Starting phenix.real_space_refine on Sun Feb 8 03:38:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cru_45883/02_2026/9cru_45883.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cru_45883/02_2026/9cru_45883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cru_45883/02_2026/9cru_45883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cru_45883/02_2026/9cru_45883.map" model { file = "/net/cci-nas-00/data/ceres_data/9cru_45883/02_2026/9cru_45883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cru_45883/02_2026/9cru_45883.cif" } resolution = 3.89 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2017 atoms to isotropic. 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 31 5.49 5 S 158 5.16 5 C 23379 2.51 5 N 6494 2.21 5 O 7313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37375 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3928 Classifications: {'peptide': 505} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 484} Chain breaks: 2 Chain: "B" Number of atoms: 5688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5688 Classifications: {'peptide': 728} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 698} Chain breaks: 2 Chain: "C" Number of atoms: 5785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5785 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 711} Chain: "D" Number of atoms: 5785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5785 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 711} Chain: "E" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4089 Classifications: {'peptide': 527} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 506} Chain: "F" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3867 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 475} Chain breaks: 2 Chain: "G" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2306 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "H" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2306 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "J" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "K" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1805 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 1, 'TRANS': 222} Chain: "L" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1015 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'TRANS': 128} Chain breaks: 1 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.54, per 1000 atoms: 0.23 Number of scatterers: 37375 At special positions: 0 Unit cell: (153.44, 193.992, 234.544, 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 158 16.00 P 31 15.00 O 7313 8.00 N 6494 7.00 C 23379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8868 Finding SS restraints... Secondary structure from input PDB file: 227 helices and 23 sheets defined 59.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.875A pdb=" N GLY A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 312 Processing helix chain 'A' and resid 317 through 326 removed outlier: 4.391A pdb=" N ILE A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 367 through 380 removed outlier: 3.697A pdb=" N ASP A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 4.098A pdb=" N LEU A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 400 " --> pdb=" O LYS A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 400' Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.653A pdb=" N LEU A 404 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 405 " --> pdb=" O SER A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 446 through 454 Processing helix chain 'A' and resid 460 through 478 removed outlier: 3.711A pdb=" N GLY A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 509 removed outlier: 3.747A pdb=" N PHE A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.903A pdb=" N LEU A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 removed outlier: 3.776A pdb=" N SER A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 removed outlier: 4.407A pdb=" N LEU A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 595 removed outlier: 3.782A pdb=" N LEU A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 614 removed outlier: 4.293A pdb=" N ALA A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 631 removed outlier: 3.906A pdb=" N LEU A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 651 removed outlier: 3.795A pdb=" N LEU A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 677 Processing helix chain 'A' and resid 678 through 682 removed outlier: 3.524A pdb=" N PHE A 682 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 705 removed outlier: 4.098A pdb=" N LEU A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 723 Processing helix chain 'A' and resid 729 through 743 removed outlier: 3.621A pdb=" N THR A 733 " --> pdb=" O GLY A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 758 removed outlier: 3.684A pdb=" N GLU A 749 " --> pdb=" O ASP A 745 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 43 removed outlier: 3.601A pdb=" N ALA B 40 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 103 through 109 Processing helix chain 'B' and resid 135 through 148 removed outlier: 4.041A pdb=" N LEU B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.611A pdb=" N ASP B 238 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 262 through 268 removed outlier: 3.521A pdb=" N ILE B 266 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.908A pdb=" N ILE B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 326 removed outlier: 3.782A pdb=" N GLU B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.595A pdb=" N ALA B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 4.281A pdb=" N SER B 353 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B 354 " --> pdb=" O LEU B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 354' Processing helix chain 'B' and resid 367 through 380 removed outlier: 3.756A pdb=" N ASP B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.576A pdb=" N LEU B 399 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 446 through 454 removed outlier: 3.672A pdb=" N LEU B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 478 Processing helix chain 'B' and resid 490 through 495 removed outlier: 3.837A pdb=" N ALA B 493 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 506 removed outlier: 3.582A pdb=" N PHE B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 3.768A pdb=" N LEU B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 551 removed outlier: 4.043A pdb=" N ASN B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 580 removed outlier: 3.908A pdb=" N LEU B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 580 " --> pdb=" O GLU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 614 removed outlier: 3.920A pdb=" N ALA B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR B 614 " --> pdb=" O PHE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 651 Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.648A pdb=" N PHE B 682 " --> pdb=" O LEU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 705 Processing helix chain 'B' and resid 708 through 723 removed outlier: 3.707A pdb=" N VAL B 713 " --> pdb=" O ASP B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 743 removed outlier: 3.684A pdb=" N HIS B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 758 removed outlier: 4.338A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 43 Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 103 through 109 removed outlier: 3.705A pdb=" N TYR C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.655A pdb=" N ALA C 129 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 Processing helix chain 'C' and resid 235 through 239 removed outlier: 3.593A pdb=" N LEU C 239 " --> pdb=" O PHE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 255 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 262 through 269 Processing helix chain 'C' and resid 286 through 297 Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.955A pdb=" N LEU C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 337 Processing helix chain 'C' and resid 350 through 354 removed outlier: 4.112A pdb=" N SER C 353 " --> pdb=" O GLU C 350 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 354 " --> pdb=" O LEU C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 354' Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.593A pdb=" N ASP C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 4.184A pdb=" N ARG C 406 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 433 through 438 removed outlier: 3.500A pdb=" N GLU C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 433 through 438' Processing helix chain 'C' and resid 446 through 454 Processing helix chain 'C' and resid 458 through 476 removed outlier: 3.786A pdb=" N ILE C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLY C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 498 through 506 Processing helix chain 'C' and resid 514 through 523 removed outlier: 4.200A pdb=" N GLU C 518 " --> pdb=" O GLY C 514 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP C 519 " --> pdb=" O ILE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 552 removed outlier: 4.509A pdb=" N ASN C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 537 " --> pdb=" O GLU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 582 removed outlier: 3.995A pdb=" N LEU C 573 " --> pdb=" O GLY C 569 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY C 582 " --> pdb=" O ALA C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 595 removed outlier: 3.803A pdb=" N SER C 595 " --> pdb=" O ASN C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 612 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 625 through 630 Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.631A pdb=" N LEU C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 677 Processing helix chain 'C' and resid 694 through 705 removed outlier: 3.565A pdb=" N ASN C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 722 removed outlier: 3.797A pdb=" N ARG C 721 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 722 " --> pdb=" O GLU C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 741 Processing helix chain 'C' and resid 746 through 758 removed outlier: 4.231A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 43 removed outlier: 3.639A pdb=" N ALA D 40 " --> pdb=" O ASN D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.647A pdb=" N ALA D 129 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 147 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 246 through 255 Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.895A pdb=" N ILE D 260 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 256 through 261' Processing helix chain 'D' and resid 262 through 270 removed outlier: 3.594A pdb=" N ILE D 266 " --> pdb=" O PRO D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 297 Processing helix chain 'D' and resid 318 through 324 Processing helix chain 'D' and resid 327 through 338 removed outlier: 3.770A pdb=" N ALA D 336 " --> pdb=" O ALA D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.636A pdb=" N SER D 353 " --> pdb=" O GLU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 380 removed outlier: 4.068A pdb=" N ASN D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 433 through 438 Processing helix chain 'D' and resid 446 through 454 removed outlier: 3.722A pdb=" N LEU D 450 " --> pdb=" O ASN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 479 removed outlier: 4.304A pdb=" N GLY D 464 " --> pdb=" O ALA D 460 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR D 477 " --> pdb=" O ALA D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 493 Processing helix chain 'D' and resid 498 through 506 removed outlier: 3.732A pdb=" N PHE D 502 " --> pdb=" O THR D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 524 removed outlier: 3.777A pdb=" N LEU D 520 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 552 removed outlier: 4.494A pdb=" N ASN D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 580 removed outlier: 3.520A pdb=" N LYS D 580 " --> pdb=" O GLU D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 595 removed outlier: 3.897A pdb=" N LEU D 594 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 613 Processing helix chain 'D' and resid 625 through 630 Processing helix chain 'D' and resid 640 through 651 removed outlier: 3.594A pdb=" N LEU D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 677 removed outlier: 3.610A pdb=" N LEU D 673 " --> pdb=" O ALA D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.842A pdb=" N PHE D 682 " --> pdb=" O LEU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 705 removed outlier: 4.019A pdb=" N LEU D 697 " --> pdb=" O ASN D 693 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 703 " --> pdb=" O ASN D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 722 Processing helix chain 'D' and resid 729 through 744 removed outlier: 4.185A pdb=" N HIS D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP D 743 " --> pdb=" O THR D 739 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU D 744 " --> pdb=" O ALA D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 758 removed outlier: 4.378A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 239 removed outlier: 3.788A pdb=" N LEU E 239 " --> pdb=" O PHE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 256 Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 262 through 270 removed outlier: 4.509A pdb=" N ILE E 266 " --> pdb=" O PRO E 262 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU E 267 " --> pdb=" O PRO E 263 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS E 268 " --> pdb=" O SER E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 298 removed outlier: 4.622A pdb=" N GLY E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N THR E 296 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 317 through 327 removed outlier: 3.699A pdb=" N ILE E 323 " --> pdb=" O SER E 319 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG E 324 " --> pdb=" O GLU E 320 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 326 " --> pdb=" O ASN E 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 338 Processing helix chain 'E' and resid 339 through 341 No H-bonds generated for 'chain 'E' and resid 339 through 341' Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.610A pdb=" N VAL E 354 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 381 removed outlier: 4.364A pdb=" N VAL E 372 " --> pdb=" O GLY E 368 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 400 removed outlier: 3.816A pdb=" N LEU E 399 " --> pdb=" O ARG E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 405 Processing helix chain 'E' and resid 420 through 438 removed outlier: 5.298A pdb=" N LYS E 434 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N MET E 435 " --> pdb=" O GLN E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 454 removed outlier: 3.710A pdb=" N LEU E 450 " --> pdb=" O ASN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 475 Processing helix chain 'E' and resid 488 through 494 removed outlier: 4.118A pdb=" N ALA E 493 " --> pdb=" O THR E 489 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS E 494 " --> pdb=" O LYS E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 509 Processing helix chain 'E' and resid 518 through 524 Processing helix chain 'E' and resid 532 through 552 removed outlier: 4.051A pdb=" N ASN E 536 " --> pdb=" O SER E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 582 removed outlier: 3.703A pdb=" N GLY E 582 " --> pdb=" O ALA E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 595 removed outlier: 3.568A pdb=" N LEU E 594 " --> pdb=" O SER E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 614 removed outlier: 3.522A pdb=" N TYR E 614 " --> pdb=" O PHE E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 631 Processing helix chain 'E' and resid 640 through 651 removed outlier: 3.780A pdb=" N LEU E 644 " --> pdb=" O SER E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 677 Processing helix chain 'E' and resid 678 through 682 removed outlier: 3.841A pdb=" N PHE E 682 " --> pdb=" O LEU E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 705 Processing helix chain 'E' and resid 708 through 723 removed outlier: 3.670A pdb=" N ILE E 716 " --> pdb=" O ARG E 712 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG E 721 " --> pdb=" O ASN E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 744 Processing helix chain 'E' and resid 746 through 758 removed outlier: 4.010A pdb=" N LEU E 750 " --> pdb=" O PRO E 746 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU E 752 " --> pdb=" O ASN E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 255 removed outlier: 3.741A pdb=" N PHE F 252 " --> pdb=" O PHE F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 261 Processing helix chain 'F' and resid 262 through 270 removed outlier: 3.833A pdb=" N ILE F 266 " --> pdb=" O PRO F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 298 removed outlier: 3.517A pdb=" N ILE F 290 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 312 Processing helix chain 'F' and resid 317 through 327 removed outlier: 4.155A pdb=" N PHE F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 337 Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.549A pdb=" N VAL F 354 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 380 removed outlier: 4.117A pdb=" N VAL F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP F 380 " --> pdb=" O LEU F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 400 removed outlier: 3.878A pdb=" N LEU F 399 " --> pdb=" O ARG F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 438 removed outlier: 4.952A pdb=" N LYS F 434 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N MET F 435 " --> pdb=" O GLN F 431 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 454 removed outlier: 3.570A pdb=" N LEU F 450 " --> pdb=" O ASN F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 478 Processing helix chain 'F' and resid 491 through 495 Processing helix chain 'F' and resid 498 through 506 removed outlier: 3.546A pdb=" N PHE F 502 " --> pdb=" O THR F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 523 removed outlier: 4.039A pdb=" N LEU F 520 " --> pdb=" O SER F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 552 removed outlier: 3.945A pdb=" N ASN F 536 " --> pdb=" O SER F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 582 removed outlier: 3.506A pdb=" N GLY F 582 " --> pdb=" O ALA F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 595 removed outlier: 3.587A pdb=" N SER F 595 " --> pdb=" O ASN F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 613 Processing helix chain 'F' and resid 625 through 631 removed outlier: 3.547A pdb=" N LEU F 629 " --> pdb=" O SER F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 652 removed outlier: 3.585A pdb=" N LEU F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS F 652 " --> pdb=" O LYS F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 676 Processing helix chain 'F' and resid 677 through 682 removed outlier: 4.020A pdb=" N SER F 680 " --> pdb=" O ASP F 677 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE F 682 " --> pdb=" O LEU F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 693 through 705 removed outlier: 3.616A pdb=" N LEU F 697 " --> pdb=" O ASN F 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 708 through 721 removed outlier: 4.016A pdb=" N ILE F 716 " --> pdb=" O ARG F 712 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG F 721 " --> pdb=" O ASN F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 744 removed outlier: 4.168A pdb=" N HIS F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 757 removed outlier: 4.221A pdb=" N LEU F 750 " --> pdb=" O PRO F 746 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLU F 752 " --> pdb=" O ASN F 748 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 15 Processing helix chain 'G' and resid 20 through 24 Processing helix chain 'G' and resid 29 through 50 Processing helix chain 'G' and resid 52 through 71 Processing helix chain 'G' and resid 72 through 90 Processing helix chain 'G' and resid 92 through 110 Processing helix chain 'G' and resid 112 through 130 Processing helix chain 'G' and resid 133 through 151 Processing helix chain 'G' and resid 153 through 171 Processing helix chain 'G' and resid 173 through 189 Processing helix chain 'G' and resid 194 through 212 removed outlier: 4.106A pdb=" N LEU G 203 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 229 Processing helix chain 'G' and resid 229 through 234 removed outlier: 3.550A pdb=" N ASP G 234 " --> pdb=" O PRO G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 251 Processing helix chain 'G' and resid 252 through 267 removed outlier: 3.514A pdb=" N PHE G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 291 Processing helix chain 'H' and resid 3 through 15 Processing helix chain 'H' and resid 19 through 25 removed outlier: 4.093A pdb=" N MET H 22 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 50 Processing helix chain 'H' and resid 52 through 71 Processing helix chain 'H' and resid 72 through 90 Processing helix chain 'H' and resid 92 through 110 Processing helix chain 'H' and resid 112 through 130 Processing helix chain 'H' and resid 133 through 151 Processing helix chain 'H' and resid 153 through 171 Processing helix chain 'H' and resid 173 through 189 Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 194 through 212 Processing helix chain 'H' and resid 214 through 229 Processing helix chain 'H' and resid 229 through 234 Processing helix chain 'H' and resid 235 through 251 Processing helix chain 'H' and resid 252 through 267 removed outlier: 3.593A pdb=" N PHE H 266 " --> pdb=" O GLU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 292 Processing helix chain 'J' and resid 28 through 86 Processing helix chain 'K' and resid 35 through 67 Processing helix chain 'K' and resid 70 through 77 Processing helix chain 'K' and resid 80 through 105 removed outlier: 5.151A pdb=" N GLN K 86 " --> pdb=" O ASN K 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA K 87 " --> pdb=" O PHE K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 149 removed outlier: 3.709A pdb=" N TYR K 148 " --> pdb=" O ALA K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 257 removed outlier: 3.651A pdb=" N GLN K 198 " --> pdb=" O GLN K 194 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU K 226 " --> pdb=" O ILE K 222 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN K 227 " --> pdb=" O GLU K 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 434 through 499 Processing helix chain 'L' and resid 590 through 649 removed outlier: 3.653A pdb=" N GLY L 649 " --> pdb=" O ASN L 645 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 307 removed outlier: 6.795A pdb=" N LYS A 304 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ASP A 349 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL A 306 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N HIS A 344 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE A 391 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 346 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N MET A 393 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE A 348 " --> pdb=" O MET A 393 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 394 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 585 through 589 removed outlier: 3.710A pdb=" N PHE A 585 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 587 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN A 619 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N MET A 664 " --> pdb=" O ASN A 619 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 621 " --> pdb=" O MET A 664 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N THR A 666 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE A 623 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 558 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR A 665 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 560 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N THR A 667 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 562 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN A 684 " --> pdb=" O SER A 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 27 through 33 removed outlier: 6.789A pdb=" N ILE B 79 " --> pdb=" O HIS B 28 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS B 30 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE B 81 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER B 32 " --> pdb=" O PHE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 157 through 162 removed outlier: 6.744A pdb=" N ASP B 118 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL B 174 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER B 116 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA B 176 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU B 114 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N GLN B 203 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY B 115 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ASN B 205 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE B 117 " --> pdb=" O ASN B 205 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N PHE B 207 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 119 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 304 through 307 removed outlier: 6.352A pdb=" N LYS B 304 " --> pdb=" O ILE B 347 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP B 349 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL B 306 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET B 393 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 394 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU B 278 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 557 through 559 removed outlier: 6.649A pdb=" N VAL B 558 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N THR B 665 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE B 585 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N VAL B 622 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG B 587 " --> pdb=" O VAL B 622 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 557 through 559 removed outlier: 6.649A pdb=" N VAL B 558 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N THR B 665 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AB1, first strand: chain 'C' and resid 157 through 162 removed outlier: 7.390A pdb=" N ASP C 118 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL C 174 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER C 116 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA C 176 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 114 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 151 through 152 Processing sheet with id=AB3, first strand: chain 'C' and resid 304 through 306 removed outlier: 3.674A pdb=" N ILE C 347 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET C 393 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 277 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR C 394 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU C 279 " --> pdb=" O THR C 394 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 586 through 589 removed outlier: 6.311A pdb=" N LEU C 621 " --> pdb=" O MET C 664 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR C 666 " --> pdb=" O LEU C 621 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE C 623 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 558 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N THR C 665 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU C 560 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR C 667 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE C 562 " --> pdb=" O THR C 667 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN C 684 " --> pdb=" O SER C 559 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 45 through 47 removed outlier: 7.070A pdb=" N ILE D 79 " --> pdb=" O HIS D 28 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS D 30 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 157 through 159 removed outlier: 7.156A pdb=" N ASP D 118 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL D 174 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER D 116 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA D 176 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU D 114 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 9.461A pdb=" N GLN D 203 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY D 115 " --> pdb=" O GLN D 203 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASN D 205 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE D 117 " --> pdb=" O ASN D 205 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N PHE D 207 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE D 119 " --> pdb=" O PHE D 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 134 through 135 removed outlier: 7.422A pdb=" N PHE D 134 " --> pdb=" O LYS D 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AB9, first strand: chain 'D' and resid 304 through 306 removed outlier: 3.579A pdb=" N LYS D 304 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D 347 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 306 " --> pdb=" O ILE D 347 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 391 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET D 393 " --> pdb=" O PHE D 348 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU D 278 " --> pdb=" O VAL D 414 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 585 through 589 removed outlier: 3.866A pdb=" N PHE D 585 " --> pdb=" O LEU D 618 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL D 558 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N THR D 665 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU D 560 " --> pdb=" O THR D 665 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 304 through 307 removed outlier: 6.201A pdb=" N LYS E 304 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP E 349 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL E 306 " --> pdb=" O ASP E 349 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR E 394 " --> pdb=" O LEU E 279 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY E 276 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N VAL E 414 " --> pdb=" O GLY E 276 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU E 278 " --> pdb=" O VAL E 414 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 585 through 589 removed outlier: 4.090A pdb=" N PHE E 585 " --> pdb=" O LEU E 618 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG E 587 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL E 622 " --> pdb=" O ARG E 587 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN E 619 " --> pdb=" O ARG E 660 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL E 558 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR E 665 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU E 560 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR E 667 " --> pdb=" O LEU E 560 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE E 562 " --> pdb=" O THR E 667 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN E 684 " --> pdb=" O SER E 559 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 304 through 306 removed outlier: 5.770A pdb=" N LYS F 304 " --> pdb=" O ILE F 347 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N HIS F 344 " --> pdb=" O LEU F 389 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE F 391 " --> pdb=" O HIS F 344 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE F 346 " --> pdb=" O ILE F 391 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N MET F 393 " --> pdb=" O ILE F 346 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE F 348 " --> pdb=" O MET F 393 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY F 276 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL F 414 " --> pdb=" O GLY F 276 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU F 278 " --> pdb=" O VAL F 414 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 585 through 589 removed outlier: 3.643A pdb=" N ARG F 587 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL F 558 " --> pdb=" O LEU F 661 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN F 684 " --> pdb=" O SER F 559 " (cutoff:3.500A) 1973 hydrogen bonds defined for protein. 5709 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: 10.12 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9458 1.33 - 1.45: 6965 1.45 - 1.57: 21175 1.57 - 1.70: 54 1.70 - 1.82: 278 Bond restraints: 37930 Sorted by residual: bond pdb=" C GLY A 243 " pdb=" N LEU A 244 " ideal model delta sigma weight residual 1.331 1.206 0.125 1.40e-02 5.10e+03 7.93e+01 bond pdb=" C ASP D 429 " pdb=" N ILE D 430 " ideal model delta sigma weight residual 1.334 1.434 -0.101 1.26e-02 6.30e+03 6.37e+01 bond pdb=" C PHE A 261 " pdb=" N PRO A 262 " ideal model delta sigma weight residual 1.329 1.418 -0.089 1.18e-02 7.18e+03 5.65e+01 bond pdb=" C4 ATP D 801 " pdb=" C5 ATP D 801 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.22e+01 bond pdb=" C4 ATP D 802 " pdb=" C5 ATP D 802 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.91e+01 ... (remaining 37925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.86: 50927 4.86 - 9.72: 249 9.72 - 14.58: 12 14.58 - 19.45: 3 19.45 - 24.31: 6 Bond angle restraints: 51197 Sorted by residual: angle pdb=" PB ATP D 801 " pdb=" O3B ATP D 801 " pdb=" PG ATP D 801 " ideal model delta sigma weight residual 139.87 115.56 24.31 1.00e+00 1.00e+00 5.91e+02 angle pdb=" PA ATP C 801 " pdb=" O3A ATP C 801 " pdb=" PB ATP C 801 " ideal model delta sigma weight residual 136.83 113.22 23.61 1.00e+00 1.00e+00 5.57e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 117.68 22.19 1.00e+00 1.00e+00 4.92e+02 angle pdb=" PA ATP D 801 " pdb=" O3A ATP D 801 " pdb=" PB ATP D 801 " ideal model delta sigma weight residual 136.83 114.75 22.08 1.00e+00 1.00e+00 4.88e+02 angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 118.84 21.03 1.00e+00 1.00e+00 4.42e+02 ... (remaining 51192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.10: 22813 31.10 - 62.19: 625 62.19 - 93.29: 69 93.29 - 124.38: 0 124.38 - 155.48: 2 Dihedral angle restraints: 23509 sinusoidal: 9832 harmonic: 13677 Sorted by residual: dihedral pdb=" C2' ADP E 801 " pdb=" C1' ADP E 801 " pdb=" N9 ADP E 801 " pdb=" C4 ADP E 801 " ideal model delta sinusoidal sigma weight residual 91.55 -112.97 -155.48 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 66.31 -126.31 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" CA GLY B 636 " pdb=" C GLY B 636 " pdb=" N PRO B 637 " pdb=" CA PRO B 637 " ideal model delta harmonic sigma weight residual 0.00 -26.55 26.55 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 23506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 5780 0.179 - 0.357: 27 0.357 - 0.536: 1 0.536 - 0.714: 0 0.714 - 0.893: 1 Chirality restraints: 5809 Sorted by residual: chirality pdb=" CG LEU G 291 " pdb=" CB LEU G 291 " pdb=" CD1 LEU G 291 " pdb=" CD2 LEU G 291 " both_signs ideal model delta sigma weight residual False -2.59 -1.70 -0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA ALA K 155 " pdb=" N ALA K 155 " pdb=" C ALA K 155 " pdb=" CB ALA K 155 " both_signs ideal model delta sigma weight residual False 2.48 2.06 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CG LEU K 200 " pdb=" CB LEU K 200 " pdb=" CD1 LEU K 200 " pdb=" CD2 LEU K 200 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 5806 not shown) Planarity restraints: 6647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 674 " -0.024 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" CD GLN A 674 " 0.083 2.00e-02 2.50e+03 pdb=" OE1 GLN A 674 " -0.031 2.00e-02 2.50e+03 pdb=" NE2 GLN A 674 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 207 " 0.027 2.00e-02 2.50e+03 3.02e-02 1.60e+01 pdb=" CG PHE B 207 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE B 207 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE B 207 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 207 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 207 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 207 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 406 " 0.062 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO E 407 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO E 407 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 407 " 0.051 5.00e-02 4.00e+02 ... (remaining 6644 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3985 2.74 - 3.28: 41315 3.28 - 3.82: 59696 3.82 - 4.36: 70498 4.36 - 4.90: 117088 Nonbonded interactions: 292582 Sorted by model distance: nonbonded pdb=" O SER G 194 " pdb=" OG SER G 197 " model vdw 2.202 3.040 nonbonded pdb=" O LEU E 298 " pdb=" O ASN E 299 " model vdw 2.325 3.040 nonbonded pdb=" O ASN D 386 " pdb=" OD1 ASN D 386 " model vdw 2.340 3.040 nonbonded pdb=" ND2 ASN C 373 " pdb=" OE2 GLU D 350 " model vdw 2.345 3.120 nonbonded pdb=" O TYR A 670 " pdb=" OE1 GLN A 674 " model vdw 2.353 3.040 ... (remaining 292577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 245 through 357 or resid 366 through 758)) selection = (chain 'E' and (resid 245 through 357 or resid 366 through 478 or resid 491 thro \ ugh 758)) selection = (chain 'F' and (resid 245 through 478 or resid 491 through 758)) } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 18 through 123 or resid 127 through 478 or resid 489 throu \ gh 802)) selection = (chain 'D' and (resid 18 through 123 or resid 127 through 478 or resid 489 throu \ gh 802)) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 37.380 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.130 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.007 0.125 37930 Z= 0.404 Angle : 1.094 24.307 51197 Z= 0.676 Chirality : 0.055 0.893 5809 Planarity : 0.006 0.092 6647 Dihedral : 14.558 155.478 14641 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.55 % Favored : 95.17 % Rotamer: Outliers : 0.51 % Allowed : 0.56 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: -0.60 (0.12), residues: 4699 helix: 0.27 (0.10), residues: 2414 sheet: -0.23 (0.20), residues: 575 loop : -1.32 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.003 ARG D 547 TYR 0.055 0.003 TYR A 670 PHE 0.069 0.003 PHE B 207 TRP 0.039 0.003 TRP H 196 HIS 0.033 0.003 HIS E 742 Details of bonding type rmsd covalent geometry : bond 0.00748 (37930) covalent geometry : angle 1.09401 (51197) hydrogen bonds : bond 0.15969 ( 1973) hydrogen bonds : angle 6.46275 ( 5709) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 636 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.9538 (mppt) cc_final: 0.9282 (mmtm) REVERT: A 379 MET cc_start: 0.8988 (tpt) cc_final: 0.8669 (tpp) REVERT: A 404 LEU cc_start: 0.9900 (mp) cc_final: 0.9690 (mp) REVERT: A 435 MET cc_start: 0.9485 (mmm) cc_final: 0.9167 (tpp) REVERT: A 440 MET cc_start: 0.9080 (mpp) cc_final: 0.8837 (mpp) REVERT: A 597 MET cc_start: 0.8960 (mtp) cc_final: 0.8498 (mtp) REVERT: A 605 TYR cc_start: 0.9641 (t80) cc_final: 0.9434 (t80) REVERT: A 670 TYR cc_start: 0.9306 (t80) cc_final: 0.9073 (t80) REVERT: A 676 MET cc_start: 0.8843 (mmp) cc_final: 0.8556 (mmm) REVERT: A 678 ILE cc_start: 0.9485 (mm) cc_final: 0.9143 (tp) REVERT: A 681 CYS cc_start: 0.8620 (m) cc_final: 0.8216 (m) REVERT: B 19 MET cc_start: -0.0079 (mtt) cc_final: -0.0343 (mtt) REVERT: B 256 PHE cc_start: 0.9599 (m-80) cc_final: 0.9328 (m-10) REVERT: B 277 LEU cc_start: 0.9669 (tp) cc_final: 0.9277 (tt) REVERT: B 315 TYR cc_start: 0.9534 (m-80) cc_final: 0.9073 (m-80) REVERT: B 349 ASP cc_start: 0.9383 (t0) cc_final: 0.8937 (t0) REVERT: B 440 MET cc_start: 0.7856 (mmm) cc_final: 0.7595 (mmm) REVERT: B 495 LEU cc_start: 0.9298 (pp) cc_final: 0.8979 (pt) REVERT: B 528 MET cc_start: 0.8844 (tpp) cc_final: 0.8425 (tpp) REVERT: B 561 LEU cc_start: 0.9819 (tt) cc_final: 0.9596 (tt) REVERT: B 588 LEU cc_start: 0.9469 (tp) cc_final: 0.9157 (tt) REVERT: B 608 ASN cc_start: 0.9740 (m-40) cc_final: 0.9438 (t0) REVERT: B 612 ASP cc_start: 0.8904 (p0) cc_final: 0.8494 (p0) REVERT: B 624 ASP cc_start: 0.9249 (t0) cc_final: 0.9001 (t0) REVERT: B 662 LEU cc_start: 0.9599 (tp) cc_final: 0.9240 (tp) REVERT: B 664 MET cc_start: 0.9064 (mpp) cc_final: 0.8786 (mpp) REVERT: B 754 MET cc_start: 0.9516 (mmp) cc_final: 0.9277 (mmp) REVERT: C 19 MET cc_start: 0.4931 (mmm) cc_final: 0.4572 (mmm) REVERT: C 22 MET cc_start: -0.0003 (ttt) cc_final: -0.1202 (tpt) REVERT: C 311 ILE cc_start: 0.9637 (mm) cc_final: 0.9130 (tp) REVERT: C 313 SER cc_start: 0.8680 (t) cc_final: 0.8434 (m) REVERT: C 355 PHE cc_start: 0.9139 (m-80) cc_final: 0.8808 (m-80) REVERT: C 369 ASP cc_start: 0.9489 (m-30) cc_final: 0.9094 (p0) REVERT: C 380 ASP cc_start: 0.9246 (t70) cc_final: 0.8909 (t0) REVERT: C 519 ASP cc_start: 0.9595 (m-30) cc_final: 0.9299 (m-30) REVERT: C 648 LYS cc_start: 0.9659 (tttt) cc_final: 0.9345 (tppt) REVERT: C 662 LEU cc_start: 0.9687 (tp) cc_final: 0.9471 (tt) REVERT: C 678 ILE cc_start: 0.9600 (pt) cc_final: 0.9342 (pt) REVERT: C 697 LEU cc_start: 0.9677 (tt) cc_final: 0.9291 (tt) REVERT: D 19 MET cc_start: -0.3791 (mtm) cc_final: -0.5119 (ptp) REVERT: D 207 PHE cc_start: 0.8894 (m-80) cc_final: 0.8688 (m-80) REVERT: D 275 LYS cc_start: 0.9787 (ptpt) cc_final: 0.9231 (mmtt) REVERT: D 337 LYS cc_start: 0.9066 (ttpt) cc_final: 0.8769 (ttpt) REVERT: D 348 PHE cc_start: 0.9444 (m-80) cc_final: 0.9162 (m-80) REVERT: D 440 MET cc_start: 0.8619 (mtm) cc_final: 0.8193 (mtm) REVERT: D 518 GLU cc_start: 0.9647 (mm-30) cc_final: 0.9421 (mp0) REVERT: D 519 ASP cc_start: 0.9489 (m-30) cc_final: 0.9116 (m-30) REVERT: D 594 LEU cc_start: 0.9679 (mm) cc_final: 0.9292 (mm) REVERT: D 603 ILE cc_start: 0.9845 (mm) cc_final: 0.9614 (mm) REVERT: D 611 ARG cc_start: 0.9198 (ttm110) cc_final: 0.8951 (mtm110) REVERT: D 648 LYS cc_start: 0.9564 (ttpt) cc_final: 0.9308 (tppt) REVERT: E 349 ASP cc_start: 0.9392 (t0) cc_final: 0.9096 (p0) REVERT: E 410 PHE cc_start: 0.9609 (m-10) cc_final: 0.9311 (m-80) REVERT: E 517 GLU cc_start: 0.9451 (pm20) cc_final: 0.9201 (pm20) REVERT: E 531 TYR cc_start: 0.8125 (p90) cc_final: 0.7399 (p90) REVERT: E 594 LEU cc_start: 0.9679 (mm) cc_final: 0.9198 (mm) REVERT: E 691 MET cc_start: 0.8539 (ppp) cc_final: 0.7029 (tmm) REVERT: E 742 HIS cc_start: 0.9071 (t70) cc_final: 0.8837 (t-90) REVERT: F 280 TYR cc_start: 0.8887 (p90) cc_final: 0.8393 (p90) REVERT: F 326 LEU cc_start: 0.8381 (mt) cc_final: 0.8008 (mt) REVERT: F 348 PHE cc_start: 0.9559 (m-80) cc_final: 0.8753 (m-80) REVERT: F 349 ASP cc_start: 0.9557 (m-30) cc_final: 0.9325 (m-30) REVERT: F 379 MET cc_start: 0.8268 (ttp) cc_final: 0.8011 (ptp) REVERT: F 393 MET cc_start: 0.7721 (pmm) cc_final: 0.7308 (pmm) REVERT: F 439 ASN cc_start: 0.9032 (t0) cc_final: 0.8724 (p0) REVERT: F 608 ASN cc_start: 0.9548 (m-40) cc_final: 0.9302 (m110) REVERT: F 614 TYR cc_start: 0.8664 (m-80) cc_final: 0.8399 (m-80) REVERT: F 648 LYS cc_start: 0.9711 (tttt) cc_final: 0.9000 (tppt) REVERT: F 651 LEU cc_start: 0.9857 (mt) cc_final: 0.9569 (mp) REVERT: F 662 LEU cc_start: 0.9579 (tp) cc_final: 0.9327 (tp) REVERT: G 1 MET cc_start: 0.4451 (ppp) cc_final: 0.4210 (ppp) REVERT: H 1 MET cc_start: 0.1854 (mtt) cc_final: 0.1114 (ttm) REVERT: J 76 ARG cc_start: 0.3087 (mtt180) cc_final: 0.2653 (ttp-110) REVERT: K 50 TYR cc_start: 0.9261 (t80) cc_final: 0.8745 (t80) REVERT: K 71 GLU cc_start: 0.8981 (pm20) cc_final: 0.8757 (tt0) REVERT: K 77 ARG cc_start: 0.9059 (mpp-170) cc_final: 0.8825 (mpp80) REVERT: K 78 HIS cc_start: 0.9002 (m-70) cc_final: 0.8682 (m90) REVERT: K 83 PHE cc_start: 0.9328 (m-80) cc_final: 0.8582 (m-80) REVERT: K 185 GLU cc_start: 0.3421 (OUTLIER) cc_final: 0.2129 (mm-30) REVERT: L 459 MET cc_start: 0.4748 (mmm) cc_final: 0.3961 (mtp) outliers start: 21 outliers final: 11 residues processed: 652 average time/residue: 0.2468 time to fit residues: 256.3582 Evaluate side-chains 461 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 449 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 645 GLN Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 175 GLN Chi-restraints excluded: chain K residue 179 ASN Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 187 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 205 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 0.0980 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 541 ASN A 645 GLN A 736 ASN B 273 HIS B 370 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 ASN C 541 ASN C 717 ASN D 374 GLN D 536 ASN ** E 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN F 413 GLN F 645 GLN ** F 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN K 56 GLN ** K 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 HIS K 140 ASN ** K 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 GLN L 446 ASN L 468 GLN L 600 GLN L 603 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.092227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.060099 restraints weight = 253381.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061077 restraints weight = 151959.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061730 restraints weight = 106912.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061872 restraints weight = 98287.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061872 restraints weight = 84043.304| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 37930 Z= 0.243 Angle : 0.752 15.383 51197 Z= 0.398 Chirality : 0.045 0.283 5809 Planarity : 0.006 0.075 6647 Dihedral : 10.276 152.019 5417 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.00 % Favored : 95.87 % Rotamer: Outliers : 2.00 % Allowed : 8.76 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.16 (0.12), residues: 4699 helix: 0.94 (0.10), residues: 2464 sheet: 0.02 (0.20), residues: 589 loop : -1.07 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 324 TYR 0.036 0.002 TYR K 50 PHE 0.039 0.002 PHE D 252 TRP 0.016 0.002 TRP H 196 HIS 0.022 0.002 HIS K 61 Details of bonding type rmsd covalent geometry : bond 0.00517 (37930) covalent geometry : angle 0.75220 (51197) hydrogen bonds : bond 0.05090 ( 1973) hydrogen bonds : angle 5.11972 ( 5709) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 478 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 MET cc_start: 0.8996 (tpt) cc_final: 0.8752 (tpp) REVERT: A 597 MET cc_start: 0.8952 (mtp) cc_final: 0.8536 (mtp) REVERT: A 605 TYR cc_start: 0.9725 (t80) cc_final: 0.9486 (t80) REVERT: A 670 TYR cc_start: 0.9202 (t80) cc_final: 0.8960 (t80) REVERT: A 675 GLN cc_start: 0.9455 (tm-30) cc_final: 0.8985 (tm-30) REVERT: A 676 MET cc_start: 0.8880 (mmp) cc_final: 0.8168 (mmm) REVERT: B 268 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.8924 (tptp) REVERT: B 277 LEU cc_start: 0.9659 (tp) cc_final: 0.9263 (tt) REVERT: B 315 TYR cc_start: 0.9349 (m-80) cc_final: 0.8891 (m-80) REVERT: B 349 ASP cc_start: 0.9459 (t0) cc_final: 0.9027 (t0) REVERT: B 588 LEU cc_start: 0.9461 (tp) cc_final: 0.9164 (tt) REVERT: B 605 TYR cc_start: 0.9520 (t80) cc_final: 0.9276 (t80) REVERT: B 611 ARG cc_start: 0.8812 (ttm110) cc_final: 0.8261 (ttm110) REVERT: B 621 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9225 (mm) REVERT: B 754 MET cc_start: 0.9656 (mmp) cc_final: 0.9329 (mmp) REVERT: C 220 ASN cc_start: 0.8923 (t0) cc_final: 0.8573 (p0) REVERT: C 311 ILE cc_start: 0.9646 (mm) cc_final: 0.9270 (tp) REVERT: C 369 ASP cc_start: 0.9500 (m-30) cc_final: 0.9115 (p0) REVERT: C 380 ASP cc_start: 0.9147 (t70) cc_final: 0.8788 (t0) REVERT: C 383 ASP cc_start: 0.9160 (t0) cc_final: 0.8958 (t0) REVERT: C 396 ARG cc_start: 0.8876 (ttp80) cc_final: 0.8537 (ttp80) REVERT: C 399 LEU cc_start: 0.9609 (mp) cc_final: 0.9358 (mt) REVERT: C 440 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8742 (mtp) REVERT: C 518 GLU cc_start: 0.9608 (tp30) cc_final: 0.9350 (tp30) REVERT: C 631 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8715 (t0) REVERT: C 648 LYS cc_start: 0.9614 (tttt) cc_final: 0.9317 (tppt) REVERT: C 678 ILE cc_start: 0.9632 (pt) cc_final: 0.9247 (pt) REVERT: D 19 MET cc_start: 0.0896 (mtm) cc_final: -0.0592 (ptp) REVERT: D 207 PHE cc_start: 0.8947 (m-80) cc_final: 0.8731 (m-80) REVERT: D 337 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8798 (ttpt) REVERT: D 348 PHE cc_start: 0.9495 (m-80) cc_final: 0.9263 (m-80) REVERT: D 379 MET cc_start: 0.9488 (mmm) cc_final: 0.9258 (mmm) REVERT: D 435 MET cc_start: 0.8989 (mmt) cc_final: 0.8439 (mmp) REVERT: D 440 MET cc_start: 0.8804 (mtm) cc_final: 0.7823 (mtm) REVERT: D 495 LEU cc_start: 0.9127 (pt) cc_final: 0.8894 (mm) REVERT: D 529 MET cc_start: 0.8772 (mpp) cc_final: 0.8507 (mpp) REVERT: D 648 LYS cc_start: 0.9701 (ttpt) cc_final: 0.9395 (tptt) REVERT: E 294 ILE cc_start: 0.9705 (tp) cc_final: 0.9440 (tp) REVERT: E 298 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8617 (pp) REVERT: E 410 PHE cc_start: 0.9535 (m-10) cc_final: 0.9266 (m-80) REVERT: E 517 GLU cc_start: 0.9479 (pm20) cc_final: 0.9220 (pm20) REVERT: E 597 MET cc_start: 0.9179 (mpp) cc_final: 0.8881 (ptp) REVERT: E 691 MET cc_start: 0.7931 (ppp) cc_final: 0.7686 (ppp) REVERT: F 280 TYR cc_start: 0.9417 (p90) cc_final: 0.9108 (p90) REVERT: F 379 MET cc_start: 0.8458 (ttp) cc_final: 0.8214 (ptt) REVERT: F 439 ASN cc_start: 0.9083 (t0) cc_final: 0.8870 (p0) REVERT: F 441 MET cc_start: 0.9469 (OUTLIER) cc_final: 0.9195 (pmm) REVERT: F 597 MET cc_start: 0.8929 (ptp) cc_final: 0.8009 (ptp) REVERT: F 608 ASN cc_start: 0.9536 (m-40) cc_final: 0.9266 (m110) REVERT: F 614 TYR cc_start: 0.8967 (m-80) cc_final: 0.8693 (m-80) REVERT: F 648 LYS cc_start: 0.9689 (tttt) cc_final: 0.9040 (tppt) REVERT: F 662 LEU cc_start: 0.9572 (tp) cc_final: 0.9361 (tp) REVERT: H 1 MET cc_start: 0.2165 (mtt) cc_final: 0.1563 (ttm) REVERT: J 43 MET cc_start: 0.4206 (ppp) cc_final: 0.2640 (ppp) REVERT: J 76 ARG cc_start: 0.3107 (mtt180) cc_final: 0.2683 (ttp-110) REVERT: K 60 LEU cc_start: 0.8976 (mm) cc_final: 0.8694 (mm) REVERT: K 61 HIS cc_start: 0.9201 (m-70) cc_final: 0.8994 (m-70) REVERT: K 83 PHE cc_start: 0.8517 (m-80) cc_final: 0.8304 (m-80) REVERT: K 205 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8632 (mmtm) REVERT: L 459 MET cc_start: 0.4659 (OUTLIER) cc_final: 0.3954 (mtp) REVERT: L 601 ILE cc_start: 0.7999 (tp) cc_final: 0.7781 (mt) outliers start: 82 outliers final: 42 residues processed: 521 average time/residue: 0.2295 time to fit residues: 194.0895 Evaluate side-chains 446 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 396 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 631 ASP Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 614 TYR Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 75 HIS Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 122 PHE Chi-restraints excluded: chain K residue 133 ASP Chi-restraints excluded: chain K residue 134 SER Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain L residue 459 MET Chi-restraints excluded: chain L residue 590 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 152 optimal weight: 0.9990 chunk 456 optimal weight: 50.0000 chunk 139 optimal weight: 40.0000 chunk 423 optimal weight: 20.0000 chunk 461 optimal weight: 40.0000 chunk 428 optimal weight: 20.0000 chunk 281 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 302 optimal weight: 10.0000 chunk 61 optimal weight: 40.0000 chunk 235 optimal weight: 10.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS A 370 ASN A 384 GLN B 84 ASN B 322 ASN B 446 ASN ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 563 HIS D 357 GLN D 373 ASN D 395 ASN D 742 HIS E 322 ASN F 426 GLN ** F 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 HIS K 143 GLN L 468 GLN L 639 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.089289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058285 restraints weight = 260127.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059405 restraints weight = 149218.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060134 restraints weight = 102802.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.060525 restraints weight = 82168.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.060525 restraints weight = 73666.726| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 37930 Z= 0.284 Angle : 0.749 9.680 51197 Z= 0.395 Chirality : 0.044 0.285 5809 Planarity : 0.006 0.087 6647 Dihedral : 10.079 149.592 5397 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.21 % Rotamer: Outliers : 2.61 % Allowed : 12.44 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.06 (0.12), residues: 4699 helix: 0.84 (0.10), residues: 2470 sheet: -0.04 (0.20), residues: 595 loop : -1.06 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 335 TYR 0.051 0.003 TYR H 148 PHE 0.030 0.002 PHE A 355 TRP 0.039 0.002 TRP H 147 HIS 0.014 0.002 HIS K 61 Details of bonding type rmsd covalent geometry : bond 0.00587 (37930) covalent geometry : angle 0.74892 (51197) hydrogen bonds : bond 0.04642 ( 1973) hydrogen bonds : angle 5.06828 ( 5709) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 418 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 MET cc_start: 0.9002 (tpt) cc_final: 0.8705 (tpp) REVERT: A 440 MET cc_start: 0.9478 (mpp) cc_final: 0.9258 (mpp) REVERT: A 545 TYR cc_start: 0.9450 (m-80) cc_final: 0.9093 (m-80) REVERT: A 597 MET cc_start: 0.8974 (mtp) cc_final: 0.8688 (mtp) REVERT: A 605 TYR cc_start: 0.9730 (t80) cc_final: 0.9516 (t80) REVERT: A 608 ASN cc_start: 0.9590 (m110) cc_final: 0.9368 (m110) REVERT: A 676 MET cc_start: 0.9062 (mmp) cc_final: 0.8689 (mmp) REVERT: B 160 MET cc_start: 0.4635 (OUTLIER) cc_final: 0.3990 (ppp) REVERT: B 315 TYR cc_start: 0.9353 (m-80) cc_final: 0.9037 (m-10) REVERT: B 349 ASP cc_start: 0.9403 (t0) cc_final: 0.8755 (t0) REVERT: B 356 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8695 (mmmt) REVERT: B 435 MET cc_start: 0.7727 (mmm) cc_final: 0.7349 (mmm) REVERT: B 495 LEU cc_start: 0.9115 (pt) cc_final: 0.8639 (mm) REVERT: B 528 MET cc_start: 0.9029 (tpp) cc_final: 0.8724 (tpp) REVERT: B 754 MET cc_start: 0.9539 (mmp) cc_final: 0.9236 (mmp) REVERT: C 157 TYR cc_start: 0.9371 (OUTLIER) cc_final: 0.9129 (t80) REVERT: C 220 ASN cc_start: 0.8661 (t0) cc_final: 0.8370 (p0) REVERT: C 311 ILE cc_start: 0.9596 (mm) cc_final: 0.9116 (tp) REVERT: C 355 PHE cc_start: 0.9420 (m-80) cc_final: 0.9029 (m-80) REVERT: C 369 ASP cc_start: 0.9498 (m-30) cc_final: 0.9149 (p0) REVERT: C 383 ASP cc_start: 0.9140 (t0) cc_final: 0.8925 (t0) REVERT: C 396 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8556 (ttp80) REVERT: C 428 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8825 (m-80) REVERT: C 607 ASP cc_start: 0.9312 (t0) cc_final: 0.8632 (t0) REVERT: C 648 LYS cc_start: 0.9561 (tttt) cc_final: 0.9176 (tppt) REVERT: C 678 ILE cc_start: 0.9652 (pt) cc_final: 0.9378 (pt) REVERT: D 19 MET cc_start: -0.2690 (mtm) cc_final: -0.3931 (ptp) REVERT: D 207 PHE cc_start: 0.8892 (m-80) cc_final: 0.8629 (m-80) REVERT: D 275 LYS cc_start: 0.9656 (ptpt) cc_final: 0.9181 (mmmt) REVERT: D 379 MET cc_start: 0.9492 (mmm) cc_final: 0.9027 (mmm) REVERT: D 396 ARG cc_start: 0.8963 (ptp-170) cc_final: 0.8698 (ptp-110) REVERT: D 440 MET cc_start: 0.8776 (mtm) cc_final: 0.8440 (mtm) REVERT: D 495 LEU cc_start: 0.9158 (pt) cc_final: 0.8896 (mm) REVERT: D 529 MET cc_start: 0.8836 (mpp) cc_final: 0.8453 (mpp) REVERT: D 648 LYS cc_start: 0.9701 (ttpt) cc_final: 0.9437 (ptmm) REVERT: E 298 LEU cc_start: 0.9252 (mm) cc_final: 0.8661 (mm) REVERT: E 350 GLU cc_start: 0.8929 (tt0) cc_final: 0.8678 (tt0) REVERT: E 410 PHE cc_start: 0.9566 (m-10) cc_final: 0.9168 (m-80) REVERT: E 517 GLU cc_start: 0.9409 (pm20) cc_final: 0.9117 (pm20) REVERT: E 691 MET cc_start: 0.7906 (ppp) cc_final: 0.7700 (ppp) REVERT: E 701 MET cc_start: 0.9385 (ppp) cc_final: 0.9145 (ppp) REVERT: E 745 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8533 (m-30) REVERT: F 256 PHE cc_start: 0.8927 (m-10) cc_final: 0.8434 (m-80) REVERT: F 280 TYR cc_start: 0.9332 (p90) cc_final: 0.8860 (p90) REVERT: F 379 MET cc_start: 0.8601 (ttp) cc_final: 0.8341 (ptm) REVERT: F 440 MET cc_start: 0.8006 (pmm) cc_final: 0.7651 (pmm) REVERT: F 597 MET cc_start: 0.8986 (ptp) cc_final: 0.8231 (ptp) REVERT: F 614 TYR cc_start: 0.9132 (m-80) cc_final: 0.8778 (m-80) REVERT: F 648 LYS cc_start: 0.9624 (tttt) cc_final: 0.9012 (tppt) REVERT: F 662 LEU cc_start: 0.9551 (tp) cc_final: 0.9277 (tp) REVERT: G 1 MET cc_start: 0.4981 (OUTLIER) cc_final: 0.4751 (ppp) REVERT: H 1 MET cc_start: 0.1223 (mtt) cc_final: 0.0333 (ttm) REVERT: H 189 MET cc_start: 0.6573 (mmm) cc_final: 0.6232 (mmm) REVERT: J 76 ARG cc_start: 0.2972 (mtt180) cc_final: 0.2524 (ttp-110) REVERT: K 83 PHE cc_start: 0.8995 (m-80) cc_final: 0.8597 (m-80) REVERT: K 205 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8559 (mmtt) REVERT: L 459 MET cc_start: 0.4111 (OUTLIER) cc_final: 0.3253 (ptp) outliers start: 107 outliers final: 55 residues processed: 493 average time/residue: 0.2261 time to fit residues: 181.7484 Evaluate side-chains 442 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 380 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 614 TYR Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 745 ASP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 640 SER Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 134 TYR Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain K residue 52 HIS Chi-restraints excluded: chain K residue 75 HIS Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 122 PHE Chi-restraints excluded: chain K residue 129 TYR Chi-restraints excluded: chain K residue 133 ASP Chi-restraints excluded: chain K residue 134 SER Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain L residue 459 MET Chi-restraints excluded: chain L residue 590 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 416 optimal weight: 6.9990 chunk 403 optimal weight: 50.0000 chunk 104 optimal weight: 4.9990 chunk 400 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 305 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 326 optimal weight: 3.9990 chunk 415 optimal weight: 50.0000 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN B 608 ASN ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN C 395 ASN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 ASN D 674 GLN E 657 GLN ** F 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 ASN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 HIS K 127 GLN L 485 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.089666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058931 restraints weight = 255192.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059542 restraints weight = 149221.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059934 restraints weight = 102999.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.060627 restraints weight = 86207.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060711 restraints weight = 73640.373| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 37930 Z= 0.186 Angle : 0.664 12.185 51197 Z= 0.344 Chirality : 0.042 0.233 5809 Planarity : 0.005 0.070 6647 Dihedral : 9.860 147.045 5397 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 2.93 % Allowed : 14.71 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.46 (0.12), residues: 4699 helix: 1.21 (0.10), residues: 2471 sheet: 0.12 (0.20), residues: 586 loop : -0.95 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 611 TYR 0.043 0.002 TYR A 670 PHE 0.018 0.001 PHE K 122 TRP 0.041 0.002 TRP H 147 HIS 0.016 0.002 HIS K 61 Details of bonding type rmsd covalent geometry : bond 0.00393 (37930) covalent geometry : angle 0.66366 (51197) hydrogen bonds : bond 0.04161 ( 1973) hydrogen bonds : angle 4.75307 ( 5709) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 413 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8909 (mmp-170) REVERT: A 311 ILE cc_start: 0.9673 (mm) cc_final: 0.9170 (mp) REVERT: A 379 MET cc_start: 0.9132 (tpt) cc_final: 0.8829 (tpp) REVERT: A 440 MET cc_start: 0.9576 (mpp) cc_final: 0.9288 (mpp) REVERT: A 545 TYR cc_start: 0.9538 (m-80) cc_final: 0.9128 (m-80) REVERT: A 597 MET cc_start: 0.9096 (mtp) cc_final: 0.8795 (mtp) REVERT: A 608 ASN cc_start: 0.9629 (m110) cc_final: 0.9410 (m110) REVERT: A 676 MET cc_start: 0.8880 (mmp) cc_final: 0.8448 (mmm) REVERT: B 268 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9051 (tptp) REVERT: B 315 TYR cc_start: 0.9482 (m-80) cc_final: 0.9210 (m-10) REVERT: B 349 ASP cc_start: 0.9452 (t0) cc_final: 0.8734 (t0) REVERT: B 495 LEU cc_start: 0.9137 (pt) cc_final: 0.8779 (mm) REVERT: B 754 MET cc_start: 0.9581 (mmp) cc_final: 0.9256 (mmp) REVERT: C 120 ASP cc_start: 0.9876 (p0) cc_final: 0.9640 (t0) REVERT: C 157 TYR cc_start: 0.9369 (OUTLIER) cc_final: 0.9121 (t80) REVERT: C 171 ILE cc_start: 0.9433 (mm) cc_final: 0.9030 (tp) REVERT: C 293 LYS cc_start: 0.9605 (mmtt) cc_final: 0.9387 (mmmm) REVERT: C 297 MET cc_start: 0.8221 (mpp) cc_final: 0.7623 (mpp) REVERT: C 311 ILE cc_start: 0.9453 (mm) cc_final: 0.8896 (tp) REVERT: C 323 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9437 (mp) REVERT: C 369 ASP cc_start: 0.9567 (m-30) cc_final: 0.9194 (p0) REVERT: C 383 ASP cc_start: 0.9276 (t0) cc_final: 0.9067 (t0) REVERT: C 396 ARG cc_start: 0.8987 (ttp80) cc_final: 0.8665 (ttp80) REVERT: C 399 LEU cc_start: 0.9606 (mp) cc_final: 0.9369 (mp) REVERT: C 428 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8874 (m-80) REVERT: C 607 ASP cc_start: 0.9374 (t0) cc_final: 0.8681 (t0) REVERT: C 648 LYS cc_start: 0.9595 (tttt) cc_final: 0.9204 (tptt) REVERT: C 678 ILE cc_start: 0.9720 (pt) cc_final: 0.9472 (pt) REVERT: D 19 MET cc_start: -0.1872 (mtm) cc_final: -0.3068 (ptp) REVERT: D 207 PHE cc_start: 0.8890 (m-80) cc_final: 0.8640 (m-80) REVERT: D 252 PHE cc_start: 0.8914 (m-80) cc_final: 0.8702 (m-80) REVERT: D 275 LYS cc_start: 0.9662 (ptpt) cc_final: 0.9195 (mmmt) REVERT: D 379 MET cc_start: 0.9543 (mmm) cc_final: 0.9086 (mmm) REVERT: D 393 MET cc_start: 0.8940 (pmm) cc_final: 0.8708 (pmm) REVERT: D 440 MET cc_start: 0.9034 (mtm) cc_final: 0.8244 (mtm) REVERT: D 495 LEU cc_start: 0.9218 (pt) cc_final: 0.8927 (mm) REVERT: D 529 MET cc_start: 0.8974 (mpp) cc_final: 0.8713 (mpp) REVERT: D 648 LYS cc_start: 0.9740 (ttpt) cc_final: 0.9354 (ptmm) REVERT: E 294 ILE cc_start: 0.9687 (tp) cc_final: 0.9345 (tp) REVERT: E 297 MET cc_start: 0.8176 (tmm) cc_final: 0.7960 (ppp) REVERT: E 298 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8663 (mt) REVERT: E 311 ILE cc_start: 0.9763 (mm) cc_final: 0.9421 (tp) REVERT: E 375 LEU cc_start: 0.9792 (tt) cc_final: 0.9519 (pp) REVERT: E 379 MET cc_start: 0.9151 (tpp) cc_final: 0.8771 (tpt) REVERT: E 410 PHE cc_start: 0.9577 (m-10) cc_final: 0.9316 (m-80) REVERT: E 428 PHE cc_start: 0.9558 (OUTLIER) cc_final: 0.9140 (m-10) REVERT: E 440 MET cc_start: 0.8799 (mmm) cc_final: 0.8595 (mmm) REVERT: E 517 GLU cc_start: 0.9424 (pm20) cc_final: 0.9118 (pm20) REVERT: E 661 LEU cc_start: 0.9559 (tp) cc_final: 0.9056 (mm) REVERT: E 691 MET cc_start: 0.8156 (ppp) cc_final: 0.7919 (ppp) REVERT: E 745 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8557 (m-30) REVERT: F 256 PHE cc_start: 0.8955 (m-10) cc_final: 0.8409 (m-80) REVERT: F 280 TYR cc_start: 0.9332 (p90) cc_final: 0.8890 (p90) REVERT: F 379 MET cc_start: 0.8641 (ttp) cc_final: 0.8352 (ptm) REVERT: F 414 VAL cc_start: 0.9321 (t) cc_final: 0.8955 (t) REVERT: F 440 MET cc_start: 0.8072 (pmm) cc_final: 0.7754 (pmm) REVERT: F 441 MET cc_start: 0.9301 (pmm) cc_final: 0.8982 (pmm) REVERT: F 588 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8984 (tp) REVERT: F 597 MET cc_start: 0.8939 (ptp) cc_final: 0.8319 (ptp) REVERT: F 614 TYR cc_start: 0.9206 (m-80) cc_final: 0.8835 (m-80) REVERT: F 648 LYS cc_start: 0.9704 (tttt) cc_final: 0.9064 (tppt) REVERT: F 662 LEU cc_start: 0.9602 (tp) cc_final: 0.9387 (tp) REVERT: F 664 MET cc_start: 0.8665 (mpp) cc_final: 0.8214 (mpp) REVERT: G 196 TRP cc_start: -0.1910 (OUTLIER) cc_final: -0.3134 (m100) REVERT: H 1 MET cc_start: 0.1532 (mtt) cc_final: 0.0753 (ttm) REVERT: H 189 MET cc_start: 0.6798 (mmm) cc_final: 0.6441 (mmm) REVERT: J 76 ARG cc_start: 0.3008 (mtt180) cc_final: 0.2532 (ttp-110) REVERT: K 83 PHE cc_start: 0.8966 (m-80) cc_final: 0.8555 (m-80) REVERT: K 205 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8522 (mmtt) REVERT: L 459 MET cc_start: 0.3961 (OUTLIER) cc_final: 0.3053 (mtp) outliers start: 120 outliers final: 68 residues processed: 495 average time/residue: 0.2161 time to fit residues: 176.0991 Evaluate side-chains 468 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 388 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 705 ASN Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 705 ASN Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 428 PHE Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 614 TYR Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 745 ASP Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain G residue 196 TRP Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain K residue 52 HIS Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 75 HIS Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 122 PHE Chi-restraints excluded: chain K residue 129 TYR Chi-restraints excluded: chain K residue 133 ASP Chi-restraints excluded: chain K residue 134 SER Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 181 ASN Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain L residue 459 MET Chi-restraints excluded: chain L residue 590 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 362 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 387 optimal weight: 20.0000 chunk 359 optimal weight: 4.9990 chunk 237 optimal weight: 0.5980 chunk 361 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN C 748 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 GLN ** F 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 ASN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN L 639 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.090182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.058484 restraints weight = 251962.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060137 restraints weight = 151118.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060137 restraints weight = 103173.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060137 restraints weight = 103080.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060137 restraints weight = 103080.766| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37930 Z= 0.145 Angle : 0.650 15.143 51197 Z= 0.332 Chirality : 0.042 0.311 5809 Planarity : 0.004 0.064 6647 Dihedral : 9.593 144.242 5397 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 2.66 % Allowed : 15.86 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.70 (0.12), residues: 4699 helix: 1.42 (0.10), residues: 2462 sheet: 0.25 (0.20), residues: 583 loop : -0.87 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 653 TYR 0.046 0.002 TYR A 670 PHE 0.025 0.001 PHE K 92 TRP 0.053 0.002 TRP H 147 HIS 0.010 0.001 HIS G 259 Details of bonding type rmsd covalent geometry : bond 0.00308 (37930) covalent geometry : angle 0.64992 (51197) hydrogen bonds : bond 0.03930 ( 1973) hydrogen bonds : angle 4.54488 ( 5709) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 419 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ILE cc_start: 0.9511 (tp) cc_final: 0.9226 (mm) REVERT: A 379 MET cc_start: 0.9023 (tpt) cc_final: 0.8736 (tpp) REVERT: A 397 LYS cc_start: 0.9547 (ttmt) cc_final: 0.8983 (mtpt) REVERT: A 440 MET cc_start: 0.9618 (mpp) cc_final: 0.9337 (mpp) REVERT: A 545 TYR cc_start: 0.9352 (m-80) cc_final: 0.9005 (m-80) REVERT: A 608 ASN cc_start: 0.9560 (m110) cc_final: 0.9352 (m110) REVERT: A 676 MET cc_start: 0.8757 (mmp) cc_final: 0.8382 (mmp) REVERT: B 349 ASP cc_start: 0.9304 (t0) cc_final: 0.8715 (t0) REVERT: B 376 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9206 (mm) REVERT: B 495 LEU cc_start: 0.9041 (pt) cc_final: 0.8722 (mm) REVERT: B 754 MET cc_start: 0.9446 (mmp) cc_final: 0.9140 (mmp) REVERT: C 19 MET cc_start: 0.6057 (mmm) cc_final: 0.5321 (mmt) REVERT: C 171 ILE cc_start: 0.9314 (mm) cc_final: 0.8825 (tp) REVERT: C 311 ILE cc_start: 0.9496 (mm) cc_final: 0.9037 (tp) REVERT: C 323 ILE cc_start: 0.9626 (OUTLIER) cc_final: 0.9385 (mp) REVERT: C 356 LYS cc_start: 0.9421 (mmmt) cc_final: 0.9086 (mmtm) REVERT: C 369 ASP cc_start: 0.9410 (m-30) cc_final: 0.9127 (p0) REVERT: C 428 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8818 (m-80) REVERT: C 607 ASP cc_start: 0.9269 (t0) cc_final: 0.8500 (t0) REVERT: C 648 LYS cc_start: 0.9598 (tttt) cc_final: 0.9222 (tptt) REVERT: D 19 MET cc_start: -0.0377 (mtm) cc_final: -0.1432 (ptp) REVERT: D 207 PHE cc_start: 0.8863 (m-80) cc_final: 0.8611 (m-80) REVERT: D 252 PHE cc_start: 0.8904 (m-80) cc_final: 0.8653 (m-80) REVERT: D 275 LYS cc_start: 0.9603 (ptpt) cc_final: 0.9185 (mmmt) REVERT: D 379 MET cc_start: 0.9409 (mmm) cc_final: 0.9012 (mmm) REVERT: D 393 MET cc_start: 0.8775 (pmm) cc_final: 0.8559 (pmm) REVERT: D 440 MET cc_start: 0.8500 (mtm) cc_final: 0.8287 (mtm) REVERT: D 495 LEU cc_start: 0.9068 (pt) cc_final: 0.8830 (mm) REVERT: D 518 GLU cc_start: 0.9610 (mm-30) cc_final: 0.9338 (mp0) REVERT: D 529 MET cc_start: 0.8999 (mpp) cc_final: 0.8579 (mpp) REVERT: D 607 ASP cc_start: 0.9254 (t0) cc_final: 0.8872 (t0) REVERT: D 648 LYS cc_start: 0.9628 (ttpt) cc_final: 0.9392 (ptmm) REVERT: D 701 MET cc_start: 0.9125 (ppp) cc_final: 0.8826 (tmm) REVERT: E 294 ILE cc_start: 0.9714 (tp) cc_final: 0.9388 (tp) REVERT: E 297 MET cc_start: 0.8118 (tmm) cc_final: 0.7898 (ppp) REVERT: E 298 LEU cc_start: 0.9192 (mm) cc_final: 0.8606 (mt) REVERT: E 311 ILE cc_start: 0.9786 (mm) cc_final: 0.9463 (tp) REVERT: E 349 ASP cc_start: 0.9483 (t0) cc_final: 0.9243 (p0) REVERT: E 351 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9477 (pp) REVERT: E 379 MET cc_start: 0.9216 (tpp) cc_final: 0.8888 (tpt) REVERT: E 389 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9353 (mm) REVERT: E 410 PHE cc_start: 0.9524 (m-10) cc_final: 0.9231 (m-80) REVERT: E 428 PHE cc_start: 0.9484 (OUTLIER) cc_final: 0.9084 (m-10) REVERT: E 646 MET cc_start: 0.9251 (ttm) cc_final: 0.8712 (tmm) REVERT: E 661 LEU cc_start: 0.9487 (tp) cc_final: 0.9049 (mm) REVERT: E 745 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8518 (m-30) REVERT: F 256 PHE cc_start: 0.9035 (m-10) cc_final: 0.8511 (m-80) REVERT: F 280 TYR cc_start: 0.9342 (p90) cc_final: 0.8881 (p90) REVERT: F 325 ASN cc_start: 0.9382 (OUTLIER) cc_final: 0.9134 (m110) REVERT: F 379 MET cc_start: 0.8719 (ttp) cc_final: 0.8398 (ptm) REVERT: F 414 VAL cc_start: 0.9168 (t) cc_final: 0.8905 (t) REVERT: F 440 MET cc_start: 0.8062 (pmm) cc_final: 0.7803 (pmm) REVERT: F 463 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.9025 (mm-30) REVERT: F 597 MET cc_start: 0.8916 (ptp) cc_final: 0.8275 (ptp) REVERT: F 614 TYR cc_start: 0.9119 (m-80) cc_final: 0.8764 (m-80) REVERT: F 648 LYS cc_start: 0.9685 (tttt) cc_final: 0.9057 (tppt) REVERT: F 662 LEU cc_start: 0.9542 (tp) cc_final: 0.9315 (tp) REVERT: F 664 MET cc_start: 0.8471 (mpp) cc_final: 0.8150 (mpp) REVERT: G 196 TRP cc_start: -0.0989 (OUTLIER) cc_final: -0.3197 (m100) REVERT: H 1 MET cc_start: 0.1142 (mtt) cc_final: 0.0194 (ttm) REVERT: H 189 MET cc_start: 0.7226 (mmm) cc_final: 0.6951 (mmm) REVERT: J 76 ARG cc_start: 0.3004 (mtt180) cc_final: 0.2535 (ttp-110) REVERT: K 60 LEU cc_start: 0.9154 (mm) cc_final: 0.8703 (mp) REVERT: K 83 PHE cc_start: 0.8572 (m-80) cc_final: 0.8315 (m-80) REVERT: K 170 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8028 (mp10) REVERT: K 205 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8503 (mmtt) REVERT: L 459 MET cc_start: 0.3200 (OUTLIER) cc_final: 0.2430 (mtm) outliers start: 109 outliers final: 57 residues processed: 494 average time/residue: 0.2081 time to fit residues: 170.8663 Evaluate side-chains 454 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 384 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 428 PHE Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 614 TYR Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 745 ASP Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain G residue 196 TRP Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain K residue 52 HIS Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 122 PHE Chi-restraints excluded: chain K residue 129 TYR Chi-restraints excluded: chain K residue 133 ASP Chi-restraints excluded: chain K residue 134 SER Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 170 GLN Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 459 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 357 optimal weight: 3.9990 chunk 323 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 348 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 70 optimal weight: 0.0020 chunk 10 optimal weight: 0.0070 chunk 374 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 overall best weight: 2.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 ASN A 727 ASN ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 736 ASN F 325 ASN F 413 GLN ** F 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 GLN G 259 HIS ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.090571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.058932 restraints weight = 253187.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.060125 restraints weight = 141174.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060454 restraints weight = 97788.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.061285 restraints weight = 84117.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061366 restraints weight = 70124.367| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37930 Z= 0.131 Angle : 0.657 11.136 51197 Z= 0.331 Chirality : 0.042 0.204 5809 Planarity : 0.004 0.065 6647 Dihedral : 9.377 143.646 5396 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 2.24 % Allowed : 16.81 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.83 (0.12), residues: 4699 helix: 1.53 (0.10), residues: 2458 sheet: 0.31 (0.20), residues: 584 loop : -0.81 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 611 TYR 0.036 0.001 TYR D 670 PHE 0.023 0.001 PHE B 166 TRP 0.054 0.002 TRP H 147 HIS 0.012 0.001 HIS G 259 Details of bonding type rmsd covalent geometry : bond 0.00279 (37930) covalent geometry : angle 0.65680 (51197) hydrogen bonds : bond 0.03844 ( 1973) hydrogen bonds : angle 4.44892 ( 5709) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 425 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ILE cc_start: 0.9508 (tp) cc_final: 0.9239 (mm) REVERT: A 379 MET cc_start: 0.9033 (tpt) cc_final: 0.8756 (tpp) REVERT: A 397 LYS cc_start: 0.9506 (ttmt) cc_final: 0.8969 (mtpt) REVERT: A 440 MET cc_start: 0.9618 (mpp) cc_final: 0.9333 (mpp) REVERT: A 545 TYR cc_start: 0.9489 (m-80) cc_final: 0.9204 (m-80) REVERT: A 676 MET cc_start: 0.8786 (mmp) cc_final: 0.8431 (mmm) REVERT: A 754 MET cc_start: 0.9135 (tpp) cc_final: 0.8689 (mmm) REVERT: B 315 TYR cc_start: 0.9359 (m-10) cc_final: 0.8850 (m-80) REVERT: B 349 ASP cc_start: 0.9331 (t0) cc_final: 0.8877 (t0) REVERT: B 376 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9248 (mm) REVERT: B 754 MET cc_start: 0.9482 (mmp) cc_final: 0.9195 (mmp) REVERT: C 19 MET cc_start: 0.3625 (mmm) cc_final: 0.2737 (mmt) REVERT: C 157 TYR cc_start: 0.9281 (t80) cc_final: 0.9042 (t80) REVERT: C 311 ILE cc_start: 0.9485 (mm) cc_final: 0.8975 (tp) REVERT: C 323 ILE cc_start: 0.9629 (OUTLIER) cc_final: 0.9385 (mp) REVERT: C 356 LYS cc_start: 0.9325 (mmmt) cc_final: 0.9119 (mmtm) REVERT: C 369 ASP cc_start: 0.9435 (m-30) cc_final: 0.9208 (p0) REVERT: C 396 ARG cc_start: 0.8934 (ttp80) cc_final: 0.8689 (tmm-80) REVERT: C 428 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8857 (m-80) REVERT: C 607 ASP cc_start: 0.9305 (t0) cc_final: 0.8573 (t0) REVERT: C 648 LYS cc_start: 0.9610 (tttt) cc_final: 0.9186 (tptt) REVERT: D 19 MET cc_start: -0.2192 (mtm) cc_final: -0.3410 (ptp) REVERT: D 207 PHE cc_start: 0.8849 (m-80) cc_final: 0.8599 (m-80) REVERT: D 252 PHE cc_start: 0.8937 (m-80) cc_final: 0.8687 (m-80) REVERT: D 254 ARG cc_start: 0.9566 (mmm160) cc_final: 0.9183 (mmm160) REVERT: D 275 LYS cc_start: 0.9628 (ptpt) cc_final: 0.9218 (mmmt) REVERT: D 379 MET cc_start: 0.9480 (mmm) cc_final: 0.9006 (mmm) REVERT: D 393 MET cc_start: 0.8860 (pmm) cc_final: 0.8636 (pmm) REVERT: D 396 ARG cc_start: 0.8922 (ptp-110) cc_final: 0.8571 (mtm110) REVERT: D 495 LEU cc_start: 0.9090 (pt) cc_final: 0.8846 (mm) REVERT: D 518 GLU cc_start: 0.9599 (mm-30) cc_final: 0.9312 (mp0) REVERT: D 529 MET cc_start: 0.9063 (mpp) cc_final: 0.8619 (mpp) REVERT: D 597 MET cc_start: 0.9031 (mtp) cc_final: 0.8776 (mpp) REVERT: D 607 ASP cc_start: 0.9341 (t0) cc_final: 0.8977 (t0) REVERT: D 608 ASN cc_start: 0.9708 (p0) cc_final: 0.9503 (p0) REVERT: D 648 LYS cc_start: 0.9694 (ttpt) cc_final: 0.9363 (tptt) REVERT: D 701 MET cc_start: 0.9173 (ppp) cc_final: 0.8930 (tmm) REVERT: E 294 ILE cc_start: 0.9724 (tp) cc_final: 0.9335 (tp) REVERT: E 298 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8518 (mt) REVERT: E 311 ILE cc_start: 0.9776 (mm) cc_final: 0.9452 (tp) REVERT: E 351 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9510 (pp) REVERT: E 375 LEU cc_start: 0.9745 (tt) cc_final: 0.9453 (pp) REVERT: E 379 MET cc_start: 0.9187 (tpp) cc_final: 0.8813 (tpt) REVERT: E 389 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9327 (mm) REVERT: E 410 PHE cc_start: 0.9509 (m-10) cc_final: 0.9244 (m-80) REVERT: E 428 PHE cc_start: 0.9537 (OUTLIER) cc_final: 0.9113 (m-10) REVERT: E 646 MET cc_start: 0.9301 (ttm) cc_final: 0.8763 (tmm) REVERT: E 661 LEU cc_start: 0.9523 (tp) cc_final: 0.9087 (mm) REVERT: E 745 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8533 (m-30) REVERT: F 256 PHE cc_start: 0.8983 (m-10) cc_final: 0.8771 (m-10) REVERT: F 280 TYR cc_start: 0.9183 (p90) cc_final: 0.8694 (p90) REVERT: F 379 MET cc_start: 0.8768 (ttp) cc_final: 0.8379 (ptm) REVERT: F 417 HIS cc_start: 0.8153 (OUTLIER) cc_final: 0.7862 (m-70) REVERT: F 463 GLU cc_start: 0.9302 (OUTLIER) cc_final: 0.9045 (mm-30) REVERT: F 529 MET cc_start: 0.8758 (mmm) cc_final: 0.8524 (mmm) REVERT: F 560 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9335 (mm) REVERT: F 597 MET cc_start: 0.8893 (ptp) cc_final: 0.8295 (ptp) REVERT: F 614 TYR cc_start: 0.9016 (m-80) cc_final: 0.8740 (m-80) REVERT: F 648 LYS cc_start: 0.9667 (tttt) cc_final: 0.9000 (tppt) REVERT: F 662 LEU cc_start: 0.9587 (tp) cc_final: 0.9354 (tp) REVERT: F 664 MET cc_start: 0.8635 (mpp) cc_final: 0.8265 (mpp) REVERT: G 196 TRP cc_start: -0.0917 (OUTLIER) cc_final: -0.2467 (m100) REVERT: H 1 MET cc_start: 0.1531 (mtt) cc_final: 0.0764 (ttm) REVERT: H 189 MET cc_start: 0.7170 (mmm) cc_final: 0.6855 (mmm) REVERT: J 43 MET cc_start: 0.3406 (ppp) cc_final: 0.2330 (ppp) REVERT: J 76 ARG cc_start: 0.2843 (mtt180) cc_final: 0.2310 (ttp-110) REVERT: K 60 LEU cc_start: 0.9311 (mm) cc_final: 0.9051 (mm) REVERT: K 83 PHE cc_start: 0.9028 (m-80) cc_final: 0.8571 (m-80) REVERT: K 170 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8155 (mp10) REVERT: K 205 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8534 (mmtt) outliers start: 92 outliers final: 58 residues processed: 489 average time/residue: 0.2176 time to fit residues: 176.9035 Evaluate side-chains 460 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 388 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 428 PHE Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 614 TYR Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 745 ASP Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 560 LEU Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain G residue 196 TRP Chi-restraints excluded: chain G residue 259 HIS Chi-restraints excluded: chain H residue 192 ARG Chi-restraints excluded: chain K residue 52 HIS Chi-restraints excluded: chain K residue 122 PHE Chi-restraints excluded: chain K residue 129 TYR Chi-restraints excluded: chain K residue 133 ASP Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 170 GLN Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 590 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 336 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 419 optimal weight: 20.0000 chunk 428 optimal weight: 6.9990 chunk 386 optimal weight: 20.0000 chunk 357 optimal weight: 0.0050 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.0010 chunk 435 optimal weight: 3.9990 chunk 384 optimal weight: 7.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 GLN ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 GLN C 736 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 GLN G 259 HIS K 82 ASN ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 468 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.090808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059402 restraints weight = 251476.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060686 restraints weight = 143653.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.061040 restraints weight = 100335.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061744 restraints weight = 85574.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061744 restraints weight = 72213.055| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 37930 Z= 0.128 Angle : 0.668 10.815 51197 Z= 0.334 Chirality : 0.042 0.300 5809 Planarity : 0.004 0.064 6647 Dihedral : 9.203 143.321 5396 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.08 % Rotamer: Outliers : 2.34 % Allowed : 17.69 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.88 (0.12), residues: 4699 helix: 1.54 (0.10), residues: 2468 sheet: 0.38 (0.20), residues: 583 loop : -0.77 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 596 TYR 0.028 0.001 TYR H 148 PHE 0.019 0.001 PHE F 327 TRP 0.045 0.002 TRP H 147 HIS 0.015 0.001 HIS G 259 Details of bonding type rmsd covalent geometry : bond 0.00276 (37930) covalent geometry : angle 0.66765 (51197) hydrogen bonds : bond 0.03768 ( 1973) hydrogen bonds : angle 4.41903 ( 5709) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 409 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ILE cc_start: 0.9515 (tp) cc_final: 0.9258 (mm) REVERT: A 379 MET cc_start: 0.9051 (tpt) cc_final: 0.8773 (tpp) REVERT: A 397 LYS cc_start: 0.9492 (ttmt) cc_final: 0.8956 (mtpt) REVERT: A 440 MET cc_start: 0.9623 (mpp) cc_final: 0.9317 (mpp) REVERT: A 676 MET cc_start: 0.8823 (mmp) cc_final: 0.8478 (mmm) REVERT: A 754 MET cc_start: 0.9149 (tpp) cc_final: 0.8757 (mmm) REVERT: B 315 TYR cc_start: 0.9407 (m-10) cc_final: 0.8961 (m-80) REVERT: B 349 ASP cc_start: 0.9342 (t0) cc_final: 0.8909 (t0) REVERT: B 376 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9234 (mm) REVERT: B 754 MET cc_start: 0.9491 (mmp) cc_final: 0.9210 (mmp) REVERT: C 19 MET cc_start: 0.4029 (mmm) cc_final: 0.3139 (mmt) REVERT: C 120 ASP cc_start: 0.9858 (p0) cc_final: 0.9613 (t0) REVERT: C 157 TYR cc_start: 0.9337 (OUTLIER) cc_final: 0.9116 (t80) REVERT: C 311 ILE cc_start: 0.9462 (mm) cc_final: 0.8912 (tp) REVERT: C 323 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9399 (mp) REVERT: C 356 LYS cc_start: 0.9321 (mmmt) cc_final: 0.9096 (mmtm) REVERT: C 369 ASP cc_start: 0.9462 (m-30) cc_final: 0.9225 (p0) REVERT: C 428 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8862 (m-80) REVERT: C 607 ASP cc_start: 0.9331 (t0) cc_final: 0.8616 (t0) REVERT: C 648 LYS cc_start: 0.9602 (tttt) cc_final: 0.9162 (tptt) REVERT: D 19 MET cc_start: -0.2125 (mtm) cc_final: -0.3378 (ptp) REVERT: D 207 PHE cc_start: 0.8837 (m-80) cc_final: 0.8589 (m-80) REVERT: D 252 PHE cc_start: 0.8961 (m-80) cc_final: 0.8685 (m-80) REVERT: D 254 ARG cc_start: 0.9593 (mmm160) cc_final: 0.9187 (mmm160) REVERT: D 275 LYS cc_start: 0.9637 (ptpt) cc_final: 0.9227 (mmmt) REVERT: D 379 MET cc_start: 0.9508 (mmm) cc_final: 0.9076 (mmm) REVERT: D 393 MET cc_start: 0.8890 (pmm) cc_final: 0.8644 (pmm) REVERT: D 396 ARG cc_start: 0.8945 (ptp-110) cc_final: 0.8584 (mtm110) REVERT: D 495 LEU cc_start: 0.9133 (pt) cc_final: 0.8908 (mm) REVERT: D 518 GLU cc_start: 0.9645 (mm-30) cc_final: 0.9332 (mp0) REVERT: D 529 MET cc_start: 0.9098 (mpp) cc_final: 0.8611 (mpp) REVERT: D 597 MET cc_start: 0.9028 (mtp) cc_final: 0.8777 (mpp) REVERT: D 607 ASP cc_start: 0.9381 (t0) cc_final: 0.9012 (t0) REVERT: D 648 LYS cc_start: 0.9722 (ttpt) cc_final: 0.9344 (tptt) REVERT: D 675 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8410 (tm-30) REVERT: D 701 MET cc_start: 0.9225 (ppp) cc_final: 0.8977 (tmm) REVERT: E 294 ILE cc_start: 0.9648 (tp) cc_final: 0.9354 (tp) REVERT: E 298 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8621 (mt) REVERT: E 311 ILE cc_start: 0.9760 (mm) cc_final: 0.9451 (tp) REVERT: E 351 LEU cc_start: 0.9780 (OUTLIER) cc_final: 0.9543 (pp) REVERT: E 375 LEU cc_start: 0.9748 (tt) cc_final: 0.9452 (pp) REVERT: E 379 MET cc_start: 0.9213 (tpp) cc_final: 0.8816 (tpt) REVERT: E 389 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9344 (mm) REVERT: E 410 PHE cc_start: 0.9526 (m-80) cc_final: 0.9279 (m-80) REVERT: E 428 PHE cc_start: 0.9569 (OUTLIER) cc_final: 0.9128 (m-10) REVERT: E 646 MET cc_start: 0.9350 (ttm) cc_final: 0.8748 (tmm) REVERT: E 661 LEU cc_start: 0.9558 (tp) cc_final: 0.9198 (mm) REVERT: E 691 MET cc_start: 0.7937 (ppp) cc_final: 0.7439 (ppp) REVERT: E 745 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8521 (m-30) REVERT: F 280 TYR cc_start: 0.9151 (p90) cc_final: 0.8854 (p90) REVERT: F 379 MET cc_start: 0.8805 (ttp) cc_final: 0.8466 (ptm) REVERT: F 417 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7922 (m-70) REVERT: F 440 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7856 (pmm) REVERT: F 463 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.9072 (mm-30) REVERT: F 529 MET cc_start: 0.8767 (mmm) cc_final: 0.8548 (mmm) REVERT: F 560 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9386 (mm) REVERT: F 597 MET cc_start: 0.8861 (ptp) cc_final: 0.8287 (ptp) REVERT: F 614 TYR cc_start: 0.9018 (m-80) cc_final: 0.8785 (m-80) REVERT: F 648 LYS cc_start: 0.9690 (tttt) cc_final: 0.9010 (tppt) REVERT: F 662 LEU cc_start: 0.9622 (tp) cc_final: 0.9360 (tp) REVERT: F 664 MET cc_start: 0.8676 (mpp) cc_final: 0.8249 (mpp) REVERT: G 196 TRP cc_start: -0.0806 (OUTLIER) cc_final: -0.1810 (m-90) REVERT: H 1 MET cc_start: 0.1612 (mtt) cc_final: 0.0810 (ttm) REVERT: H 189 MET cc_start: 0.7244 (mmm) cc_final: 0.6936 (mmm) REVERT: J 43 MET cc_start: 0.3456 (ppp) cc_final: 0.2531 (ppp) REVERT: J 76 ARG cc_start: 0.2585 (mtt180) cc_final: 0.2065 (ttp-110) REVERT: K 60 LEU cc_start: 0.9318 (mm) cc_final: 0.9053 (mm) REVERT: K 78 HIS cc_start: 0.9158 (m-70) cc_final: 0.8694 (t-90) REVERT: K 83 PHE cc_start: 0.8963 (m-80) cc_final: 0.8541 (m-80) REVERT: K 103 ARG cc_start: 0.9534 (mtm110) cc_final: 0.9298 (mtm180) REVERT: K 170 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8136 (mp10) REVERT: K 205 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8521 (mmtt) REVERT: L 459 MET cc_start: 0.2355 (mmt) cc_final: 0.1048 (mpp) outliers start: 96 outliers final: 64 residues processed: 471 average time/residue: 0.2004 time to fit residues: 156.5688 Evaluate side-chains 475 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 395 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 676 MET Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 428 PHE Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 614 TYR Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 745 ASP Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 440 MET Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 560 LEU Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain G residue 196 TRP Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 52 HIS Chi-restraints excluded: chain K residue 122 PHE Chi-restraints excluded: chain K residue 129 TYR Chi-restraints excluded: chain K residue 133 ASP Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 170 GLN Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 590 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 391 optimal weight: 9.9990 chunk 146 optimal weight: 0.0970 chunk 139 optimal weight: 0.0370 chunk 79 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 321 optimal weight: 8.9990 chunk 429 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 294 optimal weight: 8.9990 overall best weight: 3.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 ASN ** F 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.090302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.058577 restraints weight = 254782.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059957 restraints weight = 152578.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.060388 restraints weight = 101318.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060435 restraints weight = 100042.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060560 restraints weight = 84057.011| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37930 Z= 0.150 Angle : 0.672 11.134 51197 Z= 0.338 Chirality : 0.042 0.231 5809 Planarity : 0.004 0.064 6647 Dihedral : 9.012 143.627 5396 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 2.44 % Allowed : 18.13 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.88 (0.12), residues: 4699 helix: 1.54 (0.10), residues: 2455 sheet: 0.34 (0.20), residues: 583 loop : -0.73 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 596 TYR 0.027 0.001 TYR H 148 PHE 0.024 0.001 PHE F 256 TRP 0.065 0.002 TRP H 147 HIS 0.006 0.001 HIS K 61 Details of bonding type rmsd covalent geometry : bond 0.00319 (37930) covalent geometry : angle 0.67211 (51197) hydrogen bonds : bond 0.03695 ( 1973) hydrogen bonds : angle 4.48797 ( 5709) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 397 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ILE cc_start: 0.9495 (tp) cc_final: 0.9221 (mm) REVERT: A 379 MET cc_start: 0.9047 (tpt) cc_final: 0.8772 (tpp) REVERT: A 393 MET cc_start: 0.8005 (mmm) cc_final: 0.7717 (mtt) REVERT: A 440 MET cc_start: 0.9609 (mpp) cc_final: 0.9313 (mpp) REVERT: A 676 MET cc_start: 0.8886 (mmp) cc_final: 0.8641 (mmm) REVERT: A 754 MET cc_start: 0.9151 (tpp) cc_final: 0.8866 (mmm) REVERT: B 315 TYR cc_start: 0.9366 (m-10) cc_final: 0.8921 (m-80) REVERT: B 349 ASP cc_start: 0.9330 (t0) cc_final: 0.8897 (t0) REVERT: B 376 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9259 (mm) REVERT: B 396 ARG cc_start: 0.8822 (mtp180) cc_final: 0.8435 (mtp-110) REVERT: B 428 PHE cc_start: 0.9505 (OUTLIER) cc_final: 0.8949 (m-80) REVERT: B 754 MET cc_start: 0.9555 (mmp) cc_final: 0.9241 (mmp) REVERT: C 311 ILE cc_start: 0.9502 (mm) cc_final: 0.8957 (tp) REVERT: C 323 ILE cc_start: 0.9644 (OUTLIER) cc_final: 0.9412 (mp) REVERT: C 396 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7742 (ttp80) REVERT: C 428 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8872 (m-80) REVERT: C 607 ASP cc_start: 0.9303 (t0) cc_final: 0.8836 (t0) REVERT: C 624 ASP cc_start: 0.9077 (t0) cc_final: 0.8763 (p0) REVERT: C 648 LYS cc_start: 0.9585 (tttt) cc_final: 0.9180 (tptt) REVERT: D 19 MET cc_start: -0.0138 (mtm) cc_final: -0.1227 (ptp) REVERT: D 207 PHE cc_start: 0.8868 (m-80) cc_final: 0.8648 (m-80) REVERT: D 252 PHE cc_start: 0.8933 (m-80) cc_final: 0.8650 (m-80) REVERT: D 254 ARG cc_start: 0.9572 (mmm160) cc_final: 0.9189 (mmm160) REVERT: D 261 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.8666 (t80) REVERT: D 275 LYS cc_start: 0.9623 (ptpt) cc_final: 0.9230 (mmmt) REVERT: D 379 MET cc_start: 0.9429 (mmm) cc_final: 0.8986 (mmm) REVERT: D 393 MET cc_start: 0.8902 (pmm) cc_final: 0.8678 (pmm) REVERT: D 518 GLU cc_start: 0.9597 (mm-30) cc_final: 0.9306 (mp0) REVERT: D 607 ASP cc_start: 0.9307 (t0) cc_final: 0.8947 (t0) REVERT: D 648 LYS cc_start: 0.9697 (ttpt) cc_final: 0.9308 (tptt) REVERT: D 675 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8023 (tm-30) REVERT: D 701 MET cc_start: 0.9231 (ppp) cc_final: 0.8972 (tmm) REVERT: E 294 ILE cc_start: 0.9625 (tp) cc_final: 0.9317 (tp) REVERT: E 298 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8674 (mt) REVERT: E 311 ILE cc_start: 0.9764 (mm) cc_final: 0.9464 (tp) REVERT: E 351 LEU cc_start: 0.9809 (OUTLIER) cc_final: 0.9598 (pp) REVERT: E 375 LEU cc_start: 0.9762 (tt) cc_final: 0.9495 (pp) REVERT: E 379 MET cc_start: 0.9227 (tpp) cc_final: 0.8916 (tpt) REVERT: E 389 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9369 (mm) REVERT: E 410 PHE cc_start: 0.9536 (m-80) cc_final: 0.9278 (m-80) REVERT: E 428 PHE cc_start: 0.9549 (OUTLIER) cc_final: 0.9133 (m-10) REVERT: E 646 MET cc_start: 0.9319 (ttm) cc_final: 0.8743 (tmm) REVERT: E 651 LEU cc_start: 0.9786 (OUTLIER) cc_final: 0.9584 (mm) REVERT: E 661 LEU cc_start: 0.9552 (tp) cc_final: 0.9107 (mm) REVERT: E 691 MET cc_start: 0.7877 (ppp) cc_final: 0.7416 (ppp) REVERT: E 745 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8518 (m-30) REVERT: F 256 PHE cc_start: 0.8960 (m-10) cc_final: 0.8547 (m-80) REVERT: F 280 TYR cc_start: 0.9240 (p90) cc_final: 0.9016 (p90) REVERT: F 379 MET cc_start: 0.8889 (ttp) cc_final: 0.8556 (ptm) REVERT: F 463 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.9098 (mm-30) REVERT: F 560 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9331 (mm) REVERT: F 597 MET cc_start: 0.8828 (ptp) cc_final: 0.8238 (ptp) REVERT: F 614 TYR cc_start: 0.9064 (m-80) cc_final: 0.8821 (m-80) REVERT: F 648 LYS cc_start: 0.9669 (tttt) cc_final: 0.8976 (tppt) REVERT: F 664 MET cc_start: 0.8669 (mpp) cc_final: 0.8430 (mpp) REVERT: G 196 TRP cc_start: -0.1029 (OUTLIER) cc_final: -0.3465 (m100) REVERT: H 1 MET cc_start: 0.1382 (mtt) cc_final: 0.0520 (ttm) REVERT: H 189 MET cc_start: 0.7392 (mmm) cc_final: 0.7141 (mmm) REVERT: J 43 MET cc_start: 0.3263 (ppp) cc_final: 0.2352 (ppp) REVERT: J 76 ARG cc_start: 0.2526 (mtt180) cc_final: 0.2005 (ttp-110) REVERT: K 78 HIS cc_start: 0.9037 (m-70) cc_final: 0.8811 (t-90) REVERT: K 170 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: L 459 MET cc_start: 0.2205 (mmt) cc_final: 0.0950 (mtt) outliers start: 100 outliers final: 68 residues processed: 463 average time/residue: 0.2145 time to fit residues: 164.9418 Evaluate side-chains 460 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 377 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 428 PHE Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 745 ASP Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 560 LEU Chi-restraints excluded: chain G residue 196 TRP Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain K residue 52 HIS Chi-restraints excluded: chain K residue 122 PHE Chi-restraints excluded: chain K residue 129 TYR Chi-restraints excluded: chain K residue 133 ASP Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 170 GLN Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 590 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 283 optimal weight: 30.0000 chunk 364 optimal weight: 7.9990 chunk 121 optimal weight: 0.0020 chunk 349 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 358 optimal weight: 0.3980 chunk 320 optimal weight: 6.9990 chunk 348 optimal weight: 7.9990 chunk 156 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 overall best weight: 2.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 ASN ** F 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 ASN ** K 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.090262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.059448 restraints weight = 254324.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.060616 restraints weight = 146290.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061552 restraints weight = 102270.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.061691 restraints weight = 81123.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.061813 restraints weight = 76068.611| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37930 Z= 0.135 Angle : 0.686 15.368 51197 Z= 0.342 Chirality : 0.042 0.318 5809 Planarity : 0.004 0.112 6647 Dihedral : 8.823 143.424 5394 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 2.20 % Allowed : 18.32 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.12), residues: 4699 helix: 1.57 (0.10), residues: 2461 sheet: 0.41 (0.20), residues: 583 loop : -0.69 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 45 TYR 0.026 0.001 TYR H 148 PHE 0.036 0.001 PHE G 263 TRP 0.059 0.002 TRP H 147 HIS 0.008 0.001 HIS K 61 Details of bonding type rmsd covalent geometry : bond 0.00292 (37930) covalent geometry : angle 0.68580 (51197) hydrogen bonds : bond 0.03666 ( 1973) hydrogen bonds : angle 4.43188 ( 5709) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 388 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ILE cc_start: 0.9476 (tp) cc_final: 0.9205 (mm) REVERT: A 379 MET cc_start: 0.8958 (tpt) cc_final: 0.8718 (tpp) REVERT: A 397 LYS cc_start: 0.9498 (ttmt) cc_final: 0.8988 (mtpt) REVERT: A 440 MET cc_start: 0.9558 (mpp) cc_final: 0.9307 (mpp) REVERT: A 676 MET cc_start: 0.8910 (mmp) cc_final: 0.8604 (mmm) REVERT: A 754 MET cc_start: 0.9146 (tpp) cc_final: 0.8874 (mmm) REVERT: B 349 ASP cc_start: 0.9216 (t0) cc_final: 0.8783 (t0) REVERT: B 376 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9207 (mm) REVERT: B 396 ARG cc_start: 0.8784 (mtp180) cc_final: 0.8423 (mtp-110) REVERT: B 428 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.8888 (m-80) REVERT: B 754 MET cc_start: 0.9429 (mmp) cc_final: 0.9168 (mmp) REVERT: C 157 TYR cc_start: 0.9223 (t80) cc_final: 0.9003 (t80) REVERT: C 172 ARG cc_start: 0.8085 (ttt180) cc_final: 0.7739 (ttt180) REVERT: C 311 ILE cc_start: 0.9506 (mm) cc_final: 0.8961 (tp) REVERT: C 323 ILE cc_start: 0.9630 (OUTLIER) cc_final: 0.9403 (mp) REVERT: C 396 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7838 (ttp80) REVERT: C 428 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8798 (m-80) REVERT: C 607 ASP cc_start: 0.9208 (t0) cc_final: 0.8711 (t0) REVERT: C 612 ASP cc_start: 0.8973 (p0) cc_final: 0.8768 (p0) REVERT: C 624 ASP cc_start: 0.9022 (t0) cc_final: 0.8757 (p0) REVERT: C 648 LYS cc_start: 0.9529 (tttt) cc_final: 0.9131 (tptt) REVERT: D 19 MET cc_start: -0.2762 (mtm) cc_final: -0.3994 (ptp) REVERT: D 207 PHE cc_start: 0.8815 (m-80) cc_final: 0.8556 (m-80) REVERT: D 254 ARG cc_start: 0.9515 (mmm160) cc_final: 0.9191 (mmm160) REVERT: D 261 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8620 (t80) REVERT: D 275 LYS cc_start: 0.9610 (ptpt) cc_final: 0.9236 (mmmt) REVERT: D 379 MET cc_start: 0.9388 (mmm) cc_final: 0.8969 (mmm) REVERT: D 393 MET cc_start: 0.8869 (pmm) cc_final: 0.8648 (pmm) REVERT: D 518 GLU cc_start: 0.9582 (mm-30) cc_final: 0.9305 (mp0) REVERT: D 597 MET cc_start: 0.8925 (mtp) cc_final: 0.8721 (mpp) REVERT: D 607 ASP cc_start: 0.9217 (t0) cc_final: 0.8847 (t0) REVERT: D 648 LYS cc_start: 0.9674 (ttpt) cc_final: 0.9303 (tptt) REVERT: D 675 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7969 (tm-30) REVERT: D 701 MET cc_start: 0.9137 (ppp) cc_final: 0.8911 (tmm) REVERT: E 294 ILE cc_start: 0.9637 (tp) cc_final: 0.9337 (tp) REVERT: E 298 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8594 (mt) REVERT: E 311 ILE cc_start: 0.9762 (mm) cc_final: 0.9485 (tp) REVERT: E 314 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7930 (tppt) REVERT: E 375 LEU cc_start: 0.9740 (tt) cc_final: 0.9493 (pp) REVERT: E 379 MET cc_start: 0.9214 (tpp) cc_final: 0.8897 (tpt) REVERT: E 389 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9313 (mm) REVERT: E 410 PHE cc_start: 0.9478 (m-80) cc_final: 0.9173 (m-80) REVERT: E 428 PHE cc_start: 0.9479 (OUTLIER) cc_final: 0.9098 (m-10) REVERT: E 646 MET cc_start: 0.9256 (ttm) cc_final: 0.8704 (tmm) REVERT: E 651 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9570 (mm) REVERT: E 661 LEU cc_start: 0.9520 (tp) cc_final: 0.9087 (mm) REVERT: E 691 MET cc_start: 0.7848 (ppp) cc_final: 0.7392 (ppp) REVERT: E 745 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8528 (m-30) REVERT: F 256 PHE cc_start: 0.8848 (m-10) cc_final: 0.8378 (m-80) REVERT: F 280 TYR cc_start: 0.9223 (p90) cc_final: 0.8956 (p90) REVERT: F 379 MET cc_start: 0.8848 (ttp) cc_final: 0.8487 (ptm) REVERT: F 463 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.9006 (mm-30) REVERT: F 529 MET cc_start: 0.8771 (mmm) cc_final: 0.7952 (mmm) REVERT: F 560 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9214 (mm) REVERT: F 597 MET cc_start: 0.8883 (ptp) cc_final: 0.8266 (ptp) REVERT: F 614 TYR cc_start: 0.9014 (m-80) cc_final: 0.8790 (m-80) REVERT: F 648 LYS cc_start: 0.9607 (tttt) cc_final: 0.8895 (tppt) REVERT: F 664 MET cc_start: 0.8581 (mpp) cc_final: 0.8367 (mpp) REVERT: G 196 TRP cc_start: -0.0911 (OUTLIER) cc_final: -0.3212 (m100) REVERT: H 1 MET cc_start: 0.1546 (mtt) cc_final: 0.0732 (ttm) REVERT: H 189 MET cc_start: 0.7101 (mmm) cc_final: 0.6793 (mmm) REVERT: J 43 MET cc_start: 0.3258 (ppp) cc_final: 0.2463 (ppp) REVERT: J 76 ARG cc_start: 0.2350 (mtt180) cc_final: 0.1813 (ttp-110) REVERT: L 459 MET cc_start: 0.1547 (mmt) cc_final: 0.0571 (mpp) outliers start: 90 outliers final: 66 residues processed: 452 average time/residue: 0.2131 time to fit residues: 160.5315 Evaluate side-chains 455 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 375 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 314 LYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 428 PHE Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 745 ASP Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 560 LEU Chi-restraints excluded: chain G residue 196 TRP Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain K residue 52 HIS Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 122 PHE Chi-restraints excluded: chain K residue 129 TYR Chi-restraints excluded: chain K residue 133 ASP Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 590 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 160 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 385 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 467 optimal weight: 50.0000 chunk 421 optimal weight: 30.0000 chunk 109 optimal weight: 0.3980 chunk 103 optimal weight: 6.9990 chunk 400 optimal weight: 0.0870 chunk 438 optimal weight: 20.0000 overall best weight: 2.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.090508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.060005 restraints weight = 254261.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.061048 restraints weight = 147254.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.061555 restraints weight = 110244.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.062276 restraints weight = 89758.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.062165 restraints weight = 81210.074| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37930 Z= 0.131 Angle : 0.701 15.862 51197 Z= 0.346 Chirality : 0.043 0.337 5809 Planarity : 0.004 0.064 6647 Dihedral : 8.659 143.062 5394 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.81 % Rotamer: Outliers : 2.10 % Allowed : 18.49 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.13), residues: 4699 helix: 1.59 (0.11), residues: 2470 sheet: 0.45 (0.20), residues: 582 loop : -0.68 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 45 TYR 0.026 0.001 TYR H 148 PHE 0.045 0.001 PHE D 252 TRP 0.053 0.002 TRP H 147 HIS 0.006 0.001 HIS K 61 Details of bonding type rmsd covalent geometry : bond 0.00283 (37930) covalent geometry : angle 0.70076 (51197) hydrogen bonds : bond 0.03609 ( 1973) hydrogen bonds : angle 4.40980 ( 5709) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 390 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.9628 (mmtt) cc_final: 0.9372 (mmtp) REVERT: A 305 ILE cc_start: 0.9522 (tp) cc_final: 0.9279 (mm) REVERT: A 379 MET cc_start: 0.9085 (tpt) cc_final: 0.8814 (tpp) REVERT: A 396 ARG cc_start: 0.8965 (tpp80) cc_final: 0.8703 (tpp80) REVERT: A 397 LYS cc_start: 0.9467 (ttmt) cc_final: 0.8991 (mtpt) REVERT: A 440 MET cc_start: 0.9592 (mpp) cc_final: 0.9301 (mpp) REVERT: A 676 MET cc_start: 0.9014 (mmp) cc_final: 0.8757 (mmp) REVERT: A 754 MET cc_start: 0.9167 (tpp) cc_final: 0.8907 (mmm) REVERT: B 297 MET cc_start: 0.8878 (mpp) cc_final: 0.8394 (mpp) REVERT: B 349 ASP cc_start: 0.9296 (t0) cc_final: 0.8842 (t0) REVERT: B 356 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8679 (mmtm) REVERT: B 376 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9234 (mm) REVERT: B 396 ARG cc_start: 0.8839 (mtp180) cc_final: 0.8591 (mtp-110) REVERT: B 428 PHE cc_start: 0.9524 (OUTLIER) cc_final: 0.8956 (m-80) REVERT: B 754 MET cc_start: 0.9515 (mmp) cc_final: 0.9239 (mmp) REVERT: C 19 MET cc_start: 0.3607 (mmm) cc_final: 0.2657 (mmt) REVERT: C 120 ASP cc_start: 0.9890 (p0) cc_final: 0.9628 (t0) REVERT: C 157 TYR cc_start: 0.9311 (t80) cc_final: 0.9102 (t80) REVERT: C 172 ARG cc_start: 0.8130 (ttt180) cc_final: 0.7773 (ttt180) REVERT: C 298 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8894 (mm) REVERT: C 311 ILE cc_start: 0.9433 (mm) cc_final: 0.8833 (tp) REVERT: C 323 ILE cc_start: 0.9656 (OUTLIER) cc_final: 0.9410 (mp) REVERT: C 369 ASP cc_start: 0.9387 (p0) cc_final: 0.9108 (p0) REVERT: C 396 ARG cc_start: 0.8325 (ttp80) cc_final: 0.7868 (ttp80) REVERT: C 428 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8844 (m-80) REVERT: C 607 ASP cc_start: 0.9343 (t0) cc_final: 0.8884 (t0) REVERT: C 624 ASP cc_start: 0.9177 (t0) cc_final: 0.8715 (p0) REVERT: C 648 LYS cc_start: 0.9632 (tttt) cc_final: 0.9191 (tptt) REVERT: C 673 LEU cc_start: 0.9789 (tt) cc_final: 0.9567 (pp) REVERT: D 19 MET cc_start: -0.2098 (mtm) cc_final: -0.3315 (ptp) REVERT: D 207 PHE cc_start: 0.8839 (m-80) cc_final: 0.8590 (m-80) REVERT: D 254 ARG cc_start: 0.9614 (mmm160) cc_final: 0.9146 (mmm160) REVERT: D 261 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.8679 (t80) REVERT: D 275 LYS cc_start: 0.9629 (ptpt) cc_final: 0.9234 (mmmt) REVERT: D 379 MET cc_start: 0.9458 (mmm) cc_final: 0.9001 (mmm) REVERT: D 393 MET cc_start: 0.8961 (pmm) cc_final: 0.8715 (pmm) REVERT: D 518 GLU cc_start: 0.9629 (mm-30) cc_final: 0.9320 (mp0) REVERT: D 597 MET cc_start: 0.9053 (mtp) cc_final: 0.8736 (mpp) REVERT: D 607 ASP cc_start: 0.9319 (t0) cc_final: 0.8941 (t0) REVERT: D 648 LYS cc_start: 0.9685 (ttpt) cc_final: 0.9316 (tptt) REVERT: D 675 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7995 (tm-30) REVERT: D 701 MET cc_start: 0.9256 (ppp) cc_final: 0.9017 (tmm) REVERT: E 294 ILE cc_start: 0.9628 (tp) cc_final: 0.9352 (tp) REVERT: E 298 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8583 (mt) REVERT: E 311 ILE cc_start: 0.9744 (mm) cc_final: 0.9471 (tp) REVERT: E 314 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7867 (tppt) REVERT: E 375 LEU cc_start: 0.9754 (tt) cc_final: 0.9501 (pp) REVERT: E 379 MET cc_start: 0.9258 (tpp) cc_final: 0.8962 (tpt) REVERT: E 389 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9349 (mm) REVERT: E 428 PHE cc_start: 0.9559 (OUTLIER) cc_final: 0.9140 (m-10) REVERT: E 482 LYS cc_start: 0.9287 (pttm) cc_final: 0.9015 (mmpt) REVERT: E 646 MET cc_start: 0.9348 (ttm) cc_final: 0.8779 (tmm) REVERT: E 647 LEU cc_start: 0.9876 (OUTLIER) cc_final: 0.9608 (mm) REVERT: E 651 LEU cc_start: 0.9782 (OUTLIER) cc_final: 0.9572 (mm) REVERT: E 661 LEU cc_start: 0.9594 (tp) cc_final: 0.9152 (mm) REVERT: E 691 MET cc_start: 0.8092 (ppp) cc_final: 0.7525 (ppp) REVERT: E 745 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8547 (m-30) REVERT: F 256 PHE cc_start: 0.8912 (m-10) cc_final: 0.8448 (m-80) REVERT: F 280 TYR cc_start: 0.9263 (p90) cc_final: 0.9053 (p90) REVERT: F 379 MET cc_start: 0.8880 (ttp) cc_final: 0.8498 (ptm) REVERT: F 463 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.9058 (mm-30) REVERT: F 529 MET cc_start: 0.8689 (mmm) cc_final: 0.7795 (mmm) REVERT: F 560 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9358 (mm) REVERT: F 597 MET cc_start: 0.8857 (ptp) cc_final: 0.8260 (ptp) REVERT: F 607 ASP cc_start: 0.9474 (t0) cc_final: 0.9148 (t0) REVERT: F 614 TYR cc_start: 0.9095 (m-80) cc_final: 0.8831 (m-80) REVERT: F 648 LYS cc_start: 0.9697 (tttt) cc_final: 0.8981 (tppt) REVERT: F 664 MET cc_start: 0.8680 (mpp) cc_final: 0.8427 (mpp) REVERT: G 196 TRP cc_start: -0.0700 (OUTLIER) cc_final: -0.3091 (m100) REVERT: H 1 MET cc_start: 0.1694 (mtt) cc_final: 0.0873 (ttm) REVERT: H 189 MET cc_start: 0.7211 (mmm) cc_final: 0.6908 (mmm) REVERT: J 43 MET cc_start: 0.3164 (ppp) cc_final: 0.2360 (ppp) REVERT: J 76 ARG cc_start: 0.2158 (mtt180) cc_final: 0.1641 (ttp-110) REVERT: K 78 HIS cc_start: 0.9155 (m-70) cc_final: 0.8664 (t-90) REVERT: K 149 MET cc_start: 0.6949 (pmm) cc_final: 0.6544 (pmm) REVERT: L 452 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: L 459 MET cc_start: 0.1880 (mmt) cc_final: 0.0901 (mpp) outliers start: 86 outliers final: 64 residues processed: 451 average time/residue: 0.1972 time to fit residues: 149.4540 Evaluate side-chains 460 residues out of total 4099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 379 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 314 LYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 428 PHE Chi-restraints excluded: chain E residue 458 SER Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 677 ASP Chi-restraints excluded: chain E residue 745 ASP Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 440 MET Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 560 LEU Chi-restraints excluded: chain G residue 196 TRP Chi-restraints excluded: chain H residue 134 TYR Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain K residue 52 HIS Chi-restraints excluded: chain K residue 122 PHE Chi-restraints excluded: chain K residue 129 TYR Chi-restraints excluded: chain K residue 133 ASP Chi-restraints excluded: chain K residue 158 ASP Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 590 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 45 optimal weight: 7.9990 chunk 267 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 275 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 406 optimal weight: 50.0000 chunk 435 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN F 536 ASN ** F 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.089506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060037 restraints weight = 257007.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061019 restraints weight = 149794.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.061645 restraints weight = 109392.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063019 restraints weight = 84566.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062814 restraints weight = 67084.022| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37930 Z= 0.157 Angle : 0.696 13.246 51197 Z= 0.347 Chirality : 0.043 0.313 5809 Planarity : 0.004 0.066 6647 Dihedral : 8.642 143.651 5394 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 2.10 % Allowed : 18.76 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 4699 helix: 1.56 (0.10), residues: 2483 sheet: 0.41 (0.20), residues: 581 loop : -0.68 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 45 TYR 0.025 0.001 TYR H 148 PHE 0.052 0.001 PHE D 252 TRP 0.054 0.002 TRP H 147 HIS 0.006 0.001 HIS K 61 Details of bonding type rmsd covalent geometry : bond 0.00335 (37930) covalent geometry : angle 0.69590 (51197) hydrogen bonds : bond 0.03595 ( 1973) hydrogen bonds : angle 4.49481 ( 5709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8647.00 seconds wall clock time: 149 minutes 33.41 seconds (8973.41 seconds total)