Starting phenix.real_space_refine on Fri Feb 16 14:26:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7z_9002/02_2024/6e7z_9002_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7z_9002/02_2024/6e7z_9002.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7z_9002/02_2024/6e7z_9002_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7z_9002/02_2024/6e7z_9002_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7z_9002/02_2024/6e7z_9002_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7z_9002/02_2024/6e7z_9002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7z_9002/02_2024/6e7z_9002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7z_9002/02_2024/6e7z_9002_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7z_9002/02_2024/6e7z_9002_updated.pdb" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.038 sd= 0.428 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 100 5.16 5 C 10192 2.51 5 N 2568 2.21 5 O 2744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 318": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D ARG 419": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15616 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "B" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "C" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "D" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'AQV': 1, 'HZ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'AQV': 1, 'HZ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'AQV': 1, 'HZ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'AQV': 1, 'HZ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.88, per 1000 atoms: 0.57 Number of scatterers: 15616 At special positions: 0 Unit cell: (123.05, 123.05, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 12 15.00 O 2744 8.00 N 2568 7.00 C 10192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.05 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.06 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.05 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.05 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.05 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.06 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.05 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.27 Conformation dependent library (CDL) restraints added in 2.8 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 4 sheets defined 53.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 removed outlier: 3.661A pdb=" N TYR A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.562A pdb=" N PHE A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 57 " --> pdb=" O CYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 105 removed outlier: 4.784A pdb=" N LEU A 68 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 71 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 72 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 76 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N THR A 77 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 82 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU A 85 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 87 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 89 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 91 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE A 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU A 96 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN A 97 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 100 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 102 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 104 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 137 removed outlier: 3.578A pdb=" N TYR A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 No H-bonds generated for 'chain 'A' and resid 139 through 142' Processing helix chain 'A' and resid 295 through 326 removed outlier: 3.879A pdb=" N LEU A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 354 through 377 removed outlier: 3.535A pdb=" N LEU A 358 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 359 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 363 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 364 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 366 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 367 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 369 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE A 370 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 376 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA A 377 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 402 removed outlier: 4.170A pdb=" N THR A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 445 removed outlier: 3.629A pdb=" N ILE A 413 " --> pdb=" O HIS A 409 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 415 " --> pdb=" O TYR A 411 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 4.240A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N CYS A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 467 removed outlier: 4.096A pdb=" N SER A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 483 removed outlier: 4.515A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 505 removed outlier: 3.537A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 501 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 524 removed outlier: 4.073A pdb=" N ILE A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.661A pdb=" N TYR B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.561A pdb=" N PHE B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 57 " --> pdb=" O CYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 105 removed outlier: 4.785A pdb=" N LEU B 68 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 71 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 72 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 76 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N THR B 77 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU B 85 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN B 88 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 89 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL B 91 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE B 93 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU B 96 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 97 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 100 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 102 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 104 " --> pdb=" O PHE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.578A pdb=" N TYR B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 142 No H-bonds generated for 'chain 'B' and resid 139 through 142' Processing helix chain 'B' and resid 295 through 326 removed outlier: 3.878A pdb=" N LEU B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 354 through 377 removed outlier: 3.535A pdb=" N LEU B 358 " --> pdb=" O TYR B 355 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 359 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 363 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 364 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 366 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 367 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 369 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE B 370 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 373 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 376 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA B 377 " --> pdb=" O GLY B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 402 removed outlier: 4.170A pdb=" N THR B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 402 " --> pdb=" O TRP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 445 removed outlier: 3.629A pdb=" N ILE B 413 " --> pdb=" O HIS B 409 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 415 " --> pdb=" O TYR B 411 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B 417 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 4.240A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 432 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 467 removed outlier: 4.096A pdb=" N SER B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 4.514A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 505 removed outlier: 3.538A pdb=" N LEU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 501 " --> pdb=" O TYR B 497 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 503 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 524 removed outlier: 4.073A pdb=" N ILE B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.660A pdb=" N TYR C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 removed outlier: 3.561A pdb=" N PHE C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C 57 " --> pdb=" O CYS C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 105 removed outlier: 4.785A pdb=" N LEU C 68 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 71 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 72 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 76 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR C 77 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU C 85 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 87 " --> pdb=" O GLY C 84 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN C 88 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 89 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL C 91 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE C 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU C 96 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN C 97 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 100 " --> pdb=" O ASN C 97 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG C 102 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 104 " --> pdb=" O PHE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 removed outlier: 3.579A pdb=" N TYR C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 135 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 No H-bonds generated for 'chain 'C' and resid 139 through 142' Processing helix chain 'C' and resid 295 through 326 removed outlier: 3.879A pdb=" N LEU C 299 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 312 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 354 through 377 removed outlier: 3.536A pdb=" N LEU C 358 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 359 " --> pdb=" O ILE C 356 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 363 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 364 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 366 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 367 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 369 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE C 370 " --> pdb=" O SER C 367 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 373 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 376 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA C 377 " --> pdb=" O GLY C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 402 removed outlier: 4.171A pdb=" N THR C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP C 398 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE C 402 " --> pdb=" O TRP C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 445 removed outlier: 3.629A pdb=" N ILE C 413 " --> pdb=" O HIS C 409 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE C 415 " --> pdb=" O TYR C 411 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 4.240A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 432 " --> pdb=" O PHE C 428 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY C 443 " --> pdb=" O TYR C 439 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 467 removed outlier: 4.096A pdb=" N SER C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 483 removed outlier: 4.514A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA C 482 " --> pdb=" O ALA C 478 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 505 removed outlier: 3.538A pdb=" N LEU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 501 " --> pdb=" O TYR C 497 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 502 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 503 " --> pdb=" O TYR C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 524 removed outlier: 4.072A pdb=" N ILE C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 519 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.661A pdb=" N TYR D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE D 48 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 58 removed outlier: 3.561A pdb=" N PHE D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG D 57 " --> pdb=" O CYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 105 removed outlier: 4.784A pdb=" N LEU D 68 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 71 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 72 " --> pdb=" O GLN D 69 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 76 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR D 77 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 82 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU D 85 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN D 87 " --> pdb=" O GLY D 84 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 89 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL D 91 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE D 93 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU D 96 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN D 97 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 100 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG D 102 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 104 " --> pdb=" O PHE D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 removed outlier: 3.579A pdb=" N TYR D 126 " --> pdb=" O ARG D 122 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D 135 " --> pdb=" O HIS D 131 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 142 No H-bonds generated for 'chain 'D' and resid 139 through 142' Processing helix chain 'D' and resid 295 through 326 removed outlier: 3.879A pdb=" N LEU D 299 " --> pdb=" O ASN D 295 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 311 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER D 312 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 354 through 377 removed outlier: 3.536A pdb=" N LEU D 358 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL D 359 " --> pdb=" O ILE D 356 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL D 363 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 364 " --> pdb=" O SER D 361 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 366 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER D 367 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 369 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE D 370 " --> pdb=" O SER D 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 373 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU D 376 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA D 377 " --> pdb=" O GLY D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 402 removed outlier: 4.170A pdb=" N THR D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 395 " --> pdb=" O GLY D 391 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP D 398 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 445 removed outlier: 3.628A pdb=" N ILE D 413 " --> pdb=" O HIS D 409 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE D 415 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR D 417 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 4.240A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 432 " --> pdb=" O PHE D 428 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS D 442 " --> pdb=" O GLY D 438 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY D 443 " --> pdb=" O TYR D 439 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 467 removed outlier: 4.097A pdb=" N SER D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE D 465 " --> pdb=" O SER D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 483 removed outlier: 4.515A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA D 482 " --> pdb=" O ALA D 478 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 505 removed outlier: 3.538A pdb=" N LEU D 492 " --> pdb=" O SER D 488 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 501 " --> pdb=" O TYR D 497 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 502 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER D 503 " --> pdb=" O TYR D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 524 removed outlier: 4.072A pdb=" N ILE D 517 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 519 " --> pdb=" O ALA D 515 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 520 " --> pdb=" O LEU D 516 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 191 through 195 removed outlier: 3.617A pdb=" N ASP A 191 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN A 167 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 165 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 231 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 237 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS A 253 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 191 through 195 removed outlier: 3.615A pdb=" N ASP B 191 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN B 167 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 165 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 231 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 237 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS B 253 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 191 through 195 removed outlier: 3.616A pdb=" N ASP C 191 " --> pdb=" O GLN C 167 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN C 167 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 165 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 231 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 237 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS C 253 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 191 through 195 removed outlier: 3.616A pdb=" N ASP D 191 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN D 167 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 165 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 231 " --> pdb=" O PHE D 262 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 237 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS D 253 " --> pdb=" O GLN D 282 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1296 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: 3.63 Time building geometry restraints manager: 6.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2340 1.30 - 1.44: 4673 1.44 - 1.57: 8827 1.57 - 1.71: 28 1.71 - 1.84: 140 Bond restraints: 16008 Sorted by residual: bond pdb=" C7 AQV D 802 " pdb=" O3 AQV D 802 " ideal model delta sigma weight residual 1.209 1.468 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C7 AQV C 802 " pdb=" O3 AQV C 802 " ideal model delta sigma weight residual 1.209 1.468 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C7 AQV B 802 " pdb=" O3 AQV B 802 " ideal model delta sigma weight residual 1.209 1.468 -0.259 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C7 AQV A 802 " pdb=" O3 AQV A 802 " ideal model delta sigma weight residual 1.209 1.467 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C8 AQV B 802 " pdb=" O2 AQV B 802 " ideal model delta sigma weight residual 1.213 1.450 -0.237 2.00e-02 2.50e+03 1.41e+02 ... (remaining 16003 not shown) Histogram of bond angle deviations from ideal: 96.78 - 104.34: 204 104.34 - 111.90: 7560 111.90 - 119.46: 5621 119.46 - 127.02: 8184 127.02 - 134.57: 179 Bond angle restraints: 21748 Sorted by residual: angle pdb=" C ASN C 247 " pdb=" N ASN C 248 " pdb=" CA ASN C 248 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C ASN D 247 " pdb=" N ASN D 248 " pdb=" CA ASN D 248 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C ASN B 247 " pdb=" N ASN B 248 " pdb=" CA ASN B 248 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C ASN A 247 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 angle pdb=" C21 AQV B 802 " pdb=" C11 AQV B 802 " pdb=" C22 AQV B 802 " ideal model delta sigma weight residual 110.45 96.78 13.67 3.00e+00 1.11e-01 2.08e+01 ... (remaining 21743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 9229 34.61 - 69.21: 99 69.21 - 103.82: 28 103.82 - 138.43: 16 138.43 - 173.03: 20 Dihedral angle restraints: 9392 sinusoidal: 3828 harmonic: 5564 Sorted by residual: dihedral pdb=" CA ASN B 179 " pdb=" C ASN B 179 " pdb=" N ASP B 180 " pdb=" CA ASP B 180 " ideal model delta harmonic sigma weight residual -180.00 -148.08 -31.92 0 5.00e+00 4.00e-02 4.07e+01 dihedral pdb=" CA ASN D 179 " pdb=" C ASN D 179 " pdb=" N ASP D 180 " pdb=" CA ASP D 180 " ideal model delta harmonic sigma weight residual -180.00 -148.09 -31.91 0 5.00e+00 4.00e-02 4.07e+01 dihedral pdb=" CA ASN A 179 " pdb=" C ASN A 179 " pdb=" N ASP A 180 " pdb=" CA ASP A 180 " ideal model delta harmonic sigma weight residual -180.00 -148.10 -31.90 0 5.00e+00 4.00e-02 4.07e+01 ... (remaining 9389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.013: 2448 1.013 - 2.026: 0 2.026 - 3.039: 0 3.039 - 4.053: 0 4.053 - 5.066: 24 Chirality restraints: 2472 Sorted by residual: chirality pdb=" C4 HZ7 C 801 " pdb=" C3 HZ7 C 801 " pdb=" C5 HZ7 C 801 " pdb=" O6 HZ7 C 801 " both_signs ideal model delta sigma weight residual False -2.50 2.56 -5.07 2.00e-01 2.50e+01 6.42e+02 chirality pdb=" C4 HZ7 B 801 " pdb=" C3 HZ7 B 801 " pdb=" C5 HZ7 B 801 " pdb=" O6 HZ7 B 801 " both_signs ideal model delta sigma weight residual False -2.50 2.56 -5.07 2.00e-01 2.50e+01 6.41e+02 chirality pdb=" C4 HZ7 A 801 " pdb=" C3 HZ7 A 801 " pdb=" C5 HZ7 A 801 " pdb=" O6 HZ7 A 801 " both_signs ideal model delta sigma weight residual False -2.50 2.56 -5.06 2.00e-01 2.50e+01 6.41e+02 ... (remaining 2469 not shown) Planarity restraints: 2660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 AQV C 802 " 0.039 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" C14 AQV C 802 " -0.033 2.00e-02 2.50e+03 pdb=" C15 AQV C 802 " -0.002 2.00e-02 2.50e+03 pdb=" C16 AQV C 802 " 0.039 2.00e-02 2.50e+03 pdb=" C17 AQV C 802 " 0.001 2.00e-02 2.50e+03 pdb=" C18 AQV C 802 " -0.010 2.00e-02 2.50e+03 pdb=" C19 AQV C 802 " -0.008 2.00e-02 2.50e+03 pdb=" N2 AQV C 802 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 AQV D 802 " 0.039 2.00e-02 2.50e+03 2.48e-02 1.23e+01 pdb=" C14 AQV D 802 " -0.033 2.00e-02 2.50e+03 pdb=" C15 AQV D 802 " -0.003 2.00e-02 2.50e+03 pdb=" C16 AQV D 802 " 0.038 2.00e-02 2.50e+03 pdb=" C17 AQV D 802 " 0.002 2.00e-02 2.50e+03 pdb=" C18 AQV D 802 " -0.010 2.00e-02 2.50e+03 pdb=" C19 AQV D 802 " -0.008 2.00e-02 2.50e+03 pdb=" N2 AQV D 802 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 AQV B 802 " 0.039 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" C14 AQV B 802 " -0.033 2.00e-02 2.50e+03 pdb=" C15 AQV B 802 " -0.003 2.00e-02 2.50e+03 pdb=" C16 AQV B 802 " 0.038 2.00e-02 2.50e+03 pdb=" C17 AQV B 802 " 0.002 2.00e-02 2.50e+03 pdb=" C18 AQV B 802 " -0.010 2.00e-02 2.50e+03 pdb=" C19 AQV B 802 " -0.007 2.00e-02 2.50e+03 pdb=" N2 AQV B 802 " -0.026 2.00e-02 2.50e+03 ... (remaining 2657 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3920 2.78 - 3.31: 14345 3.31 - 3.84: 24806 3.84 - 4.37: 28329 4.37 - 4.90: 46546 Nonbonded interactions: 117946 Sorted by model distance: nonbonded pdb=" CE2 TYR D 355 " pdb=" NH2 ARG D 403 " model vdw 2.249 3.420 nonbonded pdb=" OH TYR B 355 " pdb=" O11 HZ7 B 801 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR C 355 " pdb=" O11 HZ7 C 801 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR A 355 " pdb=" O11 HZ7 A 801 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR D 355 " pdb=" O11 HZ7 D 801 " model vdw 2.276 2.440 ... (remaining 117941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.680 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 41.630 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.011 0.259 16008 Z= 0.690 Angle : 1.205 13.668 21748 Z= 0.619 Chirality : 0.492 5.066 2472 Planarity : 0.008 0.072 2660 Dihedral : 17.178 173.034 5784 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.80 (0.13), residues: 1884 helix: -3.93 (0.09), residues: 988 sheet: -2.19 (0.39), residues: 160 loop : -3.91 (0.18), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 491 HIS 0.010 0.003 HIS D 451 PHE 0.026 0.003 PHE A 182 TYR 0.034 0.004 TYR A 436 ARG 0.005 0.001 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 416 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7801 (t80) cc_final: 0.7471 (t80) REVERT: A 495 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8367 (tp40) REVERT: A 511 SER cc_start: 0.9283 (m) cc_final: 0.8736 (p) REVERT: B 93 PHE cc_start: 0.7839 (t80) cc_final: 0.7563 (t80) REVERT: B 495 GLN cc_start: 0.8751 (tp-100) cc_final: 0.8395 (tp40) REVERT: B 511 SER cc_start: 0.9253 (m) cc_final: 0.8696 (p) REVERT: C 47 TYR cc_start: 0.7491 (m-80) cc_final: 0.7267 (m-80) REVERT: C 495 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8335 (tp40) REVERT: C 511 SER cc_start: 0.9158 (m) cc_final: 0.8580 (p) REVERT: D 335 TRP cc_start: 0.7082 (m-10) cc_final: 0.6829 (m-90) REVERT: D 495 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8358 (tp40) REVERT: D 511 SER cc_start: 0.9268 (m) cc_final: 0.8714 (p) outliers start: 1 outliers final: 0 residues processed: 416 average time/residue: 0.2544 time to fit residues: 158.4086 Evaluate side-chains 200 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 0.0270 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 HIS A 234 HIS A 352 ASN A 469 ASN B 69 GLN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 HIS B 234 HIS B 352 ASN B 469 ASN C 69 GLN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS C 234 HIS C 469 ASN D 69 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 HIS D 234 HIS D 352 ASN D 469 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16008 Z= 0.216 Angle : 0.793 9.489 21748 Z= 0.381 Chirality : 0.044 0.233 2472 Planarity : 0.006 0.049 2660 Dihedral : 19.101 165.840 2280 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 3.72 % Allowed : 10.40 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.16), residues: 1884 helix: -2.37 (0.13), residues: 1012 sheet: -0.16 (0.43), residues: 176 loop : -3.60 (0.19), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 157 HIS 0.010 0.001 HIS B 286 PHE 0.023 0.002 PHE C 474 TYR 0.019 0.002 TYR C 436 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 268 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9140 (tptt) cc_final: 0.8843 (tppt) REVERT: A 93 PHE cc_start: 0.7686 (t80) cc_final: 0.7408 (t80) REVERT: A 499 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7496 (m-80) REVERT: A 511 SER cc_start: 0.9229 (m) cc_final: 0.8792 (p) REVERT: B 46 LYS cc_start: 0.9148 (tptt) cc_final: 0.8836 (tppt) REVERT: B 93 PHE cc_start: 0.7689 (t80) cc_final: 0.7398 (t80) REVERT: B 499 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7194 (m-80) REVERT: B 511 SER cc_start: 0.9228 (m) cc_final: 0.8767 (p) REVERT: C 46 LYS cc_start: 0.9139 (tptt) cc_final: 0.8820 (tppt) REVERT: C 297 PHE cc_start: 0.7169 (m-10) cc_final: 0.6967 (t80) REVERT: C 499 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: C 511 SER cc_start: 0.9193 (m) cc_final: 0.8779 (p) REVERT: D 46 LYS cc_start: 0.9096 (tptt) cc_final: 0.8816 (tppt) REVERT: D 242 LEU cc_start: 0.9011 (mt) cc_final: 0.8471 (tp) REVERT: D 297 PHE cc_start: 0.7293 (m-10) cc_final: 0.6972 (t80) REVERT: D 467 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8924 (tp) REVERT: D 499 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: D 511 SER cc_start: 0.9224 (m) cc_final: 0.8780 (p) outliers start: 63 outliers final: 30 residues processed: 322 average time/residue: 0.2479 time to fit residues: 126.6739 Evaluate side-chains 224 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 189 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 499 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16008 Z= 0.279 Angle : 0.768 9.592 21748 Z= 0.372 Chirality : 0.043 0.236 2472 Planarity : 0.005 0.050 2660 Dihedral : 17.769 160.289 2280 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 5.85 % Allowed : 11.82 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.18), residues: 1884 helix: -1.83 (0.14), residues: 1000 sheet: 0.11 (0.46), residues: 184 loop : -3.41 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 157 HIS 0.007 0.002 HIS B 286 PHE 0.020 0.002 PHE C 474 TYR 0.017 0.002 TYR B 404 ARG 0.004 0.001 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 202 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9171 (tptt) cc_final: 0.8832 (tppt) REVERT: A 82 LEU cc_start: 0.9392 (mm) cc_final: 0.9033 (tp) REVERT: A 495 GLN cc_start: 0.8279 (tp40) cc_final: 0.7883 (mp10) REVERT: A 499 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: A 511 SER cc_start: 0.9161 (m) cc_final: 0.8801 (p) REVERT: B 46 LYS cc_start: 0.9168 (tptt) cc_final: 0.8840 (tppt) REVERT: B 82 LEU cc_start: 0.9432 (mm) cc_final: 0.9058 (tp) REVERT: B 495 GLN cc_start: 0.8176 (tp40) cc_final: 0.7967 (mp10) REVERT: B 499 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: B 511 SER cc_start: 0.9174 (m) cc_final: 0.8812 (p) REVERT: B 516 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8872 (mp) REVERT: C 46 LYS cc_start: 0.9207 (tptt) cc_final: 0.8904 (tppt) REVERT: C 82 LEU cc_start: 0.9422 (mm) cc_final: 0.9087 (tp) REVERT: C 499 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: C 511 SER cc_start: 0.9156 (m) cc_final: 0.8767 (p) REVERT: D 46 LYS cc_start: 0.9163 (tptt) cc_final: 0.8832 (tppt) REVERT: D 82 LEU cc_start: 0.9415 (mm) cc_final: 0.9064 (tp) REVERT: D 297 PHE cc_start: 0.7144 (m-10) cc_final: 0.6932 (t80) REVERT: D 334 MET cc_start: 0.5849 (mtp) cc_final: 0.5492 (mmp) REVERT: D 459 MET cc_start: 0.8534 (tmm) cc_final: 0.7979 (tmm) REVERT: D 467 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9037 (tp) REVERT: D 495 GLN cc_start: 0.8187 (tp40) cc_final: 0.7982 (mp10) REVERT: D 499 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: D 511 SER cc_start: 0.9178 (m) cc_final: 0.8817 (p) outliers start: 99 outliers final: 68 residues processed: 281 average time/residue: 0.2120 time to fit residues: 98.9490 Evaluate side-chains 262 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 188 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 88 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 171 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B 97 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16008 Z= 0.217 Angle : 0.712 9.439 21748 Z= 0.337 Chirality : 0.041 0.189 2472 Planarity : 0.005 0.044 2660 Dihedral : 16.948 158.085 2280 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 5.38 % Allowed : 14.72 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.18), residues: 1884 helix: -1.52 (0.15), residues: 992 sheet: 0.69 (0.46), residues: 176 loop : -3.29 (0.20), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 157 HIS 0.007 0.001 HIS B 286 PHE 0.015 0.001 PHE B 474 TYR 0.016 0.002 TYR C 436 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 198 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.9355 (mm) cc_final: 0.9020 (tp) REVERT: A 467 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8955 (tt) REVERT: A 499 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: A 511 SER cc_start: 0.9186 (m) cc_final: 0.8831 (p) REVERT: B 46 LYS cc_start: 0.9179 (tptt) cc_final: 0.8828 (tppt) REVERT: B 82 LEU cc_start: 0.9352 (mm) cc_final: 0.9016 (tp) REVERT: B 334 MET cc_start: 0.5795 (mtp) cc_final: 0.5421 (mmp) REVERT: B 467 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9009 (tt) REVERT: B 495 GLN cc_start: 0.8214 (tp40) cc_final: 0.7887 (mp10) REVERT: B 499 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: B 511 SER cc_start: 0.9182 (m) cc_final: 0.8826 (p) REVERT: C 46 LYS cc_start: 0.9177 (tptt) cc_final: 0.8833 (tppt) REVERT: C 82 LEU cc_start: 0.9383 (mm) cc_final: 0.9047 (tp) REVERT: C 467 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8786 (tt) REVERT: C 499 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: C 511 SER cc_start: 0.9173 (m) cc_final: 0.8795 (p) REVERT: D 46 LYS cc_start: 0.9176 (tptt) cc_final: 0.8811 (tppt) REVERT: D 82 LEU cc_start: 0.9335 (mm) cc_final: 0.9020 (tp) REVERT: D 334 MET cc_start: 0.5933 (mtp) cc_final: 0.5492 (mmp) REVERT: D 459 MET cc_start: 0.8473 (tmm) cc_final: 0.7920 (tmm) REVERT: D 467 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8698 (tt) REVERT: D 495 GLN cc_start: 0.8232 (tp40) cc_final: 0.7907 (mp10) REVERT: D 499 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: D 511 SER cc_start: 0.9184 (m) cc_final: 0.8834 (p) outliers start: 91 outliers final: 65 residues processed: 270 average time/residue: 0.2055 time to fit residues: 92.2384 Evaluate side-chains 252 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 179 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 155 optimal weight: 40.0000 chunk 125 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16008 Z= 0.193 Angle : 0.686 9.352 21748 Z= 0.320 Chirality : 0.040 0.229 2472 Planarity : 0.004 0.045 2660 Dihedral : 16.352 156.077 2280 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 6.09 % Allowed : 14.95 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.18), residues: 1884 helix: -1.29 (0.16), residues: 992 sheet: 0.00 (0.43), residues: 200 loop : -3.10 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 157 HIS 0.007 0.001 HIS C 286 PHE 0.014 0.001 PHE B 474 TYR 0.015 0.002 TYR C 436 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 197 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.9355 (mm) cc_final: 0.9009 (tp) REVERT: A 408 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.5172 (m-80) REVERT: A 467 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8949 (tt) REVERT: A 499 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: A 511 SER cc_start: 0.9205 (m) cc_final: 0.8839 (p) REVERT: B 82 LEU cc_start: 0.9355 (mm) cc_final: 0.8977 (tp) REVERT: B 334 MET cc_start: 0.5747 (mtp) cc_final: 0.5529 (mmp) REVERT: B 408 PHE cc_start: 0.5539 (OUTLIER) cc_final: 0.5016 (m-80) REVERT: B 467 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9038 (tt) REVERT: B 495 GLN cc_start: 0.8233 (tp40) cc_final: 0.7874 (mp10) REVERT: B 499 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: B 511 SER cc_start: 0.9200 (m) cc_final: 0.8847 (p) REVERT: B 516 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8851 (mp) REVERT: C 46 LYS cc_start: 0.9165 (tptt) cc_final: 0.8915 (tppp) REVERT: C 82 LEU cc_start: 0.9335 (mm) cc_final: 0.9010 (tp) REVERT: C 408 PHE cc_start: 0.5505 (OUTLIER) cc_final: 0.5249 (m-80) REVERT: C 467 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8861 (tt) REVERT: C 499 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: C 511 SER cc_start: 0.9178 (m) cc_final: 0.8806 (p) REVERT: D 82 LEU cc_start: 0.9308 (mm) cc_final: 0.9003 (tp) REVERT: D 334 MET cc_start: 0.5897 (mtp) cc_final: 0.5541 (mmp) REVERT: D 408 PHE cc_start: 0.5601 (OUTLIER) cc_final: 0.5257 (m-80) REVERT: D 459 MET cc_start: 0.8397 (tmm) cc_final: 0.7920 (tmm) REVERT: D 467 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8688 (tt) REVERT: D 495 GLN cc_start: 0.8260 (tp40) cc_final: 0.7888 (mp10) REVERT: D 499 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: D 511 SER cc_start: 0.9198 (m) cc_final: 0.8833 (p) outliers start: 103 outliers final: 71 residues processed: 276 average time/residue: 0.2009 time to fit residues: 92.9884 Evaluate side-chains 263 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 179 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16008 Z= 0.195 Angle : 0.688 9.287 21748 Z= 0.323 Chirality : 0.041 0.251 2472 Planarity : 0.004 0.042 2660 Dihedral : 16.117 155.082 2280 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 6.56 % Allowed : 15.37 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.19), residues: 1884 helix: -1.11 (0.16), residues: 960 sheet: 0.80 (0.43), residues: 176 loop : -2.83 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 157 HIS 0.008 0.001 HIS A 451 PHE 0.013 0.001 PHE A 313 TYR 0.014 0.002 TYR C 436 ARG 0.002 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 204 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.9352 (mm) cc_final: 0.8981 (tp) REVERT: A 334 MET cc_start: 0.5864 (mtm) cc_final: 0.5567 (mmp) REVERT: A 408 PHE cc_start: 0.5480 (OUTLIER) cc_final: 0.5156 (m-80) REVERT: A 467 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8977 (tt) REVERT: A 499 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: A 511 SER cc_start: 0.9205 (m) cc_final: 0.8845 (p) REVERT: B 82 LEU cc_start: 0.9361 (mm) cc_final: 0.8993 (tp) REVERT: B 499 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7186 (m-80) REVERT: B 511 SER cc_start: 0.9204 (m) cc_final: 0.8828 (p) REVERT: B 516 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8917 (mp) REVERT: C 46 LYS cc_start: 0.9168 (tptt) cc_final: 0.8926 (tppt) REVERT: C 50 MET cc_start: 0.7543 (ttt) cc_final: 0.6930 (tmm) REVERT: C 82 LEU cc_start: 0.9344 (mm) cc_final: 0.9040 (tp) REVERT: C 334 MET cc_start: 0.5741 (mtp) cc_final: 0.5509 (mmp) REVERT: C 408 PHE cc_start: 0.5405 (OUTLIER) cc_final: 0.5141 (m-80) REVERT: C 467 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8887 (tt) REVERT: C 499 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: C 511 SER cc_start: 0.9177 (m) cc_final: 0.8781 (p) REVERT: D 82 LEU cc_start: 0.9329 (mm) cc_final: 0.9008 (tp) REVERT: D 408 PHE cc_start: 0.5556 (OUTLIER) cc_final: 0.5221 (m-80) REVERT: D 459 MET cc_start: 0.8343 (tmm) cc_final: 0.7937 (tmm) REVERT: D 467 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8661 (tt) REVERT: D 499 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: D 511 SER cc_start: 0.9197 (m) cc_final: 0.8827 (p) outliers start: 111 outliers final: 73 residues processed: 290 average time/residue: 0.2093 time to fit residues: 99.1270 Evaluate side-chains 268 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 184 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16008 Z= 0.210 Angle : 0.687 9.272 21748 Z= 0.321 Chirality : 0.040 0.196 2472 Planarity : 0.004 0.041 2660 Dihedral : 16.046 154.702 2280 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 6.09 % Allowed : 16.08 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.19), residues: 1884 helix: -1.04 (0.16), residues: 960 sheet: 0.01 (0.42), residues: 200 loop : -2.70 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 398 HIS 0.009 0.001 HIS A 451 PHE 0.014 0.001 PHE D 474 TYR 0.013 0.002 TYR B 436 ARG 0.002 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 202 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7235 (ttt) cc_final: 0.6795 (tmm) REVERT: A 82 LEU cc_start: 0.9361 (mm) cc_final: 0.8998 (tp) REVERT: A 408 PHE cc_start: 0.5454 (OUTLIER) cc_final: 0.5133 (m-80) REVERT: A 467 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8959 (tt) REVERT: A 499 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: A 511 SER cc_start: 0.9224 (m) cc_final: 0.8874 (p) REVERT: B 50 MET cc_start: 0.7511 (ttt) cc_final: 0.6853 (tmm) REVERT: B 82 LEU cc_start: 0.9368 (mm) cc_final: 0.9019 (tp) REVERT: B 495 GLN cc_start: 0.8264 (tp40) cc_final: 0.7842 (mp10) REVERT: B 499 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7173 (m-80) REVERT: B 511 SER cc_start: 0.9162 (m) cc_final: 0.8808 (p) REVERT: B 516 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8913 (mp) REVERT: C 82 LEU cc_start: 0.9352 (mm) cc_final: 0.9009 (tp) REVERT: C 334 MET cc_start: 0.5760 (mtp) cc_final: 0.5531 (mmp) REVERT: C 408 PHE cc_start: 0.5319 (OUTLIER) cc_final: 0.5039 (m-80) REVERT: C 467 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8860 (tt) REVERT: C 499 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7152 (m-80) REVERT: C 511 SER cc_start: 0.9226 (m) cc_final: 0.8862 (p) REVERT: D 50 MET cc_start: 0.7403 (ttt) cc_final: 0.6751 (tmm) REVERT: D 62 LYS cc_start: 0.6203 (mttm) cc_final: 0.5972 (mmtp) REVERT: D 82 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9013 (tp) REVERT: D 408 PHE cc_start: 0.5531 (OUTLIER) cc_final: 0.5229 (m-80) REVERT: D 459 MET cc_start: 0.8355 (tmm) cc_final: 0.7972 (tmm) REVERT: D 467 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8642 (tt) REVERT: D 499 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: D 511 SER cc_start: 0.9156 (m) cc_final: 0.8801 (p) outliers start: 103 outliers final: 79 residues processed: 278 average time/residue: 0.2086 time to fit residues: 94.1134 Evaluate side-chains 278 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 187 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 115 optimal weight: 8.9990 chunk 123 optimal weight: 0.4980 chunk 89 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16008 Z= 0.222 Angle : 0.733 13.620 21748 Z= 0.341 Chirality : 0.042 0.301 2472 Planarity : 0.004 0.041 2660 Dihedral : 15.930 154.803 2280 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 6.91 % Allowed : 15.60 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.19), residues: 1884 helix: -1.05 (0.16), residues: 984 sheet: 0.05 (0.41), residues: 200 loop : -2.72 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 398 HIS 0.008 0.001 HIS A 451 PHE 0.013 0.001 PHE D 474 TYR 0.013 0.002 TYR D 436 ARG 0.001 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 209 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7320 (ttt) cc_final: 0.6899 (tmm) REVERT: A 82 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8996 (tp) REVERT: A 408 PHE cc_start: 0.5351 (OUTLIER) cc_final: 0.5022 (m-80) REVERT: A 499 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: A 511 SER cc_start: 0.9213 (m) cc_final: 0.8870 (p) REVERT: B 50 MET cc_start: 0.7556 (ttt) cc_final: 0.6995 (tmm) REVERT: B 82 LEU cc_start: 0.9360 (mm) cc_final: 0.8989 (tp) REVERT: B 467 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8716 (tt) REVERT: B 495 GLN cc_start: 0.8261 (tp40) cc_final: 0.7875 (mp10) REVERT: B 499 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: B 511 SER cc_start: 0.9228 (m) cc_final: 0.8891 (p) REVERT: B 516 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8866 (mp) REVERT: C 50 MET cc_start: 0.7572 (ttt) cc_final: 0.7142 (tmm) REVERT: C 82 LEU cc_start: 0.9351 (mm) cc_final: 0.9034 (tp) REVERT: C 334 MET cc_start: 0.5749 (mtp) cc_final: 0.5522 (mmp) REVERT: C 408 PHE cc_start: 0.5340 (OUTLIER) cc_final: 0.5033 (m-80) REVERT: C 467 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8840 (tt) REVERT: C 499 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: C 511 SER cc_start: 0.9228 (m) cc_final: 0.8850 (p) REVERT: D 50 MET cc_start: 0.7483 (ttt) cc_final: 0.6890 (tmm) REVERT: D 62 LYS cc_start: 0.6172 (mttm) cc_final: 0.5960 (mmtp) REVERT: D 82 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9012 (tp) REVERT: D 334 MET cc_start: 0.5919 (mtp) cc_final: 0.5580 (mmp) REVERT: D 408 PHE cc_start: 0.5514 (OUTLIER) cc_final: 0.5211 (m-80) REVERT: D 459 MET cc_start: 0.8341 (tmm) cc_final: 0.7959 (tmm) REVERT: D 467 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8693 (tt) REVERT: D 495 GLN cc_start: 0.8281 (tp40) cc_final: 0.7870 (mp10) REVERT: D 499 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7102 (m-80) REVERT: D 511 SER cc_start: 0.9222 (m) cc_final: 0.8871 (p) outliers start: 117 outliers final: 82 residues processed: 293 average time/residue: 0.2129 time to fit residues: 100.9443 Evaluate side-chains 283 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 188 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.0060 chunk 158 optimal weight: 0.8980 chunk 168 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 152 optimal weight: 0.2980 chunk 159 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 178 optimal weight: 7.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS C 469 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16008 Z= 0.161 Angle : 0.701 14.950 21748 Z= 0.315 Chirality : 0.040 0.282 2472 Planarity : 0.004 0.038 2660 Dihedral : 15.602 153.911 2280 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.73 % Allowed : 17.91 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.19), residues: 1884 helix: -0.83 (0.17), residues: 968 sheet: 0.18 (0.41), residues: 200 loop : -2.54 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 398 HIS 0.010 0.001 HIS C 286 PHE 0.012 0.001 PHE A 49 TYR 0.012 0.001 TYR D 436 ARG 0.002 0.000 ARG D 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 227 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7346 (ttt) cc_final: 0.6787 (tmm) REVERT: A 82 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9008 (tp) REVERT: A 408 PHE cc_start: 0.5358 (OUTLIER) cc_final: 0.5135 (m-80) REVERT: A 499 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: A 511 SER cc_start: 0.9204 (m) cc_final: 0.8828 (p) REVERT: B 46 LYS cc_start: 0.9196 (tptt) cc_final: 0.8956 (tppt) REVERT: B 50 MET cc_start: 0.7474 (ttt) cc_final: 0.6969 (tmm) REVERT: B 82 LEU cc_start: 0.9252 (mm) cc_final: 0.9004 (tp) REVERT: B 499 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: B 511 SER cc_start: 0.9221 (m) cc_final: 0.8841 (p) REVERT: C 46 LYS cc_start: 0.9177 (tptt) cc_final: 0.8949 (tppp) REVERT: C 50 MET cc_start: 0.7510 (ttt) cc_final: 0.7193 (tmm) REVERT: C 82 LEU cc_start: 0.9269 (mm) cc_final: 0.9012 (tp) REVERT: C 467 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8799 (tt) REVERT: C 499 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7085 (m-80) REVERT: C 511 SER cc_start: 0.9219 (m) cc_final: 0.8821 (p) REVERT: D 46 LYS cc_start: 0.9183 (tptt) cc_final: 0.8942 (tppt) REVERT: D 50 MET cc_start: 0.7402 (ttt) cc_final: 0.6961 (tmm) REVERT: D 82 LEU cc_start: 0.9300 (mm) cc_final: 0.9028 (tp) REVERT: D 334 MET cc_start: 0.5901 (mtp) cc_final: 0.5553 (mmp) REVERT: D 459 MET cc_start: 0.8303 (tmm) cc_final: 0.7923 (tmm) REVERT: D 467 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9000 (tt) REVERT: D 499 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7112 (m-80) REVERT: D 511 SER cc_start: 0.9201 (m) cc_final: 0.8840 (p) outliers start: 80 outliers final: 52 residues processed: 282 average time/residue: 0.2205 time to fit residues: 99.9252 Evaluate side-chains 260 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 200 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 158 optimal weight: 6.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 ASN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 16008 Z= 0.346 Angle : 0.857 16.129 21748 Z= 0.409 Chirality : 0.047 0.323 2472 Planarity : 0.005 0.047 2660 Dihedral : 16.021 157.438 2280 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 5.02 % Allowed : 17.97 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.19), residues: 1884 helix: -1.03 (0.16), residues: 968 sheet: -0.63 (0.38), residues: 240 loop : -2.42 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 398 HIS 0.008 0.002 HIS A 451 PHE 0.036 0.002 PHE B 48 TYR 0.021 0.002 TYR B 404 ARG 0.002 0.000 ARG B 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 201 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9168 (mm) REVERT: A 408 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.5228 (m-80) REVERT: A 467 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8838 (tt) REVERT: A 499 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: A 511 SER cc_start: 0.9228 (m) cc_final: 0.8924 (p) REVERT: B 82 LEU cc_start: 0.9416 (mm) cc_final: 0.9196 (mm) REVERT: B 334 MET cc_start: 0.6007 (mtp) cc_final: 0.5768 (mmp) REVERT: B 495 GLN cc_start: 0.8385 (tp40) cc_final: 0.7883 (mp10) REVERT: B 499 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7122 (m-80) REVERT: B 511 SER cc_start: 0.9228 (m) cc_final: 0.8950 (p) REVERT: C 50 MET cc_start: 0.7344 (ttt) cc_final: 0.7111 (tmm) REVERT: C 82 LEU cc_start: 0.9414 (mm) cc_final: 0.9187 (mm) REVERT: C 467 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8842 (tt) REVERT: C 499 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: C 511 SER cc_start: 0.9230 (m) cc_final: 0.8908 (p) REVERT: D 82 LEU cc_start: 0.9413 (mm) cc_final: 0.9188 (mm) REVERT: D 334 MET cc_start: 0.5871 (mtp) cc_final: 0.5530 (mmp) REVERT: D 459 MET cc_start: 0.8439 (tmm) cc_final: 0.8037 (tmm) REVERT: D 467 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8775 (tt) REVERT: D 495 GLN cc_start: 0.8363 (tp40) cc_final: 0.7879 (mp10) REVERT: D 499 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: D 511 SER cc_start: 0.9222 (m) cc_final: 0.8925 (p) outliers start: 85 outliers final: 67 residues processed: 267 average time/residue: 0.2098 time to fit residues: 91.9643 Evaluate side-chains 259 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 183 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 499 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 TYR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 499 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 345 TRP Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 499 TYR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.8980 chunk 137 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.103903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089662 restraints weight = 48696.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.091865 restraints weight = 26980.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.093277 restraints weight = 17618.837| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 16008 Z= 0.190 Angle : 0.768 15.446 21748 Z= 0.350 Chirality : 0.043 0.278 2472 Planarity : 0.004 0.038 2660 Dihedral : 15.597 156.917 2280 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.20 % Allowed : 19.62 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.19), residues: 1884 helix: -0.72 (0.17), residues: 952 sheet: -0.56 (0.37), residues: 240 loop : -2.26 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 398 HIS 0.008 0.001 HIS C 286 PHE 0.015 0.001 PHE B 48 TYR 0.016 0.001 TYR A 411 ARG 0.003 0.000 ARG C 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2931.25 seconds wall clock time: 55 minutes 25.42 seconds (3325.42 seconds total)