Starting phenix.real_space_refine on Thu Mar 5 11:15:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjx_25939/03_2026/7tjx_25939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjx_25939/03_2026/7tjx_25939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tjx_25939/03_2026/7tjx_25939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjx_25939/03_2026/7tjx_25939.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjx_25939/03_2026/7tjx_25939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjx_25939/03_2026/7tjx_25939.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 25 5.16 5 C 13686 2.51 5 N 3896 2.21 5 O 4036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21663 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3384 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 450} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 21, 'ASP:plan': 8, 'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3375 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 23, 'ASP:plan': 10, 'GLN:plan1': 4, 'ARG:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 171 Chain: "C" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3523 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 17, 'GLN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 130 Chain: "D" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3206 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 430} Chain breaks: 1 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 14, 'GLN:plan1': 6, 'GLU:plan': 17, 'ASN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 157 Chain: "E" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3105 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 433} Chain breaks: 2 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 430 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 28, 'GLN:plan1': 8, 'ASN:plan1': 1, 'TYR:plan': 2, 'ARG:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 243 Chain: "F" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3349 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 443} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 23, 'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "G" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1560 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 513 Unresolved non-hydrogen angles: 640 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 7, 'PHE:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 14, 'ASP:plan': 10, 'HIS:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 247 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.21, per 1000 atoms: 0.24 Number of scatterers: 21663 At special positions: 0 Unit cell: (126.665, 126.665, 154.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 15 15.00 Mg 5 11.99 O 4036 8.00 N 3896 7.00 C 13686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 23 sheets defined 49.9% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.515A pdb=" N LEU A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 111 through 115 removed outlier: 4.319A pdb=" N ASN A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.673A pdb=" N VAL A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.763A pdb=" N ASN A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 226 through 229 removed outlier: 3.875A pdb=" N LYS A 229 " --> pdb=" O ASP A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 241 through 262 removed outlier: 3.583A pdb=" N GLN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.637A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.633A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 298 No H-bonds generated for 'chain 'A' and resid 297 through 298' Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.801A pdb=" N GLN A 381 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 402 removed outlier: 3.596A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 439 through 453 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 459 through 478 removed outlier: 3.891A pdb=" N ILE A 463 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 489 Processing helix chain 'A' and resid 492 through 508 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.723A pdb=" N LEU B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.546A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.728A pdb=" N VAL B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 241 through 262 removed outlier: 3.639A pdb=" N GLN B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Proline residue: B 249 - end of helix removed outlier: 3.530A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 297 through 298 No H-bonds generated for 'chain 'B' and resid 297 through 298' Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.646A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 335 removed outlier: 3.802A pdb=" N ASP B 335 " --> pdb=" O GLN B 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 332 through 335' Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.696A pdb=" N VAL B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.641A pdb=" N PHE B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.620A pdb=" N VAL B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 removed outlier: 3.655A pdb=" N GLN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 4.152A pdb=" N GLY B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 476 removed outlier: 3.530A pdb=" N SER B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 4.460A pdb=" N GLU B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY B 489 " --> pdb=" O ILE B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 508 removed outlier: 3.686A pdb=" N GLU B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.652A pdb=" N LEU C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.830A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 211 through 225 removed outlier: 3.512A pdb=" N VAL C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 241 through 262 removed outlier: 3.509A pdb=" N GLN C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Proline residue: C 249 - end of helix removed outlier: 3.657A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.599A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 309 removed outlier: 3.635A pdb=" N ARG C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 319 removed outlier: 3.622A pdb=" N GLY C 319 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 380 Processing helix chain 'C' and resid 382 through 407 removed outlier: 5.587A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 430 removed outlier: 4.237A pdb=" N THR C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 453 Proline residue: C 445 - end of helix removed outlier: 3.578A pdb=" N GLY C 453 " --> pdb=" O ALA C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 removed outlier: 4.243A pdb=" N GLY C 457 " --> pdb=" O HIS C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 478 removed outlier: 4.039A pdb=" N LEU C 471 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 489 removed outlier: 3.938A pdb=" N LEU C 482 " --> pdb=" O HIS C 478 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 509 removed outlier: 3.510A pdb=" N ALA C 497 " --> pdb=" O LYS C 493 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 removed outlier: 3.830A pdb=" N LYS D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 177 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.645A pdb=" N LYS D 202 " --> pdb=" O TYR D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 246 removed outlier: 5.007A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 273 removed outlier: 3.549A pdb=" N PHE D 261 " --> pdb=" O ASN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 294 removed outlier: 3.671A pdb=" N LEU D 291 " --> pdb=" O THR D 287 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 319 through 326 Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.507A pdb=" N SER D 340 " --> pdb=" O SER D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 385 removed outlier: 3.606A pdb=" N LYS D 373 " --> pdb=" O ASP D 369 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER D 383 " --> pdb=" O GLN D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 404 through 414 removed outlier: 3.743A pdb=" N LYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 462 through 475 removed outlier: 3.887A pdb=" N ALA D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 178 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 246 removed outlier: 5.148A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 273 removed outlier: 3.567A pdb=" N THR E 262 " --> pdb=" O ILE E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 284 through 294 removed outlier: 3.756A pdb=" N GLY E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 removed outlier: 4.052A pdb=" N ASP E 315 " --> pdb=" O VAL E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.871A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 341 removed outlier: 4.131A pdb=" N SER E 340 " --> pdb=" O SER E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 385 removed outlier: 3.677A pdb=" N GLN E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 removed outlier: 3.619A pdb=" N THR E 437 " --> pdb=" O ARG E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 474 removed outlier: 3.997A pdb=" N ASP E 465 " --> pdb=" O GLY E 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 190 through 204 removed outlier: 3.598A pdb=" N LYS F 202 " --> pdb=" O TYR F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 246 removed outlier: 4.891A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 239 " --> pdb=" O THR F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 removed outlier: 3.963A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 282 through 283 No H-bonds generated for 'chain 'F' and resid 282 through 283' Processing helix chain 'F' and resid 284 through 294 Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 326 Processing helix chain 'F' and resid 327 through 329 No H-bonds generated for 'chain 'F' and resid 327 through 329' Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 364 through 392 removed outlier: 3.897A pdb=" N VAL F 370 " --> pdb=" O GLU F 366 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 396 removed outlier: 3.924A pdb=" N LEU F 396 " --> pdb=" O MET F 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 393 through 396' Processing helix chain 'F' and resid 397 through 414 removed outlier: 3.603A pdb=" N ARG F 412 " --> pdb=" O ARG F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 475 Processing helix chain 'G' and resid 3 through 54 removed outlier: 4.351A pdb=" N SER G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 101 removed outlier: 3.758A pdb=" N ALA G 92 " --> pdb=" O HIS G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 120 Processing helix chain 'G' and resid 139 through 153 removed outlier: 4.077A pdb=" N VAL G 153 " --> pdb=" O LYS G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 Processing helix chain 'G' and resid 184 through 190 Processing helix chain 'G' and resid 204 through 276 removed outlier: 3.602A pdb=" N SER G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 37 removed outlier: 6.703A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU A 68 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 93 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.208A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR A 202 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL A 269 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 204 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASP A 271 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL A 206 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.208A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR A 202 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL A 269 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 204 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASP A 271 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL A 206 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A 172 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 77 through 78 removed outlier: 6.773A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS F 24 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL F 13 " --> pdb=" O HIS F 24 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 31 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.593A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA B 266 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LEU B 326 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 268 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 328 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR B 270 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLU B 330 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.593A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA B 266 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LEU B 326 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 268 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 328 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR B 270 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLU B 330 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 62 through 68 removed outlier: 6.627A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN C 67 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LYS D 75 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS D 40 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA D 36 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN D 35 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 110 removed outlier: 6.279A pdb=" N ARG C 108 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA C 235 " --> pdb=" O ARG C 108 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 110 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR C 202 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL C 269 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 204 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASP C 271 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 206 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR C 270 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 108 through 110 removed outlier: 6.279A pdb=" N ARG C 108 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA C 235 " --> pdb=" O ARG C 108 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 110 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR C 202 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL C 269 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 204 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASP C 271 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 206 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR C 270 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.921A pdb=" N SER D 182 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL D 218 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE D 184 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLY D 220 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY D 186 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE D 153 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL D 310 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU D 155 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.449A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 17 removed outlier: 6.834A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.722A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.722A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE E 153 " --> pdb=" O GLN E 308 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS E 152 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N THR E 333 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY E 154 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU E 335 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE E 156 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC3, first strand: chain 'F' and resid 95 through 96 removed outlier: 3.717A pdb=" N PHE F 219 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS F 152 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N THR F 333 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY F 154 " --> pdb=" O THR F 333 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU F 335 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE F 156 " --> pdb=" O LEU F 335 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL F 334 " --> pdb=" O ASP F 352 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP F 352 " --> pdb=" O VAL F 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.322A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 105 through 109 removed outlier: 5.954A pdb=" N GLU G 72 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL G 108 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 2.55 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 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.240 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- 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 : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3044 helix: 0.41 (0.14), residues: 1204 sheet: -0.04 (0.23), residues: 487 loop : -0.04 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 462 TYR 0.021 0.002 TYR G 255 PHE 0.020 0.001 PHE E 326 TRP 0.020 0.001 TRP C 258 HIS 0.010 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00269 (21978) covalent geometry : angle 0.61945 (29983) hydrogen bonds : bond 0.14670 ( 1099) hydrogen bonds : angle 6.83134 ( 3159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 932 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 SER cc_start: 0.8135 (m) cc_final: 0.7486 (t) REVERT: A 199 LYS cc_start: 0.8227 (mttt) cc_final: 0.8015 (mttt) REVERT: A 246 TYR cc_start: 0.8430 (t80) cc_final: 0.8216 (t80) REVERT: A 308 LEU cc_start: 0.8225 (mt) cc_final: 0.8006 (mt) REVERT: A 466 PHE cc_start: 0.8507 (t80) cc_final: 0.8202 (t80) REVERT: A 477 ASN cc_start: 0.7900 (m-40) cc_final: 0.7417 (t0) REVERT: B 44 PHE cc_start: 0.8880 (t80) cc_final: 0.8676 (t80) REVERT: B 84 VAL cc_start: 0.9030 (t) cc_final: 0.8820 (p) REVERT: B 91 LYS cc_start: 0.8322 (mttt) cc_final: 0.8109 (mtpp) REVERT: B 146 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 150 THR cc_start: 0.8241 (p) cc_final: 0.7996 (p) REVERT: B 187 ASN cc_start: 0.9155 (t0) cc_final: 0.8849 (t0) REVERT: B 228 MET cc_start: 0.8885 (tpt) cc_final: 0.8436 (tpp) REVERT: B 251 THR cc_start: 0.9275 (p) cc_final: 0.9061 (p) REVERT: B 262 ASN cc_start: 0.8614 (m-40) cc_final: 0.8401 (m-40) REVERT: B 448 TYR cc_start: 0.7986 (t80) cc_final: 0.7267 (t80) REVERT: B 480 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8296 (tm-30) REVERT: B 486 ARG cc_start: 0.8639 (ttt180) cc_final: 0.8398 (mtp85) REVERT: C 72 GLN cc_start: 0.7238 (pt0) cc_final: 0.6767 (pt0) REVERT: C 115 ASN cc_start: 0.8774 (m-40) cc_final: 0.8548 (m-40) REVERT: C 130 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7461 (ttp80) REVERT: C 152 LEU cc_start: 0.9388 (mt) cc_final: 0.9173 (mt) REVERT: C 178 THR cc_start: 0.8418 (m) cc_final: 0.8213 (m) REVERT: C 294 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8719 (mt-10) REVERT: C 364 ARG cc_start: 0.8862 (mtt180) cc_final: 0.8112 (mtt180) REVERT: C 368 ASN cc_start: 0.8266 (t0) cc_final: 0.7826 (t0) REVERT: C 369 VAL cc_start: 0.8931 (t) cc_final: 0.8564 (p) REVERT: C 383 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7914 (mmmt) REVERT: C 398 GLN cc_start: 0.8867 (mt0) cc_final: 0.8350 (mt0) REVERT: C 425 ARG cc_start: 0.8592 (mtt90) cc_final: 0.8331 (mtt90) REVERT: C 455 LEU cc_start: 0.8316 (tp) cc_final: 0.7990 (tp) REVERT: C 478 HIS cc_start: 0.7669 (m-70) cc_final: 0.7326 (m-70) REVERT: D 12 LYS cc_start: 0.8633 (mptt) cc_final: 0.8142 (mtpp) REVERT: D 77 LEU cc_start: 0.8134 (tp) cc_final: 0.7909 (tt) REVERT: D 90 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7323 (mm-30) REVERT: D 110 LYS cc_start: 0.8187 (mttt) cc_final: 0.7920 (mttt) REVERT: D 176 LYS cc_start: 0.8498 (tttt) cc_final: 0.8173 (tppt) REVERT: D 198 TYR cc_start: 0.8910 (t80) cc_final: 0.8704 (t80) REVERT: D 203 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8258 (mt-10) REVERT: D 332 THR cc_start: 0.8562 (p) cc_final: 0.8322 (m) REVERT: D 356 ARG cc_start: 0.7799 (ttt90) cc_final: 0.7418 (ttm-80) REVERT: D 375 GLN cc_start: 0.7918 (mt0) cc_final: 0.7392 (tm-30) REVERT: D 412 ARG cc_start: 0.7794 (mtt90) cc_final: 0.7296 (mtt-85) REVERT: D 440 SER cc_start: 0.9096 (m) cc_final: 0.8888 (t) REVERT: E 128 SER cc_start: 0.9125 (t) cc_final: 0.8891 (p) REVERT: E 196 ASP cc_start: 0.8218 (t0) cc_final: 0.7830 (t0) REVERT: E 207 ILE cc_start: 0.9180 (mt) cc_final: 0.8863 (tt) REVERT: E 277 SER cc_start: 0.8320 (t) cc_final: 0.8097 (m) REVERT: E 308 GLN cc_start: 0.8923 (mt0) cc_final: 0.8696 (mt0) REVERT: E 352 ASP cc_start: 0.7559 (m-30) cc_final: 0.7280 (m-30) REVERT: E 353 SER cc_start: 0.8538 (m) cc_final: 0.8308 (p) REVERT: E 441 PHE cc_start: 0.8718 (m-80) cc_final: 0.8469 (m-80) REVERT: F 35 ASN cc_start: 0.9145 (m-40) cc_final: 0.8752 (m-40) REVERT: F 128 SER cc_start: 0.9222 (t) cc_final: 0.8997 (m) REVERT: F 201 MET cc_start: 0.8546 (mmt) cc_final: 0.8221 (mmt) REVERT: F 202 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8199 (mtmm) REVERT: F 237 LEU cc_start: 0.8781 (mp) cc_final: 0.8519 (mp) REVERT: F 259 PHE cc_start: 0.7704 (t80) cc_final: 0.7400 (t80) REVERT: F 262 THR cc_start: 0.8989 (m) cc_final: 0.8695 (p) REVERT: F 281 TYR cc_start: 0.8866 (m-80) cc_final: 0.8362 (m-80) REVERT: F 285 LEU cc_start: 0.8474 (tt) cc_final: 0.8043 (tp) REVERT: F 288 ASP cc_start: 0.7783 (m-30) cc_final: 0.7093 (m-30) REVERT: F 293 GLN cc_start: 0.8727 (tt0) cc_final: 0.8195 (tt0) REVERT: F 349 ASP cc_start: 0.8479 (t0) cc_final: 0.8104 (t0) REVERT: F 351 LEU cc_start: 0.9363 (mt) cc_final: 0.9095 (mt) REVERT: F 356 ARG cc_start: 0.8273 (tpt170) cc_final: 0.7985 (ttp-170) REVERT: F 369 ASP cc_start: 0.8180 (t0) cc_final: 0.7939 (t70) REVERT: F 375 GLN cc_start: 0.9037 (mt0) cc_final: 0.8540 (mm-40) REVERT: F 449 TYR cc_start: 0.8735 (m-80) cc_final: 0.8473 (m-80) REVERT: F 463 ILE cc_start: 0.7868 (tp) cc_final: 0.7566 (tp) REVERT: F 464 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8138 (mt-10) REVERT: G 3 LEU cc_start: 0.6845 (tt) cc_final: 0.6538 (tp) REVERT: G 4 LYS cc_start: 0.8312 (tptt) cc_final: 0.7969 (tppp) REVERT: G 24 LYS cc_start: 0.4822 (tmtt) cc_final: 0.4323 (mtmt) REVERT: G 214 LEU cc_start: 0.8397 (tp) cc_final: 0.8126 (tp) REVERT: G 247 MET cc_start: 0.7066 (tpt) cc_final: 0.6599 (tpp) outliers start: 1 outliers final: 0 residues processed: 933 average time/residue: 0.1446 time to fit residues: 207.6020 Evaluate side-chains 747 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 747 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 308 GLN ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN F 379 GLN G 217 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.131555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.113720 restraints weight = 36220.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.117201 restraints weight = 18713.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.119356 restraints weight = 11169.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.120950 restraints weight = 7514.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.121930 restraints weight = 5458.657| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21978 Z= 0.194 Angle : 0.642 8.065 29983 Z= 0.337 Chirality : 0.047 0.161 3681 Planarity : 0.005 0.054 3859 Dihedral : 7.809 94.898 3423 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 3044 helix: 1.01 (0.15), residues: 1206 sheet: -0.07 (0.23), residues: 485 loop : 0.06 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 166 TYR 0.020 0.002 TYR A 399 PHE 0.027 0.002 PHE D 441 TRP 0.016 0.002 TRP B 191 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00431 (21978) covalent geometry : angle 0.64192 (29983) hydrogen bonds : bond 0.04939 ( 1099) hydrogen bonds : angle 5.39534 ( 3159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 779 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 SER cc_start: 0.8510 (m) cc_final: 0.7974 (t) REVERT: A 159 VAL cc_start: 0.9193 (t) cc_final: 0.8825 (m) REVERT: A 246 TYR cc_start: 0.8547 (t80) cc_final: 0.8191 (t80) REVERT: A 308 LEU cc_start: 0.8187 (mt) cc_final: 0.7963 (mt) REVERT: A 309 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 399 TYR cc_start: 0.7634 (t80) cc_final: 0.7153 (t80) REVERT: A 477 ASN cc_start: 0.7873 (m-40) cc_final: 0.7433 (t0) REVERT: B 84 VAL cc_start: 0.8911 (t) cc_final: 0.8608 (p) REVERT: B 91 LYS cc_start: 0.8351 (mttt) cc_final: 0.8115 (mtpp) REVERT: B 228 MET cc_start: 0.8879 (tpt) cc_final: 0.8398 (tpp) REVERT: B 309 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7515 (mm-30) REVERT: B 317 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8173 (ptmm) REVERT: B 342 THR cc_start: 0.9403 (p) cc_final: 0.9161 (t) REVERT: B 349 ASP cc_start: 0.8089 (m-30) cc_final: 0.6870 (m-30) REVERT: B 448 TYR cc_start: 0.8114 (t80) cc_final: 0.7260 (t80) REVERT: B 480 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8343 (tm-30) REVERT: B 486 ARG cc_start: 0.8506 (ttt180) cc_final: 0.8178 (mtp85) REVERT: C 78 PHE cc_start: 0.9005 (m-80) cc_final: 0.8753 (m-10) REVERT: C 93 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7824 (t) REVERT: C 142 ARG cc_start: 0.8637 (tmm-80) cc_final: 0.8321 (tmm-80) REVERT: C 223 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8701 (mm-30) REVERT: C 364 ARG cc_start: 0.8887 (mtt180) cc_final: 0.8493 (mtt180) REVERT: C 383 LYS cc_start: 0.8409 (mmtm) cc_final: 0.8127 (mmmt) REVERT: C 398 GLN cc_start: 0.8697 (mt0) cc_final: 0.8491 (mt0) REVERT: C 425 ARG cc_start: 0.8688 (mtt90) cc_final: 0.8042 (mtt90) REVERT: C 428 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8686 (mm110) REVERT: C 434 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: C 440 THR cc_start: 0.8859 (p) cc_final: 0.8613 (t) REVERT: D 12 LYS cc_start: 0.8644 (mptt) cc_final: 0.8256 (mtpp) REVERT: D 89 ARG cc_start: 0.8417 (mmt-90) cc_final: 0.7293 (ttp80) REVERT: D 90 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7275 (mm-30) REVERT: D 110 LYS cc_start: 0.7906 (mttt) cc_final: 0.7664 (mttt) REVERT: D 132 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7618 (mt-10) REVERT: D 168 GLN cc_start: 0.8867 (mt0) cc_final: 0.8666 (tt0) REVERT: D 267 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7915 (mt-10) REVERT: D 277 SER cc_start: 0.8720 (t) cc_final: 0.8354 (m) REVERT: D 282 GLN cc_start: 0.9313 (pm20) cc_final: 0.8730 (pm20) REVERT: D 329 LEU cc_start: 0.8860 (mt) cc_final: 0.8477 (mt) REVERT: D 332 THR cc_start: 0.8513 (p) cc_final: 0.8255 (m) REVERT: D 356 ARG cc_start: 0.7623 (ttt90) cc_final: 0.7363 (ttm-80) REVERT: D 375 GLN cc_start: 0.8062 (mt0) cc_final: 0.7583 (tm-30) REVERT: E 103 ILE cc_start: 0.9129 (pt) cc_final: 0.8908 (pt) REVERT: E 128 SER cc_start: 0.9084 (t) cc_final: 0.8805 (p) REVERT: E 201 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8057 (mpp) REVERT: E 207 ILE cc_start: 0.9068 (mt) cc_final: 0.8651 (tt) REVERT: E 353 SER cc_start: 0.8858 (m) cc_final: 0.8539 (p) REVERT: E 354 LYS cc_start: 0.8049 (mtpt) cc_final: 0.7722 (mtpp) REVERT: F 35 ASN cc_start: 0.9170 (m-40) cc_final: 0.8794 (m-40) REVERT: F 61 THR cc_start: 0.8434 (p) cc_final: 0.8223 (t) REVERT: F 192 ARG cc_start: 0.9051 (ttp-110) cc_final: 0.8566 (ttp80) REVERT: F 201 MET cc_start: 0.8632 (mmt) cc_final: 0.8236 (mmt) REVERT: F 202 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8178 (mtmm) REVERT: F 237 LEU cc_start: 0.8771 (mp) cc_final: 0.8466 (mp) REVERT: F 262 THR cc_start: 0.8955 (m) cc_final: 0.8532 (p) REVERT: F 281 TYR cc_start: 0.9005 (m-80) cc_final: 0.8708 (m-80) REVERT: F 282 GLN cc_start: 0.9282 (pm20) cc_final: 0.8212 (pm20) REVERT: F 288 ASP cc_start: 0.8114 (m-30) cc_final: 0.7593 (m-30) REVERT: F 293 GLN cc_start: 0.8560 (tt0) cc_final: 0.8339 (tt0) REVERT: F 349 ASP cc_start: 0.8523 (t0) cc_final: 0.8203 (t0) REVERT: F 351 LEU cc_start: 0.9348 (mt) cc_final: 0.8687 (mt) REVERT: F 356 ARG cc_start: 0.8470 (tpt170) cc_final: 0.8200 (ttp-170) REVERT: F 375 GLN cc_start: 0.8995 (mt0) cc_final: 0.8582 (mm-40) REVERT: F 449 TYR cc_start: 0.8867 (m-80) cc_final: 0.8637 (m-80) REVERT: F 463 ILE cc_start: 0.7882 (tp) cc_final: 0.7572 (tp) REVERT: F 464 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7917 (mt-10) REVERT: G 4 LYS cc_start: 0.8380 (tptt) cc_final: 0.8042 (tppp) REVERT: G 24 LYS cc_start: 0.5198 (tmtt) cc_final: 0.4643 (mtpt) REVERT: G 214 LEU cc_start: 0.8455 (tp) cc_final: 0.8219 (tp) REVERT: G 247 MET cc_start: 0.7334 (tpt) cc_final: 0.6891 (tpp) REVERT: G 250 ARG cc_start: 0.8219 (mtp-110) cc_final: 0.7769 (mtm180) outliers start: 69 outliers final: 42 residues processed: 806 average time/residue: 0.1355 time to fit residues: 171.5006 Evaluate side-chains 759 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 714 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain G residue 29 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 207 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 271 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 387 GLN E 24 HIS E 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.134583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.116762 restraints weight = 35989.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.120234 restraints weight = 18735.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.122526 restraints weight = 11225.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.123962 restraints weight = 7481.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.125050 restraints weight = 5473.220| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2457 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= 0.126 Angle : 0.571 8.110 29983 Z= 0.297 Chirality : 0.044 0.158 3681 Planarity : 0.004 0.055 3859 Dihedral : 7.223 96.139 3423 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.14 % Allowed : 19.17 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.16), residues: 3044 helix: 1.25 (0.15), residues: 1213 sheet: -0.12 (0.23), residues: 480 loop : 0.19 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 337 TYR 0.020 0.001 TYR C 246 PHE 0.019 0.002 PHE A 44 TRP 0.007 0.001 TRP A 258 HIS 0.006 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00277 (21978) covalent geometry : angle 0.57131 (29983) hydrogen bonds : bond 0.04128 ( 1099) hydrogen bonds : angle 4.97042 ( 3159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 766 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 129 SER cc_start: 0.8512 (m) cc_final: 0.7947 (t) REVERT: A 159 VAL cc_start: 0.9199 (t) cc_final: 0.8817 (m) REVERT: A 187 ASN cc_start: 0.9017 (t0) cc_final: 0.8577 (t0) REVERT: A 196 ASP cc_start: 0.7016 (t0) cc_final: 0.6623 (t0) REVERT: A 199 LYS cc_start: 0.8179 (mttt) cc_final: 0.7930 (mmtp) REVERT: A 221 THR cc_start: 0.8622 (m) cc_final: 0.8350 (p) REVERT: A 308 LEU cc_start: 0.8192 (mt) cc_final: 0.7951 (mt) REVERT: A 309 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 477 ASN cc_start: 0.7831 (m-40) cc_final: 0.7469 (t0) REVERT: B 84 VAL cc_start: 0.8753 (t) cc_final: 0.8482 (p) REVERT: B 91 LYS cc_start: 0.8376 (mttt) cc_final: 0.8155 (mtpp) REVERT: B 124 ASP cc_start: 0.6317 (p0) cc_final: 0.5884 (p0) REVERT: B 228 MET cc_start: 0.8778 (tpt) cc_final: 0.8300 (tpp) REVERT: B 309 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7581 (mm-30) REVERT: B 349 ASP cc_start: 0.8035 (m-30) cc_final: 0.7052 (m-30) REVERT: B 448 TYR cc_start: 0.7970 (t80) cc_final: 0.7271 (t80) REVERT: B 480 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8446 (tm-30) REVERT: B 486 ARG cc_start: 0.8554 (ttt180) cc_final: 0.8238 (mtp85) REVERT: C 44 PHE cc_start: 0.8155 (t80) cc_final: 0.7845 (t80) REVERT: C 78 PHE cc_start: 0.8828 (m-80) cc_final: 0.8622 (m-10) REVERT: C 106 LEU cc_start: 0.9091 (tp) cc_final: 0.8589 (mp) REVERT: C 223 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8648 (mm-30) REVERT: C 345 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8318 (mp) REVERT: C 349 ASP cc_start: 0.7086 (m-30) cc_final: 0.6781 (m-30) REVERT: C 364 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8557 (mtt180) REVERT: C 428 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8787 (mm110) REVERT: C 478 HIS cc_start: 0.7930 (m-70) cc_final: 0.7640 (m-70) REVERT: D 77 LEU cc_start: 0.8362 (tp) cc_final: 0.8057 (tt) REVERT: D 89 ARG cc_start: 0.8241 (mmt-90) cc_final: 0.6948 (ttp80) REVERT: D 90 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7387 (mm-30) REVERT: D 110 LYS cc_start: 0.7894 (mttt) cc_final: 0.7666 (mttp) REVERT: D 132 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7650 (mt-10) REVERT: D 168 GLN cc_start: 0.8915 (mt0) cc_final: 0.8629 (tt0) REVERT: D 267 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7934 (mt-10) REVERT: D 282 GLN cc_start: 0.9286 (pm20) cc_final: 0.8828 (pm20) REVERT: D 315 ASP cc_start: 0.7098 (t0) cc_final: 0.6856 (t0) REVERT: D 329 LEU cc_start: 0.8782 (mt) cc_final: 0.8576 (mt) REVERT: D 375 GLN cc_start: 0.8024 (mt0) cc_final: 0.7509 (tm-30) REVERT: E 101 GLU cc_start: 0.8196 (pm20) cc_final: 0.7830 (pm20) REVERT: E 103 ILE cc_start: 0.9140 (pt) cc_final: 0.8930 (pt) REVERT: E 128 SER cc_start: 0.9079 (t) cc_final: 0.8831 (p) REVERT: E 201 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8111 (mpp) REVERT: E 207 ILE cc_start: 0.9010 (mt) cc_final: 0.8739 (tt) REVERT: E 293 GLN cc_start: 0.8860 (mm110) cc_final: 0.8267 (mm110) REVERT: E 354 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7833 (mtpp) REVERT: F 35 ASN cc_start: 0.9147 (m-40) cc_final: 0.8789 (m110) REVERT: F 56 GLU cc_start: 0.8099 (pm20) cc_final: 0.7896 (pm20) REVERT: F 92 LEU cc_start: 0.9153 (mt) cc_final: 0.8937 (mt) REVERT: F 191 THR cc_start: 0.9100 (m) cc_final: 0.8789 (m) REVERT: F 201 MET cc_start: 0.8566 (mmt) cc_final: 0.8139 (mmt) REVERT: F 237 LEU cc_start: 0.8746 (mp) cc_final: 0.8463 (mp) REVERT: F 263 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8354 (tp-100) REVERT: F 281 TYR cc_start: 0.8986 (m-80) cc_final: 0.8773 (m-80) REVERT: F 282 GLN cc_start: 0.9129 (pm20) cc_final: 0.8922 (pm20) REVERT: F 288 ASP cc_start: 0.8048 (m-30) cc_final: 0.7493 (m-30) REVERT: F 349 ASP cc_start: 0.8549 (t0) cc_final: 0.8229 (t0) REVERT: F 352 ASP cc_start: 0.7651 (t0) cc_final: 0.7346 (t0) REVERT: F 356 ARG cc_start: 0.8396 (tpt170) cc_final: 0.8062 (ttp-170) REVERT: F 375 GLN cc_start: 0.8936 (mt0) cc_final: 0.8493 (tp40) REVERT: F 449 TYR cc_start: 0.8858 (m-80) cc_final: 0.8625 (m-80) REVERT: F 463 ILE cc_start: 0.7881 (tp) cc_final: 0.7577 (tp) REVERT: F 464 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8019 (mt-10) REVERT: G 4 LYS cc_start: 0.8236 (tptt) cc_final: 0.7877 (tppp) REVERT: G 24 LYS cc_start: 0.5288 (tmtt) cc_final: 0.4696 (mtpt) REVERT: G 211 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6155 (mt-10) REVERT: G 214 LEU cc_start: 0.8424 (tp) cc_final: 0.8185 (tp) REVERT: G 247 MET cc_start: 0.7164 (tpt) cc_final: 0.6475 (tpp) outliers start: 62 outliers final: 41 residues processed: 788 average time/residue: 0.1352 time to fit residues: 167.2553 Evaluate side-chains 773 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 728 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 182 LEU Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 93 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 180 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 23 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 376 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 211 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 14 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 288 optimal weight: 0.0970 chunk 199 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 270 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN B 67 ASN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN D 35 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 195 ASN E 223 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.133456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.115582 restraints weight = 36104.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.119115 restraints weight = 18773.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.121460 restraints weight = 11257.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.122985 restraints weight = 7470.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.123993 restraints weight = 5393.683| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21978 Z= 0.135 Angle : 0.564 7.540 29983 Z= 0.291 Chirality : 0.044 0.152 3681 Planarity : 0.004 0.054 3859 Dihedral : 6.919 98.092 3423 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.89 % Allowed : 21.85 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.16), residues: 3044 helix: 1.33 (0.15), residues: 1225 sheet: -0.16 (0.23), residues: 480 loop : 0.20 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 128 TYR 0.021 0.002 TYR E 242 PHE 0.031 0.002 PHE A 470 TRP 0.021 0.002 TRP B 191 HIS 0.006 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00306 (21978) covalent geometry : angle 0.56386 (29983) hydrogen bonds : bond 0.03879 ( 1099) hydrogen bonds : angle 4.84954 ( 3159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 748 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7733 (mm-30) REVERT: A 85 LYS cc_start: 0.8736 (ptpt) cc_final: 0.8412 (ptpp) REVERT: A 129 SER cc_start: 0.8503 (m) cc_final: 0.7922 (t) REVERT: A 159 VAL cc_start: 0.9204 (t) cc_final: 0.8833 (m) REVERT: A 187 ASN cc_start: 0.9025 (t0) cc_final: 0.8547 (t0) REVERT: A 196 ASP cc_start: 0.7106 (t0) cc_final: 0.6647 (t0) REVERT: A 199 LYS cc_start: 0.8281 (mttt) cc_final: 0.7908 (mmtp) REVERT: A 221 THR cc_start: 0.8653 (m) cc_final: 0.8308 (p) REVERT: A 308 LEU cc_start: 0.8270 (mt) cc_final: 0.8000 (mt) REVERT: A 309 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7231 (mm-30) REVERT: A 399 TYR cc_start: 0.7580 (t80) cc_final: 0.7299 (t80) REVERT: A 480 GLU cc_start: 0.8384 (pm20) cc_final: 0.8027 (pm20) REVERT: B 84 VAL cc_start: 0.8734 (t) cc_final: 0.8504 (p) REVERT: B 91 LYS cc_start: 0.8431 (mttt) cc_final: 0.8173 (mtpp) REVERT: B 173 ARG cc_start: 0.8616 (ttm110) cc_final: 0.8356 (mtm110) REVERT: B 228 MET cc_start: 0.8838 (tpt) cc_final: 0.8313 (tpp) REVERT: B 309 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7153 (mm-30) REVERT: B 349 ASP cc_start: 0.8039 (m-30) cc_final: 0.6594 (m-30) REVERT: B 448 TYR cc_start: 0.7895 (t80) cc_final: 0.7140 (t80) REVERT: B 480 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8476 (tm-30) REVERT: B 486 ARG cc_start: 0.8598 (ttt180) cc_final: 0.8354 (mtp85) REVERT: C 44 PHE cc_start: 0.8193 (t80) cc_final: 0.7946 (t80) REVERT: C 78 PHE cc_start: 0.8884 (m-80) cc_final: 0.8616 (m-10) REVERT: C 155 VAL cc_start: 0.8704 (m) cc_final: 0.8232 (t) REVERT: C 196 ASP cc_start: 0.7553 (t0) cc_final: 0.7060 (p0) REVERT: C 223 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8702 (mm-30) REVERT: C 345 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8402 (mp) REVERT: C 349 ASP cc_start: 0.6937 (m-30) cc_final: 0.6638 (m-30) REVERT: C 398 GLN cc_start: 0.8751 (mt0) cc_final: 0.8465 (mm-40) REVERT: C 428 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8798 (mm110) REVERT: C 471 LEU cc_start: 0.9121 (mt) cc_final: 0.8896 (mm) REVERT: C 478 HIS cc_start: 0.7920 (m-70) cc_final: 0.7644 (m-70) REVERT: D 77 LEU cc_start: 0.8423 (tp) cc_final: 0.8120 (tt) REVERT: D 89 ARG cc_start: 0.8189 (mmt-90) cc_final: 0.6912 (ttp80) REVERT: D 90 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7388 (mm-30) REVERT: D 132 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7542 (mt-10) REVERT: D 168 GLN cc_start: 0.8967 (mt0) cc_final: 0.8659 (tt0) REVERT: D 267 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7994 (mt-10) REVERT: D 282 GLN cc_start: 0.9276 (pm20) cc_final: 0.8759 (pm20) REVERT: D 315 ASP cc_start: 0.7203 (t0) cc_final: 0.6976 (t70) REVERT: D 356 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7480 (ttm-80) REVERT: D 375 GLN cc_start: 0.8100 (mt0) cc_final: 0.7605 (tm-30) REVERT: E 103 ILE cc_start: 0.9131 (pt) cc_final: 0.8867 (pt) REVERT: E 128 SER cc_start: 0.9079 (t) cc_final: 0.8813 (p) REVERT: E 293 GLN cc_start: 0.8835 (mm110) cc_final: 0.8281 (mm110) REVERT: E 353 SER cc_start: 0.8856 (m) cc_final: 0.8566 (p) REVERT: F 35 ASN cc_start: 0.9111 (m-40) cc_final: 0.8769 (m-40) REVERT: F 56 GLU cc_start: 0.8290 (pm20) cc_final: 0.8065 (pm20) REVERT: F 61 THR cc_start: 0.8441 (p) cc_final: 0.8224 (t) REVERT: F 192 ARG cc_start: 0.9147 (ttp-110) cc_final: 0.8383 (ttp80) REVERT: F 201 MET cc_start: 0.8578 (mmt) cc_final: 0.8134 (mmt) REVERT: F 237 LEU cc_start: 0.8763 (mp) cc_final: 0.8488 (mp) REVERT: F 263 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8301 (tp-100) REVERT: F 281 TYR cc_start: 0.8998 (m-80) cc_final: 0.8718 (m-80) REVERT: F 282 GLN cc_start: 0.9063 (pm20) cc_final: 0.7999 (pm20) REVERT: F 288 ASP cc_start: 0.8007 (m-30) cc_final: 0.7497 (m-30) REVERT: F 349 ASP cc_start: 0.8590 (t0) cc_final: 0.8340 (t0) REVERT: F 356 ARG cc_start: 0.8418 (tpt170) cc_final: 0.7991 (ttp-170) REVERT: F 391 LEU cc_start: 0.7651 (mp) cc_final: 0.7365 (mp) REVERT: F 463 ILE cc_start: 0.7878 (tp) cc_final: 0.7651 (tp) REVERT: F 464 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8027 (mt-10) REVERT: G 4 LYS cc_start: 0.8202 (tptt) cc_final: 0.7875 (tppp) REVERT: G 24 LYS cc_start: 0.4890 (tmtt) cc_final: 0.4393 (mtpt) REVERT: G 214 LEU cc_start: 0.8425 (tp) cc_final: 0.8211 (tp) REVERT: G 247 MET cc_start: 0.6917 (tpt) cc_final: 0.6269 (tpp) outliers start: 77 outliers final: 58 residues processed: 776 average time/residue: 0.1350 time to fit residues: 166.0399 Evaluate side-chains 764 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 704 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 23 VAL 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 251 VAL 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 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 241 SER Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 278 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 297 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 241 optimal weight: 0.1980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN D 35 ASN D 52 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 223 ASN E 293 GLN E 308 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.132734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.115036 restraints weight = 35796.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.118497 restraints weight = 18795.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.120783 restraints weight = 11308.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.122255 restraints weight = 7549.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.123320 restraints weight = 5506.626| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21978 Z= 0.150 Angle : 0.571 7.742 29983 Z= 0.294 Chirality : 0.044 0.156 3681 Planarity : 0.004 0.054 3859 Dihedral : 6.833 99.208 3423 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 5.01 % Allowed : 21.90 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.16), residues: 3044 helix: 1.38 (0.15), residues: 1220 sheet: -0.19 (0.23), residues: 475 loop : 0.17 (0.18), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 190 TYR 0.029 0.002 TYR E 242 PHE 0.022 0.001 PHE A 466 TRP 0.020 0.001 TRP B 191 HIS 0.008 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00342 (21978) covalent geometry : angle 0.57120 (29983) hydrogen bonds : bond 0.03831 ( 1099) hydrogen bonds : angle 4.78270 ( 3159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 733 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8727 (ptpt) cc_final: 0.8349 (ptpp) REVERT: A 129 SER cc_start: 0.8560 (m) cc_final: 0.7966 (t) REVERT: A 159 VAL cc_start: 0.9232 (t) cc_final: 0.8871 (m) REVERT: A 187 ASN cc_start: 0.9034 (t0) cc_final: 0.8463 (t0) REVERT: A 196 ASP cc_start: 0.7187 (t0) cc_final: 0.6764 (t0) REVERT: A 199 LYS cc_start: 0.8292 (mttt) cc_final: 0.7901 (mmtp) REVERT: A 308 LEU cc_start: 0.8252 (mt) cc_final: 0.7994 (mt) REVERT: A 309 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7187 (mm-30) REVERT: A 399 TYR cc_start: 0.7676 (t80) cc_final: 0.7166 (t80) REVERT: B 84 VAL cc_start: 0.8743 (t) cc_final: 0.8516 (p) REVERT: B 91 LYS cc_start: 0.8418 (mttt) cc_final: 0.8166 (mtpp) REVERT: B 228 MET cc_start: 0.8861 (tpt) cc_final: 0.8420 (tpp) REVERT: B 246 TYR cc_start: 0.8465 (t80) cc_final: 0.8172 (t80) REVERT: B 309 GLU cc_start: 0.8584 (mm-30) cc_final: 0.7062 (mm-30) REVERT: B 349 ASP cc_start: 0.7925 (m-30) cc_final: 0.6408 (m-30) REVERT: B 448 TYR cc_start: 0.7876 (t80) cc_final: 0.7122 (t80) REVERT: B 480 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 44 PHE cc_start: 0.8116 (t80) cc_final: 0.7887 (t80) REVERT: C 78 PHE cc_start: 0.8924 (m-80) cc_final: 0.8612 (m-10) REVERT: C 155 VAL cc_start: 0.8773 (m) cc_final: 0.8291 (t) REVERT: C 159 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8637 (m) REVERT: C 196 ASP cc_start: 0.7496 (t0) cc_final: 0.7029 (p0) REVERT: C 223 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8725 (mm-30) REVERT: C 345 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8441 (mp) REVERT: C 349 ASP cc_start: 0.6964 (m-30) cc_final: 0.6558 (m-30) REVERT: C 359 PHE cc_start: 0.8764 (t80) cc_final: 0.8545 (t80) REVERT: C 398 GLN cc_start: 0.8843 (mt0) cc_final: 0.8552 (mm-40) REVERT: C 428 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8724 (mm110) REVERT: C 471 LEU cc_start: 0.9125 (mt) cc_final: 0.8920 (mm) REVERT: C 478 HIS cc_start: 0.8021 (m-70) cc_final: 0.7811 (m-70) REVERT: D 77 LEU cc_start: 0.8512 (tp) cc_final: 0.8249 (tt) REVERT: D 89 ARG cc_start: 0.8243 (mmt-90) cc_final: 0.6861 (tmt170) REVERT: D 90 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7354 (mm-30) REVERT: D 132 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7574 (mt-10) REVERT: D 168 GLN cc_start: 0.8953 (mt0) cc_final: 0.8716 (tt0) REVERT: D 282 GLN cc_start: 0.9228 (pm20) cc_final: 0.8758 (pm20) REVERT: D 315 ASP cc_start: 0.7189 (t0) cc_final: 0.6861 (t70) REVERT: D 356 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7501 (ttm-80) REVERT: D 373 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7725 (tppt) REVERT: D 375 GLN cc_start: 0.8221 (mt0) cc_final: 0.7713 (tm-30) REVERT: E 101 GLU cc_start: 0.8051 (pm20) cc_final: 0.7718 (pm20) REVERT: E 103 ILE cc_start: 0.9113 (pt) cc_final: 0.8905 (pt) REVERT: E 128 SER cc_start: 0.9086 (t) cc_final: 0.8805 (p) REVERT: E 293 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8327 (mm110) REVERT: E 353 SER cc_start: 0.8774 (m) cc_final: 0.8482 (p) REVERT: F 35 ASN cc_start: 0.9114 (m-40) cc_final: 0.8804 (m-40) REVERT: F 56 GLU cc_start: 0.8359 (pm20) cc_final: 0.8066 (pm20) REVERT: F 192 ARG cc_start: 0.9149 (ttp-170) cc_final: 0.8370 (ttp80) REVERT: F 201 MET cc_start: 0.8606 (mmt) cc_final: 0.8173 (mmt) REVERT: F 237 LEU cc_start: 0.8726 (mp) cc_final: 0.8473 (mp) REVERT: F 263 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8282 (tp-100) REVERT: F 277 SER cc_start: 0.9316 (t) cc_final: 0.9107 (t) REVERT: F 282 GLN cc_start: 0.9044 (pm20) cc_final: 0.7916 (pm20) REVERT: F 288 ASP cc_start: 0.8006 (m-30) cc_final: 0.7520 (m-30) REVERT: F 349 ASP cc_start: 0.8588 (t0) cc_final: 0.8328 (t0) REVERT: F 356 ARG cc_start: 0.8483 (tpt170) cc_final: 0.8056 (ttp-170) REVERT: F 391 LEU cc_start: 0.7651 (mp) cc_final: 0.7189 (mp) REVERT: F 449 TYR cc_start: 0.8532 (m-80) cc_final: 0.8272 (m-10) REVERT: F 464 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8082 (mt-10) REVERT: G 4 LYS cc_start: 0.8257 (tptt) cc_final: 0.8025 (tppp) REVERT: G 24 LYS cc_start: 0.4948 (tmtt) cc_final: 0.4400 (ttpt) REVERT: G 211 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6099 (mt-10) REVERT: G 214 LEU cc_start: 0.8427 (tp) cc_final: 0.8214 (tp) REVERT: G 247 MET cc_start: 0.6879 (tpt) cc_final: 0.6121 (tpp) outliers start: 99 outliers final: 75 residues processed: 773 average time/residue: 0.1322 time to fit residues: 161.4964 Evaluate side-chains 781 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 701 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 83 LEU 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 278 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain 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 110 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 LEU 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 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 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 266 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 91 THR 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 269 SER Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 369 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 209 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 220 optimal weight: 0.0070 chunk 238 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- 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** C 387 GLN D 35 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 195 ASN E 308 GLN F 127 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.136780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.118944 restraints weight = 36020.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.122419 restraints weight = 19075.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.124717 restraints weight = 11586.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.126226 restraints weight = 7766.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.127258 restraints weight = 5671.221| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21978 Z= 0.135 Angle : 0.562 8.064 29983 Z= 0.290 Chirality : 0.044 0.159 3681 Planarity : 0.004 0.054 3859 Dihedral : 6.698 100.126 3423 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.75 % Allowed : 23.52 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 3044 helix: 1.40 (0.15), residues: 1229 sheet: -0.14 (0.23), residues: 470 loop : 0.16 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 32 TYR 0.028 0.001 TYR E 242 PHE 0.018 0.001 PHE F 259 TRP 0.021 0.001 TRP B 191 HIS 0.006 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00304 (21978) covalent geometry : angle 0.56191 (29983) hydrogen bonds : bond 0.03706 ( 1099) hydrogen bonds : angle 4.72279 ( 3159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 728 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7832 (mt) REVERT: A 85 LYS cc_start: 0.8734 (ptpt) cc_final: 0.8363 (ptpp) REVERT: A 129 SER cc_start: 0.8551 (m) cc_final: 0.7967 (t) REVERT: A 159 VAL cc_start: 0.9252 (t) cc_final: 0.8887 (m) REVERT: A 187 ASN cc_start: 0.9020 (t0) cc_final: 0.8485 (t0) REVERT: A 196 ASP cc_start: 0.7193 (t0) cc_final: 0.6773 (t0) REVERT: A 199 LYS cc_start: 0.8241 (mttt) cc_final: 0.7878 (mmtp) REVERT: A 247 LEU cc_start: 0.9271 (mt) cc_final: 0.8924 (tp) REVERT: A 308 LEU cc_start: 0.8217 (mt) cc_final: 0.7962 (mt) REVERT: A 309 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7111 (mm-30) REVERT: A 399 TYR cc_start: 0.7828 (t80) cc_final: 0.7359 (t80) REVERT: B 84 VAL cc_start: 0.8721 (t) cc_final: 0.8502 (p) REVERT: B 91 LYS cc_start: 0.8406 (mttt) cc_final: 0.8146 (mtpp) REVERT: B 228 MET cc_start: 0.8854 (tpt) cc_final: 0.8403 (tpp) REVERT: B 246 TYR cc_start: 0.8480 (t80) cc_final: 0.8219 (t80) REVERT: B 309 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7011 (mm-30) REVERT: B 349 ASP cc_start: 0.7829 (m-30) cc_final: 0.6913 (m-30) REVERT: B 448 TYR cc_start: 0.7847 (t80) cc_final: 0.7124 (t80) REVERT: B 480 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8458 (tm-30) REVERT: C 78 PHE cc_start: 0.8944 (m-80) cc_final: 0.8585 (m-10) REVERT: C 155 VAL cc_start: 0.8796 (m) cc_final: 0.8321 (t) REVERT: C 159 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8603 (m) REVERT: C 196 ASP cc_start: 0.7499 (t0) cc_final: 0.7050 (p0) REVERT: C 223 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8745 (mm-30) REVERT: C 345 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8435 (mp) REVERT: C 349 ASP cc_start: 0.6850 (m-30) cc_final: 0.6465 (m-30) REVERT: C 364 ARG cc_start: 0.8690 (mtt180) cc_final: 0.8486 (mtt180) REVERT: C 398 GLN cc_start: 0.8860 (mt0) cc_final: 0.8609 (mm-40) REVERT: C 428 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8707 (mm110) REVERT: D 77 LEU cc_start: 0.8552 (tp) cc_final: 0.8289 (tt) REVERT: D 89 ARG cc_start: 0.8269 (mmt-90) cc_final: 0.6943 (ttp80) REVERT: D 90 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7326 (mm-30) REVERT: D 132 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7644 (mt-10) REVERT: D 168 GLN cc_start: 0.8937 (mt0) cc_final: 0.8685 (tt0) REVERT: D 282 GLN cc_start: 0.9222 (pm20) cc_final: 0.8764 (pm20) REVERT: D 289 MET cc_start: 0.8775 (mtp) cc_final: 0.8554 (ttp) REVERT: D 315 ASP cc_start: 0.7196 (t0) cc_final: 0.6680 (t0) REVERT: D 356 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7503 (ttm-80) REVERT: D 373 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7768 (tppt) REVERT: D 375 GLN cc_start: 0.8220 (mt0) cc_final: 0.7721 (tm-30) REVERT: E 101 GLU cc_start: 0.7952 (pm20) cc_final: 0.7679 (pm20) REVERT: E 128 SER cc_start: 0.9084 (t) cc_final: 0.8801 (p) REVERT: E 293 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8350 (mm110) REVERT: E 353 SER cc_start: 0.8767 (m) cc_final: 0.8466 (p) REVERT: F 35 ASN cc_start: 0.9085 (m-40) cc_final: 0.8767 (m-40) REVERT: F 56 GLU cc_start: 0.8387 (pm20) cc_final: 0.8121 (pm20) REVERT: F 72 ARG cc_start: 0.8947 (mtm-85) cc_final: 0.8460 (ttm110) REVERT: F 201 MET cc_start: 0.8645 (mmt) cc_final: 0.8205 (mmt) REVERT: F 237 LEU cc_start: 0.8689 (mp) cc_final: 0.8430 (mp) REVERT: F 263 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8272 (tp-100) REVERT: F 281 TYR cc_start: 0.8927 (m-80) cc_final: 0.8651 (m-80) REVERT: F 282 GLN cc_start: 0.9025 (pm20) cc_final: 0.7930 (pm20) REVERT: F 288 ASP cc_start: 0.7998 (m-30) cc_final: 0.7512 (m-30) REVERT: F 356 ARG cc_start: 0.8495 (tpt170) cc_final: 0.8050 (ttp-170) REVERT: F 464 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8142 (mt-10) REVERT: G 24 LYS cc_start: 0.4815 (tmtt) cc_final: 0.4216 (ttpt) REVERT: G 211 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5826 (mt-10) REVERT: G 214 LEU cc_start: 0.8408 (tp) cc_final: 0.8199 (tp) REVERT: G 247 MET cc_start: 0.6770 (tpt) cc_final: 0.6007 (tpp) outliers start: 94 outliers final: 73 residues processed: 767 average time/residue: 0.1357 time to fit residues: 164.1234 Evaluate side-chains 784 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 705 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 96 ILE 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 186 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 LEU 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 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 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 440 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 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 263 GLN Chi-restraints excluded: chain F residue 269 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 105 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 120 optimal weight: 0.0870 chunk 124 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- 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** C 387 GLN 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 223 ASN E 308 GLN F 127 GLN F 293 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.135162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.117484 restraints weight = 35861.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.120943 restraints weight = 18947.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.123237 restraints weight = 11493.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.124733 restraints weight = 7674.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.125787 restraints weight = 5598.677| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21978 Z= 0.142 Angle : 0.576 8.529 29983 Z= 0.296 Chirality : 0.044 0.172 3681 Planarity : 0.004 0.054 3859 Dihedral : 6.628 104.702 3423 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.06 % Allowed : 24.28 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.16), residues: 3044 helix: 1.43 (0.15), residues: 1230 sheet: -0.15 (0.23), residues: 474 loop : 0.15 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 400 TYR 0.034 0.002 TYR E 242 PHE 0.012 0.001 PHE D 441 TRP 0.023 0.001 TRP B 191 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00323 (21978) covalent geometry : angle 0.57616 (29983) hydrogen bonds : bond 0.03672 ( 1099) hydrogen bonds : angle 4.69166 ( 3159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 721 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7755 (mt) REVERT: A 85 LYS cc_start: 0.8756 (ptpt) cc_final: 0.8387 (ptpp) REVERT: A 129 SER cc_start: 0.8573 (m) cc_final: 0.7978 (t) REVERT: A 159 VAL cc_start: 0.9236 (t) cc_final: 0.8873 (m) REVERT: A 187 ASN cc_start: 0.9006 (t0) cc_final: 0.8432 (t0) REVERT: A 196 ASP cc_start: 0.7226 (t0) cc_final: 0.6786 (t0) REVERT: A 199 LYS cc_start: 0.8236 (mttt) cc_final: 0.7871 (mmtp) REVERT: A 308 LEU cc_start: 0.8201 (mt) cc_final: 0.7962 (mt) REVERT: A 309 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7075 (mm-30) REVERT: A 349 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: A 399 TYR cc_start: 0.7828 (t80) cc_final: 0.7348 (t80) REVERT: B 84 VAL cc_start: 0.8724 (t) cc_final: 0.8519 (p) REVERT: B 91 LYS cc_start: 0.8410 (mttt) cc_final: 0.8124 (mtpp) REVERT: B 228 MET cc_start: 0.8853 (tpt) cc_final: 0.8412 (tpp) REVERT: B 246 TYR cc_start: 0.8504 (t80) cc_final: 0.8294 (t80) REVERT: B 309 GLU cc_start: 0.8429 (mm-30) cc_final: 0.6670 (mm-30) REVERT: B 349 ASP cc_start: 0.7807 (m-30) cc_final: 0.6871 (m-30) REVERT: B 448 TYR cc_start: 0.7826 (t80) cc_final: 0.7119 (t80) REVERT: B 480 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8463 (tm-30) REVERT: C 78 PHE cc_start: 0.8967 (m-80) cc_final: 0.8641 (m-10) REVERT: C 159 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8699 (m) REVERT: C 196 ASP cc_start: 0.7469 (t0) cc_final: 0.6978 (p0) REVERT: C 345 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8496 (mp) REVERT: C 349 ASP cc_start: 0.6792 (m-30) cc_final: 0.6412 (m-30) REVERT: C 398 GLN cc_start: 0.8825 (mt0) cc_final: 0.8547 (mm-40) REVERT: C 428 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8717 (mm110) REVERT: D 35 ASN cc_start: 0.7376 (m110) cc_final: 0.6016 (m110) REVERT: D 77 LEU cc_start: 0.8546 (tp) cc_final: 0.8290 (tt) REVERT: D 89 ARG cc_start: 0.8256 (mmt-90) cc_final: 0.6918 (ttp80) REVERT: D 90 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7316 (mm-30) REVERT: D 282 GLN cc_start: 0.9238 (pm20) cc_final: 0.8787 (pm20) REVERT: D 315 ASP cc_start: 0.7158 (t0) cc_final: 0.6677 (t0) REVERT: D 356 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7544 (ttm-80) REVERT: D 373 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7839 (tppt) REVERT: D 375 GLN cc_start: 0.8052 (mt0) cc_final: 0.7700 (tm-30) REVERT: E 101 GLU cc_start: 0.7888 (pm20) cc_final: 0.7651 (pm20) REVERT: E 128 SER cc_start: 0.9083 (t) cc_final: 0.8802 (p) REVERT: E 293 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8368 (mm110) REVERT: E 353 SER cc_start: 0.8774 (m) cc_final: 0.8464 (p) REVERT: F 35 ASN cc_start: 0.9067 (m-40) cc_final: 0.8756 (m-40) REVERT: F 56 GLU cc_start: 0.8223 (pm20) cc_final: 0.7955 (pm20) REVERT: F 61 THR cc_start: 0.8389 (p) cc_final: 0.8155 (t) REVERT: F 201 MET cc_start: 0.8629 (mmt) cc_final: 0.8206 (mmt) REVERT: F 237 LEU cc_start: 0.8664 (mp) cc_final: 0.8394 (mp) REVERT: F 263 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8266 (tp-100) REVERT: F 281 TYR cc_start: 0.8883 (m-80) cc_final: 0.8652 (m-80) REVERT: F 282 GLN cc_start: 0.9041 (pm20) cc_final: 0.7966 (pm20) REVERT: F 288 ASP cc_start: 0.7988 (m-30) cc_final: 0.7477 (m-30) REVERT: F 391 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7207 (mt) REVERT: F 449 TYR cc_start: 0.8590 (m-80) cc_final: 0.8228 (m-80) REVERT: F 464 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8146 (mt-10) REVERT: G 17 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6828 (mm-30) REVERT: G 211 GLU cc_start: 0.6139 (OUTLIER) cc_final: 0.5835 (mt-10) REVERT: G 214 LEU cc_start: 0.8408 (tp) cc_final: 0.8205 (tp) REVERT: G 247 MET cc_start: 0.6734 (tpt) cc_final: 0.6032 (tpp) outliers start: 100 outliers final: 78 residues processed: 763 average time/residue: 0.1329 time to fit residues: 161.1297 Evaluate side-chains 790 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 704 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 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 349 ASP Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 LEU 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 159 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 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 182 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 155 LEU 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 376 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 169 optimal weight: 0.3980 chunk 243 optimal weight: 3.9990 chunk 275 optimal weight: 0.0670 chunk 248 optimal weight: 0.7980 chunk 26 optimal weight: 0.0270 chunk 12 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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** C 387 GLN D 52 GLN E 24 HIS E 308 GLN F 127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.140451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.122601 restraints weight = 35386.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.126117 restraints weight = 18788.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.128428 restraints weight = 11344.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.129877 restraints weight = 7574.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.130953 restraints weight = 5535.056| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 21978 Z= 0.111 Angle : 0.572 10.915 29983 Z= 0.291 Chirality : 0.044 0.173 3681 Planarity : 0.004 0.053 3859 Dihedral : 6.393 107.364 3423 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.84 % Allowed : 26.15 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 3044 helix: 1.49 (0.15), residues: 1231 sheet: -0.09 (0.23), residues: 483 loop : 0.24 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 114 TYR 0.032 0.001 TYR E 242 PHE 0.027 0.001 PHE A 466 TRP 0.022 0.001 TRP B 191 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00249 (21978) covalent geometry : angle 0.57208 (29983) hydrogen bonds : bond 0.03365 ( 1099) hydrogen bonds : angle 4.59174 ( 3159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 742 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7832 (mt) REVERT: A 85 LYS cc_start: 0.8751 (ptpt) cc_final: 0.8375 (ptpp) REVERT: A 105 LEU cc_start: 0.9044 (tp) cc_final: 0.8768 (tt) REVERT: A 129 SER cc_start: 0.8514 (m) cc_final: 0.7946 (t) REVERT: A 159 VAL cc_start: 0.9288 (t) cc_final: 0.8950 (m) REVERT: A 186 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9053 (mt) REVERT: A 187 ASN cc_start: 0.8936 (t0) cc_final: 0.8295 (t0) REVERT: A 196 ASP cc_start: 0.7255 (t0) cc_final: 0.6704 (t0) REVERT: A 199 LYS cc_start: 0.8192 (mttt) cc_final: 0.7819 (mmtp) REVERT: A 308 LEU cc_start: 0.8156 (mt) cc_final: 0.7921 (mt) REVERT: A 309 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 349 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: A 399 TYR cc_start: 0.7832 (t80) cc_final: 0.7476 (t80) REVERT: B 91 LYS cc_start: 0.8369 (mttt) cc_final: 0.8063 (mtpp) REVERT: B 228 MET cc_start: 0.8806 (tpt) cc_final: 0.8357 (tpp) REVERT: B 309 GLU cc_start: 0.8578 (mm-30) cc_final: 0.6917 (mm-30) REVERT: B 349 ASP cc_start: 0.7667 (m-30) cc_final: 0.6195 (m-30) REVERT: B 448 TYR cc_start: 0.7727 (t80) cc_final: 0.7105 (t80) REVERT: B 480 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8412 (tm-30) REVERT: C 128 ARG cc_start: 0.7476 (mmm-85) cc_final: 0.7265 (mmm-85) REVERT: C 142 ARG cc_start: 0.8680 (tmm-80) cc_final: 0.8444 (tmm-80) REVERT: C 159 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8691 (m) REVERT: C 196 ASP cc_start: 0.7426 (t0) cc_final: 0.6982 (p0) REVERT: C 349 ASP cc_start: 0.6374 (m-30) cc_final: 0.5964 (m-30) REVERT: C 398 GLN cc_start: 0.8786 (mt0) cc_final: 0.8514 (mm-40) REVERT: C 408 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6872 (p90) REVERT: C 425 ARG cc_start: 0.8710 (mtt90) cc_final: 0.8282 (mtt90) REVERT: C 428 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8666 (mm110) REVERT: C 495 LEU cc_start: 0.8623 (tp) cc_final: 0.8406 (tp) REVERT: D 35 ASN cc_start: 0.7153 (m110) cc_final: 0.6432 (m-40) REVERT: D 77 LEU cc_start: 0.8545 (tp) cc_final: 0.8306 (tt) REVERT: D 90 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7379 (mm-30) REVERT: D 201 MET cc_start: 0.8707 (mmp) cc_final: 0.8400 (mmp) REVERT: D 282 GLN cc_start: 0.9235 (pm20) cc_final: 0.8787 (pm20) REVERT: D 315 ASP cc_start: 0.7033 (t0) cc_final: 0.6667 (t0) REVERT: D 345 TYR cc_start: 0.8045 (m-80) cc_final: 0.7839 (m-80) REVERT: D 356 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7470 (ttm-80) REVERT: D 375 GLN cc_start: 0.7896 (mt0) cc_final: 0.7588 (tm-30) REVERT: E 41 THR cc_start: 0.7334 (OUTLIER) cc_final: 0.7022 (m) REVERT: E 101 GLU cc_start: 0.7751 (pm20) cc_final: 0.7497 (pm20) REVERT: E 128 SER cc_start: 0.9062 (t) cc_final: 0.8804 (p) REVERT: E 293 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8314 (mm110) REVERT: E 353 SER cc_start: 0.8751 (m) cc_final: 0.8487 (p) REVERT: F 35 ASN cc_start: 0.9046 (m-40) cc_final: 0.8594 (m-40) REVERT: F 56 GLU cc_start: 0.8296 (pm20) cc_final: 0.8035 (pm20) REVERT: F 61 THR cc_start: 0.8414 (p) cc_final: 0.8153 (t) REVERT: F 72 ARG cc_start: 0.8953 (mtm-85) cc_final: 0.8437 (ttm110) REVERT: F 106 ARG cc_start: 0.7713 (mtm180) cc_final: 0.7444 (mtm180) REVERT: F 192 ARG cc_start: 0.9120 (ttp-170) cc_final: 0.8301 (ttp80) REVERT: F 201 MET cc_start: 0.8580 (mmt) cc_final: 0.8135 (mmt) REVERT: F 237 LEU cc_start: 0.8678 (mp) cc_final: 0.8410 (mp) REVERT: F 263 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8305 (tp-100) REVERT: F 282 GLN cc_start: 0.9000 (pm20) cc_final: 0.8525 (pm20) REVERT: F 288 ASP cc_start: 0.7909 (m-30) cc_final: 0.7430 (m-30) REVERT: F 391 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7151 (mt) REVERT: F 449 TYR cc_start: 0.8631 (m-80) cc_final: 0.8394 (m-80) REVERT: F 464 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8127 (mt-10) REVERT: G 11 LYS cc_start: 0.7912 (mttt) cc_final: 0.7614 (mttm) REVERT: G 17 GLU cc_start: 0.7227 (mm-30) cc_final: 0.7016 (mm-30) REVERT: G 211 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5883 (mt-10) REVERT: G 247 MET cc_start: 0.6673 (tpt) cc_final: 0.5994 (tpp) outliers start: 76 outliers final: 53 residues processed: 778 average time/residue: 0.1342 time to fit residues: 165.7110 Evaluate side-chains 775 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 713 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR 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 97 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 186 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 110 VAL Chi-restraints excluded: chain B residue 123 ILE 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 C residue 30 THR 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 159 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 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 182 SER 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 E residue 17 ILE Chi-restraints excluded: chain E residue 41 THR 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 206 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 263 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 390 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 285 optimal weight: 0.0030 chunk 250 optimal weight: 0.0570 chunk 4 optimal weight: 0.8980 chunk 284 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 289 optimal weight: 0.0270 chunk 25 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 overall best weight: 0.3566 ------------------------------------------------------------------------------- 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** ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN E 24 HIS E 223 ASN F 127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.140509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.122786 restraints weight = 35373.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.126305 restraints weight = 18596.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.128600 restraints weight = 11174.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.130130 restraints weight = 7450.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.131158 restraints weight = 5398.489| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21978 Z= 0.112 Angle : 0.587 9.630 29983 Z= 0.297 Chirality : 0.044 0.210 3681 Planarity : 0.004 0.053 3859 Dihedral : 6.175 109.125 3423 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.24 % Allowed : 27.47 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 3044 helix: 1.47 (0.15), residues: 1242 sheet: 0.01 (0.24), residues: 471 loop : 0.31 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 114 TYR 0.034 0.001 TYR E 242 PHE 0.011 0.001 PHE B 259 TRP 0.029 0.002 TRP B 191 HIS 0.007 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00252 (21978) covalent geometry : angle 0.58696 (29983) hydrogen bonds : bond 0.03243 ( 1099) hydrogen bonds : angle 4.53407 ( 3159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 739 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8760 (ptpt) cc_final: 0.8426 (ptpp) REVERT: A 129 SER cc_start: 0.8462 (m) cc_final: 0.7828 (t) REVERT: A 141 ARG cc_start: 0.8723 (mtt-85) cc_final: 0.8502 (mtt-85) REVERT: A 142 ARG cc_start: 0.7023 (ttt90) cc_final: 0.6672 (ttt-90) REVERT: A 159 VAL cc_start: 0.9289 (t) cc_final: 0.8971 (m) REVERT: A 187 ASN cc_start: 0.8924 (t0) cc_final: 0.8263 (t0) REVERT: A 196 ASP cc_start: 0.7155 (t0) cc_final: 0.6328 (t0) REVERT: A 199 LYS cc_start: 0.8174 (mttt) cc_final: 0.7780 (mmtp) REVERT: A 247 LEU cc_start: 0.9327 (tp) cc_final: 0.8864 (tp) REVERT: A 308 LEU cc_start: 0.8140 (mt) cc_final: 0.7871 (mt) REVERT: A 309 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7577 (mm-30) REVERT: A 399 TYR cc_start: 0.7814 (t80) cc_final: 0.7399 (t80) REVERT: B 91 LYS cc_start: 0.8238 (mttt) cc_final: 0.7900 (mtpp) REVERT: B 153 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8023 (ttpp) REVERT: B 228 MET cc_start: 0.8751 (tpt) cc_final: 0.8321 (tpp) REVERT: B 309 GLU cc_start: 0.8475 (mm-30) cc_final: 0.6752 (mm-30) REVERT: B 349 ASP cc_start: 0.7499 (m-30) cc_final: 0.6662 (m-30) REVERT: B 448 TYR cc_start: 0.7675 (t80) cc_final: 0.7088 (t80) REVERT: B 480 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8403 (tm-30) REVERT: C 155 VAL cc_start: 0.8549 (m) cc_final: 0.8091 (t) REVERT: C 159 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8603 (m) REVERT: C 196 ASP cc_start: 0.7421 (t0) cc_final: 0.7000 (p0) REVERT: C 224 GLN cc_start: 0.8335 (tp40) cc_final: 0.7987 (tp40) REVERT: C 345 ILE cc_start: 0.8213 (mp) cc_final: 0.7890 (mp) REVERT: C 349 ASP cc_start: 0.6627 (m-30) cc_final: 0.6146 (m-30) REVERT: C 398 GLN cc_start: 0.8796 (mt0) cc_final: 0.8553 (mm-40) REVERT: C 425 ARG cc_start: 0.8609 (mtt90) cc_final: 0.8124 (mtt90) REVERT: C 428 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8671 (mm110) REVERT: C 495 LEU cc_start: 0.8690 (tp) cc_final: 0.8449 (tp) REVERT: D 12 LYS cc_start: 0.8770 (mttp) cc_final: 0.8176 (mtpp) REVERT: D 77 LEU cc_start: 0.8611 (tp) cc_final: 0.8355 (tt) REVERT: D 90 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7220 (mm-30) REVERT: D 144 LEU cc_start: 0.7797 (mt) cc_final: 0.7483 (mt) REVERT: D 201 MET cc_start: 0.8711 (mmp) cc_final: 0.8465 (mmp) REVERT: D 203 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7575 (mt-10) REVERT: D 282 GLN cc_start: 0.9215 (pm20) cc_final: 0.8817 (pm20) REVERT: D 315 ASP cc_start: 0.6983 (t0) cc_final: 0.6748 (t0) REVERT: D 356 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7514 (ttm-80) REVERT: D 375 GLN cc_start: 0.7811 (mt0) cc_final: 0.7548 (tm-30) REVERT: E 41 THR cc_start: 0.7250 (OUTLIER) cc_final: 0.6877 (m) REVERT: E 101 GLU cc_start: 0.7759 (pm20) cc_final: 0.7493 (pm20) REVERT: E 128 SER cc_start: 0.9042 (t) cc_final: 0.8765 (p) REVERT: E 277 SER cc_start: 0.8382 (p) cc_final: 0.8017 (m) REVERT: E 293 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8269 (mm110) REVERT: E 353 SER cc_start: 0.8704 (m) cc_final: 0.8448 (p) REVERT: E 354 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7548 (tttm) REVERT: E 358 LEU cc_start: 0.8210 (tp) cc_final: 0.7846 (mt) REVERT: F 35 ASN cc_start: 0.8989 (m-40) cc_final: 0.8515 (m-40) REVERT: F 56 GLU cc_start: 0.8300 (pm20) cc_final: 0.8045 (pm20) REVERT: F 61 THR cc_start: 0.8498 (p) cc_final: 0.8234 (t) REVERT: F 72 ARG cc_start: 0.8955 (mtm-85) cc_final: 0.8449 (ttm110) REVERT: F 201 MET cc_start: 0.8486 (mmt) cc_final: 0.7998 (mmt) REVERT: F 237 LEU cc_start: 0.8710 (mp) cc_final: 0.8437 (mp) REVERT: F 263 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8305 (tp-100) REVERT: F 282 GLN cc_start: 0.9003 (pm20) cc_final: 0.8768 (pm20) REVERT: F 288 ASP cc_start: 0.7911 (m-30) cc_final: 0.7423 (m-30) REVERT: F 356 ARG cc_start: 0.8553 (tpp-160) cc_final: 0.7996 (ttp-170) REVERT: F 375 GLN cc_start: 0.8875 (mt0) cc_final: 0.8553 (tp40) REVERT: F 391 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7039 (mp) REVERT: G 11 LYS cc_start: 0.7891 (mttt) cc_final: 0.7606 (mttm) REVERT: G 247 MET cc_start: 0.6641 (tpt) cc_final: 0.5974 (tpp) REVERT: G 250 ARG cc_start: 0.8248 (mtp-110) cc_final: 0.8008 (ptp-170) outliers start: 64 outliers final: 47 residues processed: 769 average time/residue: 0.1344 time to fit residues: 162.5569 Evaluate side-chains 757 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 706 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR 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 97 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 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 110 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 452 ASN 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 182 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 263 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 390 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 257 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 299 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 280 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS B 67 ASN C 192 ASN D 52 GLN E 24 HIS E 308 GLN F 127 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.134783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.117067 restraints weight = 36084.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.120479 restraints weight = 19362.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.122716 restraints weight = 11808.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.124093 restraints weight = 7998.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.125212 restraints weight = 5925.654| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21978 Z= 0.219 Angle : 0.673 12.567 29983 Z= 0.344 Chirality : 0.047 0.238 3681 Planarity : 0.005 0.055 3859 Dihedral : 6.738 117.711 3423 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.29 % Allowed : 27.77 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 3044 helix: 1.22 (0.15), residues: 1231 sheet: -0.28 (0.23), residues: 485 loop : 0.14 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 32 TYR 0.032 0.002 TYR E 242 PHE 0.023 0.002 PHE A 466 TRP 0.015 0.002 TRP B 191 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00506 (21978) covalent geometry : angle 0.67327 (29983) hydrogen bonds : bond 0.04021 ( 1099) hydrogen bonds : angle 4.78615 ( 3159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 704 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7923 (mt) REVERT: A 85 LYS cc_start: 0.8802 (ptpt) cc_final: 0.8458 (ptpp) REVERT: A 129 SER cc_start: 0.8733 (m) cc_final: 0.8135 (t) REVERT: A 141 ARG cc_start: 0.8854 (mtt-85) cc_final: 0.8610 (mtt-85) REVERT: A 159 VAL cc_start: 0.9329 (t) cc_final: 0.8941 (m) REVERT: A 160 PRO cc_start: 0.9464 (Cg_exo) cc_final: 0.9140 (Cg_endo) REVERT: A 187 ASN cc_start: 0.9018 (t0) cc_final: 0.8570 (t0) REVERT: A 196 ASP cc_start: 0.7215 (t0) cc_final: 0.6682 (t0) REVERT: A 199 LYS cc_start: 0.8303 (mttt) cc_final: 0.7926 (mmtp) REVERT: A 230 TYR cc_start: 0.9130 (p90) cc_final: 0.8886 (p90) REVERT: A 240 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7545 (mm-30) REVERT: A 247 LEU cc_start: 0.9387 (tp) cc_final: 0.8918 (tp) REVERT: A 308 LEU cc_start: 0.8155 (mt) cc_final: 0.7928 (mt) REVERT: A 309 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7449 (mm-30) REVERT: A 399 TYR cc_start: 0.7849 (t80) cc_final: 0.7307 (t80) REVERT: B 91 LYS cc_start: 0.8388 (mttt) cc_final: 0.8064 (mtpp) REVERT: B 228 MET cc_start: 0.8888 (tpt) cc_final: 0.8503 (tpp) REVERT: B 349 ASP cc_start: 0.7722 (m-30) cc_final: 0.6836 (m-30) REVERT: B 448 TYR cc_start: 0.7821 (t80) cc_final: 0.7016 (t80) REVERT: B 480 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8349 (tm-30) REVERT: C 78 PHE cc_start: 0.9029 (m-80) cc_final: 0.8748 (m-10) REVERT: C 159 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8616 (m) REVERT: C 196 ASP cc_start: 0.7474 (t0) cc_final: 0.6929 (p0) REVERT: C 349 ASP cc_start: 0.7067 (m-30) cc_final: 0.6732 (m-30) REVERT: C 398 GLN cc_start: 0.8882 (mt0) cc_final: 0.8652 (mm-40) REVERT: C 408 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.7081 (p90) REVERT: C 428 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8650 (mm110) REVERT: D 12 LYS cc_start: 0.8733 (mttp) cc_final: 0.8154 (mtpp) REVERT: D 77 LEU cc_start: 0.8586 (tp) cc_final: 0.8329 (tt) REVERT: D 89 ARG cc_start: 0.8402 (mmt-90) cc_final: 0.7089 (ttp80) REVERT: D 90 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7328 (mm-30) REVERT: D 282 GLN cc_start: 0.9323 (pm20) cc_final: 0.8768 (pm20) REVERT: D 375 GLN cc_start: 0.7972 (mt0) cc_final: 0.7627 (tm-30) REVERT: E 101 GLU cc_start: 0.7813 (pm20) cc_final: 0.7489 (pm20) REVERT: E 128 SER cc_start: 0.9099 (t) cc_final: 0.8769 (p) REVERT: E 201 MET cc_start: 0.8347 (mtm) cc_final: 0.7817 (mtm) REVERT: E 293 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8301 (mm110) REVERT: E 353 SER cc_start: 0.8649 (m) cc_final: 0.8446 (p) REVERT: F 35 ASN cc_start: 0.8977 (m-40) cc_final: 0.8617 (m-40) REVERT: F 56 GLU cc_start: 0.8335 (pm20) cc_final: 0.8119 (pm20) REVERT: F 61 THR cc_start: 0.8395 (p) cc_final: 0.8155 (t) REVERT: F 237 LEU cc_start: 0.8706 (mp) cc_final: 0.8469 (mp) REVERT: F 263 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: F 288 ASP cc_start: 0.8017 (m-30) cc_final: 0.7562 (m-30) REVERT: F 289 MET cc_start: 0.8902 (tpp) cc_final: 0.8383 (tpp) REVERT: F 391 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7443 (mt) REVERT: G 247 MET cc_start: 0.6736 (tpt) cc_final: 0.6128 (tpp) REVERT: G 250 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7989 (ptp-170) outliers start: 65 outliers final: 44 residues processed: 733 average time/residue: 0.1313 time to fit residues: 152.5275 Evaluate side-chains 738 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 689 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 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 97 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 237 THR 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 376 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 452 ASN 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 182 SER Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 98 VAL 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 71 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 76 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 163 optimal weight: 0.6980 chunk 233 optimal weight: 0.9990 chunk 205 optimal weight: 0.7980 chunk 247 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 263 GLN E 24 HIS E 308 GLN F 127 GLN F 168 GLN ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.136003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.118241 restraints weight = 35734.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.121757 restraints weight = 18779.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.124064 restraints weight = 11295.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.125633 restraints weight = 7528.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.126665 restraints weight = 5404.000| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21978 Z= 0.125 Angle : 0.615 10.914 29983 Z= 0.312 Chirality : 0.045 0.230 3681 Planarity : 0.004 0.053 3859 Dihedral : 6.396 115.837 3423 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.78 % Allowed : 28.73 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.16), residues: 3044 helix: 1.33 (0.15), residues: 1232 sheet: -0.20 (0.23), residues: 475 loop : 0.20 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 114 TYR 0.030 0.002 TYR E 242 PHE 0.040 0.001 PHE A 466 TRP 0.024 0.002 TRP B 191 HIS 0.007 0.001 HIS F 328 Details of bonding type rmsd covalent geometry : bond 0.00287 (21978) covalent geometry : angle 0.61463 (29983) hydrogen bonds : bond 0.03459 ( 1099) hydrogen bonds : angle 4.61260 ( 3159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3852.21 seconds wall clock time: 66 minutes 59.05 seconds (4019.05 seconds total)