cc_final: 0.8205 (tp) REVERT: G 247 MET cc_start: 0.6943 (tpt) cc_final: 0.6287 (tpp) outliers start: 89 outliers final: 69 residues processed: 761 average time/residue: 0.1328 time to fit residues: 158.9914 Evaluate side-chains 772 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 700 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 278 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 54 optimal weight: 0.0070 chunk 297 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 HIS ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN D 35 ASN D 52 GLN E 24 HIS E 223 ASN E 293 GLN E 308 GLN F 168 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.128197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.110386 restraints weight = 36464.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.113807 restraints weight = 19099.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.116110 restraints weight = 11551.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.117612 restraints weight = 7728.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.118683 restraints weight = 5628.431| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 21978 Z= 0.255 Angle : 0.664 7.246 29983 Z= 0.343 Chirality : 0.047 0.158 3681 Planarity : 0.005 0.056 3859 Dihedral : 5.529 103.114 3299 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 6.02 % Allowed : 21.35 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.15), residues: 3044 helix: 1.14 (0.15), residues: 1217 sheet: -0.24 (0.23), residues: 492 loop : -0.07 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 32 TYR 0.029 0.002 TYR E 242 PHE 0.027 0.002 PHE A 466 TRP 0.010 0.002 TRP B 191 HIS 0.006 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.26 (21978) covalent geometry : angle 0.66404 / 0.34 (29983) hydrogen bonds : bond 0.04520 / 3.10 ( 1099) hydrogen bonds : angle 5.05865 / 3.66 ( 3159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 727 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: A 83 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8055 (mt) REVERT: A 85 LYS cc_start: 0.8751 (ptpt) cc_final: 0.8361 (ptpp) REVERT: A 98 ASP cc_start: 0.8509 (p0) cc_final: 0.8265 (p0) REVERT: A 129 SER cc_start: 0.8607 (m) cc_final: 0.8042 (t) REVERT: A 159 VAL cc_start: 0.9176 (t) cc_final: 0.8783 (m) REVERT: A 187 ASN cc_start: 0.9141 (t0) cc_final: 0.8799 (t0) REVERT: A 308 LEU cc_start: 0.8289 (mt) cc_final: 0.8048 (mt) REVERT: A 309 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7261 (mm-30) REVERT: A 399 TYR cc_start: 0.7711 (t80) cc_final: 0.7305 (t80) REVERT: A 480 GLU cc_start: 0.8455 (pm20) cc_final: 0.8209 (pm20) REVERT: B 84 VAL cc_start: 0.8845 (t) cc_final: 0.8575 (p) REVERT: B 91 LYS cc_start: 0.8409 (mttt) cc_final: 0.8128 (mtpp) REVERT: B 228 MET cc_start: 0.8958 (tpt) cc_final: 0.8588 (tpp) REVERT: B 309 GLU cc_start: 0.8404 (mm-30) cc_final: 0.6715 (mm-30) REVERT: B 349 ASP cc_start: 0.7942 (m-30) cc_final: 0.7177 (m-30) REVERT: B 448 TYR cc_start: 0.7888 (t80) cc_final: 0.7027 (t80) REVERT: B 480 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8379 (tm-30) REVERT: B 486 ARG cc_start: 0.8556 (ttt180) cc_final: 0.8341 (mtp85) REVERT: C 44 PHE cc_start: 0.8213 (t80) cc_final: 0.7968 (t80) REVERT: C 106 LEU cc_start: 0.9167 (tp) cc_final: 0.8663 (mp) REVERT: C 196 ASP cc_start: 0.7522 (t0) cc_final: 0.6930 (p0) REVERT: C 223 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8795 (mm-30) REVERT: C 282 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: C 345 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8594 (mp) REVERT: C 349 ASP cc_start: 0.7078 (m-30) cc_final: 0.6618 (m-30) REVERT: C 364 ARG cc_start: 0.8844 (mtt180) cc_final: 0.8622 (mtt180) REVERT: C 428 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8591 (mm110) REVERT: D 77 LEU cc_start: 0.8474 (tp) cc_final: 0.8232 (tt) REVERT: D 89 ARG cc_start: 0.8270 (mmt-90) cc_final: 0.6965 (ttp80) REVERT: D 90 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7321 (mm-30) REVERT: D 190 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8362 (mtt90) REVERT: D 193 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7486 (mt-10) REVERT: D 267 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8072 (mt-10) REVERT: D 282 GLN cc_start: 0.9374 (pm20) cc_final: 0.8866 (pm20) REVERT: D 315 ASP cc_start: 0.7200 (t0) cc_final: 0.6937 (t70) REVERT: D 373 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7783 (tppt) REVERT: D 375 GLN cc_start: 0.8219 (mt0) cc_final: 0.7705 (tm-30) REVERT: E 9 ILE cc_start: 0.8662 (mt) cc_final: 0.8319 (mt) REVERT: E 101 GLU cc_start: 0.7973 (pm20) cc_final: 0.7506 (pm20) REVERT: E 114 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7561 (mmm-85) REVERT: E 128 SER cc_start: 0.9110 (t) cc_final: 0.8783 (p) REVERT: E 293 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8359 (mm110) REVERT: E 353 SER cc_start: 0.8705 (m) cc_final: 0.8472 (p) REVERT: E 354 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7794 (tttm) REVERT: F 35 ASN cc_start: 0.9140 (m-40) cc_final: 0.8851 (m-40) REVERT: F 156 PHE cc_start: 0.8677 (m-80) cc_final: 0.8357 (m-80) REVERT: F 201 MET cc_start: 0.8680 (mmt) cc_final: 0.8246 (mmt) REVERT: F 237 LEU cc_start: 0.8811 (mp) cc_final: 0.8529 (mp) REVERT: F 263 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8234 (tp-100) REVERT: F 281 TYR cc_start: 0.9046 (m-80) cc_final: 0.8845 (m-80) REVERT: F 288 ASP cc_start: 0.8038 (m-30) cc_final: 0.7617 (m-30) REVERT: F 289 MET cc_start: 0.8953 (tpp) cc_final: 0.8414 (tpp) REVERT: F 349 ASP cc_start: 0.8678 (t0) cc_final: 0.8427 (t0) REVERT: F 375 GLN cc_start: 0.9088 (mt0) cc_final: 0.8784 (mm-40) REVERT: F 391 LEU cc_start: 0.7751 (mp) cc_final: 0.7388 (mp) REVERT: G 4 LYS cc_start: 0.8296 (tptt) cc_final: 0.8076 (tppp) REVERT: G 17 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6684 (mm-30) REVERT: G 24 LYS cc_start: 0.4965 (tmtt) cc_final: 0.4401 (ttpt) REVERT: G 211 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6201 (mt-10) REVERT: G 247 MET cc_start: 0.7020 (tpt) cc_final: 0.6294 (tpp) outliers start: 119 outliers final: 88 residues processed: 774 average time/residue: 0.1354 time to fit residues: 165.3999 Evaluate side-chains 797 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 702 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 209 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS C 387 GLN D 52 GLN E 24 HIS E 308 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.131516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.113818 restraints weight = 36243.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.117260 restraints weight = 19081.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.119569 restraints weight = 11554.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.121071 restraints weight = 7711.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.122048 restraints weight = 5609.108| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21978 Z= 0.151 Angle : 0.586 8.487 29983 Z= 0.302 Chirality : 0.044 0.160 3681 Planarity : 0.004 0.054 3859 Dihedral : 5.269 103.098 3299 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.40 % Allowed : 24.68 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 3044 helix: 1.24 (0.15), residues: 1224 sheet: -0.18 (0.23), residues: 479 loop : -0.02 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 106 TYR 0.034 0.002 TYR E 242 PHE 0.023 0.002 PHE A 466 TRP 0.024 0.002 TRP B 191 HIS 0.006 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (21978) covalent geometry : angle 0.58582 / 0.30 (29983) hydrogen bonds : bond 0.03939 / 2.70 ( 1099) hydrogen bonds : angle 4.84237 / 3.51 ( 3159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 709 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7843 (mt) REVERT: A 85 LYS cc_start: 0.8766 (ptpt) cc_final: 0.8409 (ptpp) REVERT: A 159 VAL cc_start: 0.9235 (t) cc_final: 0.8909 (m) REVERT: A 187 ASN cc_start: 0.9020 (t0) cc_final: 0.8503 (t0) REVERT: A 199 LYS cc_start: 0.8264 (mttt) cc_final: 0.8058 (mmtp) REVERT: A 247 LEU cc_start: 0.9324 (mt) cc_final: 0.8957 (tp) REVERT: A 308 LEU cc_start: 0.8284 (mt) cc_final: 0.8030 (mt) REVERT: A 309 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7187 (mm-30) REVERT: A 349 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: A 399 TYR cc_start: 0.7686 (t80) cc_final: 0.7286 (t80) REVERT: A 480 GLU cc_start: 0.8264 (pm20) cc_final: 0.7936 (pm20) REVERT: B 84 VAL cc_start: 0.8814 (t) cc_final: 0.8547 (p) REVERT: B 91 LYS cc_start: 0.8375 (mttt) cc_final: 0.8099 (mtpp) REVERT: B 228 MET cc_start: 0.8903 (tpt) cc_final: 0.8525 (tpp) REVERT: B 309 GLU cc_start: 0.8460 (mm-30) cc_final: 0.6724 (mm-30) REVERT: B 349 ASP cc_start: 0.7834 (m-30) cc_final: 0.6886 (m-30) REVERT: B 448 TYR cc_start: 0.7874 (t80) cc_final: 0.7085 (t80) REVERT: B 480 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8345 (tm-30) REVERT: C 196 ASP cc_start: 0.7487 (t0) cc_final: 0.6945 (p0) REVERT: C 220 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8198 (tp40) REVERT: C 224 GLN cc_start: 0.8796 (tp40) cc_final: 0.8535 (tp40) REVERT: C 345 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8555 (mp) REVERT: C 349 ASP cc_start: 0.6907 (m-30) cc_final: 0.6439 (m-30) REVERT: C 398 GLN cc_start: 0.8872 (mt0) cc_final: 0.8599 (mm-40) REVERT: C 401 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7243 (mt-10) REVERT: C 428 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8693 (mm110) REVERT: D 77 LEU cc_start: 0.8565 (tp) cc_final: 0.8298 (tt) REVERT: D 89 ARG cc_start: 0.8263 (mmt-90) cc_final: 0.6793 (tmt170) REVERT: D 90 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7407 (mm-30) REVERT: D 190 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8350 (mtt90) REVERT: D 282 GLN cc_start: 0.9340 (pm20) cc_final: 0.8806 (pm20) REVERT: D 315 ASP cc_start: 0.7149 (t0) cc_final: 0.6691 (t0) REVERT: D 373 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7849 (tppt) REVERT: D 375 GLN cc_start: 0.8116 (mt0) cc_final: 0.7618 (tm-30) REVERT: E 9 ILE cc_start: 0.8558 (mt) cc_final: 0.8174 (mt) REVERT: E 101 GLU cc_start: 0.7950 (pm20) cc_final: 0.7512 (pm20) REVERT: E 128 SER cc_start: 0.9100 (t) cc_final: 0.8812 (p) REVERT: E 293 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8379 (mm110) REVERT: E 354 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7718 (tttp) REVERT: F 35 ASN cc_start: 0.9083 (m-40) cc_final: 0.8795 (m-40) REVERT: F 106 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7614 (mtm180) REVERT: F 237 LEU cc_start: 0.8702 (mp) cc_final: 0.8438 (mp) REVERT: F 263 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8219 (tp-100) REVERT: F 281 TYR cc_start: 0.9061 (m-80) cc_final: 0.8809 (m-80) REVERT: F 288 ASP cc_start: 0.7906 (m-30) cc_final: 0.7538 (m-30) REVERT: F 356 ARG cc_start: 0.8546 (tpp-160) cc_final: 0.7905 (ttp-170) REVERT: G 17 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6778 (mm-30) REVERT: G 211 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5883 (mt-10) REVERT: G 247 MET cc_start: 0.6849 (tpt) cc_final: 0.6163 (tpp) outliers start: 87 outliers final: 69 residues processed: 745 average time/residue: 0.1316 time to fit residues: 156.2147 Evaluate side-chains 768 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 692 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 304 HIS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 105 optimal weight: 0.0470 chunk 129 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 120 optimal weight: 0.0670 chunk 124 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 overall best weight: 0.9618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN C 387 GLN E 24 HIS E 223 ASN E 308 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.132937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.114817 restraints weight = 35930.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.118354 restraints weight = 18791.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.120705 restraints weight = 11288.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.122133 restraints weight = 7498.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.123264 restraints weight = 5513.060| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21978 Z= 0.131 Angle : 0.574 8.386 29983 Z= 0.295 Chirality : 0.044 0.188 3681 Planarity : 0.004 0.054 3859 Dihedral : 5.107 106.349 3299 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.35 % Allowed : 24.99 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.16), residues: 3044 helix: 1.35 (0.15), residues: 1221 sheet: -0.18 (0.23), residues: 485 loop : 0.03 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 82 TYR 0.035 0.002 TYR E 242 PHE 0.022 0.001 PHE A 466 TRP 0.013 0.001 TRP B 191 HIS 0.025 0.001 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (21978) covalent geometry : angle 0.57430 / 0.30 (29983) hydrogen bonds : bond 0.03742 / 2.57 ( 1099) hydrogen bonds : angle 4.73024 / 3.43 ( 3159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 721 time to evaluate : 0.767 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 83 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7795 (mt) REVERT: A 85 LYS cc_start: 0.8774 (ptpt) cc_final: 0.8412 (ptpp) REVERT: A 129 SER cc_start: 0.8627 (m) cc_final: 0.7933 (t) REVERT: A 159 VAL cc_start: 0.9242 (t) cc_final: 0.8873 (m) REVERT: A 187 ASN cc_start: 0.8997 (t0) cc_final: 0.8409 (t0) REVERT: A 240 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 247 LEU cc_start: 0.9355 (mt) cc_final: 0.9106 (tp) REVERT: A 308 LEU cc_start: 0.8279 (mt) cc_final: 0.8013 (mt) REVERT: A 309 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7180 (mm-30) REVERT: A 349 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: A 399 TYR cc_start: 0.7754 (t80) cc_final: 0.7347 (t80) REVERT: B 84 VAL cc_start: 0.8770 (t) cc_final: 0.8520 (p) REVERT: B 91 LYS cc_start: 0.8372 (mttt) cc_final: 0.8070 (mtpp) REVERT: B 228 MET cc_start: 0.8883 (tpt) cc_final: 0.8492 (tpp) REVERT: B 246 TYR cc_start: 0.8522 (t80) cc_final: 0.8282 (t80) REVERT: B 309 GLU cc_start: 0.8470 (mm-30) cc_final: 0.6693 (mm-30) REVERT: B 349 ASP cc_start: 0.7777 (m-30) cc_final: 0.6904 (m-30) REVERT: B 448 TYR cc_start: 0.7847 (t80) cc_final: 0.7119 (t80) REVERT: B 480 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8350 (tm-30) REVERT: C 142 ARG cc_start: 0.8516 (tmm-80) cc_final: 0.8242 (tmm-80) REVERT: C 196 ASP cc_start: 0.7453 (t0) cc_final: 0.6863 (p0) REVERT: C 198 SER cc_start: 0.9235 (m) cc_final: 0.8845 (p) REVERT: C 220 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8117 (tp40) REVERT: C 224 GLN cc_start: 0.8791 (tp40) cc_final: 0.8310 (tp40) REVERT: C 345 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8504 (mp) REVERT: C 349 ASP cc_start: 0.6933 (m-30) cc_final: 0.6574 (m-30) REVERT: C 398 GLN cc_start: 0.8886 (mt0) cc_final: 0.8633 (mm-40) REVERT: C 401 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7338 (mt-10) REVERT: C 428 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8762 (mm110) REVERT: D 77 LEU cc_start: 0.8569 (tp) cc_final: 0.8320 (tt) REVERT: D 89 ARG cc_start: 0.8232 (mmt-90) cc_final: 0.6890 (ttp80) REVERT: D 90 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7423 (mm-30) REVERT: D 144 LEU cc_start: 0.7915 (mt) cc_final: 0.7631 (mt) REVERT: D 267 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7812 (mm-30) REVERT: D 282 GLN cc_start: 0.9255 (pm20) cc_final: 0.8772 (pm20) REVERT: D 315 ASP cc_start: 0.7142 (t0) cc_final: 0.6653 (t0) REVERT: D 345 TYR cc_start: 0.8120 (m-80) cc_final: 0.7916 (m-80) REVERT: D 373 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7763 (tppt) REVERT: D 375 GLN cc_start: 0.8097 (mt0) cc_final: 0.7672 (tm-30) REVERT: E 101 GLU cc_start: 0.7773 (pm20) cc_final: 0.7346 (pm20) REVERT: E 128 SER cc_start: 0.9082 (t) cc_final: 0.8805 (p) REVERT: E 147 TYR cc_start: 0.8986 (m-10) cc_final: 0.8730 (m-10) REVERT: E 293 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8373 (mm110) REVERT: E 354 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7829 (tttp) REVERT: F 35 ASN cc_start: 0.9064 (m-40) cc_final: 0.8772 (m-40) REVERT: F 237 LEU cc_start: 0.8693 (mp) cc_final: 0.8438 (mp) REVERT: F 263 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8309 (tp-100) REVERT: F 288 ASP cc_start: 0.7869 (m-30) cc_final: 0.7512 (m-30) REVERT: F 356 ARG cc_start: 0.8530 (tpp-160) cc_final: 0.7897 (ttp-170) REVERT: G 17 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6726 (mm-30) REVERT: G 211 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5831 (mt-10) REVERT: G 247 MET cc_start: 0.6891 (tpt) cc_final: 0.6215 (tpp) outliers start: 86 outliers final: 72 residues processed: 758 average time/residue: 0.1361 time to fit residues: 163.9511 Evaluate side-chains 776 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 697 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 169 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN C 304 HIS D 52 GLN D 168 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 118 HIS E 308 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.135624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.117755 restraints weight = 35810.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.121219 restraints weight = 18963.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.123519 restraints weight = 11492.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.124885 restraints weight = 7681.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.125973 restraints weight = 5705.653| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21978 Z= 0.134 Angle : 0.580 10.582 29983 Z= 0.298 Chirality : 0.044 0.180 3681 Planarity : 0.004 0.053 3859 Dihedral : 5.031 110.430 3299 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.86 % Allowed : 26.00 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 3044 helix: 1.37 (0.15), residues: 1220 sheet: -0.12 (0.23), residues: 481 loop : 0.03 (0.18), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 32 TYR 0.033 0.002 TYR E 242 PHE 0.027 0.001 PHE A 466 TRP 0.029 0.002 TRP B 191 HIS 0.006 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (21978) covalent geometry : angle 0.58026 / 0.30 (29983) hydrogen bonds : bond 0.03660 / 2.50 ( 1099) hydrogen bonds : angle 4.65815 / 3.37 ( 3159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 710 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7852 (mt) REVERT: A 85 LYS cc_start: 0.8786 (ptpt) cc_final: 0.8427 (ptpp) REVERT: A 129 SER cc_start: 0.8718 (m) cc_final: 0.8035 (t) REVERT: A 159 VAL cc_start: 0.9237 (t) cc_final: 0.8884 (m) REVERT: A 187 ASN cc_start: 0.9016 (t0) cc_final: 0.8467 (t0) REVERT: A 217 GLN cc_start: 0.8186 (tp40) cc_final: 0.7862 (tp40) REVERT: A 240 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 247 LEU cc_start: 0.9348 (mt) cc_final: 0.9100 (tp) REVERT: A 308 LEU cc_start: 0.8220 (mt) cc_final: 0.7950 (mt) REVERT: A 309 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 399 TYR cc_start: 0.7748 (t80) cc_final: 0.7337 (t80) REVERT: B 84 VAL cc_start: 0.8725 (t) cc_final: 0.8505 (p) REVERT: B 91 LYS cc_start: 0.8346 (mttt) cc_final: 0.8042 (mtpp) REVERT: B 228 MET cc_start: 0.8842 (tpt) cc_final: 0.8462 (tpp) REVERT: B 309 GLU cc_start: 0.8437 (mm-30) cc_final: 0.6681 (mm-30) REVERT: B 349 ASP cc_start: 0.7723 (m-30) cc_final: 0.6817 (m-30) REVERT: B 448 TYR cc_start: 0.7819 (t80) cc_final: 0.7115 (t80) REVERT: B 480 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8477 (tm-30) REVERT: C 174 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8692 (mm-40) REVERT: C 196 ASP cc_start: 0.7455 (t0) cc_final: 0.6819 (p0) REVERT: C 220 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8046 (tp40) REVERT: C 224 GLN cc_start: 0.8772 (tp40) cc_final: 0.8302 (tp40) REVERT: C 344 VAL cc_start: 0.9283 (t) cc_final: 0.9061 (t) REVERT: C 345 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8504 (mp) REVERT: C 349 ASP cc_start: 0.6808 (m-30) cc_final: 0.6495 (m-30) REVERT: C 398 GLN cc_start: 0.8869 (mt0) cc_final: 0.8628 (mm-40) REVERT: C 408 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6939 (p90) REVERT: C 426 LEU cc_start: 0.8953 (mt) cc_final: 0.8721 (mt) REVERT: C 428 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8629 (mm110) REVERT: D 12 LYS cc_start: 0.8784 (mttp) cc_final: 0.8214 (mtpp) REVERT: D 35 ASN cc_start: 0.7154 (m110) cc_final: 0.6449 (m-40) REVERT: D 77 LEU cc_start: 0.8571 (tp) cc_final: 0.8312 (tt) REVERT: D 89 ARG cc_start: 0.8295 (mmt-90) cc_final: 0.6925 (ttp80) REVERT: D 90 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7363 (mm-30) REVERT: D 282 GLN cc_start: 0.9218 (pm20) cc_final: 0.8759 (pm20) REVERT: D 315 ASP cc_start: 0.7013 (t0) cc_final: 0.6692 (t0) REVERT: D 373 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7834 (tppt) REVERT: D 375 GLN cc_start: 0.7940 (mt0) cc_final: 0.7604 (tm-30) REVERT: E 101 GLU cc_start: 0.7760 (pm20) cc_final: 0.7347 (pm20) REVERT: E 128 SER cc_start: 0.9084 (t) cc_final: 0.8814 (p) REVERT: E 147 TYR cc_start: 0.9009 (m-10) cc_final: 0.8751 (m-10) REVERT: E 293 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8336 (mm110) REVERT: E 354 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7696 (tttm) REVERT: F 35 ASN cc_start: 0.9043 (m-40) cc_final: 0.8747 (m-40) REVERT: F 56 GLU cc_start: 0.8298 (pm20) cc_final: 0.8033 (pm20) REVERT: F 237 LEU cc_start: 0.8699 (mp) cc_final: 0.8437 (mp) REVERT: F 263 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8315 (tp-100) REVERT: F 281 TYR cc_start: 0.8946 (m-80) cc_final: 0.8669 (m-80) REVERT: F 288 ASP cc_start: 0.7889 (m-30) cc_final: 0.7538 (m-30) REVERT: F 356 ARG cc_start: 0.8505 (tpp-160) cc_final: 0.7920 (ttp-170) REVERT: G 17 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6741 (mm-30) REVERT: G 211 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5936 (mt-10) REVERT: G 247 MET cc_start: 0.6769 (tpt) cc_final: 0.6110 (tpp) outliers start: 96 outliers final: 80 residues processed: 748 average time/residue: 0.1316 time to fit residues: 155.9708 Evaluate side-chains 779 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 692 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 304 HIS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 285 optimal weight: 10.0000 chunk 250 optimal weight: 0.0030 chunk 4 optimal weight: 2.9990 chunk 284 optimal weight: 20.0000 chunk 219 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN C 225 HIS C 304 HIS C 387 GLN D 52 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 223 ASN E 308 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.130468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.112670 restraints weight = 36242.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.116120 restraints weight = 19052.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.118388 restraints weight = 11534.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.119956 restraints weight = 7759.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.120972 restraints weight = 5637.685| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21978 Z= 0.202 Angle : 0.636 13.362 29983 Z= 0.327 Chirality : 0.046 0.202 3681 Planarity : 0.005 0.054 3859 Dihedral : 5.194 117.579 3299 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.26 % Allowed : 25.80 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 3044 helix: 1.24 (0.15), residues: 1216 sheet: -0.20 (0.23), residues: 477 loop : -0.08 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 32 TYR 0.032 0.002 TYR E 242 PHE 0.020 0.002 PHE B 44 TRP 0.020 0.002 TRP B 191 HIS 0.012 0.001 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (21978) covalent geometry : angle 0.63573 / 0.33 (29983) hydrogen bonds : bond 0.04031 / 2.77 ( 1099) hydrogen bonds : angle 4.79495 / 3.47 ( 3159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 701 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8777 (ptpt) cc_final: 0.8433 (ptpp) REVERT: A 129 SER cc_start: 0.8645 (m) cc_final: 0.8012 (t) REVERT: A 159 VAL cc_start: 0.9184 (t) cc_final: 0.8805 (m) REVERT: A 187 ASN cc_start: 0.9042 (t0) cc_final: 0.8571 (t0) REVERT: A 199 LYS cc_start: 0.8291 (mttt) cc_final: 0.8054 (mmtp) REVERT: A 240 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7599 (mm-30) REVERT: A 247 LEU cc_start: 0.9393 (mt) cc_final: 0.9112 (tp) REVERT: A 308 LEU cc_start: 0.8266 (mt) cc_final: 0.7994 (mt) REVERT: A 309 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 349 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: A 399 TYR cc_start: 0.7687 (t80) cc_final: 0.7109 (t80) REVERT: B 84 VAL cc_start: 0.8819 (t) cc_final: 0.8545 (p) REVERT: B 91 LYS cc_start: 0.8361 (mttt) cc_final: 0.8046 (mtpp) REVERT: B 228 MET cc_start: 0.8927 (tpt) cc_final: 0.8551 (tpp) REVERT: B 309 GLU cc_start: 0.8500 (mm-30) cc_final: 0.6756 (mm-30) REVERT: B 349 ASP cc_start: 0.7787 (m-30) cc_final: 0.6831 (m-30) REVERT: B 448 TYR cc_start: 0.7864 (t80) cc_final: 0.6982 (t80) REVERT: B 480 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8366 (tm-30) REVERT: C 142 ARG cc_start: 0.8594 (tmm-80) cc_final: 0.8280 (tmm-80) REVERT: C 174 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8810 (mm-40) REVERT: C 196 ASP cc_start: 0.7495 (t0) cc_final: 0.6761 (p0) REVERT: C 224 GLN cc_start: 0.8749 (tp40) cc_final: 0.8338 (tp40) REVERT: C 344 VAL cc_start: 0.9294 (t) cc_final: 0.9065 (t) REVERT: C 345 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8553 (mp) REVERT: C 349 ASP cc_start: 0.7116 (m-30) cc_final: 0.6807 (m-30) REVERT: C 398 GLN cc_start: 0.8941 (mt0) cc_final: 0.8699 (mm-40) REVERT: C 408 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.7026 (p90) REVERT: C 426 LEU cc_start: 0.8975 (mt) cc_final: 0.8752 (mt) REVERT: C 428 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8630 (mm110) REVERT: D 12 LYS cc_start: 0.8785 (mttp) cc_final: 0.8170 (mtpp) REVERT: D 35 ASN cc_start: 0.7508 (m110) cc_final: 0.6823 (m-40) REVERT: D 77 LEU cc_start: 0.8558 (tp) cc_final: 0.8308 (tt) REVERT: D 89 ARG cc_start: 0.8367 (mmt-90) cc_final: 0.7036 (ttp80) REVERT: D 90 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7415 (mm-30) REVERT: D 267 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7615 (mm-30) REVERT: D 282 GLN cc_start: 0.9283 (pm20) cc_final: 0.8726 (pm20) REVERT: D 315 ASP cc_start: 0.7130 (t0) cc_final: 0.6884 (t0) REVERT: D 373 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7811 (tppt) REVERT: D 375 GLN cc_start: 0.8148 (mt0) cc_final: 0.7657 (tm-30) REVERT: E 9 ILE cc_start: 0.8682 (mt) cc_final: 0.8250 (mt) REVERT: E 101 GLU cc_start: 0.7617 (pm20) cc_final: 0.7227 (pm20) REVERT: E 114 ARG cc_start: 0.7849 (mmm-85) cc_final: 0.7169 (mmm-85) REVERT: E 128 SER cc_start: 0.9084 (t) cc_final: 0.8791 (p) REVERT: E 293 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8326 (mm110) REVERT: E 354 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7726 (tttm) REVERT: F 35 ASN cc_start: 0.8997 (m-40) cc_final: 0.8690 (m-40) REVERT: F 237 LEU cc_start: 0.8726 (mp) cc_final: 0.8464 (mp) REVERT: F 263 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8213 (tp-100) REVERT: F 281 TYR cc_start: 0.8923 (m-80) cc_final: 0.8701 (m-80) REVERT: F 288 ASP cc_start: 0.8014 (m-30) cc_final: 0.7623 (m-30) REVERT: F 289 MET cc_start: 0.8959 (tpp) cc_final: 0.8455 (tpp) REVERT: F 356 ARG cc_start: 0.8572 (tpp-160) cc_final: 0.7970 (ttp-170) REVERT: F 391 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7068 (mt) REVERT: G 17 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6732 (mm-30) REVERT: G 211 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.6027 (mt-10) REVERT: G 247 MET cc_start: 0.6734 (tpt) cc_final: 0.6088 (tpp) outliers start: 104 outliers final: 85 residues processed: 739 average time/residue: 0.1288 time to fit residues: 151.1967 Evaluate side-chains 788 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 696 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 304 HIS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 299 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 236 optimal weight: 0.9990 chunk 245 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 280 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 ASN B 67 ASN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN C 304 HIS D 52 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 308 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.133101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.115045 restraints weight = 35978.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.118598 restraints weight = 18850.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.120931 restraints weight = 11349.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.122515 restraints weight = 7579.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.123583 restraints weight = 5465.991| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21978 Z= 0.130 Angle : 0.600 12.317 29983 Z= 0.305 Chirality : 0.045 0.209 3681 Planarity : 0.004 0.053 3859 Dihedral : 5.060 119.257 3299 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.00 % Allowed : 27.72 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.16), residues: 3044 helix: 1.29 (0.15), residues: 1225 sheet: -0.22 (0.23), residues: 478 loop : 0.01 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 32 TYR 0.033 0.002 TYR E 242 PHE 0.022 0.001 PHE F 259 TRP 0.024 0.002 TRP B 191 HIS 0.016 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (21978) covalent geometry : angle 0.59997 / 0.31 (29983) hydrogen bonds : bond 0.03660 / 2.51 ( 1099) hydrogen bonds : angle 4.67391 / 3.38 ( 3159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 711 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8740 (ptpt) cc_final: 0.8416 (ptpp) REVERT: A 129 SER cc_start: 0.8645 (m) cc_final: 0.7992 (t) REVERT: A 159 VAL cc_start: 0.9272 (t) cc_final: 0.8910 (m) REVERT: A 187 ASN cc_start: 0.9048 (t0) cc_final: 0.8494 (t0) REVERT: A 199 LYS cc_start: 0.8244 (mttt) cc_final: 0.7977 (mmtp) REVERT: A 240 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 308 LEU cc_start: 0.8233 (mt) cc_final: 0.7957 (mt) REVERT: A 309 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 349 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: A 399 TYR cc_start: 0.7733 (t80) cc_final: 0.7340 (t80) REVERT: B 84 VAL cc_start: 0.8751 (t) cc_final: 0.8483 (p) REVERT: B 91 LYS cc_start: 0.8343 (mttt) cc_final: 0.8037 (mtpp) REVERT: B 228 MET cc_start: 0.8885 (tpt) cc_final: 0.8501 (tpp) REVERT: B 309 GLU cc_start: 0.8506 (mm-30) cc_final: 0.6677 (mm-30) REVERT: B 349 ASP cc_start: 0.7710 (m-30) cc_final: 0.6831 (m-30) REVERT: B 448 TYR cc_start: 0.7812 (t80) cc_final: 0.7031 (t80) REVERT: B 480 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8488 (tm-30) REVERT: C 142 ARG cc_start: 0.8524 (tmm-80) cc_final: 0.8226 (tmm-80) REVERT: C 174 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8726 (mm-40) REVERT: C 196 ASP cc_start: 0.7490 (t0) cc_final: 0.6756 (p0) REVERT: C 224 GLN cc_start: 0.8735 (tp40) cc_final: 0.8332 (tp40) REVERT: C 230 TYR cc_start: 0.9004 (p90) cc_final: 0.8651 (p90) REVERT: C 344 VAL cc_start: 0.9257 (t) cc_final: 0.9033 (t) REVERT: C 345 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8461 (mp) REVERT: C 349 ASP cc_start: 0.6806 (m-30) cc_final: 0.6525 (m-30) REVERT: C 398 GLN cc_start: 0.8902 (mt0) cc_final: 0.8681 (mm-40) REVERT: C 408 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6944 (p90) REVERT: C 428 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8656 (mm110) REVERT: D 12 LYS cc_start: 0.8766 (mttp) cc_final: 0.8127 (mtpp) REVERT: D 77 LEU cc_start: 0.8555 (tp) cc_final: 0.8301 (tt) REVERT: D 89 ARG cc_start: 0.8323 (mmt-90) cc_final: 0.6801 (tmt170) REVERT: D 90 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7386 (mm-30) REVERT: D 267 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7536 (mm-30) REVERT: D 282 GLN cc_start: 0.9239 (pm20) cc_final: 0.8773 (pm20) REVERT: D 315 ASP cc_start: 0.7094 (t0) cc_final: 0.6879 (t0) REVERT: D 375 GLN cc_start: 0.8054 (mt0) cc_final: 0.7584 (tm-30) REVERT: E 101 GLU cc_start: 0.7670 (pm20) cc_final: 0.7238 (pm20) REVERT: E 114 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.6839 (mmm-85) REVERT: E 128 SER cc_start: 0.9086 (t) cc_final: 0.8792 (p) REVERT: E 147 TYR cc_start: 0.9002 (m-10) cc_final: 0.8747 (m-10) REVERT: E 293 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8340 (mm110) REVERT: E 354 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7642 (tttm) REVERT: F 35 ASN cc_start: 0.8981 (m-40) cc_final: 0.8677 (m-40) REVERT: F 56 GLU cc_start: 0.8300 (pm20) cc_final: 0.8043 (pm20) REVERT: F 237 LEU cc_start: 0.8707 (mp) cc_final: 0.8430 (mp) REVERT: F 263 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8278 (tp-100) REVERT: F 281 TYR cc_start: 0.8957 (m-80) cc_final: 0.8725 (m-80) REVERT: F 288 ASP cc_start: 0.7907 (m-30) cc_final: 0.7559 (m-30) REVERT: F 289 MET cc_start: 0.8899 (tpp) cc_final: 0.8412 (tpp) REVERT: F 356 ARG cc_start: 0.8556 (tpp-160) cc_final: 0.7959 (ttp-170) REVERT: F 391 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7177 (mt) REVERT: G 11 LYS cc_start: 0.8117 (mttt) cc_final: 0.7819 (mttm) REVERT: G 17 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6820 (mm-30) REVERT: G 211 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.6020 (mt-10) REVERT: G 247 MET cc_start: 0.6773 (tpt) cc_final: 0.6103 (tpp) outliers start: 79 outliers final: 70 residues processed: 742 average time/residue: 0.1270 time to fit residues: 150.5000 Evaluate side-chains 765 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 689 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 304 HIS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 76 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.134582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.116749 restraints weight = 35957.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.120300 restraints weight = 18798.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.122580 restraints weight = 11297.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.124134 restraints weight = 7594.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.125193 restraints weight = 5487.670| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21978 Z= 0.119 Angle : 0.588 11.762 29983 Z= 0.299 Chirality : 0.044 0.250 3681 Planarity : 0.004 0.053 3859 Dihedral : 4.982 122.111 3299 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.54 % Allowed : 28.17 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.16), residues: 3044 helix: 1.33 (0.15), residues: 1234 sheet: -0.14 (0.24), residues: 471 loop : 0.09 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 108 TYR 0.034 0.002 TYR A 230 PHE 0.028 0.001 PHE A 466 TRP 0.023 0.002 TRP B 191 HIS 0.012 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (21978) covalent geometry : angle 0.58779 / 0.30 (29983) hydrogen bonds : bond 0.03508 / 2.41 ( 1099) hydrogen bonds : angle 4.58404 / 3.32 ( 3159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3900.15 seconds wall clock time: 67 minutes 54.47 seconds (4074.47 seconds total)