Starting phenix.real_space_refine on Tue May 5 09:07:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qlv_53235/05_2026/9qlv_53235.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qlv_53235/05_2026/9qlv_53235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qlv_53235/05_2026/9qlv_53235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qlv_53235/05_2026/9qlv_53235.map" model { file = "/net/cci-nas-00/data/ceres_data/9qlv_53235/05_2026/9qlv_53235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qlv_53235/05_2026/9qlv_53235.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 8 5.49 5 S 176 5.16 5 C 17616 2.51 5 N 4724 2.21 5 O 5224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27748 Number of models: 1 Model: "" Number of chains: 12 Chain: "P" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 583 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "Q" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 583 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "R" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 583 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "S" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 583 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "A" Number of atoms: 6327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6327 Classifications: {'peptide': 799} Link IDs: {'PTRANS': 30, 'TRANS': 768} Chain breaks: 1 Chain: "B" Number of atoms: 6327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6327 Classifications: {'peptide': 799} Link IDs: {'PTRANS': 30, 'TRANS': 768} Chain breaks: 1 Chain: "C" Number of atoms: 6327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6327 Classifications: {'peptide': 799} Link IDs: {'PTRANS': 30, 'TRANS': 768} Chain breaks: 1 Chain: "D" Number of atoms: 6327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6327 Classifications: {'peptide': 799} Link IDs: {'PTRANS': 30, 'TRANS': 768} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.37, per 1000 atoms: 0.19 Number of scatterers: 27748 At special positions: 0 Unit cell: (196.236, 196.236, 97.704, 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 176 16.00 P 8 15.00 O 5224 8.00 N 4724 7.00 C 17616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS P 40 " - pdb=" SG CYS P 87 " distance=2.03 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 81 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 40 " - pdb=" SG CYS Q 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 43 " - pdb=" SG CYS Q 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 87 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS S 40 " - pdb=" SG CYS S 87 " distance=2.03 Simple disulfide: pdb=" SG CYS S 43 " - pdb=" SG CYS S 81 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.2 seconds 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6648 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 28 sheets defined 29.4% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'P' and resid 33 through 40 removed outlier: 4.046A pdb=" N LEU P 37 " --> pdb=" O SER P 33 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER P 38 " --> pdb=" O ARG P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 45 Processing helix chain 'P' and resid 70 through 76 removed outlier: 3.746A pdb=" N PHE P 74 " --> pdb=" O SER P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 85 Processing helix chain 'Q' and resid 34 through 47 removed outlier: 4.078A pdb=" N SER Q 38 " --> pdb=" O ARG Q 34 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN Q 41 " --> pdb=" O LEU Q 37 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA Q 42 " --> pdb=" O SER Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 76 removed outlier: 3.612A pdb=" N PHE Q 74 " --> pdb=" O SER Q 70 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN Q 76 " --> pdb=" O PHE Q 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 47 removed outlier: 4.364A pdb=" N SER R 38 " --> pdb=" O ARG R 34 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA R 42 " --> pdb=" O SER R 38 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU R 45 " --> pdb=" O GLN R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 76 removed outlier: 3.689A pdb=" N PHE R 74 " --> pdb=" O SER R 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 47 removed outlier: 4.258A pdb=" N CYS S 40 " --> pdb=" O SER S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 76 Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'A' and resid 188 through 201 Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 254 through 270 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 310 through 314 removed outlier: 4.034A pdb=" N PHE A 314 " --> pdb=" O MET A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 removed outlier: 4.206A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 removed outlier: 3.759A pdb=" N THR A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 379 removed outlier: 3.826A pdb=" N GLU A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 396 through 408 Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 414 through 424 removed outlier: 3.555A pdb=" N LYS A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 439 removed outlier: 3.840A pdb=" N ALA A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 452 removed outlier: 4.106A pdb=" N LEU A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 476 through 479 removed outlier: 3.687A pdb=" N LYS A 479 " --> pdb=" O HIS A 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 479' Processing helix chain 'A' and resid 485 through 499 Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.897A pdb=" N LYS A 503 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 504 " --> pdb=" O PRO A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 504' Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 543 through 549 removed outlier: 4.320A pdb=" N GLU A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 670 removed outlier: 3.681A pdb=" N ILE A 667 " --> pdb=" O PRO A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 851 Processing helix chain 'A' and resid 896 through 900 Processing helix chain 'B' and resid 188 through 201 removed outlier: 3.825A pdb=" N HIS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'B' and resid 254 through 270 Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 301 through 307 removed outlier: 3.620A pdb=" N LEU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 4.085A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 379 removed outlier: 4.007A pdb=" N ASP B 372 " --> pdb=" O MET B 368 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 392 Processing helix chain 'B' and resid 396 through 408 Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 414 through 424 removed outlier: 4.775A pdb=" N VAL B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 439 removed outlier: 3.694A pdb=" N LEU B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 453 Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.527A pdb=" N LYS B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 499 Processing helix chain 'B' and resid 509 through 519 Processing helix chain 'B' and resid 543 through 549 removed outlier: 4.255A pdb=" N GLU B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 670 removed outlier: 3.565A pdb=" N ILE B 667 " --> pdb=" O PRO B 664 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 669 " --> pdb=" O SER B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 782 removed outlier: 4.190A pdb=" N ILE B 780 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 782 " --> pdb=" O ASP B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 849 removed outlier: 3.575A pdb=" N ARG B 846 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 847 " --> pdb=" O GLU B 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 removed outlier: 3.920A pdb=" N HIS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 231 Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 254 through 270 Processing helix chain 'C' and resid 281 through 288 Processing helix chain 'C' and resid 310 through 314 removed outlier: 3.822A pdb=" N PHE C 314 " --> pdb=" O MET C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 333 removed outlier: 4.420A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.969A pdb=" N ASP C 372 " --> pdb=" O MET C 368 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU C 373 " --> pdb=" O ASP C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 391 Processing helix chain 'C' and resid 396 through 408 Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 414 through 424 removed outlier: 4.027A pdb=" N LEU C 418 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLY C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 440 removed outlier: 3.831A pdb=" N LEU C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 476 through 479 removed outlier: 4.027A pdb=" N LYS C 479 " --> pdb=" O HIS C 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 476 through 479' Processing helix chain 'C' and resid 485 through 499 Processing helix chain 'C' and resid 499 through 504 removed outlier: 4.315A pdb=" N SER C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 518 removed outlier: 3.554A pdb=" N ILE C 513 " --> pdb=" O ASP C 509 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA C 514 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 664 through 670 removed outlier: 3.612A pdb=" N ILE C 667 " --> pdb=" O PRO C 664 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN C 669 " --> pdb=" O SER C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 783 Processing helix chain 'C' and resid 841 through 851 Processing helix chain 'C' and resid 918 through 922 removed outlier: 3.906A pdb=" N SER C 922 " --> pdb=" O SER C 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 removed outlier: 3.913A pdb=" N HIS D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 232 Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 254 through 270 Processing helix chain 'D' and resid 281 through 288 Processing helix chain 'D' and resid 326 through 333 removed outlier: 4.087A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 Processing helix chain 'D' and resid 367 through 379 removed outlier: 4.182A pdb=" N ASP D 372 " --> pdb=" O MET D 368 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D 373 " --> pdb=" O ASP D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 392 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 414 through 424 removed outlier: 4.768A pdb=" N VAL D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLY D 421 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 439 removed outlier: 3.885A pdb=" N LEU D 432 " --> pdb=" O LYS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 452 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 485 through 499 Processing helix chain 'D' and resid 509 through 519 Processing helix chain 'D' and resid 543 through 549 removed outlier: 4.168A pdb=" N GLU D 547 " --> pdb=" O PRO D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 670 removed outlier: 3.772A pdb=" N ASN D 669 " --> pdb=" O SER D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 783 removed outlier: 3.575A pdb=" N LEU D 783 " --> pdb=" O ILE D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 843 through 848 removed outlier: 3.817A pdb=" N ILE D 848 " --> pdb=" O ALA D 844 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 52 through 58 removed outlier: 5.645A pdb=" N MET P 53 " --> pdb=" O THR P 68 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR P 68 " --> pdb=" O MET P 53 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU P 55 " --> pdb=" O LYS P 66 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS P 66 " --> pdb=" O LEU P 55 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN P 57 " --> pdb=" O THR P 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 23 through 29 removed outlier: 3.881A pdb=" N ASN Q 57 " --> pdb=" O THR Q 64 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS Q 66 " --> pdb=" O LEU Q 55 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU Q 55 " --> pdb=" O LYS Q 66 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N THR Q 68 " --> pdb=" O MET Q 53 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N MET Q 53 " --> pdb=" O THR Q 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 52 through 58 removed outlier: 6.934A pdb=" N THR R 64 " --> pdb=" O ILE R 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 24 through 28 removed outlier: 3.512A pdb=" N LEU S 26 " --> pdb=" O TYR S 65 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG S 52 " --> pdb=" O THR S 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 removed outlier: 6.440A pdb=" N CYS A 239 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP A 297 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL A 241 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 299 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP A 337 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'A' and resid 530 through 532 removed outlier: 6.434A pdb=" N PHE A 584 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL A 606 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 629 " --> pdb=" O TYR A 653 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU A 652 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE A 676 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 719 through 721 removed outlier: 6.492A pdb=" N ILE A 743 " --> pdb=" O ASN A 766 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 831 through 833 Processing sheet with id=AB1, first strand: chain 'A' and resid 877 through 880 Processing sheet with id=AB2, first strand: chain 'A' and resid 912 through 915 removed outlier: 3.911A pdb=" N VAL A 915 " --> pdb=" O SER A 921 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER A 921 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 237 through 241 removed outlier: 4.898A pdb=" N ASP B 337 " --> pdb=" O MET B 209 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 472 through 475 Processing sheet with id=AB5, first strand: chain 'B' and resid 530 through 532 removed outlier: 5.937A pdb=" N LEU B 555 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE B 584 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL B 606 " --> pdb=" O ASP B 630 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 629 " --> pdb=" O TYR B 653 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 652 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 700 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE B 743 " --> pdb=" O ASN B 766 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 855 through 857 removed outlier: 4.262A pdb=" N GLY B 856 " --> pdb=" O HIS B 951 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU B 986 " --> pdb=" O VAL B 893 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS B 871 " --> pdb=" O VAL B 989 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 878 through 880 removed outlier: 3.615A pdb=" N ILE B 971 " --> pdb=" O ILE B 880 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 911 through 912 Processing sheet with id=AB9, first strand: chain 'C' and resid 237 through 241 removed outlier: 6.663A pdb=" N HIS C 237 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE C 295 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS C 239 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASP C 297 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 241 " --> pdb=" O ASP C 297 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C 299 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 319 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N TYR C 339 " --> pdb=" O MET C 209 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY C 211 " --> pdb=" O TYR C 339 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AC2, first strand: chain 'C' and resid 530 through 532 removed outlier: 6.851A pdb=" N PHE C 531 " --> pdb=" O TYR C 558 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU C 555 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE C 584 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL C 606 " --> pdb=" O ASP C 630 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE C 629 " --> pdb=" O TYR C 653 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU C 652 " --> pdb=" O MET C 677 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 723 " --> pdb=" O MET C 701 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 720 " --> pdb=" O LYS C 744 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N SER C 746 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C 722 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 743 " --> pdb=" O ASN C 766 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N SER C 768 " --> pdb=" O ILE C 743 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 745 " --> pdb=" O SER C 768 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU C 791 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE C 767 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 809 through 811 removed outlier: 6.304A pdb=" N LEU C 810 " --> pdb=" O TYR C 833 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU C 832 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 871 through 873 removed outlier: 3.585A pdb=" N ALA C 873 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS C 987 " --> pdb=" O ALA C 873 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 877 through 878 Processing sheet with id=AC6, first strand: chain 'D' and resid 237 through 241 removed outlier: 6.363A pdb=" N HIS D 237 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE D 295 " --> pdb=" O HIS D 237 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N CYS D 239 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASP D 297 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL D 241 " --> pdb=" O ASP D 297 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 299 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET D 209 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N TYR D 339 " --> pdb=" O MET D 209 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY D 211 " --> pdb=" O TYR D 339 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 473 through 475 removed outlier: 3.540A pdb=" N ARG D 481 " --> pdb=" O ASP D 475 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 506 through 507 removed outlier: 6.429A pdb=" N LEU D 507 " --> pdb=" O SER D 530 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP D 532 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL D 529 " --> pdb=" O LYS D 556 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N TYR D 558 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE D 531 " --> pdb=" O TYR D 558 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL D 606 " --> pdb=" O ASP D 630 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE D 629 " --> pdb=" O TYR D 653 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU D 652 " --> pdb=" O MET D 677 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 699 " --> pdb=" O ASP D 719 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 857 through 860 Processing sheet with id=AD1, first strand: chain 'D' and resid 913 through 915 729 hydrogen bonds defined for protein. 2046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9076 1.34 - 1.46: 5905 1.46 - 1.58: 13038 1.58 - 1.70: 13 1.70 - 1.82: 244 Bond restraints: 28276 Sorted by residual: bond pdb=" CA TYR C 833 " pdb=" CB TYR C 833 " ideal model delta sigma weight residual 1.527 1.585 -0.058 1.75e-02 3.27e+03 1.09e+01 bond pdb=" N ARG A 706 " pdb=" CA ARG A 706 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.27e-02 6.20e+03 7.77e+00 bond pdb=" N LEU A 707 " pdb=" CA LEU A 707 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.08e+00 bond pdb=" N VAL C 661 " pdb=" CA VAL C 661 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.19e-02 7.06e+03 6.88e+00 bond pdb=" N GLN C 741 " pdb=" CA GLN C 741 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.22e-02 6.72e+03 6.72e+00 ... (remaining 28271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 37098 2.02 - 4.05: 988 4.05 - 6.07: 145 6.07 - 8.10: 25 8.10 - 10.12: 8 Bond angle restraints: 38264 Sorted by residual: angle pdb=" N LYS C 752 " pdb=" CA LYS C 752 " pdb=" C LYS C 752 " ideal model delta sigma weight residual 114.75 106.28 8.47 1.26e+00 6.30e-01 4.52e+01 angle pdb=" N VAL D 798 " pdb=" CA VAL D 798 " pdb=" C VAL D 798 " ideal model delta sigma weight residual 112.96 106.58 6.38 1.00e+00 1.00e+00 4.07e+01 angle pdb=" N VAL B 654 " pdb=" CA VAL B 654 " pdb=" C VAL B 654 " ideal model delta sigma weight residual 113.20 107.55 5.65 9.60e-01 1.09e+00 3.46e+01 angle pdb=" C SER D 705 " pdb=" CA SER D 705 " pdb=" CB SER D 705 " ideal model delta sigma weight residual 116.54 110.14 6.40 1.15e+00 7.56e-01 3.10e+01 angle pdb=" C MET A 186 " pdb=" CA MET A 186 " pdb=" CB MET A 186 " ideal model delta sigma weight residual 116.54 110.59 5.95 1.15e+00 7.56e-01 2.68e+01 ... (remaining 38259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 16637 33.38 - 66.75: 519 66.75 - 100.13: 46 100.13 - 133.50: 0 133.50 - 166.88: 2 Dihedral angle restraints: 17204 sinusoidal: 6996 harmonic: 10208 Sorted by residual: dihedral pdb=" C2' ADP A1301 " pdb=" C1' ADP A1301 " pdb=" N9 ADP A1301 " pdb=" C4 ADP A1301 " ideal model delta sinusoidal sigma weight residual 91.55 -75.33 166.88 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" CB CYS S 43 " pdb=" SG CYS S 43 " pdb=" SG CYS S 81 " pdb=" CB CYS S 81 " ideal model delta sinusoidal sigma weight residual 93.00 150.19 -57.19 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" O2A ADP C1301 " pdb=" O3A ADP C1301 " pdb=" PA ADP C1301 " pdb=" PB ADP C1301 " ideal model delta sinusoidal sigma weight residual 300.00 165.15 134.86 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 17201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3053 0.041 - 0.083: 974 0.083 - 0.124: 346 0.124 - 0.165: 43 0.165 - 0.207: 12 Chirality restraints: 4428 Sorted by residual: chirality pdb=" CB ILE A 571 " pdb=" CA ILE A 571 " pdb=" CG1 ILE A 571 " pdb=" CG2 ILE A 571 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU A 707 " pdb=" N LEU A 707 " pdb=" C LEU A 707 " pdb=" CB LEU A 707 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE A 575 " pdb=" CA ILE A 575 " pdb=" CG1 ILE A 575 " pdb=" CG2 ILE A 575 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 4425 not shown) Planarity restraints: 4848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 730 " 0.049 5.00e-02 4.00e+02 7.43e-02 8.82e+00 pdb=" N PRO A 731 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 731 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 731 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 749 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" C VAL C 749 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL C 749 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN C 750 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 593 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C ARG D 593 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG D 593 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU D 594 " 0.013 2.00e-02 2.50e+03 ... (remaining 4845 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 392 2.64 - 3.20: 25919 3.20 - 3.77: 41976 3.77 - 4.33: 58815 4.33 - 4.90: 97290 Nonbonded interactions: 224392 Sorted by model distance: nonbonded pdb=" O ARG P 34 " pdb=" NH1 ARG P 34 " model vdw 2.072 3.120 nonbonded pdb=" OD2 ASP R 80 " pdb=" ND2 ASN R 88 " model vdw 2.203 3.120 nonbonded pdb=" O HIS C 931 " pdb=" ND1 HIS C 931 " model vdw 2.206 3.120 nonbonded pdb=" O ILE A 536 " pdb=" NZ LYS A 568 " model vdw 2.221 3.120 nonbonded pdb=" O ALA D 624 " pdb=" ND2 ASN D 648 " model vdw 2.227 3.120 ... (remaining 224387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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=0.00 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 23.350 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28284 Z= 0.178 Angle : 0.787 10.120 38280 Z= 0.450 Chirality : 0.046 0.207 4428 Planarity : 0.004 0.074 4848 Dihedral : 15.676 166.881 10532 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.30 % Favored : 91.24 % Rotamer: Outliers : 2.66 % Allowed : 15.30 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.14), residues: 3480 helix: -0.54 (0.17), residues: 911 sheet: -1.53 (0.21), residues: 571 loop : -2.08 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 706 TYR 0.021 0.002 TYR A 515 PHE 0.029 0.002 PHE A 927 TRP 0.024 0.002 TRP A 857 HIS 0.004 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00338 (28276) covalent geometry : angle 0.78743 (38264) SS BOND : bond 0.00223 ( 8) SS BOND : angle 0.72762 ( 16) hydrogen bonds : bond 0.19832 ( 729) hydrogen bonds : angle 7.96804 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 220 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 74 PHE cc_start: 0.8290 (m-80) cc_final: 0.7750 (m-10) REVERT: R 52 ARG cc_start: 0.5120 (tpp-160) cc_final: 0.4842 (tpp-160) REVERT: A 271 LYS cc_start: 0.7724 (pttt) cc_final: 0.7143 (mtmt) REVERT: A 362 SER cc_start: 0.8503 (t) cc_final: 0.8047 (p) REVERT: A 593 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6893 (ttm-80) REVERT: A 615 LYS cc_start: 0.7309 (tptt) cc_final: 0.6999 (mmmt) REVERT: A 690 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6964 (pp) REVERT: A 991 ILE cc_start: 0.6024 (OUTLIER) cc_final: 0.5577 (mt) REVERT: B 403 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7170 (mm-30) REVERT: B 544 LYS cc_start: 0.6818 (mppt) cc_final: 0.6546 (pttm) REVERT: C 379 ASP cc_start: 0.8362 (t0) cc_final: 0.8041 (t70) REVERT: C 752 LYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5248 (ptmm) REVERT: C 832 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6685 (pp) REVERT: C 932 MET cc_start: 0.3727 (tpt) cc_final: 0.2881 (tpt) REVERT: D 541 ILE cc_start: 0.8481 (mm) cc_final: 0.8274 (mm) REVERT: D 568 LYS cc_start: 0.3558 (OUTLIER) cc_final: 0.1347 (pptt) REVERT: D 797 LEU cc_start: -0.2373 (OUTLIER) cc_final: -0.2714 (tt) REVERT: D 941 LYS cc_start: 0.3819 (OUTLIER) cc_final: 0.2652 (tmtt) outliers start: 84 outliers final: 49 residues processed: 289 average time/residue: 0.1766 time to fit residues: 81.9004 Evaluate side-chains 260 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 203 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 933 PHE Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 TRP Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain C residue 598 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 658 THR Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 752 LYS Chi-restraints excluded: chain C residue 786 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 568 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 941 LYS Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0060 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 ASN S 76 ASN A 441 ASN A 897 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 HIS C 750 ASN ** C 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 ASN C 931 HIS D 247 ASN D 441 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.191185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.144515 restraints weight = 41286.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133807 restraints weight = 62314.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130411 restraints weight = 45279.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128492 restraints weight = 44725.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129592 restraints weight = 37023.924| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28284 Z= 0.152 Angle : 0.688 10.875 38280 Z= 0.351 Chirality : 0.047 0.215 4428 Planarity : 0.004 0.068 4848 Dihedral : 8.981 164.312 3856 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.07 % Favored : 91.47 % Rotamer: Outliers : 3.77 % Allowed : 15.15 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.13), residues: 3480 helix: -0.31 (0.17), residues: 920 sheet: -1.53 (0.21), residues: 561 loop : -2.13 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 582 TYR 0.023 0.002 TYR A 515 PHE 0.023 0.002 PHE A 950 TRP 0.020 0.002 TRP A 502 HIS 0.004 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00354 (28276) covalent geometry : angle 0.68794 (38264) SS BOND : bond 0.00257 ( 8) SS BOND : angle 0.83794 ( 16) hydrogen bonds : bond 0.04385 ( 729) hydrogen bonds : angle 5.92049 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 217 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 27 ARG cc_start: 0.7820 (mtp-110) cc_final: 0.7600 (mtp-110) REVERT: Q 52 ARG cc_start: 0.6028 (tpm170) cc_final: 0.5386 (tpm170) REVERT: Q 61 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6119 (pm20) REVERT: Q 74 PHE cc_start: 0.8200 (m-80) cc_final: 0.7642 (m-10) REVERT: A 271 LYS cc_start: 0.7866 (pttt) cc_final: 0.7232 (mtmt) REVERT: A 403 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7494 (mm-30) REVERT: A 544 LYS cc_start: 0.7395 (tppt) cc_final: 0.6876 (pttm) REVERT: A 615 LYS cc_start: 0.7289 (tptt) cc_final: 0.6947 (mmmt) REVERT: A 690 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6999 (pp) REVERT: A 991 ILE cc_start: 0.6096 (OUTLIER) cc_final: 0.5650 (mt) REVERT: B 403 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7295 (mm-30) REVERT: B 607 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7934 (m110) REVERT: C 244 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8500 (pp) REVERT: C 379 ASP cc_start: 0.8377 (t0) cc_final: 0.8082 (t70) REVERT: C 740 LEU cc_start: 0.5251 (pt) cc_final: 0.5011 (pt) REVERT: C 752 LYS cc_start: 0.5930 (OUTLIER) cc_final: 0.5330 (ptmm) REVERT: C 832 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6565 (pp) REVERT: C 932 MET cc_start: 0.3783 (tpt) cc_final: 0.3004 (tpt) REVERT: D 541 ILE cc_start: 0.8473 (mm) cc_final: 0.8267 (mm) REVERT: D 568 LYS cc_start: 0.3179 (OUTLIER) cc_final: 0.0884 (pptt) REVERT: D 593 ARG cc_start: 0.6936 (tpp-160) cc_final: 0.6731 (tpp-160) REVERT: D 745 ILE cc_start: 0.5610 (OUTLIER) cc_final: 0.5167 (tt) outliers start: 119 outliers final: 65 residues processed: 312 average time/residue: 0.1663 time to fit residues: 84.8462 Evaluate side-chains 281 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 207 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 933 PHE Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 TRP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain C residue 598 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 752 LYS Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 446 ASP Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 568 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 312 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 chunk 205 optimal weight: 0.0770 chunk 257 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 92 optimal weight: 30.0000 chunk 238 optimal weight: 7.9990 overall best weight: 2.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS A 441 ASN ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 HIS A 934 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 HIS ** B 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN ** C 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 HIS D 441 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.187854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.142250 restraints weight = 41502.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129360 restraints weight = 60876.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125626 restraints weight = 43850.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125013 restraints weight = 40651.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126002 restraints weight = 36867.476| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 28284 Z= 0.250 Angle : 0.753 12.140 38280 Z= 0.382 Chirality : 0.049 0.214 4428 Planarity : 0.004 0.061 4848 Dihedral : 9.018 163.794 3816 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.97 % Favored : 90.55 % Rotamer: Outliers : 4.82 % Allowed : 16.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.13), residues: 3480 helix: -0.63 (0.16), residues: 921 sheet: -1.63 (0.21), residues: 587 loop : -2.20 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 593 TYR 0.029 0.002 TYR A 515 PHE 0.023 0.002 PHE A 948 TRP 0.021 0.002 TRP A 245 HIS 0.012 0.001 HIS C 931 Details of bonding type rmsd covalent geometry : bond 0.00609 (28276) covalent geometry : angle 0.74993 (38264) SS BOND : bond 0.00416 ( 8) SS BOND : angle 3.59717 ( 16) hydrogen bonds : bond 0.04653 ( 729) hydrogen bonds : angle 5.80679 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 223 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 27 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.7301 (mtp-110) REVERT: Q 52 ARG cc_start: 0.6156 (tpm170) cc_final: 0.5583 (tpm170) REVERT: Q 61 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6090 (pm20) REVERT: Q 74 PHE cc_start: 0.8292 (m-80) cc_final: 0.7630 (m-10) REVERT: R 53 MET cc_start: 0.2554 (pmm) cc_final: 0.2196 (pmm) REVERT: A 244 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8513 (pp) REVERT: A 271 LYS cc_start: 0.7937 (pttt) cc_final: 0.7330 (mtmt) REVERT: A 539 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6575 (pt) REVERT: A 544 LYS cc_start: 0.7451 (tppt) cc_final: 0.7057 (pttm) REVERT: A 608 MET cc_start: 0.8318 (mmm) cc_final: 0.8013 (mtm) REVERT: A 615 LYS cc_start: 0.7359 (tptt) cc_final: 0.7132 (mmmt) REVERT: A 991 ILE cc_start: 0.6245 (OUTLIER) cc_final: 0.5657 (mt) REVERT: B 277 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9051 (pp) REVERT: B 403 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7446 (mm-30) REVERT: B 418 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8706 (mp) REVERT: B 452 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5486 (mm) REVERT: B 607 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8008 (m110) REVERT: B 609 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7086 (mt0) REVERT: B 756 THR cc_start: 0.5904 (OUTLIER) cc_final: 0.5692 (m) REVERT: C 244 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8480 (pp) REVERT: C 290 LYS cc_start: 0.7075 (mmtt) cc_final: 0.6625 (mttt) REVERT: C 379 ASP cc_start: 0.8389 (t0) cc_final: 0.8023 (t70) REVERT: C 515 TYR cc_start: 0.3311 (OUTLIER) cc_final: 0.2428 (t80) REVERT: C 718 GLU cc_start: 0.6452 (tm-30) cc_final: 0.6186 (tm-30) REVERT: C 740 LEU cc_start: 0.5459 (pt) cc_final: 0.5111 (pt) REVERT: C 768 SER cc_start: 0.6116 (p) cc_final: 0.5873 (p) REVERT: C 832 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6811 (pp) REVERT: C 932 MET cc_start: 0.3959 (tpt) cc_final: 0.3250 (tpt) REVERT: D 373 GLU cc_start: 0.7767 (tp30) cc_final: 0.7543 (tp30) REVERT: D 452 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5538 (mm) REVERT: D 526 ILE cc_start: 0.7663 (mt) cc_final: 0.7285 (mm) REVERT: D 541 ILE cc_start: 0.8501 (mm) cc_final: 0.8289 (mm) REVERT: D 593 ARG cc_start: 0.7118 (tpp-160) cc_final: 0.6855 (tpp-160) REVERT: D 727 LEU cc_start: -0.1641 (OUTLIER) cc_final: -0.2574 (tt) REVERT: D 797 LEU cc_start: -0.2346 (OUTLIER) cc_final: -0.2580 (tt) outliers start: 152 outliers final: 92 residues processed: 346 average time/residue: 0.1635 time to fit residues: 93.7149 Evaluate side-chains 317 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 209 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 72 PHE Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 933 PHE Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 TRP Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 672 LYS Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain C residue 598 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 410 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 441 ASN Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 79 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 319 optimal weight: 0.4980 chunk 116 optimal weight: 0.2980 chunk 280 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 216 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 HIS C 441 ASN C 609 GLN ** C 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.190610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133141 restraints weight = 40431.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131898 restraints weight = 35356.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.132676 restraints weight = 22827.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131337 restraints weight = 17586.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131971 restraints weight = 18903.379| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28284 Z= 0.122 Angle : 0.649 11.685 38280 Z= 0.329 Chirality : 0.045 0.265 4428 Planarity : 0.004 0.070 4848 Dihedral : 8.492 163.833 3804 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.96 % Favored : 91.58 % Rotamer: Outliers : 3.83 % Allowed : 17.59 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.14), residues: 3480 helix: -0.20 (0.17), residues: 918 sheet: -1.68 (0.21), residues: 589 loop : -2.12 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 706 TYR 0.019 0.001 TYR A 515 PHE 0.024 0.001 PHE C 439 TRP 0.015 0.001 TRP A 857 HIS 0.010 0.001 HIS C 931 Details of bonding type rmsd covalent geometry : bond 0.00268 (28276) covalent geometry : angle 0.64709 (38264) SS BOND : bond 0.00469 ( 8) SS BOND : angle 2.64321 ( 16) hydrogen bonds : bond 0.03461 ( 729) hydrogen bonds : angle 5.42113 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 227 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 52 ARG cc_start: 0.6299 (tpm170) cc_final: 0.5427 (tpt170) REVERT: Q 74 PHE cc_start: 0.8139 (m-80) cc_final: 0.7685 (m-10) REVERT: A 271 LYS cc_start: 0.7905 (pttt) cc_final: 0.7332 (mtmt) REVERT: A 544 LYS cc_start: 0.7045 (tppt) cc_final: 0.6804 (pttm) REVERT: A 608 MET cc_start: 0.8200 (mmm) cc_final: 0.7945 (mtm) REVERT: A 745 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7569 (pt) REVERT: A 897 ASN cc_start: 0.3521 (OUTLIER) cc_final: 0.3022 (t0) REVERT: A 991 ILE cc_start: 0.6023 (OUTLIER) cc_final: 0.5446 (mt) REVERT: B 418 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8797 (mp) REVERT: B 607 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7844 (m110) REVERT: B 609 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7227 (mt0) REVERT: B 756 THR cc_start: 0.5796 (OUTLIER) cc_final: 0.5575 (m) REVERT: B 972 MET cc_start: 0.5052 (tpp) cc_final: 0.4816 (tpt) REVERT: C 244 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8367 (pp) REVERT: C 290 LYS cc_start: 0.7059 (mmtt) cc_final: 0.6680 (mttt) REVERT: C 379 ASP cc_start: 0.8309 (t0) cc_final: 0.8000 (t70) REVERT: C 515 TYR cc_start: 0.3114 (OUTLIER) cc_final: 0.2787 (t80) REVERT: C 718 GLU cc_start: 0.6517 (tm-30) cc_final: 0.6203 (tm-30) REVERT: C 740 LEU cc_start: 0.5623 (pt) cc_final: 0.5230 (pt) REVERT: C 768 SER cc_start: 0.6098 (p) cc_final: 0.5816 (p) REVERT: C 932 MET cc_start: 0.4279 (tpt) cc_final: 0.3641 (tpt) REVERT: C 972 MET cc_start: 0.2185 (mpp) cc_final: 0.1562 (ptp) REVERT: D 452 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5364 (mm) REVERT: D 541 ILE cc_start: 0.8449 (mm) cc_final: 0.8236 (mm) REVERT: D 544 LYS cc_start: 0.7253 (ttpt) cc_final: 0.6969 (ttpt) REVERT: D 745 ILE cc_start: 0.5389 (OUTLIER) cc_final: 0.5033 (tt) REVERT: D 797 LEU cc_start: -0.2550 (OUTLIER) cc_final: -0.2778 (tt) outliers start: 121 outliers final: 77 residues processed: 331 average time/residue: 0.1622 time to fit residues: 88.4129 Evaluate side-chains 303 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 214 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 72 PHE Chi-restraints excluded: chain R residue 51 SER Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 TRP Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 672 LYS Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain C residue 598 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 786 LEU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 100 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 88 optimal weight: 9.9990 chunk 307 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 15 optimal weight: 30.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 ASN A 441 ASN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 GLN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 ASN D 851 GLN D 951 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.186744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136591 restraints weight = 40419.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126426 restraints weight = 56716.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123685 restraints weight = 38932.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122882 restraints weight = 33001.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123516 restraints weight = 27840.304| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 28284 Z= 0.246 Angle : 0.735 12.439 38280 Z= 0.369 Chirality : 0.050 0.396 4428 Planarity : 0.004 0.061 4848 Dihedral : 8.762 163.848 3799 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.11 % Favored : 90.43 % Rotamer: Outliers : 4.72 % Allowed : 17.14 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.13), residues: 3480 helix: -0.53 (0.17), residues: 924 sheet: -1.76 (0.21), residues: 605 loop : -2.16 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 260 TYR 0.025 0.002 TYR A 515 PHE 0.027 0.002 PHE B 950 TRP 0.021 0.002 TRP C 245 HIS 0.008 0.001 HIS C 931 Details of bonding type rmsd covalent geometry : bond 0.00599 (28276) covalent geometry : angle 0.73396 (38264) SS BOND : bond 0.00357 ( 8) SS BOND : angle 2.39627 ( 16) hydrogen bonds : bond 0.04261 ( 729) hydrogen bonds : angle 5.57263 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 226 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 52 ARG cc_start: 0.6135 (tpm170) cc_final: 0.5618 (tpm170) REVERT: Q 61 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6192 (pm20) REVERT: Q 74 PHE cc_start: 0.8253 (m-80) cc_final: 0.7678 (m-10) REVERT: A 271 LYS cc_start: 0.8046 (pttt) cc_final: 0.7401 (mtmt) REVERT: A 539 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6632 (pt) REVERT: A 544 LYS cc_start: 0.7443 (tppt) cc_final: 0.7024 (pttm) REVERT: A 576 LYS cc_start: 0.5766 (mttm) cc_final: 0.5050 (mmtm) REVERT: A 608 MET cc_start: 0.8327 (mmm) cc_final: 0.8020 (mtm) REVERT: A 745 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7835 (pt) REVERT: A 752 LYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5934 (tptp) REVERT: A 897 ASN cc_start: 0.3241 (OUTLIER) cc_final: 0.2805 (t0) REVERT: A 991 ILE cc_start: 0.6177 (OUTLIER) cc_final: 0.5546 (mt) REVERT: B 414 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8859 (mt) REVERT: B 418 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8643 (mp) REVERT: B 452 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5469 (mm) REVERT: B 519 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: B 607 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8013 (m110) REVERT: B 609 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7208 (mt0) REVERT: B 718 GLU cc_start: 0.6327 (tm-30) cc_final: 0.5898 (tm-30) REVERT: B 756 THR cc_start: 0.5978 (OUTLIER) cc_final: 0.5752 (m) REVERT: B 815 CYS cc_start: 0.3094 (OUTLIER) cc_final: 0.2115 (t) REVERT: B 894 MET cc_start: 0.2906 (OUTLIER) cc_final: 0.2638 (tmm) REVERT: C 244 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8470 (pp) REVERT: C 290 LYS cc_start: 0.7158 (mmtt) cc_final: 0.6815 (mttt) REVERT: C 291 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6084 (tppp) REVERT: C 379 ASP cc_start: 0.8425 (t0) cc_final: 0.8197 (t70) REVERT: C 515 TYR cc_start: 0.3235 (OUTLIER) cc_final: 0.2438 (t80) REVERT: C 709 ARG cc_start: 0.5539 (OUTLIER) cc_final: 0.4368 (tpt-90) REVERT: C 740 LEU cc_start: 0.5733 (pt) cc_final: 0.5435 (pt) REVERT: C 932 MET cc_start: 0.3942 (tpt) cc_final: 0.3420 (tpt) REVERT: D 452 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5714 (mm) REVERT: D 544 LYS cc_start: 0.7600 (ttpt) cc_final: 0.7236 (ttpt) REVERT: D 727 LEU cc_start: -0.1657 (OUTLIER) cc_final: -0.2633 (tt) REVERT: D 745 ILE cc_start: 0.5841 (OUTLIER) cc_final: 0.5352 (tt) REVERT: D 797 LEU cc_start: -0.2467 (OUTLIER) cc_final: -0.2726 (tt) outliers start: 149 outliers final: 97 residues processed: 350 average time/residue: 0.1631 time to fit residues: 93.8741 Evaluate side-chains 328 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 208 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 72 PHE Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 TRP Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 672 LYS Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 894 MET Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 598 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 786 LEU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 410 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 236 optimal weight: 8.9990 chunk 138 optimal weight: 0.7980 chunk 173 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 ASN A 441 ASN A 473 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN C 741 GLN ** C 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.189724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.143721 restraints weight = 41239.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130564 restraints weight = 57470.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.128842 restraints weight = 40811.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127352 restraints weight = 35335.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128021 restraints weight = 31094.927| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28284 Z= 0.145 Angle : 0.666 11.225 38280 Z= 0.334 Chirality : 0.046 0.298 4428 Planarity : 0.004 0.060 4848 Dihedral : 8.544 163.699 3799 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.48 % Favored : 91.09 % Rotamer: Outliers : 4.28 % Allowed : 17.97 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.14), residues: 3480 helix: -0.26 (0.17), residues: 919 sheet: -1.68 (0.22), residues: 568 loop : -2.14 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 593 TYR 0.019 0.001 TYR A 515 PHE 0.024 0.002 PHE A 948 TRP 0.016 0.002 TRP C 245 HIS 0.007 0.001 HIS C 931 Details of bonding type rmsd covalent geometry : bond 0.00341 (28276) covalent geometry : angle 0.66453 (38264) SS BOND : bond 0.00297 ( 8) SS BOND : angle 2.32291 ( 16) hydrogen bonds : bond 0.03515 ( 729) hydrogen bonds : angle 5.33307 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 216 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: P 21 LEU cc_start: 0.3348 (OUTLIER) cc_final: 0.3017 (pp) REVERT: Q 52 ARG cc_start: 0.6125 (tpm170) cc_final: 0.5500 (tpt170) REVERT: Q 61 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6374 (pm20) REVERT: Q 74 PHE cc_start: 0.8138 (m-80) cc_final: 0.7583 (m-10) REVERT: R 53 MET cc_start: 0.2935 (pmm) cc_final: 0.2708 (pmm) REVERT: A 271 LYS cc_start: 0.8016 (pttt) cc_final: 0.7414 (mtmt) REVERT: A 544 LYS cc_start: 0.7246 (tppt) cc_final: 0.6866 (pttm) REVERT: A 608 MET cc_start: 0.8245 (mmm) cc_final: 0.7967 (mtm) REVERT: A 615 LYS cc_start: 0.7467 (mmmt) cc_final: 0.7244 (mmmt) REVERT: A 745 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7753 (pt) REVERT: A 752 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5882 (tptp) REVERT: A 991 ILE cc_start: 0.6095 (OUTLIER) cc_final: 0.5400 (mt) REVERT: B 519 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: B 607 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7978 (m110) REVERT: B 718 GLU cc_start: 0.6307 (tm-30) cc_final: 0.5901 (tm-30) REVERT: B 756 THR cc_start: 0.5920 (OUTLIER) cc_final: 0.5678 (m) REVERT: B 815 CYS cc_start: 0.3072 (OUTLIER) cc_final: 0.2101 (t) REVERT: B 894 MET cc_start: 0.2881 (OUTLIER) cc_final: 0.2588 (tmm) REVERT: B 950 PHE cc_start: 0.5357 (t80) cc_final: 0.4668 (t80) REVERT: B 972 MET cc_start: 0.4962 (tpp) cc_final: 0.4707 (tpt) REVERT: C 244 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8410 (pp) REVERT: C 290 LYS cc_start: 0.7112 (mmtt) cc_final: 0.6588 (mmtt) REVERT: C 379 ASP cc_start: 0.8338 (t0) cc_final: 0.8031 (t70) REVERT: C 394 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7372 (mpt-90) REVERT: C 515 TYR cc_start: 0.3051 (OUTLIER) cc_final: 0.2684 (t80) REVERT: C 740 LEU cc_start: 0.5586 (pt) cc_final: 0.5322 (pt) REVERT: C 741 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6651 (pm20) REVERT: C 932 MET cc_start: 0.3969 (tpt) cc_final: 0.3294 (tpt) REVERT: D 324 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8729 (t) REVERT: D 452 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5550 (mm) REVERT: D 544 LYS cc_start: 0.7533 (ttpt) cc_final: 0.7167 (ttpt) REVERT: D 727 LEU cc_start: -0.1670 (OUTLIER) cc_final: -0.2660 (tt) REVERT: D 745 ILE cc_start: 0.5715 (OUTLIER) cc_final: 0.5247 (tt) outliers start: 135 outliers final: 92 residues processed: 327 average time/residue: 0.1684 time to fit residues: 89.7350 Evaluate side-chains 311 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 201 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 72 PHE Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 TRP Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 672 LYS Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 894 MET Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 598 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 741 GLN Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 786 LEU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 410 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 163 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 304 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 0.0470 chunk 143 optimal weight: 0.4980 chunk 71 optimal weight: 0.0970 chunk 144 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN ** C 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 HIS ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 ASN ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.191663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145713 restraints weight = 40924.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.132953 restraints weight = 55398.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.130070 restraints weight = 38165.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.129757 restraints weight = 33435.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129743 restraints weight = 29989.626| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28284 Z= 0.110 Angle : 0.639 13.073 38280 Z= 0.319 Chirality : 0.045 0.282 4428 Planarity : 0.004 0.055 4848 Dihedral : 8.220 164.437 3799 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.10 % Favored : 91.47 % Rotamer: Outliers : 3.77 % Allowed : 18.73 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.14), residues: 3480 helix: -0.01 (0.17), residues: 931 sheet: -1.74 (0.21), residues: 601 loop : -2.08 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 593 TYR 0.014 0.001 TYR A 515 PHE 0.024 0.001 PHE A 948 TRP 0.014 0.001 TRP A 857 HIS 0.007 0.001 HIS C 931 Details of bonding type rmsd covalent geometry : bond 0.00243 (28276) covalent geometry : angle 0.63830 (38264) SS BOND : bond 0.00220 ( 8) SS BOND : angle 1.92323 ( 16) hydrogen bonds : bond 0.03095 ( 729) hydrogen bonds : angle 5.12814 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 228 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 21 LEU cc_start: 0.3297 (OUTLIER) cc_final: 0.2986 (pp) REVERT: Q 52 ARG cc_start: 0.5983 (tpm170) cc_final: 0.5375 (tpt170) REVERT: Q 61 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6409 (pm20) REVERT: Q 74 PHE cc_start: 0.8157 (m-80) cc_final: 0.7655 (m-10) REVERT: R 53 MET cc_start: 0.3074 (pmm) cc_final: 0.2771 (pmm) REVERT: A 271 LYS cc_start: 0.7911 (pttt) cc_final: 0.7283 (mtmt) REVERT: A 362 SER cc_start: 0.8569 (t) cc_final: 0.8093 (p) REVERT: A 452 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.6077 (mm) REVERT: A 544 LYS cc_start: 0.7215 (tppt) cc_final: 0.6833 (pttm) REVERT: A 608 MET cc_start: 0.8268 (mmm) cc_final: 0.7949 (mtm) REVERT: A 745 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7811 (pt) REVERT: A 752 LYS cc_start: 0.6173 (OUTLIER) cc_final: 0.5861 (tptp) REVERT: A 991 ILE cc_start: 0.6094 (OUTLIER) cc_final: 0.5448 (mt) REVERT: B 503 LYS cc_start: 0.5915 (OUTLIER) cc_final: 0.5388 (ptpp) REVERT: B 506 ILE cc_start: 0.5711 (OUTLIER) cc_final: 0.5080 (mp) REVERT: B 607 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7939 (m110) REVERT: B 756 THR cc_start: 0.5915 (OUTLIER) cc_final: 0.5664 (m) REVERT: B 815 CYS cc_start: 0.3187 (OUTLIER) cc_final: 0.2240 (t) REVERT: B 894 MET cc_start: 0.2808 (OUTLIER) cc_final: 0.2533 (tmm) REVERT: C 244 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8408 (pp) REVERT: C 290 LYS cc_start: 0.7037 (mmtt) cc_final: 0.6372 (mttt) REVERT: C 291 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6002 (tppp) REVERT: C 379 ASP cc_start: 0.8351 (t0) cc_final: 0.8067 (t70) REVERT: C 452 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5792 (mm) REVERT: D 324 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8640 (t) REVERT: D 452 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.5363 (mm) REVERT: D 544 LYS cc_start: 0.7393 (ttpt) cc_final: 0.7021 (ttpt) REVERT: D 549 MET cc_start: 0.7467 (tpp) cc_final: 0.7225 (tpp) REVERT: D 745 ILE cc_start: 0.5333 (OUTLIER) cc_final: 0.4979 (tt) outliers start: 119 outliers final: 81 residues processed: 328 average time/residue: 0.1617 time to fit residues: 86.7473 Evaluate side-chains 304 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 205 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 TRP Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 672 LYS Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 894 MET Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 441 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain C residue 598 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 786 LEU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 410 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 441 ASN Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 326 optimal weight: 20.0000 chunk 273 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.0270 chunk 206 optimal weight: 1.9990 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 441 ASN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.189335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139743 restraints weight = 40372.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133564 restraints weight = 49347.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128000 restraints weight = 33987.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127350 restraints weight = 34468.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127942 restraints weight = 29014.650| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28284 Z= 0.160 Angle : 0.668 10.827 38280 Z= 0.333 Chirality : 0.047 0.324 4428 Planarity : 0.004 0.057 4848 Dihedral : 8.234 164.828 3795 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.30 % Favored : 91.26 % Rotamer: Outliers : 4.18 % Allowed : 18.63 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.14), residues: 3480 helix: -0.05 (0.17), residues: 926 sheet: -1.65 (0.21), residues: 582 loop : -2.09 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 907 TYR 0.027 0.002 TYR C 589 PHE 0.038 0.002 PHE C 948 TRP 0.016 0.001 TRP C 245 HIS 0.005 0.001 HIS C 931 Details of bonding type rmsd covalent geometry : bond 0.00381 (28276) covalent geometry : angle 0.66614 (38264) SS BOND : bond 0.00390 ( 8) SS BOND : angle 2.23431 ( 16) hydrogen bonds : bond 0.03416 ( 729) hydrogen bonds : angle 5.16820 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 211 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 21 LEU cc_start: 0.3297 (OUTLIER) cc_final: 0.2967 (pp) REVERT: Q 52 ARG cc_start: 0.6049 (tpm170) cc_final: 0.5573 (tpm170) REVERT: Q 61 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6273 (pm20) REVERT: Q 74 PHE cc_start: 0.8197 (m-80) cc_final: 0.7735 (m-10) REVERT: R 53 MET cc_start: 0.3117 (pmm) cc_final: 0.2845 (pmm) REVERT: A 271 LYS cc_start: 0.7951 (pttt) cc_final: 0.7346 (mtmt) REVERT: A 362 SER cc_start: 0.8553 (t) cc_final: 0.8089 (p) REVERT: A 452 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6048 (mm) REVERT: A 539 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6636 (pt) REVERT: A 544 LYS cc_start: 0.7288 (tppt) cc_final: 0.6988 (pttm) REVERT: A 608 MET cc_start: 0.8294 (mmm) cc_final: 0.8001 (mtm) REVERT: A 615 LYS cc_start: 0.7404 (mmmt) cc_final: 0.7089 (mmmt) REVERT: A 745 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7809 (pt) REVERT: A 991 ILE cc_start: 0.5945 (OUTLIER) cc_final: 0.5286 (mt) REVERT: B 519 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: B 607 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8021 (m110) REVERT: B 756 THR cc_start: 0.5905 (OUTLIER) cc_final: 0.5635 (m) REVERT: B 815 CYS cc_start: 0.3023 (OUTLIER) cc_final: 0.2167 (t) REVERT: B 894 MET cc_start: 0.2788 (OUTLIER) cc_final: 0.2550 (tmm) REVERT: C 244 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8432 (pp) REVERT: C 290 LYS cc_start: 0.7134 (mmtt) cc_final: 0.6454 (mttt) REVERT: C 291 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6041 (tppp) REVERT: C 379 ASP cc_start: 0.8353 (t0) cc_final: 0.8051 (t70) REVERT: C 394 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7209 (mpt-90) REVERT: C 452 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5846 (mm) REVERT: C 709 ARG cc_start: 0.5315 (OUTLIER) cc_final: 0.4327 (tpt-90) REVERT: C 932 MET cc_start: 0.4522 (tpt) cc_final: 0.3853 (tpt) REVERT: D 324 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8756 (t) REVERT: D 452 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5545 (mm) REVERT: D 568 LYS cc_start: 0.3160 (OUTLIER) cc_final: 0.0996 (pptt) REVERT: D 745 ILE cc_start: 0.5441 (OUTLIER) cc_final: 0.5074 (tt) REVERT: D 750 ASN cc_start: 0.6046 (OUTLIER) cc_final: 0.5790 (m110) outliers start: 132 outliers final: 92 residues processed: 324 average time/residue: 0.1669 time to fit residues: 88.6592 Evaluate side-chains 318 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 205 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 81 CYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 TRP Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 672 LYS Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 894 MET Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain C residue 598 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 786 LEU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 410 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 568 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 750 ASN Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 149 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 291 optimal weight: 0.3980 chunk 90 optimal weight: 50.0000 chunk 273 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN B 648 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN ** C 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.189598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.142687 restraints weight = 40988.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.129901 restraints weight = 58072.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.127288 restraints weight = 46076.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126736 restraints weight = 39206.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127284 restraints weight = 31424.940| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28284 Z= 0.166 Angle : 0.686 13.430 38280 Z= 0.341 Chirality : 0.047 0.315 4428 Planarity : 0.004 0.053 4848 Dihedral : 8.271 164.486 3794 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.51 % Favored : 91.03 % Rotamer: Outliers : 4.02 % Allowed : 18.85 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.14), residues: 3480 helix: -0.12 (0.17), residues: 925 sheet: -1.65 (0.21), residues: 581 loop : -2.11 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 706 TYR 0.027 0.002 TYR C 589 PHE 0.036 0.002 PHE B 950 TRP 0.016 0.001 TRP C 245 HIS 0.006 0.001 HIS C 931 Details of bonding type rmsd covalent geometry : bond 0.00396 (28276) covalent geometry : angle 0.68039 (38264) SS BOND : bond 0.00777 ( 8) SS BOND : angle 4.23009 ( 16) hydrogen bonds : bond 0.03510 ( 729) hydrogen bonds : angle 5.19531 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 211 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 21 LEU cc_start: 0.3383 (OUTLIER) cc_final: 0.3080 (pp) REVERT: Q 52 ARG cc_start: 0.6027 (tpm170) cc_final: 0.5524 (tpm170) REVERT: Q 61 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6158 (pm20) REVERT: Q 74 PHE cc_start: 0.8202 (m-80) cc_final: 0.7747 (m-10) REVERT: R 53 MET cc_start: 0.3111 (pmm) cc_final: 0.2835 (pmm) REVERT: A 271 LYS cc_start: 0.8005 (pttt) cc_final: 0.7394 (mtmt) REVERT: A 362 SER cc_start: 0.8656 (t) cc_final: 0.8168 (p) REVERT: A 452 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6084 (mm) REVERT: A 539 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6628 (pt) REVERT: A 544 LYS cc_start: 0.7403 (tppt) cc_final: 0.7103 (pttm) REVERT: A 608 MET cc_start: 0.8269 (mmm) cc_final: 0.7985 (mtm) REVERT: A 745 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7823 (pt) REVERT: A 991 ILE cc_start: 0.5985 (OUTLIER) cc_final: 0.5335 (mt) REVERT: B 519 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: B 607 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.8046 (m110) REVERT: B 718 GLU cc_start: 0.6308 (tm-30) cc_final: 0.5923 (tm-30) REVERT: B 756 THR cc_start: 0.5961 (OUTLIER) cc_final: 0.5674 (m) REVERT: B 815 CYS cc_start: 0.3128 (OUTLIER) cc_final: 0.2243 (t) REVERT: B 894 MET cc_start: 0.2786 (OUTLIER) cc_final: 0.2555 (tmm) REVERT: C 244 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8430 (pp) REVERT: C 290 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6431 (mttt) REVERT: C 291 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6040 (tppp) REVERT: C 379 ASP cc_start: 0.8369 (t0) cc_final: 0.8057 (t70) REVERT: C 394 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7371 (mpt-90) REVERT: C 452 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5844 (mm) REVERT: C 709 ARG cc_start: 0.5353 (OUTLIER) cc_final: 0.4326 (tpt-90) REVERT: C 932 MET cc_start: 0.4613 (tpt) cc_final: 0.4041 (tpt) REVERT: D 324 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8916 (t) REVERT: D 452 LEU cc_start: 0.5873 (OUTLIER) cc_final: 0.5593 (mm) REVERT: D 745 ILE cc_start: 0.5516 (OUTLIER) cc_final: 0.5128 (tt) outliers start: 127 outliers final: 97 residues processed: 319 average time/residue: 0.1634 time to fit residues: 85.9348 Evaluate side-chains 323 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 207 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 81 CYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 TRP Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 672 LYS Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 894 MET Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 598 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 709 ARG Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 786 LEU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 410 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 217 optimal weight: 0.0970 chunk 210 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 292 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 GLN A 441 ASN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN ** C 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.190371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142731 restraints weight = 40943.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.130758 restraints weight = 51476.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128589 restraints weight = 42387.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128239 restraints weight = 34607.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128478 restraints weight = 30709.653| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28284 Z= 0.137 Angle : 0.666 13.475 38280 Z= 0.331 Chirality : 0.046 0.327 4428 Planarity : 0.004 0.055 4848 Dihedral : 8.176 164.605 3794 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.13 % Favored : 91.41 % Rotamer: Outliers : 3.87 % Allowed : 19.17 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.14), residues: 3480 helix: -0.01 (0.17), residues: 923 sheet: -1.64 (0.21), residues: 581 loop : -2.09 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 706 TYR 0.025 0.001 TYR C 589 PHE 0.037 0.002 PHE B 950 TRP 0.015 0.001 TRP C 245 HIS 0.006 0.001 HIS C 931 Details of bonding type rmsd covalent geometry : bond 0.00321 (28276) covalent geometry : angle 0.66325 (38264) SS BOND : bond 0.00530 ( 8) SS BOND : angle 2.98272 ( 16) hydrogen bonds : bond 0.03292 ( 729) hydrogen bonds : angle 5.13030 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 209 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 21 LEU cc_start: 0.3442 (OUTLIER) cc_final: 0.3156 (pp) REVERT: Q 52 ARG cc_start: 0.5988 (tpm170) cc_final: 0.5496 (tpm170) REVERT: Q 61 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6336 (pm20) REVERT: Q 74 PHE cc_start: 0.8228 (m-80) cc_final: 0.7793 (m-10) REVERT: R 53 MET cc_start: 0.3021 (pmm) cc_final: 0.2772 (pmm) REVERT: A 271 LYS cc_start: 0.7975 (pttt) cc_final: 0.7362 (mtmt) REVERT: A 362 SER cc_start: 0.8646 (t) cc_final: 0.8147 (p) REVERT: A 452 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.6066 (mm) REVERT: A 544 LYS cc_start: 0.7371 (tppt) cc_final: 0.7103 (pttm) REVERT: A 608 MET cc_start: 0.8245 (mmm) cc_final: 0.7985 (mtm) REVERT: A 706 ARG cc_start: 0.7211 (mpt180) cc_final: 0.6936 (mpt-90) REVERT: A 745 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7859 (pt) REVERT: A 991 ILE cc_start: 0.5944 (OUTLIER) cc_final: 0.5297 (mt) REVERT: B 506 ILE cc_start: 0.5791 (OUTLIER) cc_final: 0.5176 (mp) REVERT: B 519 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: B 607 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8027 (m110) REVERT: B 718 GLU cc_start: 0.6314 (tm-30) cc_final: 0.5932 (tm-30) REVERT: B 756 THR cc_start: 0.5887 (OUTLIER) cc_final: 0.5619 (m) REVERT: B 815 CYS cc_start: 0.3158 (OUTLIER) cc_final: 0.2229 (t) REVERT: B 894 MET cc_start: 0.2729 (OUTLIER) cc_final: 0.2492 (tmm) REVERT: C 244 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8463 (pp) REVERT: C 290 LYS cc_start: 0.7138 (mmtt) cc_final: 0.6458 (mttt) REVERT: C 291 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6014 (tppp) REVERT: C 379 ASP cc_start: 0.8367 (t0) cc_final: 0.8052 (t70) REVERT: C 394 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7378 (mpt-90) REVERT: C 452 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5820 (mm) REVERT: C 932 MET cc_start: 0.4696 (tpt) cc_final: 0.4154 (tpt) REVERT: D 324 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8755 (t) REVERT: D 452 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5544 (mm) REVERT: D 549 MET cc_start: 0.7545 (tpp) cc_final: 0.7292 (tpp) REVERT: D 745 ILE cc_start: 0.5347 (OUTLIER) cc_final: 0.5004 (tt) outliers start: 122 outliers final: 98 residues processed: 314 average time/residue: 0.1605 time to fit residues: 83.0947 Evaluate side-chains 321 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 205 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 81 CYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 TRP Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 672 LYS Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 894 MET Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 598 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 786 LEU Chi-restraints excluded: chain C residue 880 ILE Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 410 CYS Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 942 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 250 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 159 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 318 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 204 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 ASN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN ** C 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 614 GLN D 702 ASN ** D 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.189073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125939 restraints weight = 40225.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125899 restraints weight = 23171.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124799 restraints weight = 16902.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.125264 restraints weight = 17757.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125594 restraints weight = 15679.024| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28284 Z= 0.167 Angle : 0.677 13.241 38280 Z= 0.337 Chirality : 0.047 0.322 4428 Planarity : 0.004 0.051 4848 Dihedral : 8.227 164.717 3794 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.56 % Favored : 90.98 % Rotamer: Outliers : 3.99 % Allowed : 18.98 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.14), residues: 3480 helix: -0.06 (0.17), residues: 918 sheet: -1.65 (0.21), residues: 585 loop : -2.11 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 706 TYR 0.026 0.002 TYR C 589 PHE 0.037 0.002 PHE B 950 TRP 0.017 0.002 TRP C 245 HIS 0.006 0.001 HIS C 931 Details of bonding type rmsd covalent geometry : bond 0.00400 (28276) covalent geometry : angle 0.67497 (38264) SS BOND : bond 0.00314 ( 8) SS BOND : angle 2.88379 ( 16) hydrogen bonds : bond 0.03487 ( 729) hydrogen bonds : angle 5.16650 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4801.72 seconds wall clock time: 83 minutes 52.91 seconds (5032.91 seconds total)