Starting phenix.real_space_refine on Thu Jun 19 00:07:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjx_25939/06_2025/7tjx_25939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjx_25939/06_2025/7tjx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tjx_25939/06_2025/7tjx_25939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjx_25939/06_2025/7tjx_25939.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjx_25939/06_2025/7tjx_25939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjx_25939/06_2025/7tjx_25939.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'GLU:plan': 21, 'ARG:plan': 3, 'PHE:plan': 2, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 23, 'ARG: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: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 17, '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: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 14, 'GLU:plan': 17, 'ARG: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: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 28, 'ARG:plan': 4} 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: {'GLN:plan1': 3, 'GLU:plan': 23, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5} 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: {'GLN:plan1': 7, 'ARG:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 14, 'ASP:plan': 10, 'PHE:plan': 7, 'GLU:plan': 11, 'HIS:plan': 3} 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: 12.79, per 1000 atoms: 0.59 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: 5.30 Conformation dependent library (CDL) restraints added in 2.8 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: 2.78 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: 8.14 Time building geometry restraints manager: 6.28 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: 12735 21.80 - 43.61: 381 43.61 - 65.41: 79 65.41 - 87.22: 19 87.22 - 109.02: 2 Dihedral angle restraints: 13216 sinusoidal: 4505 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 13213 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 508 or resid 600 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 49.280 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.090 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 12.053 109.023 7636 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 2.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (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 TRP 0.020 0.001 TRP C 258 HIS 0.010 0.001 HIS C 145 PHE 0.020 0.001 PHE E 326 TYR 0.021 0.002 TYR G 255 ARG 0.005 0.001 ARG B 462 Details of bonding type rmsd hydrogen bonds : bond 0.14670 ( 1099) hydrogen bonds : angle 6.83134 ( 3159) covalent geometry : bond 0.00269 (21978) covalent geometry : angle 0.61945 (29983) *********************** 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 : 2.274 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: 0.8242 (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: 0.7825 (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: 0.7668 (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: 0.9144 (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: 0.8539 (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: 0.8398 (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: 0.3523 time to fit residues: 506.1814 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 : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 4.9990 chunk 230 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 177 optimal weight: 0.0670 chunk 276 optimal weight: 0.4980 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 195 ASN 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.133613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.116063 restraints weight = 35923.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.119457 restraints weight = 18854.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.121676 restraints weight = 11360.911| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21978 Z= 0.203 Angle : 0.648 7.915 29983 Z= 0.340 Chirality : 0.047 0.163 3681 Planarity : 0.005 0.054 3859 Dihedral : 7.825 95.476 3423 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.49 % Allowed : 14.92 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3044 helix: 0.99 (0.15), residues: 1206 sheet: -0.10 (0.23), residues: 480 loop : 0.05 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 191 HIS 0.005 0.001 HIS E 24 PHE 0.028 0.002 PHE D 441 TYR 0.021 0.002 TYR B 399 ARG 0.006 0.001 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 1099) hydrogen bonds : angle 5.40591 ( 3159) covalent geometry : bond 0.00455 (21978) covalent geometry : angle 0.64764 (29983) *********************** 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 843 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 774 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 SER cc_start: 0.8545 (m) cc_final: 0.7996 (t) REVERT: A 159 VAL cc_start: 0.9233 (t) cc_final: 0.8866 (m) REVERT: A 246 TYR cc_start: 0.8546 (t80) cc_final: 0.8210 (t80) REVERT: A 308 LEU cc_start: 0.8132 (mt) cc_final: 0.7915 (mt) REVERT: A 309 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 399 TYR cc_start: 0.7680 (t80) cc_final: 0.7218 (t80) REVERT: A 477 ASN cc_start: 0.7918 (m-40) cc_final: 0.7452 (t0) REVERT: B 84 VAL cc_start: 0.8906 (t) cc_final: 0.8596 (p) REVERT: B 91 LYS cc_start: 0.8352 (mttt) cc_final: 0.8114 (mtpp) REVERT: B 228 MET cc_start: 0.8878 (tpt) cc_final: 0.8381 (tpp) REVERT: B 309 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 317 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8177 (ptmm) REVERT: B 342 THR cc_start: 0.9404 (p) cc_final: 0.9155 (t) REVERT: B 349 ASP cc_start: 0.8042 (m-30) cc_final: 0.6777 (m-30) REVERT: B 448 TYR cc_start: 0.8133 (t80) cc_final: 0.7276 (t80) REVERT: B 480 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 486 ARG cc_start: 0.8524 (ttt180) cc_final: 0.8188 (mtp85) REVERT: C 93 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7845 (t) REVERT: C 142 ARG cc_start: 0.8647 (tmm-80) cc_final: 0.8316 (tmm-80) REVERT: C 223 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8702 (mm-30) REVERT: C 364 ARG cc_start: 0.8909 (mtt180) cc_final: 0.8555 (mtt180) REVERT: C 383 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8166 (mmmt) REVERT: C 398 GLN cc_start: 0.8698 (mt0) cc_final: 0.8496 (mt0) REVERT: C 425 ARG cc_start: 0.8746 (mtt90) cc_final: 0.8088 (mtt90) REVERT: C 428 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8706 (mm110) REVERT: C 434 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7621 (mt0) REVERT: C 440 THR cc_start: 0.8856 (p) cc_final: 0.8620 (t) REVERT: C 478 HIS cc_start: 0.7936 (m-70) cc_final: 0.7719 (m90) REVERT: D 12 LYS cc_start: 0.8653 (mptt) cc_final: 0.8271 (mtpp) REVERT: D 89 ARG cc_start: 0.8453 (mmt-90) cc_final: 0.7352 (ttp80) REVERT: D 90 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7277 (mm-30) REVERT: D 110 LYS cc_start: 0.7888 (mttt) cc_final: 0.7651 (mttt) REVERT: D 168 GLN cc_start: 0.8855 (mt0) cc_final: 0.8648 (tt0) REVERT: D 190 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.8276 (mtm-85) REVERT: D 267 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7889 (mt-10) REVERT: D 277 SER cc_start: 0.8734 (t) cc_final: 0.8412 (m) REVERT: D 282 GLN cc_start: 0.9309 (pm20) cc_final: 0.8684 (pm20) REVERT: D 329 LEU cc_start: 0.8879 (mt) cc_final: 0.8495 (mt) REVERT: D 332 THR cc_start: 0.8549 (p) cc_final: 0.8270 (m) REVERT: D 356 ARG cc_start: 0.7616 (ttt90) cc_final: 0.7367 (ttm-80) REVERT: D 375 GLN cc_start: 0.8083 (mt0) cc_final: 0.7615 (tm-30) REVERT: E 128 SER cc_start: 0.9072 (t) cc_final: 0.8793 (p) REVERT: E 201 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8043 (mpp) REVERT: E 207 ILE cc_start: 0.9087 (mt) cc_final: 0.8661 (tt) REVERT: E 353 SER cc_start: 0.8859 (m) cc_final: 0.8540 (p) REVERT: E 354 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7774 (mtpp) REVERT: F 35 ASN cc_start: 0.9173 (m-40) cc_final: 0.8788 (m-40) REVERT: F 178 HIS cc_start: 0.5884 (t-90) cc_final: 0.5681 (t-170) REVERT: F 192 ARG cc_start: 0.9057 (ttp-110) cc_final: 0.8555 (ttp80) REVERT: F 201 MET cc_start: 0.8651 (mmt) cc_final: 0.8272 (mmt) REVERT: F 202 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8189 (mtmm) REVERT: F 237 LEU cc_start: 0.8774 (mp) cc_final: 0.8465 (mp) REVERT: F 262 THR cc_start: 0.8969 (m) cc_final: 0.8488 (p) REVERT: F 281 TYR cc_start: 0.9013 (m-80) cc_final: 0.8768 (m-80) REVERT: F 282 GLN cc_start: 0.9265 (pm20) cc_final: 0.8220 (pm20) REVERT: F 288 ASP cc_start: 0.8107 (m-30) cc_final: 0.7587 (m-30) REVERT: F 349 ASP cc_start: 0.8539 (t0) cc_final: 0.8291 (t0) REVERT: F 351 LEU cc_start: 0.9351 (mt) cc_final: 0.8696 (mt) REVERT: F 356 ARG cc_start: 0.8454 (tpt170) cc_final: 0.8196 (ttp-170) REVERT: F 375 GLN cc_start: 0.8975 (mt0) cc_final: 0.8566 (mm-40) REVERT: F 449 TYR cc_start: 0.8857 (m-80) cc_final: 0.8627 (m-80) REVERT: F 463 ILE cc_start: 0.7923 (tp) cc_final: 0.7609 (tp) REVERT: F 464 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7911 (mt-10) REVERT: G 4 LYS cc_start: 0.8390 (tptt) cc_final: 0.8041 (tppp) REVERT: G 24 LYS cc_start: 0.5207 (tmtt) cc_final: 0.4651 (mtpt) REVERT: G 214 LEU cc_start: 0.8464 (tp) cc_final: 0.8226 (tp) REVERT: G 247 MET cc_start: 0.7266 (tpt) cc_final: 0.6845 (tpp) REVERT: G 250 ARG cc_start: 0.8239 (mtp-110) cc_final: 0.7760 (mtm180) outliers start: 69 outliers final: 44 residues processed: 802 average time/residue: 0.3150 time to fit residues: 392.9075 Evaluate side-chains 758 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 711 time to evaluate : 2.222 ------------------------------------------------------------------------------- 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 376 VAL 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 219 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 99 ILE 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 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 99 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 387 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 300 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 275 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 278 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN C 387 GLN E 24 HIS E 195 ASN ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.130325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.112453 restraints weight = 36094.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.115904 restraints weight = 18771.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.118147 restraints weight = 11299.203| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21978 Z= 0.189 Angle : 0.615 6.786 29983 Z= 0.322 Chirality : 0.045 0.159 3681 Planarity : 0.005 0.055 3859 Dihedral : 7.482 96.124 3423 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.30 % Allowed : 18.82 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3044 helix: 1.10 (0.15), residues: 1209 sheet: -0.22 (0.23), residues: 488 loop : 0.05 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.005 0.001 HIS E 24 PHE 0.018 0.002 PHE A 44 TYR 0.019 0.002 TYR C 246 ARG 0.006 0.001 ARG F 433 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 1099) hydrogen bonds : angle 5.13543 ( 3159) covalent geometry : bond 0.00426 (21978) covalent geometry : angle 0.61550 (29983) *********************** 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 814 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 729 time to evaluate : 2.325 Fit side-chains REVERT: A 129 SER cc_start: 0.8594 (m) cc_final: 0.8027 (t) REVERT: A 159 VAL cc_start: 0.9209 (t) cc_final: 0.8859 (m) REVERT: A 196 ASP cc_start: 0.7057 (t0) cc_final: 0.6611 (t0) REVERT: A 199 LYS cc_start: 0.8300 (mttt) cc_final: 0.7999 (mmtp) REVERT: A 308 LEU cc_start: 0.8204 (mt) cc_final: 0.7940 (mt) REVERT: A 309 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7258 (mm-30) REVERT: A 399 TYR cc_start: 0.7616 (t80) cc_final: 0.7212 (t80) REVERT: A 477 ASN cc_start: 0.7941 (m-40) cc_final: 0.7488 (t0) REVERT: A 480 GLU cc_start: 0.8288 (pm20) cc_final: 0.8000 (pm20) REVERT: B 84 VAL cc_start: 0.8858 (t) cc_final: 0.8545 (p) REVERT: B 91 LYS cc_start: 0.8365 (mttt) cc_final: 0.8115 (mtpp) REVERT: B 228 MET cc_start: 0.8915 (tpt) cc_final: 0.8412 (tpp) REVERT: B 309 GLU cc_start: 0.8639 (mm-30) cc_final: 0.7512 (mm-30) REVERT: B 349 ASP cc_start: 0.8139 (m-30) cc_final: 0.7135 (m-30) REVERT: B 448 TYR cc_start: 0.8056 (t80) cc_final: 0.7226 (t80) REVERT: B 480 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8422 (tm-30) REVERT: B 486 ARG cc_start: 0.8685 (ttt180) cc_final: 0.8317 (mtp85) REVERT: C 223 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8746 (mm-30) REVERT: C 345 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8609 (mp) REVERT: C 364 ARG cc_start: 0.8942 (mtt180) cc_final: 0.8632 (mtt180) REVERT: C 383 LYS cc_start: 0.8514 (mmtm) cc_final: 0.8304 (mmmt) REVERT: C 428 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8615 (mm110) REVERT: C 478 HIS cc_start: 0.7912 (m-70) cc_final: 0.7682 (m-70) REVERT: D 77 LEU cc_start: 0.8401 (tp) cc_final: 0.8122 (tt) REVERT: D 89 ARG cc_start: 0.8314 (mmt-90) cc_final: 0.6887 (tmt170) REVERT: D 90 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7248 (mm-30) REVERT: D 110 LYS cc_start: 0.8041 (mttt) cc_final: 0.7809 (mttp) REVERT: D 168 GLN cc_start: 0.8900 (mt0) cc_final: 0.8691 (tt0) REVERT: D 267 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7884 (mt-10) REVERT: D 282 GLN cc_start: 0.9328 (pm20) cc_final: 0.8857 (pm20) REVERT: D 315 ASP cc_start: 0.7236 (t0) cc_final: 0.7022 (t0) REVERT: D 356 ARG cc_start: 0.7649 (ttt90) cc_final: 0.7419 (ttm-80) REVERT: D 375 GLN cc_start: 0.8122 (mt0) cc_final: 0.7624 (tm-30) REVERT: D 464 GLU cc_start: 0.7762 (pp20) cc_final: 0.7520 (pm20) REVERT: E 101 GLU cc_start: 0.8150 (pm20) cc_final: 0.7864 (pm20) REVERT: E 114 ARG cc_start: 0.7664 (mtp85) cc_final: 0.7233 (mmm-85) REVERT: E 128 SER cc_start: 0.9070 (t) cc_final: 0.8795 (p) REVERT: E 201 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8063 (mpp) REVERT: E 207 ILE cc_start: 0.9027 (mt) cc_final: 0.8595 (tt) REVERT: E 354 LYS cc_start: 0.8218 (mtpt) cc_final: 0.7879 (tttm) REVERT: F 35 ASN cc_start: 0.9195 (m-40) cc_final: 0.8845 (m-40) REVERT: F 191 THR cc_start: 0.9053 (m) cc_final: 0.8740 (m) REVERT: F 201 MET cc_start: 0.8639 (mmt) cc_final: 0.8228 (mmt) REVERT: F 202 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8251 (mtmm) REVERT: F 237 LEU cc_start: 0.8743 (mp) cc_final: 0.8514 (mp) REVERT: F 263 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8261 (tp-100) REVERT: F 281 TYR cc_start: 0.9085 (m-80) cc_final: 0.8854 (m-80) REVERT: F 288 ASP cc_start: 0.8145 (m-30) cc_final: 0.7578 (m-30) REVERT: F 349 ASP cc_start: 0.8613 (t0) cc_final: 0.8339 (t0) REVERT: F 356 ARG cc_start: 0.8444 (tpt170) cc_final: 0.8009 (ttp-170) REVERT: F 375 GLN cc_start: 0.9017 (mt0) cc_final: 0.8620 (mm-40) REVERT: F 449 TYR cc_start: 0.8876 (m-80) cc_final: 0.8665 (m-80) REVERT: F 463 ILE cc_start: 0.7915 (tp) cc_final: 0.7677 (tp) REVERT: F 464 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8096 (mt-10) REVERT: G 4 LYS cc_start: 0.8312 (tptt) cc_final: 0.7993 (tppp) REVERT: G 24 LYS cc_start: 0.5046 (tmtt) cc_final: 0.4447 (mtpt) REVERT: G 211 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.6041 (mt-10) REVERT: G 214 LEU cc_start: 0.8469 (tp) cc_final: 0.8224 (tp) REVERT: G 247 MET cc_start: 0.6985 (tpt) cc_final: 0.6328 (tpp) outliers start: 85 outliers final: 59 residues processed: 763 average time/residue: 0.3116 time to fit residues: 368.5390 Evaluate side-chains 753 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 690 time to evaluate : 2.461 ------------------------------------------------------------------------------- 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 81 ASP 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 342 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 143 SER 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 27 LEU 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 208 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 276 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 394 LEU Chi-restraints excluded: chain C residue 444 VAL 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 99 ILE Chi-restraints excluded: chain D residue 258 ILE 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 435 LYS Chi-restraints excluded: chain E residue 17 ILE 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 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 99 ILE 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 266 SER Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 263 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 63 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 296 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 285 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN E 24 HIS E 223 ASN F 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.131698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.113926 restraints weight = 36333.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.117381 restraints weight = 19125.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.119679 restraints weight = 11552.653| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21978 Z= 0.161 Angle : 0.587 7.909 29983 Z= 0.305 Chirality : 0.045 0.154 3681 Planarity : 0.005 0.055 3859 Dihedral : 7.164 96.797 3423 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.60 % Allowed : 20.99 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3044 helix: 1.23 (0.15), residues: 1201 sheet: -0.33 (0.23), residues: 488 loop : 0.05 (0.18), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 191 HIS 0.005 0.001 HIS E 24 PHE 0.031 0.002 PHE A 470 TYR 0.022 0.002 TYR E 242 ARG 0.007 0.001 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 1099) hydrogen bonds : angle 4.94359 ( 3159) covalent geometry : bond 0.00366 (21978) covalent geometry : angle 0.58745 (29983) *********************** 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: 91 poor density : 734 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: A 56 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7985 (mm-30) REVERT: A 83 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7937 (mt) REVERT: A 98 ASP cc_start: 0.8608 (p0) cc_final: 0.8403 (p0) REVERT: A 129 SER cc_start: 0.8623 (m) cc_final: 0.8024 (t) REVERT: A 159 VAL cc_start: 0.9270 (t) cc_final: 0.8899 (m) REVERT: A 187 ASN cc_start: 0.9075 (t0) cc_final: 0.8698 (t0) REVERT: A 247 LEU cc_start: 0.9312 (mt) cc_final: 0.8874 (tp) REVERT: A 308 LEU cc_start: 0.8256 (mt) cc_final: 0.8015 (mt) REVERT: A 309 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7254 (mm-30) REVERT: A 399 TYR cc_start: 0.7674 (t80) cc_final: 0.7223 (t80) REVERT: B 84 VAL cc_start: 0.8781 (t) cc_final: 0.8513 (p) REVERT: B 91 LYS cc_start: 0.8426 (mttt) cc_final: 0.8171 (mtpp) REVERT: B 228 MET cc_start: 0.8916 (tpt) cc_final: 0.8439 (tpp) REVERT: B 309 GLU cc_start: 0.8609 (mm-30) cc_final: 0.7112 (mm-30) REVERT: B 349 ASP cc_start: 0.7988 (m-30) cc_final: 0.6484 (m-30) REVERT: B 448 TYR cc_start: 0.7991 (t80) cc_final: 0.7164 (t80) REVERT: B 480 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8392 (tm-30) REVERT: B 486 ARG cc_start: 0.8651 (ttt180) cc_final: 0.8406 (mtp85) REVERT: C 44 PHE cc_start: 0.8175 (t80) cc_final: 0.7902 (t80) REVERT: C 196 ASP cc_start: 0.7403 (t0) cc_final: 0.7146 (p0) REVERT: C 223 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8768 (mm-30) REVERT: C 344 VAL cc_start: 0.9237 (t) cc_final: 0.9015 (t) REVERT: C 345 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8542 (mp) REVERT: C 349 ASP cc_start: 0.6822 (m-30) cc_final: 0.6505 (m-30) REVERT: C 364 ARG cc_start: 0.8919 (mtt180) cc_final: 0.8689 (mtt180) REVERT: C 428 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8774 (mm110) REVERT: C 471 LEU cc_start: 0.9144 (mt) cc_final: 0.8917 (mm) REVERT: C 478 HIS cc_start: 0.7884 (m-70) cc_final: 0.7327 (m-70) REVERT: D 77 LEU cc_start: 0.8445 (tp) cc_final: 0.8173 (tt) REVERT: D 89 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.6941 (ttp80) REVERT: D 90 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7433 (mm-30) REVERT: D 110 LYS cc_start: 0.8040 (mttt) cc_final: 0.7789 (mttp) REVERT: D 168 GLN cc_start: 0.8925 (mt0) cc_final: 0.8685 (tt0) REVERT: D 267 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7973 (mt-10) REVERT: D 282 GLN cc_start: 0.9289 (pm20) cc_final: 0.8794 (pm20) REVERT: D 315 ASP cc_start: 0.7237 (t0) cc_final: 0.6969 (t70) REVERT: D 375 GLN cc_start: 0.8203 (mt0) cc_final: 0.7727 (tm-30) REVERT: E 9 ILE cc_start: 0.8504 (mt) cc_final: 0.8130 (mt) REVERT: E 101 GLU cc_start: 0.7923 (pm20) cc_final: 0.7402 (pm20) REVERT: E 128 SER cc_start: 0.9098 (t) cc_final: 0.8824 (p) REVERT: E 293 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8310 (mm110) REVERT: E 354 LYS cc_start: 0.8303 (mtpt) cc_final: 0.7993 (tttm) REVERT: F 35 ASN cc_start: 0.9183 (m-40) cc_final: 0.8797 (m-40) REVERT: F 56 GLU cc_start: 0.8232 (pm20) cc_final: 0.8028 (pm20) REVERT: F 192 ARG cc_start: 0.9123 (ttp-170) cc_final: 0.8340 (ttp80) REVERT: F 201 MET cc_start: 0.8601 (mmt) cc_final: 0.8159 (mmt) REVERT: F 237 LEU cc_start: 0.8718 (mp) cc_final: 0.8463 (mp) REVERT: F 263 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8177 (tp-100) REVERT: F 281 TYR cc_start: 0.9095 (m-80) cc_final: 0.8867 (m-80) REVERT: F 288 ASP cc_start: 0.7993 (m-30) cc_final: 0.7602 (m-30) REVERT: F 349 ASP cc_start: 0.8638 (t0) cc_final: 0.8399 (t0) REVERT: F 356 ARG cc_start: 0.8514 (tpt170) cc_final: 0.8034 (ttp-170) REVERT: F 375 GLN cc_start: 0.8969 (mt0) cc_final: 0.8631 (mm-40) REVERT: F 449 TYR cc_start: 0.8853 (m-80) cc_final: 0.8634 (m-80) REVERT: F 463 ILE cc_start: 0.7914 (tp) cc_final: 0.7659 (tp) REVERT: F 464 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8180 (mt-10) REVERT: G 4 LYS cc_start: 0.8267 (tptt) cc_final: 0.7900 (tppp) REVERT: G 24 LYS cc_start: 0.4895 (tmtt) cc_final: 0.4364 (mtpt) REVERT: G 211 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6095 (mt-10) REVERT: G 214 LEU cc_start: 0.8453 (tp) cc_final: 0.8224 (tp) REVERT: G 247 MET cc_start: 0.6855 (tpt) cc_final: 0.6197 (tpp) outliers start: 91 outliers final: 70 residues processed: 769 average time/residue: 0.3309 time to fit residues: 396.9212 Evaluate side-chains 773 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 698 time to evaluate : 2.474 ------------------------------------------------------------------------------- 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 53 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 76 VAL 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 115 ASN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 186 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 300 VAL Chi-restraints excluded: chain A residue 342 THR 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 101 VAL Chi-restraints excluded: chain B residue 143 SER 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 27 LEU 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 180 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 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 23 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 62 ILE 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 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 47 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 103 ILE 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 71 VAL 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 269 SER Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 296 ILE 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 244 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 291 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 HIS C 262 ASN C 387 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 178 HIS E 223 ASN E 308 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.126460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.108571 restraints weight = 36881.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.111969 restraints weight = 19410.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.114234 restraints weight = 11779.309| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 21978 Z= 0.302 Angle : 0.714 8.657 29983 Z= 0.370 Chirality : 0.048 0.156 3681 Planarity : 0.005 0.055 3859 Dihedral : 7.558 99.578 3423 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 6.47 % Allowed : 21.04 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3044 helix: 0.90 (0.15), residues: 1214 sheet: -0.42 (0.23), residues: 488 loop : -0.29 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 191 HIS 0.006 0.002 HIS C 265 PHE 0.020 0.002 PHE A 466 TYR 0.028 0.002 TYR E 242 ARG 0.008 0.001 ARG F 190 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 1099) hydrogen bonds : angle 5.26422 ( 3159) covalent geometry : bond 0.00681 (21978) covalent geometry : angle 0.71364 (29983) *********************** 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 848 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 720 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8060 (mt) REVERT: A 98 ASP cc_start: 0.8653 (p0) cc_final: 0.8438 (p0) REVERT: A 129 SER cc_start: 0.8708 (m) cc_final: 0.8153 (t) REVERT: A 159 VAL cc_start: 0.9197 (t) cc_final: 0.8814 (m) REVERT: A 199 LYS cc_start: 0.8422 (mttt) cc_final: 0.8175 (mmtp) REVERT: A 217 GLN cc_start: 0.7974 (tp40) cc_final: 0.7562 (tp40) REVERT: A 230 TYR cc_start: 0.9180 (p90) cc_final: 0.8911 (p90) REVERT: A 257 GLU cc_start: 0.7517 (tt0) cc_final: 0.7224 (tt0) REVERT: A 308 LEU cc_start: 0.8270 (mt) cc_final: 0.8006 (mt) REVERT: A 309 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 399 TYR cc_start: 0.7693 (t80) cc_final: 0.7275 (t80) REVERT: B 84 VAL cc_start: 0.8890 (t) cc_final: 0.8600 (p) REVERT: B 91 LYS cc_start: 0.8398 (mttt) cc_final: 0.8105 (mtpp) REVERT: B 204 VAL cc_start: 0.9142 (t) cc_final: 0.8921 (m) REVERT: B 228 MET cc_start: 0.8994 (tpt) cc_final: 0.8617 (tpp) REVERT: B 309 GLU cc_start: 0.8553 (mm-30) cc_final: 0.6871 (mm-30) REVERT: B 349 ASP cc_start: 0.7948 (m-30) cc_final: 0.7228 (m-30) REVERT: B 448 TYR cc_start: 0.8051 (t80) cc_final: 0.7222 (t80) REVERT: B 480 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8372 (tm-30) REVERT: B 486 ARG cc_start: 0.8731 (ttt180) cc_final: 0.8525 (mtp85) REVERT: C 196 ASP cc_start: 0.7442 (t0) cc_final: 0.6925 (p0) REVERT: C 223 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8829 (mm-30) REVERT: C 282 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: C 345 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8671 (mp) REVERT: C 398 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: C 428 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8619 (mm110) REVERT: C 478 HIS cc_start: 0.7982 (m-70) cc_final: 0.7545 (m-70) REVERT: D 77 LEU cc_start: 0.8460 (tp) cc_final: 0.8193 (tt) REVERT: D 89 ARG cc_start: 0.8329 (mmt-90) cc_final: 0.6946 (ttp80) REVERT: D 90 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7281 (mm-30) REVERT: D 110 LYS cc_start: 0.8092 (mttt) cc_final: 0.7775 (mttt) REVERT: D 282 GLN cc_start: 0.9391 (pm20) cc_final: 0.8793 (pm20) REVERT: D 315 ASP cc_start: 0.7216 (t0) cc_final: 0.6968 (t70) REVERT: D 373 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7828 (tppt) REVERT: D 375 GLN cc_start: 0.8175 (mt0) cc_final: 0.7685 (tm-30) REVERT: E 9 ILE cc_start: 0.8576 (mt) cc_final: 0.8223 (mt) REVERT: E 128 SER cc_start: 0.9120 (t) cc_final: 0.8779 (p) REVERT: E 354 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7941 (tttm) REVERT: F 35 ASN cc_start: 0.9167 (m-40) cc_final: 0.8851 (m-40) REVERT: F 56 GLU cc_start: 0.8462 (pm20) cc_final: 0.8251 (pm20) REVERT: F 156 PHE cc_start: 0.8799 (m-80) cc_final: 0.8470 (m-80) REVERT: F 201 MET cc_start: 0.8714 (mmt) cc_final: 0.8289 (mmt) REVERT: F 263 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: F 288 ASP cc_start: 0.8015 (m-30) cc_final: 0.7624 (m-30) REVERT: F 289 MET cc_start: 0.8940 (tpp) cc_final: 0.8606 (tpp) REVERT: F 349 ASP cc_start: 0.8764 (t0) cc_final: 0.8519 (t0) REVERT: F 375 GLN cc_start: 0.9096 (mt0) cc_final: 0.8772 (mm-40) REVERT: F 449 TYR cc_start: 0.8919 (m-80) cc_final: 0.8692 (m-80) REVERT: F 463 ILE cc_start: 0.7971 (tp) cc_final: 0.7758 (tp) REVERT: F 464 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8187 (mt-10) REVERT: G 4 LYS cc_start: 0.8027 (tptt) cc_final: 0.7821 (tppp) REVERT: G 17 GLU cc_start: 0.6810 (tp30) cc_final: 0.6536 (mm-30) REVERT: G 24 LYS cc_start: 0.4911 (tmtt) cc_final: 0.4328 (ttpt) REVERT: G 211 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6237 (mt-10) REVERT: G 214 LEU cc_start: 0.8445 (tp) cc_final: 0.8227 (tp) REVERT: G 247 MET cc_start: 0.6915 (tpt) cc_final: 0.6210 (tpp) outliers start: 128 outliers final: 94 residues processed: 769 average time/residue: 0.3127 time to fit residues: 374.9505 Evaluate side-chains 797 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 696 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 64 MET Chi-restraints excluded: chain A residue 76 VAL 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 208 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 342 THR 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 A residue 474 LEU 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 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 B residue 430 LEU Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 THR 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 251 THR Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 398 GLN 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 C residue 463 ILE 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 99 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 258 ILE 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 362 VAL Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 444 VAL 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 23 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 61 THR 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 239 ILE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 296 ILE 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 437 THR 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 7 optimal weight: 1.9990 chunk 230 optimal weight: 0.0060 chunk 116 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 297 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 274 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 253 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN B 67 ASN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** 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 308 GLN ** F 282 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 = 0.3408 r_free = 0.3408 target = 0.136287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.118421 restraints weight = 35808.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.121869 restraints weight = 18974.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.124132 restraints weight = 11531.110| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21978 Z= 0.117 Angle : 0.567 8.554 29983 Z= 0.293 Chirality : 0.044 0.166 3681 Planarity : 0.004 0.055 3859 Dihedral : 6.854 99.266 3423 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.69 % Allowed : 25.09 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 3044 helix: 1.26 (0.15), residues: 1219 sheet: -0.39 (0.23), residues: 476 loop : -0.02 (0.18), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 191 HIS 0.006 0.001 HIS E 24 PHE 0.014 0.001 PHE D 441 TYR 0.027 0.001 TYR E 242 ARG 0.008 0.001 ARG D 337 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 1099) hydrogen bonds : angle 4.79173 ( 3159) covalent geometry : bond 0.00257 (21978) covalent geometry : angle 0.56714 (29983) *********************** 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 809 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 736 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7941 (mt) REVERT: A 129 SER cc_start: 0.8609 (m) cc_final: 0.8056 (t) REVERT: A 159 VAL cc_start: 0.9284 (t) cc_final: 0.8954 (m) REVERT: A 187 ASN cc_start: 0.9021 (t0) cc_final: 0.8711 (t0) REVERT: A 240 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7579 (mm-30) REVERT: A 247 LEU cc_start: 0.9268 (mt) cc_final: 0.8905 (tp) REVERT: A 308 LEU cc_start: 0.8240 (mt) cc_final: 0.7975 (mt) REVERT: A 309 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7376 (mm-30) REVERT: A 349 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: A 399 TYR cc_start: 0.7615 (t80) cc_final: 0.7275 (t80) REVERT: B 84 VAL cc_start: 0.8786 (t) cc_final: 0.8512 (p) REVERT: B 91 LYS cc_start: 0.8421 (mttt) cc_final: 0.8162 (mtpp) REVERT: B 228 MET cc_start: 0.8859 (tpt) cc_final: 0.8419 (tpp) REVERT: B 309 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7088 (mm-30) REVERT: B 349 ASP cc_start: 0.7798 (m-30) cc_final: 0.6928 (m-30) REVERT: B 448 TYR cc_start: 0.7864 (t80) cc_final: 0.7087 (t80) REVERT: B 480 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8378 (tm-30) REVERT: C 44 PHE cc_start: 0.8216 (t80) cc_final: 0.7985 (t80) REVERT: C 128 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.7338 (mmm-85) REVERT: C 155 VAL cc_start: 0.8774 (m) cc_final: 0.8321 (t) REVERT: C 196 ASP cc_start: 0.7421 (t0) cc_final: 0.7056 (p0) REVERT: C 220 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8217 (tp40) REVERT: C 223 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8795 (mm-30) REVERT: C 364 ARG cc_start: 0.8849 (mtt180) cc_final: 0.8628 (mtt180) REVERT: C 428 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8741 (mm110) REVERT: D 77 LEU cc_start: 0.8529 (tp) cc_final: 0.8277 (tt) REVERT: D 89 ARG cc_start: 0.8251 (mmt-90) cc_final: 0.6862 (ttp80) REVERT: D 90 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7360 (mm-30) REVERT: D 110 LYS cc_start: 0.7851 (mttt) cc_final: 0.7493 (mttp) REVERT: D 282 GLN cc_start: 0.9274 (pm20) cc_final: 0.8809 (pm20) REVERT: D 315 ASP cc_start: 0.7290 (t0) cc_final: 0.6887 (t0) REVERT: D 373 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7843 (tppt) REVERT: D 375 GLN cc_start: 0.7948 (mt0) cc_final: 0.7544 (tm-30) REVERT: E 9 ILE cc_start: 0.8433 (mt) cc_final: 0.8010 (mt) REVERT: E 128 SER cc_start: 0.9090 (t) cc_final: 0.8827 (p) REVERT: E 195 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8493 (t0) REVERT: E 293 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8375 (mm110) REVERT: F 35 ASN cc_start: 0.9046 (m-40) cc_final: 0.8759 (m-40) REVERT: F 56 GLU cc_start: 0.8223 (pm20) cc_final: 0.7970 (pm20) REVERT: F 201 MET cc_start: 0.8622 (mmt) cc_final: 0.8155 (mmt) REVERT: F 223 ASN cc_start: 0.8275 (p0) cc_final: 0.8005 (p0) REVERT: F 237 LEU cc_start: 0.8718 (mp) cc_final: 0.8451 (mp) REVERT: F 263 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8234 (tp-100) REVERT: F 288 ASP cc_start: 0.7936 (m-30) cc_final: 0.7559 (m-30) REVERT: F 449 TYR cc_start: 0.8842 (m-80) cc_final: 0.8631 (m-10) REVERT: F 463 ILE cc_start: 0.7813 (tp) cc_final: 0.7481 (tp) REVERT: F 464 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8025 (mt-10) REVERT: G 211 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5851 (mt-10) REVERT: G 214 LEU cc_start: 0.8416 (tp) cc_final: 0.8189 (tp) REVERT: G 247 MET cc_start: 0.6668 (tpt) cc_final: 0.5978 (tpp) outliers start: 73 outliers final: 52 residues processed: 768 average time/residue: 0.4110 time to fit residues: 493.5020 Evaluate side-chains 765 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 706 time to evaluate : 5.827 ------------------------------------------------------------------------------- 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 64 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 148 VAL 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 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 LEU 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 220 GLN 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 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 62 ILE 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 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 136 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 59 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 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 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 214 optimal weight: 0.0470 chunk 37 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 250 optimal weight: 0.0470 chunk 215 optimal weight: 0.8980 chunk 149 optimal weight: 0.0670 chunk 66 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 300 optimal weight: 0.9990 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN C 304 HIS C 387 GLN D 35 ASN E 24 HIS E 195 ASN E 223 ASN E 308 GLN F 127 GLN ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN F 328 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.136721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.119057 restraints weight = 35655.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.122497 restraints weight = 18687.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.124808 restraints weight = 11268.607| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 21978 Z= 0.111 Angle : 0.563 8.823 29983 Z= 0.289 Chirality : 0.044 0.159 3681 Planarity : 0.004 0.054 3859 Dihedral : 6.528 103.464 3423 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.69 % Allowed : 26.61 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 3044 helix: 1.35 (0.15), residues: 1230 sheet: -0.29 (0.23), residues: 472 loop : 0.12 (0.18), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 191 HIS 0.005 0.001 HIS E 24 PHE 0.013 0.001 PHE D 441 TYR 0.033 0.001 TYR E 242 ARG 0.010 0.001 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 1099) hydrogen bonds : angle 4.63193 ( 3159) covalent geometry : bond 0.00243 (21978) covalent geometry : angle 0.56310 (29983) *********************** 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: 73 poor density : 734 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7825 (mt) REVERT: A 98 ASP cc_start: 0.8349 (p0) cc_final: 0.8051 (p0) REVERT: A 129 SER cc_start: 0.8572 (m) cc_final: 0.7882 (t) REVERT: A 141 ARG cc_start: 0.8733 (mtt-85) cc_final: 0.8464 (mtt-85) REVERT: A 159 VAL cc_start: 0.9291 (t) cc_final: 0.8960 (m) REVERT: A 187 ASN cc_start: 0.8928 (t0) cc_final: 0.7874 (t0) REVERT: A 199 LYS cc_start: 0.8324 (mttt) cc_final: 0.8029 (mmtp) REVERT: A 217 GLN cc_start: 0.7976 (tp40) cc_final: 0.7557 (tp40) REVERT: A 240 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7500 (mm-30) REVERT: A 247 LEU cc_start: 0.9340 (mt) cc_final: 0.9036 (tp) REVERT: A 308 LEU cc_start: 0.8193 (mt) cc_final: 0.7896 (mt) REVERT: A 309 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7558 (mm-30) REVERT: B 84 VAL cc_start: 0.8695 (t) cc_final: 0.8479 (p) REVERT: B 91 LYS cc_start: 0.8363 (mttt) cc_final: 0.8016 (mtpp) REVERT: B 173 ARG cc_start: 0.8505 (ttm110) cc_final: 0.8254 (mtm110) REVERT: B 228 MET cc_start: 0.8767 (tpt) cc_final: 0.8351 (tpp) REVERT: B 309 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7030 (mm-30) REVERT: B 349 ASP cc_start: 0.7729 (m-30) cc_final: 0.6827 (m-30) REVERT: B 448 TYR cc_start: 0.7806 (t80) cc_final: 0.7198 (t80) REVERT: B 480 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8507 (tm-30) REVERT: C 155 VAL cc_start: 0.8594 (m) cc_final: 0.8212 (t) REVERT: C 196 ASP cc_start: 0.7408 (t0) cc_final: 0.7043 (p0) REVERT: C 220 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8016 (tp40) REVERT: C 223 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8789 (mm-30) REVERT: C 344 VAL cc_start: 0.9243 (t) cc_final: 0.9007 (t) REVERT: C 345 ILE cc_start: 0.8558 (mp) cc_final: 0.8268 (mp) REVERT: C 364 ARG cc_start: 0.8722 (mtt180) cc_final: 0.8478 (mtt180) REVERT: C 398 GLN cc_start: 0.8828 (mt0) cc_final: 0.8533 (mm-40) REVERT: C 408 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6856 (p90) REVERT: C 425 ARG cc_start: 0.8787 (mtt90) cc_final: 0.8394 (mtt90) REVERT: C 428 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8739 (mm110) REVERT: C 495 LEU cc_start: 0.8702 (tp) cc_final: 0.8456 (tp) REVERT: D 77 LEU cc_start: 0.8542 (tp) cc_final: 0.8293 (tt) REVERT: D 89 ARG cc_start: 0.8263 (mmt-90) cc_final: 0.6950 (ttp80) REVERT: D 90 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7413 (mm-30) REVERT: D 110 LYS cc_start: 0.7809 (mttt) cc_final: 0.7464 (mttp) REVERT: D 168 GLN cc_start: 0.8897 (mt0) cc_final: 0.8628 (tt0) REVERT: D 267 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7412 (mm-30) REVERT: D 282 GLN cc_start: 0.9200 (pm20) cc_final: 0.8725 (pm20) REVERT: D 315 ASP cc_start: 0.7206 (t0) cc_final: 0.6860 (t0) REVERT: D 356 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7645 (ttm-80) REVERT: D 375 GLN cc_start: 0.7898 (mt0) cc_final: 0.7505 (tm-30) REVERT: D 441 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: E 128 SER cc_start: 0.9064 (t) cc_final: 0.8830 (p) REVERT: E 293 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8353 (mm110) REVERT: F 35 ASN cc_start: 0.9053 (m-40) cc_final: 0.8737 (m-40) REVERT: F 56 GLU cc_start: 0.8306 (pm20) cc_final: 0.8074 (pm20) REVERT: F 201 MET cc_start: 0.8621 (mmt) cc_final: 0.8038 (mmt) REVERT: F 237 LEU cc_start: 0.8668 (mp) cc_final: 0.8414 (mp) REVERT: F 288 ASP cc_start: 0.7881 (m-30) cc_final: 0.7515 (m-30) REVERT: F 356 ARG cc_start: 0.8539 (tpp-160) cc_final: 0.8011 (ttp-170) REVERT: F 450 ASP cc_start: 0.8262 (p0) cc_final: 0.7837 (t70) REVERT: F 463 ILE cc_start: 0.7794 (tp) cc_final: 0.7479 (tp) REVERT: F 464 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8104 (mt-10) REVERT: G 4 LYS cc_start: 0.7757 (tppt) cc_final: 0.7442 (tppt) REVERT: G 247 MET cc_start: 0.6490 (tpt) cc_final: 0.5830 (tpp) outliers start: 73 outliers final: 54 residues processed: 764 average time/residue: 0.5698 time to fit residues: 713.2919 Evaluate side-chains 769 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 711 time to evaluate : 3.067 ------------------------------------------------------------------------------- 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 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 148 VAL 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 A residue 465 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 382 VAL 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 220 GLN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 62 ILE 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 222 MET Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 441 PHE 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 195 ASN Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 61 THR 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 293 GLN 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 460 VAL Chi-restraints excluded: chain G residue 241 SER 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 86 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 87 optimal weight: 0.0070 chunk 232 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN C 72 GLN D 52 GLN E 24 HIS E 308 GLN F 127 GLN ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3436 r_free = 0.3436 target = 0.138455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.120554 restraints weight = 35999.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.124004 restraints weight = 19177.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.126288 restraints weight = 11679.585| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21978 Z= 0.144 Angle : 0.588 11.730 29983 Z= 0.302 Chirality : 0.044 0.191 3681 Planarity : 0.004 0.054 3859 Dihedral : 6.543 108.013 3423 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.89 % Allowed : 27.47 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.16), residues: 3044 helix: 1.30 (0.15), residues: 1229 sheet: -0.27 (0.23), residues: 474 loop : 0.13 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 191 HIS 0.006 0.001 HIS E 24 PHE 0.015 0.001 PHE B 44 TYR 0.038 0.002 TYR E 242 ARG 0.011 0.001 ARG C 108 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 1099) hydrogen bonds : angle 4.64576 ( 3159) covalent geometry : bond 0.00331 (21978) covalent geometry : angle 0.58834 (29983) *********************** 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 802 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 725 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8774 (ttp) cc_final: 0.8457 (ttm) REVERT: A 83 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7901 (mt) REVERT: A 98 ASP cc_start: 0.8473 (p0) cc_final: 0.8239 (p0) REVERT: A 129 SER cc_start: 0.8698 (m) cc_final: 0.8034 (t) REVERT: A 141 ARG cc_start: 0.8926 (mtt-85) cc_final: 0.8676 (mtt-85) REVERT: A 159 VAL cc_start: 0.9263 (t) cc_final: 0.8910 (m) REVERT: A 187 ASN cc_start: 0.8968 (t0) cc_final: 0.7893 (t0) REVERT: A 240 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 247 LEU cc_start: 0.9316 (mt) cc_final: 0.9037 (tp) REVERT: A 308 LEU cc_start: 0.8182 (mt) cc_final: 0.7931 (mt) REVERT: A 309 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7360 (mm-30) REVERT: A 399 TYR cc_start: 0.7807 (t80) cc_final: 0.7545 (t80) REVERT: B 84 VAL cc_start: 0.8750 (t) cc_final: 0.8503 (p) REVERT: B 91 LYS cc_start: 0.8382 (mttt) cc_final: 0.8038 (mtpp) REVERT: B 228 MET cc_start: 0.8794 (tpt) cc_final: 0.8368 (tpp) REVERT: B 309 GLU cc_start: 0.8494 (mm-30) cc_final: 0.6679 (mm-30) REVERT: B 349 ASP cc_start: 0.7761 (m-30) cc_final: 0.6817 (m-30) REVERT: B 448 TYR cc_start: 0.7834 (t80) cc_final: 0.7123 (t80) REVERT: B 480 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8520 (tm-30) REVERT: C 155 VAL cc_start: 0.8720 (m) cc_final: 0.8280 (t) REVERT: C 196 ASP cc_start: 0.7414 (t0) cc_final: 0.6993 (p0) REVERT: C 220 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8016 (tp40) REVERT: C 223 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8813 (mm-30) REVERT: C 344 VAL cc_start: 0.9288 (t) cc_final: 0.9062 (t) REVERT: C 349 ASP cc_start: 0.6883 (m-30) cc_final: 0.6506 (m-30) REVERT: C 398 GLN cc_start: 0.8881 (mt0) cc_final: 0.8634 (mm-40) REVERT: C 408 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6937 (p90) REVERT: C 428 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8716 (mm110) REVERT: D 35 ASN cc_start: 0.7773 (m110) cc_final: 0.7141 (m110) REVERT: D 77 LEU cc_start: 0.8520 (tp) cc_final: 0.8289 (tt) REVERT: D 89 ARG cc_start: 0.8326 (mmt-90) cc_final: 0.6990 (ttp80) REVERT: D 90 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7439 (mm-30) REVERT: D 110 LYS cc_start: 0.7910 (mttt) cc_final: 0.7628 (mttp) REVERT: D 168 GLN cc_start: 0.8868 (mt0) cc_final: 0.8622 (tt0) REVERT: D 267 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7496 (mm-30) REVERT: D 282 GLN cc_start: 0.9227 (pm20) cc_final: 0.8756 (pm20) REVERT: D 315 ASP cc_start: 0.7141 (t0) cc_final: 0.6919 (t0) REVERT: D 356 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7707 (ttm-80) REVERT: D 375 GLN cc_start: 0.7769 (mt0) cc_final: 0.7496 (tm-30) REVERT: D 441 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: E 128 SER cc_start: 0.9079 (t) cc_final: 0.8822 (p) REVERT: E 293 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8381 (mm110) REVERT: E 354 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7801 (tttm) REVERT: F 35 ASN cc_start: 0.9038 (m-40) cc_final: 0.8740 (m-40) REVERT: F 56 GLU cc_start: 0.8333 (pm20) cc_final: 0.8088 (pm20) REVERT: F 201 MET cc_start: 0.8652 (mmt) cc_final: 0.8197 (mmt) REVERT: F 237 LEU cc_start: 0.8684 (mp) cc_final: 0.8439 (mp) REVERT: F 263 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8353 (tp-100) REVERT: F 288 ASP cc_start: 0.7908 (m-30) cc_final: 0.7564 (m-30) REVERT: F 356 ARG cc_start: 0.8507 (tpp-160) cc_final: 0.7978 (ttp-170) REVERT: F 391 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7120 (mt) REVERT: F 450 ASP cc_start: 0.8306 (p0) cc_final: 0.7839 (t70) REVERT: F 464 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8176 (mt-10) REVERT: G 11 LYS cc_start: 0.8041 (mttt) cc_final: 0.7706 (mttm) REVERT: G 211 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5945 (mt-10) REVERT: G 247 MET cc_start: 0.6320 (tpt) cc_final: 0.5703 (tpp) outliers start: 77 outliers final: 59 residues processed: 757 average time/residue: 0.3117 time to fit residues: 367.7720 Evaluate side-chains 775 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 709 time to evaluate : 2.743 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 382 VAL 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 208 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 367 ILE Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 62 ILE 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 222 MET Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 441 PHE Chi-restraints excluded: chain D residue 444 VAL 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 23 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 61 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 293 GLN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 71 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 78 optimal weight: 0.3980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 302 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN C 387 GLN D 52 GLN E 24 HIS E 195 ASN E 308 GLN F 127 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 = 0.3344 r_free = 0.3344 target = 0.131415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.113700 restraints weight = 36188.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.117133 restraints weight = 19163.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.119427 restraints weight = 11634.976| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21978 Z= 0.179 Angle : 0.617 11.819 29983 Z= 0.317 Chirality : 0.045 0.200 3681 Planarity : 0.005 0.054 3859 Dihedral : 6.730 114.447 3423 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.30 % Allowed : 26.96 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 3044 helix: 1.27 (0.15), residues: 1220 sheet: -0.34 (0.23), residues: 474 loop : 0.02 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 191 HIS 0.004 0.001 HIS E 24 PHE 0.017 0.002 PHE C 359 TYR 0.035 0.002 TYR E 242 ARG 0.008 0.001 ARG C 108 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 1099) hydrogen bonds : angle 4.70308 ( 3159) covalent geometry : bond 0.00410 (21978) covalent geometry : angle 0.61692 (29983) *********************** 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 794 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 709 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8765 (ttp) cc_final: 0.8539 (ttm) REVERT: A 129 SER cc_start: 0.8650 (m) cc_final: 0.7987 (t) REVERT: A 159 VAL cc_start: 0.9270 (t) cc_final: 0.8911 (m) REVERT: A 187 ASN cc_start: 0.9032 (t0) cc_final: 0.7956 (t0) REVERT: A 199 LYS cc_start: 0.8317 (mttt) cc_final: 0.8023 (mmtp) REVERT: A 247 LEU cc_start: 0.9274 (mt) cc_final: 0.9004 (tp) REVERT: A 308 LEU cc_start: 0.8227 (mt) cc_final: 0.7942 (mt) REVERT: B 84 VAL cc_start: 0.8796 (t) cc_final: 0.8543 (p) REVERT: B 91 LYS cc_start: 0.8424 (mttt) cc_final: 0.8044 (mtpp) REVERT: B 204 VAL cc_start: 0.9095 (t) cc_final: 0.8881 (m) REVERT: B 228 MET cc_start: 0.8872 (tpt) cc_final: 0.8445 (tpp) REVERT: B 246 TYR cc_start: 0.8499 (t80) cc_final: 0.8283 (t80) REVERT: B 309 GLU cc_start: 0.8456 (mm-30) cc_final: 0.6679 (mm-30) REVERT: B 349 ASP cc_start: 0.7829 (m-30) cc_final: 0.6975 (m-30) REVERT: B 395 PHE cc_start: 0.7444 (t80) cc_final: 0.7205 (t80) REVERT: B 448 TYR cc_start: 0.7847 (t80) cc_final: 0.6996 (t80) REVERT: B 480 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8396 (tm-30) REVERT: C 155 VAL cc_start: 0.8755 (m) cc_final: 0.8336 (t) REVERT: C 196 ASP cc_start: 0.7430 (t0) cc_final: 0.6951 (p0) REVERT: C 220 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8007 (tp40) REVERT: C 223 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8829 (mm-30) REVERT: C 344 VAL cc_start: 0.9240 (t) cc_final: 0.9019 (t) REVERT: C 345 ILE cc_start: 0.8579 (mt) cc_final: 0.8328 (mp) REVERT: C 364 ARG cc_start: 0.8862 (mtt180) cc_final: 0.8080 (mtt180) REVERT: C 398 GLN cc_start: 0.8904 (mt0) cc_final: 0.8665 (mm-40) REVERT: C 408 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.7063 (p90) REVERT: C 428 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8648 (mm110) REVERT: C 490 GLU cc_start: 0.8922 (pm20) cc_final: 0.8721 (pm20) REVERT: D 12 LYS cc_start: 0.8774 (mttp) cc_final: 0.8150 (mtpp) REVERT: D 35 ASN cc_start: 0.7852 (m110) cc_final: 0.7231 (m110) REVERT: D 77 LEU cc_start: 0.8543 (tp) cc_final: 0.8288 (tt) REVERT: D 89 ARG cc_start: 0.8359 (mmt-90) cc_final: 0.6897 (tmt170) REVERT: D 90 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7234 (mm-30) REVERT: D 110 LYS cc_start: 0.7971 (mttt) cc_final: 0.7649 (mttp) REVERT: D 168 GLN cc_start: 0.8884 (mt0) cc_final: 0.8665 (tt0) REVERT: D 267 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7590 (mm-30) REVERT: D 282 GLN cc_start: 0.9270 (pm20) cc_final: 0.8721 (pm20) REVERT: D 315 ASP cc_start: 0.7190 (t0) cc_final: 0.6973 (t0) REVERT: D 375 GLN cc_start: 0.7786 (mt0) cc_final: 0.7504 (tm-30) REVERT: D 441 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: E 9 ILE cc_start: 0.8555 (mt) cc_final: 0.8107 (mt) REVERT: E 128 SER cc_start: 0.9083 (t) cc_final: 0.8802 (p) REVERT: F 35 ASN cc_start: 0.9074 (m-40) cc_final: 0.8735 (m-40) REVERT: F 201 MET cc_start: 0.8627 (mmt) cc_final: 0.8186 (mmt) REVERT: F 237 LEU cc_start: 0.8722 (mp) cc_final: 0.8441 (mp) REVERT: F 263 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8342 (tp-100) REVERT: F 288 ASP cc_start: 0.7926 (m-30) cc_final: 0.7567 (m-30) REVERT: F 356 ARG cc_start: 0.8557 (tpp-160) cc_final: 0.8007 (ttp-170) REVERT: F 391 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7446 (mt) REVERT: F 450 ASP cc_start: 0.8347 (p0) cc_final: 0.7821 (t70) REVERT: F 464 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8211 (mt-10) REVERT: G 11 LYS cc_start: 0.8098 (mttt) cc_final: 0.7781 (mttm) REVERT: G 211 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5950 (mt-10) REVERT: G 247 MET cc_start: 0.6409 (tpt) cc_final: 0.5764 (tpp) REVERT: G 250 ARG cc_start: 0.8388 (mtp-110) cc_final: 0.8122 (ptp-170) outliers start: 85 outliers final: 71 residues processed: 743 average time/residue: 0.3536 time to fit residues: 411.9250 Evaluate side-chains 780 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 703 time to evaluate : 2.451 ------------------------------------------------------------------------------- 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 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 329 ILE 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 132 GLN Chi-restraints excluded: chain C residue 144 VAL 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 304 HIS 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 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 149 ARG Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 441 PHE Chi-restraints excluded: chain D residue 444 VAL 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 195 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 355 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 61 THR 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 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 241 SER 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 34 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 276 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 295 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS B 67 ASN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN E 24 HIS E 195 ASN E 223 ASN E 308 GLN F 127 GLN ** F 282 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 = 0.3361 r_free = 0.3361 target = 0.132682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.114745 restraints weight = 36120.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.118308 restraints weight = 18847.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.120632 restraints weight = 11295.045| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21978 Z= 0.143 Angle : 0.602 11.936 29983 Z= 0.308 Chirality : 0.045 0.214 3681 Planarity : 0.004 0.054 3859 Dihedral : 6.651 117.690 3423 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.05 % Allowed : 27.42 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 3044 helix: 1.31 (0.15), residues: 1219 sheet: -0.33 (0.23), residues: 474 loop : 0.02 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 191 HIS 0.007 0.001 HIS A 478 PHE 0.017 0.001 PHE C 359 TYR 0.034 0.002 TYR E 242 ARG 0.009 0.001 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 1099) hydrogen bonds : angle 4.64290 ( 3159) covalent geometry : bond 0.00329 (21978) covalent geometry : angle 0.60184 (29983) ********************** 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 783 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 703 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 SER cc_start: 0.8620 (m) cc_final: 0.7979 (t) REVERT: A 141 ARG cc_start: 0.8777 (mtt-85) cc_final: 0.8572 (mtt90) REVERT: A 159 VAL cc_start: 0.9259 (t) cc_final: 0.8892 (m) REVERT: A 199 LYS cc_start: 0.8345 (mttt) cc_final: 0.8039 (mmtp) REVERT: A 247 LEU cc_start: 0.9261 (mt) cc_final: 0.8954 (tp) REVERT: A 308 LEU cc_start: 0.8219 (mt) cc_final: 0.7904 (mt) REVERT: A 399 TYR cc_start: 0.7329 (t80) cc_final: 0.7113 (t80) REVERT: B 84 VAL cc_start: 0.8762 (t) cc_final: 0.8508 (p) REVERT: B 89 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7961 (pp) REVERT: B 91 LYS cc_start: 0.8376 (mttt) cc_final: 0.8006 (mtpp) REVERT: B 204 VAL cc_start: 0.9103 (t) cc_final: 0.8885 (m) REVERT: B 228 MET cc_start: 0.8897 (tpt) cc_final: 0.8417 (tpp) REVERT: B 309 GLU cc_start: 0.8532 (mm-30) cc_final: 0.6683 (mm-30) REVERT: B 349 ASP cc_start: 0.7821 (m-30) cc_final: 0.6859 (m-30) REVERT: B 395 PHE cc_start: 0.7469 (t80) cc_final: 0.7252 (t80) REVERT: B 448 TYR cc_start: 0.7828 (t80) cc_final: 0.7015 (t80) REVERT: B 480 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8528 (tm-30) REVERT: C 155 VAL cc_start: 0.8681 (m) cc_final: 0.8272 (t) REVERT: C 196 ASP cc_start: 0.7441 (t0) cc_final: 0.6945 (p0) REVERT: C 220 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7998 (tp40) REVERT: C 223 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8850 (mm-30) REVERT: C 230 TYR cc_start: 0.9024 (p90) cc_final: 0.8645 (p90) REVERT: C 344 VAL cc_start: 0.9212 (t) cc_final: 0.9005 (t) REVERT: C 345 ILE cc_start: 0.8604 (mt) cc_final: 0.8352 (mp) REVERT: C 364 ARG cc_start: 0.8813 (mtt180) cc_final: 0.7965 (mtt180) REVERT: C 398 GLN cc_start: 0.8903 (mt0) cc_final: 0.8659 (mm-40) REVERT: C 428 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8686 (mm110) REVERT: C 490 GLU cc_start: 0.8868 (pm20) cc_final: 0.8666 (pm20) REVERT: D 12 LYS cc_start: 0.8772 (mttp) cc_final: 0.8117 (mtpp) REVERT: D 35 ASN cc_start: 0.7785 (m110) cc_final: 0.7157 (m110) REVERT: D 77 LEU cc_start: 0.8551 (tp) cc_final: 0.8305 (tt) REVERT: D 89 ARG cc_start: 0.8341 (mmt-90) cc_final: 0.6962 (ttp80) REVERT: D 90 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7330 (mm-30) REVERT: D 110 LYS cc_start: 0.7968 (mttt) cc_final: 0.7650 (mttp) REVERT: D 168 GLN cc_start: 0.8893 (mt0) cc_final: 0.8662 (tt0) REVERT: D 267 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7617 (mm-30) REVERT: D 282 GLN cc_start: 0.9256 (pm20) cc_final: 0.8767 (pm20) REVERT: D 315 ASP cc_start: 0.7223 (t0) cc_final: 0.6977 (t0) REVERT: D 375 GLN cc_start: 0.7772 (mt0) cc_final: 0.7498 (tm-30) REVERT: D 441 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: E 9 ILE cc_start: 0.8515 (mt) cc_final: 0.8046 (mt) REVERT: E 128 SER cc_start: 0.9094 (t) cc_final: 0.8792 (p) REVERT: E 293 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8333 (mm110) REVERT: F 35 ASN cc_start: 0.9058 (m-40) cc_final: 0.8705 (m-40) REVERT: F 56 GLU cc_start: 0.8329 (pm20) cc_final: 0.8046 (pm20) REVERT: F 201 MET cc_start: 0.8592 (mmt) cc_final: 0.8129 (mmt) REVERT: F 263 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8317 (tp-100) REVERT: F 288 ASP cc_start: 0.7942 (m-30) cc_final: 0.7578 (m-30) REVERT: F 356 ARG cc_start: 0.8560 (tpp-160) cc_final: 0.7995 (ttp-170) REVERT: F 375 GLN cc_start: 0.8987 (mt0) cc_final: 0.8671 (mm-40) REVERT: F 391 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7426 (mt) REVERT: F 464 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8241 (mt-10) REVERT: G 11 LYS cc_start: 0.8104 (mttt) cc_final: 0.7791 (mttm) REVERT: G 211 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5903 (mt-10) REVERT: G 247 MET cc_start: 0.6419 (tpt) cc_final: 0.5757 (tpp) REVERT: G 250 ARG cc_start: 0.8366 (mtp-110) cc_final: 0.8016 (ptp-170) outliers start: 80 outliers final: 72 residues processed: 738 average time/residue: 0.3370 time to fit residues: 393.2707 Evaluate side-chains 782 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 704 time to evaluate : 2.377 ------------------------------------------------------------------------------- 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 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 329 ILE 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 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 150 THR 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 304 HIS Chi-restraints excluded: chain C residue 367 ILE 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 78 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 441 PHE Chi-restraints excluded: chain D residue 444 VAL 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 136 THR Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 238 THR 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 61 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 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 241 SER 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 191 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 222 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN A 478 HIS B 67 ASN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN E 24 HIS E 195 ASN E 308 GLN F 127 GLN ** F 282 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 = 0.3363 r_free = 0.3363 target = 0.132974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.115121 restraints weight = 36052.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.118670 restraints weight = 18840.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.121058 restraints weight = 11329.858| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3874 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= 0.139 Angle : 0.596 10.581 29983 Z= 0.305 Chirality : 0.045 0.207 3681 Planarity : 0.004 0.054 3859 Dihedral : 6.619 120.942 3423 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.50 % Allowed : 27.42 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 3044 helix: 1.33 (0.15), residues: 1223 sheet: -0.33 (0.24), residues: 464 loop : 0.03 (0.18), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 258 HIS 0.010 0.001 HIS A 478 PHE 0.040 0.001 PHE A 466 TYR 0.032 0.002 TYR E 242 ARG 0.009 0.001 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 1099) hydrogen bonds : angle 4.61277 ( 3159) covalent geometry : bond 0.00319 (21978) covalent geometry : angle 0.59573 (29983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10248.15 seconds wall clock time: 184 minutes 29.52 seconds (11069.52 seconds total)