Starting phenix.real_space_refine on Sun Jul 5 12:52:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uqj_26696/07_2026/7uqj_26696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uqj_26696/07_2026/7uqj_26696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uqj_26696/07_2026/7uqj_26696.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uqj_26696/07_2026/7uqj_26696.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uqj_26696/07_2026/7uqj_26696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uqj_26696/07_2026/7uqj_26696.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uqj_26696/07_2026/7uqj_26696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uqj_26696/07_2026/7uqj_26696.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 4 5.21 5 S 107 5.16 5 C 17881 2.51 5 N 4741 2.21 5 O 5233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27983 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4646 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 33, 'TRANS': 551} Chain breaks: 2 Chain: "B" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4573 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 541} Chain breaks: 2 Chain: "C" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4622 Classifications: {'peptide': 581} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 547} Chain breaks: 2 Chain: "D" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4622 Classifications: {'peptide': 581} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 547} Chain breaks: 2 Chain: "E" Number of atoms: 4598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4598 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 545} Chain breaks: 2 Chain: "F" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4628 Classifications: {'peptide': 581} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 548} Chain breaks: 2 Chain: "G" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 108 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.96, per 1000 atoms: 0.21 Number of scatterers: 27983 At special positions: 0 Unit cell: (125.856, 150.696, 158.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 107 16.00 P 17 15.00 Mg 4 11.99 O 5233 8.00 N 4741 7.00 C 17881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 941.0 milliseconds 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6688 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 12 sheets defined 54.5% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.880A pdb=" N GLU A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 removed outlier: 3.544A pdb=" N LEU A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.816A pdb=" N TYR A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 494 through 510 removed outlier: 4.034A pdb=" N ARG A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.580A pdb=" N LEU A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 546 removed outlier: 3.570A pdb=" N VAL A 539 " --> pdb=" O HIS A 535 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 598 Processing helix chain 'A' and resid 607 through 617 Processing helix chain 'A' and resid 622 through 642 Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.856A pdb=" N ARG A 647 " --> pdb=" O GLN A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 670 removed outlier: 3.607A pdb=" N PHE A 666 " --> pdb=" O LYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 removed outlier: 5.722A pdb=" N ASP A 698 " --> pdb=" O PRO A 694 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN A 699 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.673A pdb=" N GLN A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 757 through 765 Processing helix chain 'A' and resid 781 through 793 removed outlier: 3.609A pdb=" N ALA A 787 " --> pdb=" O GLN A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 807 Processing helix chain 'A' and resid 813 through 828 removed outlier: 3.736A pdb=" N VAL A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 845 removed outlier: 3.906A pdb=" N ASN A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 859 removed outlier: 3.587A pdb=" N ILE A 850 " --> pdb=" O PRO A 846 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 883 removed outlier: 3.878A pdb=" N VAL A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 909 through 917 removed outlier: 3.782A pdb=" N ILE A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1338 removed outlier: 3.589A pdb=" N ILE A1327 " --> pdb=" O THR A1323 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A1328 " --> pdb=" O PRO A1324 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A1333 " --> pdb=" O LYS A1329 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A1336 " --> pdb=" O ALA A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1360 removed outlier: 3.882A pdb=" N SER A1360 " --> pdb=" O ILE A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1377 Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.560A pdb=" N ILE B 415 " --> pdb=" O PHE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 430 removed outlier: 3.683A pdb=" N ASP B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.795A pdb=" N TYR B 439 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 removed outlier: 3.608A pdb=" N ALA B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 510 removed outlier: 3.676A pdb=" N ALA B 496 " --> pdb=" O TRP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.710A pdb=" N LEU B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 547 removed outlier: 3.793A pdb=" N ALA B 536 " --> pdb=" O GLU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 567 removed outlier: 3.688A pdb=" N ALA B 566 " --> pdb=" O ARG B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 572 Processing helix chain 'B' and resid 587 through 600 Processing helix chain 'B' and resid 607 through 618 Processing helix chain 'B' and resid 622 through 642 Processing helix chain 'B' and resid 643 through 647 Processing helix chain 'B' and resid 662 through 673 removed outlier: 3.547A pdb=" N LYS B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 712 removed outlier: 5.424A pdb=" N ASP B 698 " --> pdb=" O PRO B 694 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 Processing helix chain 'B' and resid 758 through 765 Processing helix chain 'B' and resid 781 through 793 removed outlier: 3.849A pdb=" N ALA B 787 " --> pdb=" O GLN B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 807 Processing helix chain 'B' and resid 813 through 828 Processing helix chain 'B' and resid 837 through 845 removed outlier: 3.759A pdb=" N ASN B 843 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 859 removed outlier: 3.532A pdb=" N ILE B 850 " --> pdb=" O PRO B 846 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B 852 " --> pdb=" O ASN B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 882 removed outlier: 3.650A pdb=" N ASN B 882 " --> pdb=" O SER B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.786A pdb=" N SER B 886 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP B 887 " --> pdb=" O ILE B 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 883 through 887' Processing helix chain 'B' and resid 901 through 917 removed outlier: 4.293A pdb=" N ASN B 911 " --> pdb=" O ARG B 907 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 912 " --> pdb=" O TYR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 1325 through 1338 Processing helix chain 'B' and resid 1342 through 1360 removed outlier: 3.576A pdb=" N VAL B1349 " --> pdb=" O GLN B1345 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B1360 " --> pdb=" O ILE B1356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1366 through 1377 removed outlier: 3.524A pdb=" N VAL B1370 " --> pdb=" O LYS B1366 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 removed outlier: 3.795A pdb=" N ILE C 415 " --> pdb=" O PHE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.585A pdb=" N ASP C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 435 through 442 removed outlier: 4.143A pdb=" N TYR C 439 " --> pdb=" O TYR C 435 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 471 Processing helix chain 'C' and resid 495 through 510 Processing helix chain 'C' and resid 520 through 523 Processing helix chain 'C' and resid 532 through 547 removed outlier: 3.586A pdb=" N ALA C 536 " --> pdb=" O GLU C 532 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL C 539 " --> pdb=" O HIS C 535 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP C 547 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'C' and resid 587 through 599 Processing helix chain 'C' and resid 607 through 618 Processing helix chain 'C' and resid 622 through 642 Processing helix chain 'C' and resid 643 through 647 removed outlier: 3.604A pdb=" N TYR C 646 " --> pdb=" O PRO C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 673 removed outlier: 3.714A pdb=" N PHE C 666 " --> pdb=" O LYS C 662 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 672 " --> pdb=" O LEU C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 679 removed outlier: 3.705A pdb=" N ARG C 679 " --> pdb=" O SER C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 712 removed outlier: 5.271A pdb=" N ASP C 698 " --> pdb=" O PRO C 694 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLN C 699 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN C 702 " --> pdb=" O ASP C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 758 through 765 Processing helix chain 'C' and resid 781 through 793 Processing helix chain 'C' and resid 802 through 807 Processing helix chain 'C' and resid 815 through 828 removed outlier: 3.586A pdb=" N ARG C 828 " --> pdb=" O GLU C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 844 removed outlier: 3.959A pdb=" N ASN C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 859 removed outlier: 3.514A pdb=" N ILE C 850 " --> pdb=" O PRO C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 882 removed outlier: 3.645A pdb=" N ASN C 882 " --> pdb=" O SER C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 4.221A pdb=" N ASP C 887 " --> pdb=" O ILE C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 917 removed outlier: 3.886A pdb=" N ASN C 911 " --> pdb=" O ARG C 907 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU C 912 " --> pdb=" O TYR C 908 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 1323 through 1338 removed outlier: 3.724A pdb=" N CYS C1338 " --> pdb=" O LEU C1334 " (cutoff:3.500A) Processing helix chain 'C' and resid 1342 through 1360 removed outlier: 3.892A pdb=" N SER C1360 " --> pdb=" O ILE C1356 " (cutoff:3.500A) Processing helix chain 'C' and resid 1366 through 1378 removed outlier: 3.643A pdb=" N ASP C1371 " --> pdb=" O THR C1367 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 removed outlier: 3.533A pdb=" N ILE D 415 " --> pdb=" O PHE D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 430 removed outlier: 3.694A pdb=" N ILE D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 435 Processing helix chain 'D' and resid 435 through 440 removed outlier: 3.844A pdb=" N TYR D 439 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 472 Processing helix chain 'D' and resid 494 through 510 removed outlier: 3.512A pdb=" N HIS D 510 " --> pdb=" O GLU D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 524 removed outlier: 3.820A pdb=" N LEU D 523 " --> pdb=" O GLU D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 547 removed outlier: 3.878A pdb=" N ALA D 536 " --> pdb=" O GLU D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 567 Processing helix chain 'D' and resid 568 through 572 Processing helix chain 'D' and resid 587 through 599 Processing helix chain 'D' and resid 607 through 617 Processing helix chain 'D' and resid 622 through 642 Processing helix chain 'D' and resid 643 through 648 Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 675 through 679 removed outlier: 3.821A pdb=" N ARG D 679 " --> pdb=" O SER D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 712 removed outlier: 5.258A pdb=" N ASP D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLN D 699 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 730 Processing helix chain 'D' and resid 759 through 764 Processing helix chain 'D' and resid 781 through 793 removed outlier: 3.556A pdb=" N ALA D 787 " --> pdb=" O GLN D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 807 Processing helix chain 'D' and resid 813 through 828 removed outlier: 3.534A pdb=" N ALA D 817 " --> pdb=" O THR D 813 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG D 828 " --> pdb=" O GLU D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 845 removed outlier: 4.492A pdb=" N ASN D 843 " --> pdb=" O ASP D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 859 removed outlier: 3.525A pdb=" N SER D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 876 through 881 removed outlier: 4.007A pdb=" N VAL D 880 " --> pdb=" O ASP D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 917 removed outlier: 3.857A pdb=" N ASN D 911 " --> pdb=" O ARG D 907 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D 912 " --> pdb=" O TYR D 908 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 914 " --> pdb=" O SER D 910 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 915 " --> pdb=" O ASN D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 1323 through 1338 Processing helix chain 'D' and resid 1342 through 1360 Processing helix chain 'D' and resid 1366 through 1377 Processing helix chain 'E' and resid 411 through 415 removed outlier: 3.668A pdb=" N ILE E 415 " --> pdb=" O PHE E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 435 removed outlier: 3.669A pdb=" N ILE E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing helix chain 'E' and resid 437 through 442 removed outlier: 3.649A pdb=" N PHE E 442 " --> pdb=" O LEU E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 471 Processing helix chain 'E' and resid 495 through 510 Processing helix chain 'E' and resid 519 through 524 removed outlier: 3.542A pdb=" N LEU E 523 " --> pdb=" O GLU E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 548 removed outlier: 4.167A pdb=" N ALA E 536 " --> pdb=" O GLU E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 587 through 599 Processing helix chain 'E' and resid 608 through 617 Processing helix chain 'E' and resid 622 through 642 Processing helix chain 'E' and resid 644 through 648 removed outlier: 3.924A pdb=" N ARG E 647 " --> pdb=" O GLN E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 659 Processing helix chain 'E' and resid 662 through 672 removed outlier: 3.765A pdb=" N LYS E 671 " --> pdb=" O MET E 667 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS E 672 " --> pdb=" O LEU E 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 679 removed outlier: 3.518A pdb=" N ARG E 679 " --> pdb=" O SER E 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 707 removed outlier: 5.639A pdb=" N ASP E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLN E 699 " --> pdb=" O LEU E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 717 removed outlier: 3.873A pdb=" N THR E 716 " --> pdb=" O ASN E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 731 Processing helix chain 'E' and resid 758 through 765 Processing helix chain 'E' and resid 781 through 793 Processing helix chain 'E' and resid 802 through 807 Processing helix chain 'E' and resid 813 through 826 Processing helix chain 'E' and resid 837 through 845 removed outlier: 3.979A pdb=" N ASN E 843 " --> pdb=" O ASP E 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 846 through 858 removed outlier: 3.621A pdb=" N ILE E 850 " --> pdb=" O PRO E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 877 through 882 removed outlier: 3.652A pdb=" N LYS E 881 " --> pdb=" O ILE E 877 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN E 882 " --> pdb=" O SER E 878 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 877 through 882' Processing helix chain 'E' and resid 883 through 888 removed outlier: 4.065A pdb=" N ASP E 887 " --> pdb=" O ILE E 884 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 910 Processing helix chain 'E' and resid 912 through 917 Processing helix chain 'E' and resid 1328 through 1338 removed outlier: 3.762A pdb=" N CYS E1333 " --> pdb=" O LYS E1329 " (cutoff:3.500A) Processing helix chain 'E' and resid 1342 through 1360 removed outlier: 3.713A pdb=" N SER E1360 " --> pdb=" O ILE E1356 " (cutoff:3.500A) Processing helix chain 'E' and resid 1366 through 1377 removed outlier: 3.882A pdb=" N GLU E1372 " --> pdb=" O GLY E1368 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 429 Processing helix chain 'F' and resid 429 through 435 Processing helix chain 'F' and resid 435 through 440 Processing helix chain 'F' and resid 459 through 470 removed outlier: 3.659A pdb=" N ALA F 464 " --> pdb=" O LYS F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 510 Processing helix chain 'F' and resid 519 through 524 removed outlier: 3.652A pdb=" N LEU F 523 " --> pdb=" O GLU F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 549 removed outlier: 3.580A pdb=" N ALA F 536 " --> pdb=" O GLU F 532 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA F 544 " --> pdb=" O SER F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 567 Processing helix chain 'F' and resid 568 through 573 removed outlier: 3.626A pdb=" N LEU F 571 " --> pdb=" O ASP F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 600 Processing helix chain 'F' and resid 607 through 617 Processing helix chain 'F' and resid 622 through 642 Processing helix chain 'F' and resid 662 through 672 removed outlier: 3.825A pdb=" N PHE F 666 " --> pdb=" O LYS F 662 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS F 671 " --> pdb=" O MET F 667 " (cutoff:3.500A) Processing helix chain 'F' and resid 696 through 712 removed outlier: 3.576A pdb=" N LEU F 700 " --> pdb=" O LEU F 696 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 731 removed outlier: 4.088A pdb=" N ASN F 727 " --> pdb=" O SER F 723 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE F 729 " --> pdb=" O LEU F 725 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP F 730 " --> pdb=" O GLN F 726 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 764 removed outlier: 4.226A pdb=" N SER F 755 " --> pdb=" O SER F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 765 through 767 No H-bonds generated for 'chain 'F' and resid 765 through 767' Processing helix chain 'F' and resid 781 through 793 removed outlier: 3.654A pdb=" N ALA F 787 " --> pdb=" O GLN F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 802 through 807 Processing helix chain 'F' and resid 813 through 828 Processing helix chain 'F' and resid 837 through 845 removed outlier: 3.824A pdb=" N ASN F 843 " --> pdb=" O ASP F 839 " (cutoff:3.500A) Processing helix chain 'F' and resid 846 through 859 Processing helix chain 'F' and resid 877 through 882 Processing helix chain 'F' and resid 883 through 887 removed outlier: 4.196A pdb=" N ASP F 887 " --> pdb=" O ILE F 884 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 917 removed outlier: 4.183A pdb=" N ASN F 911 " --> pdb=" O ARG F 907 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU F 912 " --> pdb=" O TYR F 908 " (cutoff:3.500A) Processing helix chain 'F' and resid 1323 through 1338 Processing helix chain 'F' and resid 1342 through 1360 removed outlier: 3.510A pdb=" N VAL F1349 " --> pdb=" O GLN F1345 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER F1360 " --> pdb=" O ILE F1356 " (cutoff:3.500A) Processing helix chain 'F' and resid 1367 through 1377 removed outlier: 3.556A pdb=" N GLU F1372 " --> pdb=" O GLY F1368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 479 through 483 removed outlier: 6.198A pdb=" N SER A 513 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE A 558 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE A 515 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA A 560 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 517 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 579 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 798 through 800 removed outlier: 6.099A pdb=" N GLN A 799 " --> pdb=" O PHE A 834 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 772 " --> pdb=" O CYS A 870 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA A 872 " --> pdb=" O LEU A 772 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 774 " --> pdb=" O ALA A 872 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 479 through 483 removed outlier: 6.209A pdb=" N THR B 479 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE B 516 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE B 481 " --> pdb=" O PHE B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 797 through 800 removed outlier: 6.110A pdb=" N ASN B 797 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE B 834 " --> pdb=" O ASN B 797 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN B 799 " --> pdb=" O PHE B 834 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 479 through 483 removed outlier: 6.464A pdb=" N THR C 479 " --> pdb=" O ILE C 514 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE C 516 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE C 481 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP C 518 " --> pdb=" O PHE C 481 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG C 483 " --> pdb=" O ASP C 518 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 797 through 800 removed outlier: 5.971A pdb=" N ASN C 797 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE C 834 " --> pdb=" O ASN C 797 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN C 799 " --> pdb=" O PHE C 834 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C 772 " --> pdb=" O CYS C 870 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA C 872 " --> pdb=" O LEU C 772 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE C 774 " --> pdb=" O ALA C 872 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 479 through 484 removed outlier: 6.288A pdb=" N THR D 479 " --> pdb=" O ILE D 514 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE D 516 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE D 481 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP D 518 " --> pdb=" O PHE D 481 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG D 483 " --> pdb=" O ASP D 518 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 556 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 797 through 800 Processing sheet with id=AA9, first strand: chain 'E' and resid 479 through 483 removed outlier: 6.050A pdb=" N THR E 479 " --> pdb=" O ILE E 514 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE E 516 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE E 481 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASP E 518 " --> pdb=" O PHE E 481 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG E 483 " --> pdb=" O ASP E 518 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER E 513 " --> pdb=" O ILE E 556 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE E 558 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE E 515 " --> pdb=" O ILE E 558 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA E 560 " --> pdb=" O ILE E 515 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE E 517 " --> pdb=" O ALA E 560 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 797 through 800 removed outlier: 6.218A pdb=" N ASN E 797 " --> pdb=" O VAL E 832 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE E 834 " --> pdb=" O ASN E 797 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN E 799 " --> pdb=" O PHE E 834 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE E 895 " --> pdb=" O ARG E 771 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU E 773 " --> pdb=" O PHE E 895 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 479 through 484 removed outlier: 6.102A pdb=" N THR F 479 " --> pdb=" O ILE F 514 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE F 516 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE F 481 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP F 518 " --> pdb=" O PHE F 481 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG F 483 " --> pdb=" O ASP F 518 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER F 513 " --> pdb=" O ILE F 556 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE F 558 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE F 515 " --> pdb=" O ILE F 558 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA F 560 " --> pdb=" O ILE F 515 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE F 517 " --> pdb=" O ALA F 560 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY F 449 " --> pdb=" O PHE F 577 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG F 579 " --> pdb=" O GLY F 449 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 798 through 800 1224 hydrogen bonds defined for protein. 3549 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.31: 4679 1.31 - 1.47: 10681 1.47 - 1.63: 12990 1.63 - 1.79: 117 1.79 - 1.95: 56 Bond restraints: 28523 Sorted by residual: bond pdb=" C LEU C 860 " pdb=" O LEU C 860 " ideal model delta sigma weight residual 1.234 1.151 0.084 1.33e-02 5.65e+03 3.95e+01 bond pdb=" C LEU A 912 " pdb=" O LEU A 912 " ideal model delta sigma weight residual 1.237 1.171 0.065 1.16e-02 7.43e+03 3.17e+01 bond pdb=" C GLN C 861 " pdb=" O GLN C 861 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.22e-02 6.72e+03 2.67e+01 bond pdb=" C SER C 859 " pdb=" O SER C 859 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.29e-02 6.01e+03 1.89e+01 bond pdb=" C CYS C 768 " pdb=" N LYS C 769 " ideal model delta sigma weight residual 1.332 1.299 0.033 8.60e-03 1.35e+04 1.43e+01 ... (remaining 28518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 37005 2.46 - 4.92: 1416 4.92 - 7.38: 142 7.38 - 9.83: 19 9.83 - 12.29: 3 Bond angle restraints: 38585 Sorted by residual: angle pdb=" C SER D 831 " pdb=" N VAL D 832 " pdb=" CA VAL D 832 " ideal model delta sigma weight residual 122.99 112.28 10.71 1.39e+00 5.18e-01 5.93e+01 angle pdb=" CA GLN C 861 " pdb=" C GLN C 861 " pdb=" O GLN C 861 " ideal model delta sigma weight residual 120.92 112.77 8.15 1.15e+00 7.56e-01 5.03e+01 angle pdb=" N HIS C 510 " pdb=" CA HIS C 510 " pdb=" C HIS C 510 " ideal model delta sigma weight residual 109.96 100.37 9.59 1.49e+00 4.50e-01 4.14e+01 angle pdb=" CA GLN C 861 " pdb=" C GLN C 861 " pdb=" N SER C 862 " ideal model delta sigma weight residual 115.86 123.41 -7.55 1.24e+00 6.50e-01 3.70e+01 angle pdb=" N PRO B 512 " pdb=" CA PRO B 512 " pdb=" C PRO B 512 " ideal model delta sigma weight residual 110.74 101.04 9.70 1.66e+00 3.63e-01 3.41e+01 ... (remaining 38580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.18: 16914 32.18 - 64.36: 598 64.36 - 96.54: 74 96.54 - 128.72: 5 128.72 - 160.90: 4 Dihedral angle restraints: 17595 sinusoidal: 7353 harmonic: 10242 Sorted by residual: dihedral pdb=" C5' ADP A1401 " pdb=" O5' ADP A1401 " pdb=" PA ADP A1401 " pdb=" O2A ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 100.91 -160.90 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O2A ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PA ADP A1401 " pdb=" PB ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 71.45 -131.45 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O1B ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PB ADP A1401 " pdb=" PA ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 65.20 -125.20 1 2.00e+01 2.50e-03 3.78e+01 ... (remaining 17592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3557 0.076 - 0.152: 749 0.152 - 0.228: 74 0.228 - 0.304: 17 0.304 - 0.380: 6 Chirality restraints: 4403 Sorted by residual: chirality pdb=" CA THR E 813 " pdb=" N THR E 813 " pdb=" C THR E 813 " pdb=" CB THR E 813 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE D 845 " pdb=" CA ILE D 845 " pdb=" CG1 ILE D 845 " pdb=" CG2 ILE D 845 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA ILE F 488 " pdb=" N ILE F 488 " pdb=" C ILE F 488 " pdb=" CB ILE F 488 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 4400 not shown) Planarity restraints: 4918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS D 510 " -0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C HIS D 510 " 0.058 2.00e-02 2.50e+03 pdb=" O HIS D 510 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN D 511 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 505 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C GLU D 505 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU D 505 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU D 506 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 933 " -0.050 5.00e-02 4.00e+02 7.55e-02 9.11e+00 pdb=" N PRO E 934 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 934 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 934 " -0.041 5.00e-02 4.00e+02 ... (remaining 4915 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 230 2.58 - 3.16: 21764 3.16 - 3.74: 43976 3.74 - 4.32: 63215 4.32 - 4.90: 102189 Nonbonded interactions: 231374 Sorted by model distance: nonbonded pdb=" O3G AGS D1401 " pdb="MG MG D1402 " model vdw 2.001 2.170 nonbonded pdb=" O2G AGS E1401 " pdb="MG MG E1402 " model vdw 2.025 2.170 nonbonded pdb=" OG1 THR E 461 " pdb="MG MG E1402 " model vdw 2.033 2.170 nonbonded pdb=" OG1 THR D 461 " pdb="MG MG D1402 " model vdw 2.058 2.170 nonbonded pdb=" O1B AGS C1401 " pdb="MG MG C1402 " model vdw 2.081 2.170 ... (remaining 231369 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 407 through 735 or resid 756 through 1378)) selection = (chain 'B' and (resid 407 through 939 or resid 1319 through 1378)) selection = (chain 'C' and (resid 407 through 939 or resid 1319 through 1378)) selection = (chain 'D' and (resid 407 through 939 or resid 1319 through 1378)) selection = (chain 'E' and (resid 407 through 735 or resid 756 through 939 or resid 1319 thr \ ough 1378)) selection = (chain 'F' and (resid 407 through 735 or resid 756 through 939 or resid 1319 thr \ ough 1378)) } 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 individual isotropic 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: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.400 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.050 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:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 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 : 0.010 0.126 28523 Z= 0.476 Angle : 1.075 12.292 38585 Z= 0.629 Chirality : 0.064 0.380 4403 Planarity : 0.008 0.075 4918 Dihedral : 16.880 160.904 10907 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.71 % Rotamer: Outliers : 1.08 % Allowed : 10.23 % Favored : 88.68 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.55 % 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: -3.16 (0.12), residues: 3457 helix: -2.35 (0.10), residues: 1709 sheet: -1.09 (0.26), residues: 361 loop : -1.79 (0.15), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 573 TYR 0.019 0.003 TYR C 784 PHE 0.031 0.003 PHE D1341 TRP 0.021 0.003 TRP B 841 HIS 0.010 0.003 HIS A1350 Details of bonding type rmsd/Z covalent geometry : bond 0.01039 / 0.48 (28523) covalent geometry : angle 1.07514 / 0.63 (38585) hydrogen bonds : bond 0.17152 / 10.94 ( 1224) hydrogen bonds : angle 6.74218 / 4.68 ( 3549) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 813 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 ASP cc_start: 0.6418 (OUTLIER) cc_final: 0.6213 (m-30) REVERT: A 792 TYR cc_start: 0.6952 (t80) cc_final: 0.6276 (t80) REVERT: B 728 PHE cc_start: 0.8387 (m-10) cc_final: 0.8187 (m-80) REVERT: B 757 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6116 (mp0) REVERT: B 873 GLU cc_start: 0.5808 (tt0) cc_final: 0.5537 (tt0) REVERT: B 1336 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6385 (tm-30) REVERT: C 541 THR cc_start: 0.5951 (m) cc_final: 0.4896 (p) REVERT: C 578 ASP cc_start: 0.5805 (OUTLIER) cc_final: 0.5383 (m-30) REVERT: C 731 TYR cc_start: 0.7544 (m-80) cc_final: 0.6914 (m-80) REVERT: C 1329 LYS cc_start: 0.7843 (tttt) cc_final: 0.7579 (tttt) REVERT: D 757 GLU cc_start: 0.5180 (mm-30) cc_final: 0.4242 (mm-30) REVERT: F 505 GLU cc_start: 0.6495 (tp30) cc_final: 0.6273 (tp30) REVERT: F 782 GLN cc_start: 0.7187 (mp10) cc_final: 0.6931 (mp10) REVERT: F 936 LEU cc_start: 0.8019 (mt) cc_final: 0.7425 (mt) outliers start: 34 outliers final: 17 residues processed: 838 average time/residue: 0.5878 time to fit residues: 577.5170 Evaluate side-chains 655 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 636 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 715 ASP Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 1377 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain E residue 844 THR Chi-restraints excluded: chain E residue 847 GLU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 863 ASN Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 HIS A 511 GLN A 533 GLN A 609 ASN A 639 GLN ** A 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN A 874 ASN A 904 ASN A1345 GLN B 441 ASN B 533 GLN B 535 HIS B 562 ASN B 644 GLN B 797 ASN B 829 GLN B 904 ASN B1345 GLN C 443 ASN C 531 GLN C 562 ASN C 712 ASN C 800 ASN C 861 GLN C 893 ASN C 896 GLN C1345 GLN C1350 HIS D 511 GLN D 535 HIS D 562 ASN D 596 GLN D 686 GLN D 699 GLN D 702 ASN D 775 ASN D 780 ASN D 797 ASN D 896 GLN D1340 ASN D1345 GLN E 531 GLN E 535 HIS E 699 GLN E 721 ASN E 726 GLN E 727 ASN E 782 GLN E 799 GLN E 848 ASN E1340 ASN E1345 GLN F 420 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 GLN ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 ASN ** F 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 775 ASN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 797 ASN F 799 GLN F 820 GLN F 861 GLN F 863 ASN F 893 ASN F 896 GLN F 937 GLN F1345 GLN G 20 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123551 restraints weight = 40621.830| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.93 r_work: 0.3469 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28523 Z= 0.190 Angle : 0.746 12.232 38585 Z= 0.373 Chirality : 0.046 0.280 4403 Planarity : 0.006 0.064 4918 Dihedral : 9.017 177.055 3810 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 4.11 % Allowed : 18.11 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -1.49 (0.14), residues: 3457 helix: -0.66 (0.12), residues: 1744 sheet: -0.83 (0.27), residues: 337 loop : -1.30 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 640 TYR 0.024 0.002 TYR E 421 PHE 0.035 0.002 PHE D 822 TRP 0.024 0.002 TRP A 841 HIS 0.007 0.002 HIS E1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (28523) covalent geometry : angle 0.74587 / 0.37 (38585) hydrogen bonds : bond 0.04197 / 2.75 ( 1224) hydrogen bonds : angle 4.55976 / 3.18 ( 3549) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 768 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5977 (pp) REVERT: A 424 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7336 (mt0) REVERT: A 477 LYS cc_start: 0.8316 (mppt) cc_final: 0.8045 (mppt) REVERT: A 481 PHE cc_start: 0.7937 (m-80) cc_final: 0.7470 (m-80) REVERT: A 513 SER cc_start: 0.8095 (m) cc_final: 0.7886 (m) REVERT: A 549 MET cc_start: 0.2817 (mmt) cc_final: 0.1291 (mmt) REVERT: A 619 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7227 (mttp) REVERT: A 724 LEU cc_start: 0.7617 (mt) cc_final: 0.7222 (mp) REVERT: A 727 ASN cc_start: 0.8060 (m-40) cc_final: 0.7748 (m-40) REVERT: A 728 PHE cc_start: 0.8330 (m-10) cc_final: 0.8113 (m-80) REVERT: A 902 LYS cc_start: 0.8287 (tppt) cc_final: 0.8025 (tppt) REVERT: A 907 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7950 (ttp80) REVERT: A 1319 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6809 (mt-10) REVERT: A 1365 ASP cc_start: 0.7627 (p0) cc_final: 0.7411 (p0) REVERT: B 414 ASP cc_start: 0.7968 (m-30) cc_final: 0.7763 (m-30) REVERT: B 431 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7631 (tp) REVERT: B 458 THR cc_start: 0.8275 (p) cc_final: 0.7985 (m) REVERT: B 589 LYS cc_start: 0.8628 (ttmm) cc_final: 0.8367 (mmmm) REVERT: B 627 ARG cc_start: 0.8442 (ttt180) cc_final: 0.8058 (ttt180) REVERT: B 632 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7232 (tm-30) REVERT: B 757 GLU cc_start: 0.6792 (mm-30) cc_final: 0.5840 (mp0) REVERT: B 1336 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7237 (tm-30) REVERT: B 1376 PHE cc_start: 0.8489 (t80) cc_final: 0.8262 (t80) REVERT: C 604 SER cc_start: 0.8132 (m) cc_final: 0.7865 (p) REVERT: C 612 ASP cc_start: 0.7942 (m-30) cc_final: 0.7593 (m-30) REVERT: C 613 LYS cc_start: 0.8337 (tttt) cc_final: 0.8087 (tttt) REVERT: C 731 TYR cc_start: 0.7986 (m-80) cc_final: 0.7530 (m-10) REVERT: C 802 ASP cc_start: 0.8085 (p0) cc_final: 0.7852 (p0) REVERT: C 865 LYS cc_start: 0.8381 (ttmt) cc_final: 0.8170 (ttmm) REVERT: C 1327 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7670 (tp) REVERT: C 1329 LYS cc_start: 0.8225 (tttt) cc_final: 0.7967 (tttt) REVERT: C 1336 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7543 (mm-30) REVERT: D 647 ARG cc_start: 0.7600 (tpp80) cc_final: 0.7214 (mmt90) REVERT: D 661 VAL cc_start: 0.7712 (m) cc_final: 0.7418 (t) REVERT: D 798 VAL cc_start: 0.8351 (m) cc_final: 0.8106 (t) REVERT: D 821 SER cc_start: 0.8148 (t) cc_final: 0.7851 (p) REVERT: D 865 LYS cc_start: 0.7455 (mtpt) cc_final: 0.7254 (mtpp) REVERT: D 887 ASP cc_start: 0.6889 (t70) cc_final: 0.6667 (t70) REVERT: D 903 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7607 (tp30) REVERT: D 925 MET cc_start: 0.4754 (mpp) cc_final: 0.4544 (mpp) REVERT: D 928 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.6954 (ttm-80) REVERT: E 421 TYR cc_start: 0.7065 (m-80) cc_final: 0.6316 (m-80) REVERT: E 873 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6634 (mt-10) REVERT: F 422 ILE cc_start: 0.7224 (mt) cc_final: 0.6996 (mp) REVERT: F 463 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7603 (tpp) REVERT: F 591 ARG cc_start: 0.6770 (mtm-85) cc_final: 0.6435 (mtp180) REVERT: F 601 LYS cc_start: 0.7622 (tptp) cc_final: 0.7402 (tptt) REVERT: F 612 ASP cc_start: 0.6974 (t70) cc_final: 0.6736 (t70) REVERT: F 879 GLU cc_start: 0.6817 (tp30) cc_final: 0.6604 (tp30) REVERT: F 880 VAL cc_start: 0.7305 (OUTLIER) cc_final: 0.7053 (p) REVERT: F 1361 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7493 (ttmt) outliers start: 129 outliers final: 40 residues processed: 826 average time/residue: 0.5729 time to fit residues: 554.4670 Evaluate side-chains 728 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 680 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 811 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1327 ILE Chi-restraints excluded: chain C residue 1361 LYS Chi-restraints excluded: chain D residue 440 GLN Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain D residue 797 ASN Chi-restraints excluded: chain D residue 898 HIS Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 561 THR Chi-restraints excluded: chain E residue 607 SER Chi-restraints excluded: chain E residue 665 ASP Chi-restraints excluded: chain E residue 884 ILE Chi-restraints excluded: chain E residue 1340 ASN Chi-restraints excluded: chain F residue 463 MET Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 665 ASP Chi-restraints excluded: chain F residue 725 LEU Chi-restraints excluded: chain F residue 880 VAL Chi-restraints excluded: chain F residue 1361 LYS Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 340 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 266 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 251 optimal weight: 0.6980 chunk 208 optimal weight: 0.4980 chunk 226 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 453 HIS A 554 GLN A 699 GLN A 780 ASN A 799 GLN A 800 ASN A1340 ASN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN B 797 ASN B 904 ASN B1326 GLN C 727 ASN C 791 ASN C 874 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 ASN D 780 ASN D 799 GLN D1350 HIS ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 GLN ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 820 GLN ** E1340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1350 HIS ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN F 766 GLN F 775 ASN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118564 restraints weight = 40301.174| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.00 r_work: 0.3384 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28523 Z= 0.198 Angle : 0.689 10.070 38585 Z= 0.348 Chirality : 0.045 0.249 4403 Planarity : 0.005 0.065 4918 Dihedral : 8.358 174.926 3784 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 3.73 % Allowed : 21.55 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.80 (0.14), residues: 3457 helix: -0.03 (0.12), residues: 1752 sheet: -0.65 (0.27), residues: 374 loop : -1.01 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 640 TYR 0.017 0.002 TYR A 435 PHE 0.030 0.002 PHE D 822 TRP 0.039 0.002 TRP E 841 HIS 0.007 0.001 HIS E1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (28523) covalent geometry : angle 0.68882 / 0.35 (38585) hydrogen bonds : bond 0.04356 / 2.84 ( 1224) hydrogen bonds : angle 4.28143 / 2.98 ( 3549) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 826 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 LEU cc_start: 0.7820 (tt) cc_final: 0.7465 (tm) REVERT: A 424 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7790 (mt0) REVERT: A 428 MET cc_start: 0.8111 (ttm) cc_final: 0.7824 (mtp) REVERT: A 463 MET cc_start: 0.7946 (tpp) cc_final: 0.7738 (tpp) REVERT: A 465 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7602 (mtm180) REVERT: A 477 LYS cc_start: 0.8371 (mppt) cc_final: 0.8090 (mppt) REVERT: A 481 PHE cc_start: 0.7950 (m-80) cc_final: 0.7551 (m-80) REVERT: A 500 LEU cc_start: 0.7990 (mt) cc_final: 0.7581 (mp) REVERT: A 506 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7100 (mm-30) REVERT: A 549 MET cc_start: 0.2842 (mmt) cc_final: 0.1816 (mmt) REVERT: A 598 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7639 (mm110) REVERT: A 600 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7743 (ptt180) REVERT: A 619 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7481 (mttp) REVERT: A 672 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.7081 (ptmt) REVERT: A 724 LEU cc_start: 0.7883 (mt) cc_final: 0.7656 (mp) REVERT: A 727 ASN cc_start: 0.8201 (m-40) cc_final: 0.7994 (m-40) REVERT: A 807 VAL cc_start: 0.8093 (m) cc_final: 0.7768 (t) REVERT: A 902 LYS cc_start: 0.8512 (tppt) cc_final: 0.8229 (tppt) REVERT: A 907 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.7976 (mtp-110) REVERT: A 1319 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7027 (mt-10) REVERT: A 1336 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7456 (tm-30) REVERT: A 1365 ASP cc_start: 0.7671 (p0) cc_final: 0.7442 (p0) REVERT: B 414 ASP cc_start: 0.8115 (m-30) cc_final: 0.7896 (m-30) REVERT: B 431 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8132 (mp) REVERT: B 458 THR cc_start: 0.8332 (p) cc_final: 0.8097 (m) REVERT: B 491 LYS cc_start: 0.7511 (pmtt) cc_final: 0.7194 (pmtt) REVERT: B 502 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8595 (mm) REVERT: B 549 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8242 (ttp) REVERT: B 627 ARG cc_start: 0.8484 (ttt180) cc_final: 0.8277 (ttt180) REVERT: B 728 PHE cc_start: 0.8620 (m-80) cc_final: 0.8407 (m-80) REVERT: B 815 GLU cc_start: 0.7644 (mp0) cc_final: 0.7359 (mp0) REVERT: B 862 SER cc_start: 0.8343 (m) cc_final: 0.7910 (t) REVERT: B 903 GLU cc_start: 0.7783 (mp0) cc_final: 0.7507 (mp0) REVERT: B 923 ILE cc_start: 0.8295 (mt) cc_final: 0.8091 (mm) REVERT: C 463 MET cc_start: 0.8868 (tpp) cc_final: 0.8563 (tpp) REVERT: C 482 MET cc_start: 0.7817 (tmm) cc_final: 0.7419 (tmm) REVERT: C 502 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8270 (tp) REVERT: C 546 MET cc_start: 0.8072 (mtp) cc_final: 0.7640 (mtt) REVERT: C 612 ASP cc_start: 0.7982 (m-30) cc_final: 0.7729 (m-30) REVERT: C 662 LYS cc_start: 0.8653 (mtpm) cc_final: 0.8353 (mtmm) REVERT: C 708 ASP cc_start: 0.8131 (p0) cc_final: 0.7724 (p0) REVERT: C 711 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8235 (tp) REVERT: C 778 LYS cc_start: 0.8607 (tptt) cc_final: 0.8358 (tptt) REVERT: C 802 ASP cc_start: 0.8237 (p0) cc_final: 0.8009 (p0) REVERT: C 823 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8121 (mmt) REVERT: C 864 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7564 (mm-30) REVERT: C 865 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8516 (tttp) REVERT: C 903 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7114 (tm-30) REVERT: C 1329 LYS cc_start: 0.8279 (tttt) cc_final: 0.8032 (tttt) REVERT: C 1361 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7948 (ttpp) REVERT: D 429 VAL cc_start: 0.7327 (t) cc_final: 0.7066 (t) REVERT: D 463 MET cc_start: 0.8590 (tpp) cc_final: 0.8253 (tpp) REVERT: D 495 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7309 (mm-30) REVERT: D 509 LYS cc_start: 0.8157 (ttmm) cc_final: 0.7888 (mtpt) REVERT: D 529 SER cc_start: 0.7102 (m) cc_final: 0.6830 (p) REVERT: D 531 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: D 558 ILE cc_start: 0.8273 (pt) cc_final: 0.8044 (mt) REVERT: D 647 ARG cc_start: 0.7798 (tpp80) cc_final: 0.7564 (mmt90) REVERT: D 655 ASP cc_start: 0.7553 (t70) cc_final: 0.7259 (t70) REVERT: D 661 VAL cc_start: 0.7971 (m) cc_final: 0.7769 (t) REVERT: D 662 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8311 (mttp) REVERT: D 704 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7833 (mttm) REVERT: D 795 GLU cc_start: 0.7437 (pm20) cc_final: 0.7164 (pm20) REVERT: D 821 SER cc_start: 0.8479 (t) cc_final: 0.8096 (p) REVERT: D 823 MET cc_start: 0.8510 (tpp) cc_final: 0.8020 (mpp) REVERT: D 887 ASP cc_start: 0.7063 (t70) cc_final: 0.6829 (t70) REVERT: D 938 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7490 (ttpt) REVERT: D 1329 LYS cc_start: 0.7805 (tptp) cc_final: 0.7378 (tptp) REVERT: D 1340 ASN cc_start: 0.7658 (t0) cc_final: 0.7447 (t0) REVERT: E 420 ASN cc_start: 0.8009 (t0) cc_final: 0.7782 (t0) REVERT: E 448 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7246 (mtp-110) REVERT: E 505 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6333 (mp0) REVERT: E 519 GLU cc_start: 0.6732 (mp0) cc_final: 0.6450 (mp0) REVERT: E 671 LYS cc_start: 0.7777 (mmtm) cc_final: 0.7392 (mmtm) REVERT: E 795 GLU cc_start: 0.7236 (pm20) cc_final: 0.7003 (pm20) REVERT: E 850 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.8053 (mp) REVERT: E 851 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8021 (mm) REVERT: F 422 ILE cc_start: 0.7834 (mt) cc_final: 0.7632 (mp) REVERT: F 424 GLN cc_start: 0.7481 (tt0) cc_final: 0.7258 (tt0) REVERT: F 518 ASP cc_start: 0.7397 (t0) cc_final: 0.6927 (m-30) REVERT: F 519 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6539 (mm-30) REVERT: F 601 LYS cc_start: 0.7632 (tptp) cc_final: 0.7301 (tptt) REVERT: F 612 ASP cc_start: 0.7291 (t70) cc_final: 0.7013 (t70) REVERT: F 613 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7558 (ttpt) REVERT: F 665 ASP cc_start: 0.5713 (t0) cc_final: 0.5016 (m-30) REVERT: F 708 ASP cc_start: 0.7582 (m-30) cc_final: 0.7358 (m-30) REVERT: F 713 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6420 (tt) REVERT: F 767 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7751 (mt) REVERT: F 798 VAL cc_start: 0.8757 (m) cc_final: 0.8524 (t) REVERT: F 858 ARG cc_start: 0.7694 (mtp180) cc_final: 0.7466 (mtp180) REVERT: F 879 GLU cc_start: 0.6944 (tp30) cc_final: 0.6726 (tp30) REVERT: F 905 ILE cc_start: 0.7814 (mm) cc_final: 0.7573 (mm) REVERT: F 911 ASN cc_start: 0.8170 (t0) cc_final: 0.7953 (t0) REVERT: F 1357 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.6990 (mt) REVERT: F 1361 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7772 (ttmt) outliers start: 117 outliers final: 36 residues processed: 880 average time/residue: 0.5915 time to fit residues: 607.7460 Evaluate side-chains 820 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 763 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 1361 LYS Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 704 LYS Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 801 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 448 ARG Chi-restraints excluded: chain E residue 607 SER Chi-restraints excluded: chain E residue 850 ILE Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 1341 PHE Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 688 LEU Chi-restraints excluded: chain F residue 713 ILE Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 1356 ILE Chi-restraints excluded: chain F residue 1357 ILE Chi-restraints excluded: chain F residue 1361 LYS Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 104 optimal weight: 2.9990 chunk 278 optimal weight: 0.0670 chunk 62 optimal weight: 0.5980 chunk 319 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 336 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 246 optimal weight: 0.5980 chunk 211 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 GLN A 780 ASN B 443 ASN B 797 ASN B 848 ASN C 424 GLN C 727 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 ASN D 911 ASN D 937 GLN D1339 GLN E 424 GLN ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 596 GLN E 639 GLN E1345 GLN F 441 ASN F 511 GLN F 896 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.137914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118008 restraints weight = 40003.921| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.99 r_work: 0.3382 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28523 Z= 0.132 Angle : 0.590 12.013 38585 Z= 0.294 Chirality : 0.042 0.236 4403 Planarity : 0.005 0.073 4918 Dihedral : 8.032 178.422 3782 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 4.34 % Allowed : 23.88 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.30 (0.14), residues: 3457 helix: 0.48 (0.13), residues: 1749 sheet: -0.51 (0.27), residues: 353 loop : -0.90 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 448 TYR 0.017 0.001 TYR A 756 PHE 0.025 0.001 PHE F 728 TRP 0.020 0.001 TRP E 841 HIS 0.003 0.001 HIS C1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (28523) covalent geometry : angle 0.58987 / 0.29 (38585) hydrogen bonds : bond 0.03353 / 2.22 ( 1224) hydrogen bonds : angle 4.03935 / 2.81 ( 3549) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 810 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 LEU cc_start: 0.7858 (tt) cc_final: 0.7488 (tm) REVERT: A 424 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: A 428 MET cc_start: 0.8145 (ttm) cc_final: 0.7920 (mtp) REVERT: A 451 LEU cc_start: 0.8506 (tp) cc_final: 0.8196 (tm) REVERT: A 463 MET cc_start: 0.7984 (tpp) cc_final: 0.7751 (tpp) REVERT: A 477 LYS cc_start: 0.8408 (mppt) cc_final: 0.8083 (mppt) REVERT: A 500 LEU cc_start: 0.7992 (mt) cc_final: 0.7611 (mp) REVERT: A 506 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7139 (mm-30) REVERT: A 549 MET cc_start: 0.2948 (mmt) cc_final: 0.1788 (mmt) REVERT: A 598 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7714 (mm110) REVERT: A 600 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7735 (ptt180) REVERT: A 619 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7580 (mttp) REVERT: A 662 LYS cc_start: 0.8224 (mttt) cc_final: 0.7986 (mttm) REVERT: A 672 LYS cc_start: 0.7246 (ttmt) cc_final: 0.7003 (ptmt) REVERT: A 724 LEU cc_start: 0.7833 (mt) cc_final: 0.7616 (mp) REVERT: A 807 VAL cc_start: 0.8092 (m) cc_final: 0.7781 (t) REVERT: A 879 GLU cc_start: 0.7439 (tp30) cc_final: 0.7143 (tp30) REVERT: A 902 LYS cc_start: 0.8504 (tppt) cc_final: 0.8221 (tppt) REVERT: A 907 ARG cc_start: 0.8394 (ttm-80) cc_final: 0.7990 (mtp-110) REVERT: A 1319 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 1336 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7587 (tm-30) REVERT: A 1348 ASP cc_start: 0.7919 (t0) cc_final: 0.7621 (t0) REVERT: A 1365 ASP cc_start: 0.7631 (p0) cc_final: 0.7380 (p0) REVERT: B 414 ASP cc_start: 0.8169 (m-30) cc_final: 0.7928 (m-30) REVERT: B 431 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8083 (mp) REVERT: B 433 LEU cc_start: 0.8135 (mt) cc_final: 0.7864 (mp) REVERT: B 561 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8269 (t) REVERT: B 616 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7720 (t80) REVERT: B 627 ARG cc_start: 0.8492 (ttt180) cc_final: 0.8167 (ttt180) REVERT: B 672 LYS cc_start: 0.7797 (ptpt) cc_final: 0.7561 (pttt) REVERT: B 728 PHE cc_start: 0.8707 (m-80) cc_final: 0.8402 (m-80) REVERT: B 806 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7659 (mp) REVERT: B 815 GLU cc_start: 0.7684 (mp0) cc_final: 0.7422 (mp0) REVERT: B 862 SER cc_start: 0.8367 (m) cc_final: 0.7897 (t) REVERT: B 868 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8350 (tp) REVERT: C 441 ASN cc_start: 0.8157 (t0) cc_final: 0.7732 (t0) REVERT: C 463 MET cc_start: 0.8857 (tpp) cc_final: 0.8588 (tpp) REVERT: C 482 MET cc_start: 0.7892 (tmm) cc_final: 0.7520 (tmm) REVERT: C 502 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8322 (tp) REVERT: C 538 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7936 (mt) REVERT: C 546 MET cc_start: 0.8174 (mtp) cc_final: 0.7793 (mtt) REVERT: C 612 ASP cc_start: 0.7949 (m-30) cc_final: 0.7710 (m-30) REVERT: C 802 ASP cc_start: 0.8239 (p0) cc_final: 0.7994 (p0) REVERT: C 823 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8190 (mmt) REVERT: C 839 ASP cc_start: 0.8114 (p0) cc_final: 0.7579 (p0) REVERT: C 864 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7331 (mm-30) REVERT: C 865 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8509 (tttt) REVERT: C 873 GLU cc_start: 0.7562 (mp0) cc_final: 0.6834 (mp0) REVERT: C 879 GLU cc_start: 0.8030 (tp30) cc_final: 0.7737 (tp30) REVERT: C 1361 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8006 (ttpp) REVERT: D 429 VAL cc_start: 0.7390 (t) cc_final: 0.7137 (t) REVERT: D 463 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8401 (tpp) REVERT: D 484 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7977 (mtmm) REVERT: D 495 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7349 (mm-30) REVERT: D 509 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7917 (mtpt) REVERT: D 529 SER cc_start: 0.7280 (m) cc_final: 0.6963 (p) REVERT: D 531 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: D 607 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7903 (p) REVERT: D 655 ASP cc_start: 0.7587 (t70) cc_final: 0.7284 (t70) REVERT: D 661 VAL cc_start: 0.8092 (m) cc_final: 0.7886 (t) REVERT: D 704 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7963 (mttm) REVERT: D 775 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.8024 (t0) REVERT: D 801 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7263 (mt) REVERT: D 821 SER cc_start: 0.8645 (t) cc_final: 0.8313 (p) REVERT: D 823 MET cc_start: 0.8537 (tpp) cc_final: 0.8029 (mpp) REVERT: D 887 ASP cc_start: 0.7031 (t70) cc_final: 0.6809 (t70) REVERT: D 923 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7178 (tt) REVERT: D 925 MET cc_start: 0.5158 (mpp) cc_final: 0.4933 (mpp) REVERT: D 937 GLN cc_start: 0.7480 (tm-30) cc_final: 0.7192 (tm-30) REVERT: D 1329 LYS cc_start: 0.7768 (tptp) cc_final: 0.7347 (tptp) REVERT: D 1340 ASN cc_start: 0.7658 (t0) cc_final: 0.7354 (t0) REVERT: E 420 ASN cc_start: 0.8161 (t0) cc_final: 0.7881 (t0) REVERT: E 429 VAL cc_start: 0.6514 (OUTLIER) cc_final: 0.6310 (t) REVERT: E 448 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6983 (ptt90) REVERT: E 502 LEU cc_start: 0.7847 (mm) cc_final: 0.7572 (mp) REVERT: E 518 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7382 (t0) REVERT: E 531 GLN cc_start: 0.7800 (mm110) cc_final: 0.7528 (tp40) REVERT: E 667 MET cc_start: 0.7689 (mmp) cc_final: 0.7451 (mmp) REVERT: E 671 LYS cc_start: 0.7882 (mmtm) cc_final: 0.7502 (mmtm) REVERT: E 795 GLU cc_start: 0.7484 (pm20) cc_final: 0.7244 (pm20) REVERT: E 862 SER cc_start: 0.7808 (m) cc_final: 0.7483 (p) REVERT: E 1358 TRP cc_start: 0.8121 (t-100) cc_final: 0.7877 (t-100) REVERT: F 414 ASP cc_start: 0.7401 (m-30) cc_final: 0.7096 (m-30) REVERT: F 518 ASP cc_start: 0.7503 (t0) cc_final: 0.6938 (m-30) REVERT: F 519 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6643 (mm-30) REVERT: F 593 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7724 (tptt) REVERT: F 612 ASP cc_start: 0.7338 (t70) cc_final: 0.7077 (t70) REVERT: F 613 LYS cc_start: 0.8066 (ttpt) cc_final: 0.7593 (ttpt) REVERT: F 665 ASP cc_start: 0.5746 (t0) cc_final: 0.5318 (m-30) REVERT: F 767 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7696 (mt) REVERT: F 864 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7491 (mt-10) REVERT: F 879 GLU cc_start: 0.7065 (tp30) cc_final: 0.6750 (tp30) REVERT: F 895 PHE cc_start: 0.6700 (t80) cc_final: 0.6201 (t80) REVERT: F 911 ASN cc_start: 0.8333 (t0) cc_final: 0.8123 (t0) REVERT: F 913 ILE cc_start: 0.8202 (pp) cc_final: 0.7814 (mm) REVERT: F 938 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7562 (ttmm) REVERT: F 1357 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7105 (mt) outliers start: 136 outliers final: 40 residues processed: 868 average time/residue: 0.6002 time to fit residues: 607.6362 Evaluate side-chains 851 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 785 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 616 PHE Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 1348 ASP Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 1327 ILE Chi-restraints excluded: chain C residue 1361 LYS Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 477 LYS Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 704 LYS Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 775 ASN Chi-restraints excluded: chain D residue 790 LEU Chi-restraints excluded: chain D residue 801 LEU Chi-restraints excluded: chain D residue 898 HIS Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 448 ARG Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 593 LYS Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 910 SER Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain F residue 1356 ILE Chi-restraints excluded: chain F residue 1357 ILE Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 320 optimal weight: 0.3980 chunk 192 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 699 GLN B 829 GLN B 848 ASN B1326 GLN C 727 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 GLN D1339 GLN ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN E 766 GLN F 441 ASN F 649 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.115338 restraints weight = 39719.245| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.98 r_work: 0.3337 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28523 Z= 0.168 Angle : 0.640 13.422 38585 Z= 0.317 Chirality : 0.044 0.262 4403 Planarity : 0.005 0.059 4918 Dihedral : 8.011 178.418 3782 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 5.36 % Allowed : 24.00 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.05 (0.15), residues: 3457 helix: 0.68 (0.13), residues: 1762 sheet: -0.52 (0.27), residues: 367 loop : -0.73 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 640 TYR 0.018 0.002 TYR A 435 PHE 0.024 0.002 PHE F 642 TRP 0.016 0.001 TRP A 841 HIS 0.005 0.001 HIS B 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (28523) covalent geometry : angle 0.64006 / 0.32 (38585) hydrogen bonds : bond 0.03689 / 2.44 ( 1224) hydrogen bonds : angle 4.00743 / 2.78 ( 3549) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 891 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8102 (m-10) cc_final: 0.7698 (m-10) REVERT: A 424 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: A 428 MET cc_start: 0.8413 (ttm) cc_final: 0.8206 (mtp) REVERT: A 437 GLU cc_start: 0.8020 (pm20) cc_final: 0.7572 (pm20) REVERT: A 463 MET cc_start: 0.8168 (tpp) cc_final: 0.7888 (tpp) REVERT: A 465 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7812 (mtm180) REVERT: A 477 LYS cc_start: 0.8399 (mppt) cc_final: 0.8002 (mppt) REVERT: A 499 GLN cc_start: 0.8158 (mm110) cc_final: 0.7939 (mm-40) REVERT: A 500 LEU cc_start: 0.8102 (mt) cc_final: 0.7763 (mp) REVERT: A 521 ASP cc_start: 0.8202 (p0) cc_final: 0.7958 (p0) REVERT: A 549 MET cc_start: 0.2910 (mmt) cc_final: 0.1900 (mmt) REVERT: A 598 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7999 (mm110) REVERT: A 600 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7834 (ptt180) REVERT: A 619 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7802 (ptmt) REVERT: A 667 MET cc_start: 0.7916 (mmp) cc_final: 0.7642 (mmm) REVERT: A 672 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7364 (ptmt) REVERT: A 807 VAL cc_start: 0.8045 (m) cc_final: 0.7776 (t) REVERT: A 879 GLU cc_start: 0.7458 (tp30) cc_final: 0.7138 (tp30) REVERT: A 902 LYS cc_start: 0.8478 (tppt) cc_final: 0.8156 (tppt) REVERT: A 903 GLU cc_start: 0.7956 (tp30) cc_final: 0.7648 (tp30) REVERT: A 907 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.7914 (mtp-110) REVERT: A 1336 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 1348 ASP cc_start: 0.7917 (t0) cc_final: 0.7624 (t0) REVERT: A 1365 ASP cc_start: 0.7564 (p0) cc_final: 0.7319 (p0) REVERT: B 431 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8348 (mp) REVERT: B 530 LYS cc_start: 0.7916 (ptpt) cc_final: 0.7683 (ptpt) REVERT: B 616 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7847 (t80) REVERT: B 627 ARG cc_start: 0.8444 (ttt180) cc_final: 0.8095 (ttt180) REVERT: B 671 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8182 (tppp) REVERT: B 672 LYS cc_start: 0.8330 (ptpt) cc_final: 0.8050 (pttt) REVERT: B 692 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8197 (pp) REVERT: B 792 TYR cc_start: 0.8862 (t80) cc_final: 0.8644 (t80) REVERT: B 815 GLU cc_start: 0.7745 (mp0) cc_final: 0.7485 (mp0) REVERT: B 827 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8594 (mttp) REVERT: B 840 ILE cc_start: 0.8510 (pt) cc_final: 0.8241 (pt) REVERT: B 847 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7986 (mt-10) REVERT: B 868 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8454 (tp) REVERT: B 1336 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7814 (tm-30) REVERT: C 420 ASN cc_start: 0.8241 (m-40) cc_final: 0.7917 (m-40) REVERT: C 433 LEU cc_start: 0.8220 (mt) cc_final: 0.7978 (mp) REVERT: C 441 ASN cc_start: 0.8201 (t0) cc_final: 0.7890 (t0) REVERT: C 463 MET cc_start: 0.8800 (tpp) cc_final: 0.8366 (tpp) REVERT: C 538 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8187 (mt) REVERT: C 546 MET cc_start: 0.8226 (mtp) cc_final: 0.7886 (mtt) REVERT: C 612 ASP cc_start: 0.7914 (m-30) cc_final: 0.7708 (m-30) REVERT: C 627 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7733 (ttp-110) REVERT: C 671 LYS cc_start: 0.8229 (mtpt) cc_final: 0.8012 (mtpt) REVERT: C 708 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7720 (p0) REVERT: C 762 MET cc_start: 0.8441 (mmm) cc_final: 0.8232 (mmm) REVERT: C 823 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8413 (mmt) REVERT: C 858 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7783 (ptp-170) REVERT: C 864 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7358 (mm-30) REVERT: C 865 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8494 (tttp) REVERT: C 879 GLU cc_start: 0.8000 (tp30) cc_final: 0.7596 (tp30) REVERT: C 1329 LYS cc_start: 0.8178 (tttt) cc_final: 0.7925 (ttmm) REVERT: C 1361 LYS cc_start: 0.8265 (ttpp) cc_final: 0.7991 (ttpp) REVERT: C 1372 GLU cc_start: 0.7891 (tt0) cc_final: 0.7673 (tt0) REVERT: D 419 ASP cc_start: 0.7763 (m-30) cc_final: 0.7501 (m-30) REVERT: D 420 ASN cc_start: 0.8394 (t0) cc_final: 0.8055 (t0) REVERT: D 428 MET cc_start: 0.8346 (ttm) cc_final: 0.8119 (ttp) REVERT: D 429 VAL cc_start: 0.8177 (t) cc_final: 0.7937 (t) REVERT: D 437 GLU cc_start: 0.7956 (pm20) cc_final: 0.7716 (pm20) REVERT: D 450 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8264 (p) REVERT: D 484 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7641 (mttt) REVERT: D 489 LEU cc_start: 0.8062 (mp) cc_final: 0.7860 (mm) REVERT: D 501 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7765 (ttm-80) REVERT: D 502 LEU cc_start: 0.8595 (mt) cc_final: 0.8383 (mm) REVERT: D 508 LYS cc_start: 0.8388 (tttm) cc_final: 0.8093 (ttpp) REVERT: D 509 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7940 (mtpp) REVERT: D 529 SER cc_start: 0.7981 (m) cc_final: 0.7697 (p) REVERT: D 607 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.8098 (p) REVERT: D 655 ASP cc_start: 0.7660 (t70) cc_final: 0.7054 (t70) REVERT: D 658 LYS cc_start: 0.8355 (mttt) cc_final: 0.8011 (mttt) REVERT: D 704 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8177 (mttm) REVERT: D 728 PHE cc_start: 0.7144 (m-10) cc_final: 0.6905 (m-80) REVERT: D 762 MET cc_start: 0.8058 (mmm) cc_final: 0.7759 (mmm) REVERT: D 775 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7946 (t0) REVERT: D 821 SER cc_start: 0.8771 (t) cc_final: 0.8450 (p) REVERT: D 903 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7532 (tm-30) REVERT: D 923 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7040 (tt) REVERT: D 928 ARG cc_start: 0.7404 (ttm-80) cc_final: 0.6910 (ttm-80) REVERT: D 937 GLN cc_start: 0.7462 (tm-30) cc_final: 0.7226 (tm-30) REVERT: D 1329 LYS cc_start: 0.7887 (tptp) cc_final: 0.7513 (tptp) REVERT: D 1340 ASN cc_start: 0.7909 (t0) cc_final: 0.7690 (t0) REVERT: D 1375 LYS cc_start: 0.8108 (tttm) cc_final: 0.7896 (tttm) REVERT: E 408 MET cc_start: 0.5181 (mmm) cc_final: 0.4881 (tmm) REVERT: E 420 ASN cc_start: 0.8322 (t0) cc_final: 0.8028 (t0) REVERT: E 425 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8030 (tp) REVERT: E 440 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7526 (mm-40) REVERT: E 448 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7064 (ptt90) REVERT: E 502 LEU cc_start: 0.8211 (mm) cc_final: 0.7889 (mp) REVERT: E 518 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7216 (t0) REVERT: E 519 GLU cc_start: 0.7250 (mp0) cc_final: 0.6719 (mp0) REVERT: E 528 SER cc_start: 0.8498 (t) cc_final: 0.8297 (t) REVERT: E 530 LYS cc_start: 0.8014 (mtmm) cc_final: 0.7741 (mtmm) REVERT: E 531 GLN cc_start: 0.7875 (mm110) cc_final: 0.7621 (tp40) REVERT: E 554 GLN cc_start: 0.6415 (mm-40) cc_final: 0.6157 (mp10) REVERT: E 667 MET cc_start: 0.8094 (mmp) cc_final: 0.7866 (mmp) REVERT: E 671 LYS cc_start: 0.8343 (mmtm) cc_final: 0.8072 (mmtm) REVERT: E 730 ASP cc_start: 0.7358 (m-30) cc_final: 0.6943 (m-30) REVERT: E 760 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7245 (mt-10) REVERT: E 762 MET cc_start: 0.8483 (mmm) cc_final: 0.8217 (mmm) REVERT: E 764 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7591 (mt-10) REVERT: E 778 LYS cc_start: 0.8553 (tppp) cc_final: 0.8191 (tppp) REVERT: E 862 SER cc_start: 0.8243 (m) cc_final: 0.8028 (m) REVERT: E 873 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7087 (mt-10) REVERT: E 1348 ASP cc_start: 0.8173 (t70) cc_final: 0.7795 (t0) REVERT: E 1375 LYS cc_start: 0.7948 (tptp) cc_final: 0.7632 (tptp) REVERT: F 414 ASP cc_start: 0.7688 (m-30) cc_final: 0.7274 (m-30) REVERT: F 498 ARG cc_start: 0.7238 (ttp80) cc_final: 0.6990 (ttp80) REVERT: F 508 LYS cc_start: 0.8035 (tppt) cc_final: 0.7610 (tppt) REVERT: F 540 SER cc_start: 0.8292 (t) cc_final: 0.8041 (t) REVERT: F 593 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7851 (tptt) REVERT: F 601 LYS cc_start: 0.7880 (tptp) cc_final: 0.7468 (tptt) REVERT: F 612 ASP cc_start: 0.7556 (t70) cc_final: 0.7270 (t70) REVERT: F 707 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8244 (tp) REVERT: F 815 GLU cc_start: 0.7470 (mp0) cc_final: 0.7093 (mp0) REVERT: F 827 LYS cc_start: 0.8377 (tttp) cc_final: 0.8165 (ttpp) REVERT: F 845 ILE cc_start: 0.7693 (mm) cc_final: 0.7441 (mp) REVERT: F 864 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7536 (mt-10) REVERT: F 879 GLU cc_start: 0.7304 (tp30) cc_final: 0.6899 (tp30) REVERT: F 898 HIS cc_start: 0.7734 (m-70) cc_final: 0.7533 (m-70) REVERT: F 911 ASN cc_start: 0.8504 (t0) cc_final: 0.8273 (t0) REVERT: F 913 ILE cc_start: 0.8416 (pp) cc_final: 0.8132 (mp) REVERT: F 938 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7554 (ttmm) REVERT: F 1336 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7266 (tm-30) REVERT: F 1357 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7756 (mt) REVERT: F 1359 LYS cc_start: 0.7572 (ttpt) cc_final: 0.7339 (ttpt) outliers start: 168 outliers final: 55 residues processed: 962 average time/residue: 0.6359 time to fit residues: 711.8160 Evaluate side-chains 903 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 821 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 616 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 1322 LEU Chi-restraints excluded: chain B residue 1348 ASP Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 673 ILE Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 858 ARG Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1327 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 704 LYS Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 775 ASN Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 847 GLU Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 448 ARG Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 824 GLU Chi-restraints excluded: chain E residue 840 ILE Chi-restraints excluded: chain E residue 897 LEU Chi-restraints excluded: chain E residue 1327 ILE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 593 LYS Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 847 GLU Chi-restraints excluded: chain F residue 906 THR Chi-restraints excluded: chain F residue 919 LYS Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain F residue 1357 ILE Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 289 optimal weight: 4.9990 chunk 199 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 221 optimal weight: 0.5980 chunk 154 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 GLN A 699 GLN C 554 GLN C 727 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN D 712 ASN D 911 ASN E 898 HIS F 441 ASN ** F 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1340 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113477 restraints weight = 39746.942| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.11 r_work: 0.3298 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.7412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28523 Z= 0.167 Angle : 0.606 12.435 38585 Z= 0.299 Chirality : 0.043 0.245 4403 Planarity : 0.004 0.056 4918 Dihedral : 7.846 177.072 3782 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 4.21 % Allowed : 26.78 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 0.15 (0.15), residues: 3457 helix: 0.82 (0.13), residues: 1775 sheet: -0.54 (0.27), residues: 385 loop : -0.57 (0.18), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 501 TYR 0.017 0.002 TYR A 435 PHE 0.023 0.002 PHE E 592 TRP 0.015 0.001 TRP A 841 HIS 0.004 0.001 HIS E 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (28523) covalent geometry : angle 0.60605 / 0.30 (38585) hydrogen bonds : bond 0.03426 / 2.26 ( 1224) hydrogen bonds : angle 3.94299 / 2.74 ( 3549) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 866 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6910 (mt) REVERT: A 421 TYR cc_start: 0.8110 (m-10) cc_final: 0.7713 (m-10) REVERT: A 424 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: A 437 GLU cc_start: 0.7966 (pm20) cc_final: 0.7444 (pm20) REVERT: A 451 LEU cc_start: 0.8671 (tp) cc_final: 0.8361 (tm) REVERT: A 463 MET cc_start: 0.8220 (tpp) cc_final: 0.7991 (tpp) REVERT: A 465 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7906 (mtm180) REVERT: A 477 LYS cc_start: 0.8352 (mppt) cc_final: 0.7962 (mppt) REVERT: A 495 GLU cc_start: 0.7486 (tp30) cc_final: 0.6427 (tp30) REVERT: A 499 GLN cc_start: 0.8259 (mm110) cc_final: 0.8020 (mm-40) REVERT: A 500 LEU cc_start: 0.8124 (mt) cc_final: 0.7768 (mt) REVERT: A 509 LYS cc_start: 0.7867 (tptp) cc_final: 0.7651 (tppp) REVERT: A 521 ASP cc_start: 0.8166 (p0) cc_final: 0.7960 (p0) REVERT: A 549 MET cc_start: 0.2797 (mmt) cc_final: 0.1758 (mmt) REVERT: A 598 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8052 (mm110) REVERT: A 600 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7879 (ptt180) REVERT: A 662 LYS cc_start: 0.8360 (mttm) cc_final: 0.8013 (mttt) REVERT: A 667 MET cc_start: 0.8001 (mmp) cc_final: 0.7771 (mmm) REVERT: A 672 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7484 (ptmt) REVERT: A 690 GLU cc_start: 0.7185 (tp30) cc_final: 0.6955 (tp30) REVERT: A 807 VAL cc_start: 0.8008 (m) cc_final: 0.7746 (t) REVERT: A 813 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8308 (t) REVERT: A 824 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: A 879 GLU cc_start: 0.7517 (tp30) cc_final: 0.7184 (tp30) REVERT: A 902 LYS cc_start: 0.8436 (tppt) cc_final: 0.8116 (tppt) REVERT: A 907 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8080 (mtp-110) REVERT: A 1319 GLU cc_start: 0.7872 (mt-10) cc_final: 0.6500 (tt0) REVERT: A 1336 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 1348 ASP cc_start: 0.7904 (t0) cc_final: 0.7618 (t0) REVERT: A 1365 ASP cc_start: 0.7563 (p0) cc_final: 0.7335 (p0) REVERT: B 414 ASP cc_start: 0.8189 (m-30) cc_final: 0.7940 (m-30) REVERT: B 431 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8409 (mp) REVERT: B 434 LEU cc_start: 0.8616 (mt) cc_final: 0.8403 (mp) REVERT: B 445 THR cc_start: 0.8372 (m) cc_final: 0.8163 (t) REVERT: B 477 LYS cc_start: 0.8151 (tppt) cc_final: 0.7941 (tppt) REVERT: B 483 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7877 (mmp80) REVERT: B 530 LYS cc_start: 0.7964 (ptpt) cc_final: 0.7643 (ptpt) REVERT: B 616 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7945 (t80) REVERT: B 627 ARG cc_start: 0.8439 (ttt180) cc_final: 0.8100 (ttt180) REVERT: B 671 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8277 (tppp) REVERT: B 672 LYS cc_start: 0.8554 (ptpt) cc_final: 0.8281 (pttt) REVERT: B 686 GLN cc_start: 0.7985 (mt0) cc_final: 0.7776 (tp40) REVERT: B 692 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8203 (pp) REVERT: B 815 GLU cc_start: 0.7758 (mp0) cc_final: 0.7494 (mp0) REVERT: B 827 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8632 (mttp) REVERT: B 847 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8051 (mt-10) REVERT: B 868 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8456 (tp) REVERT: B 1336 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7795 (tm-30) REVERT: C 420 ASN cc_start: 0.8243 (m-40) cc_final: 0.7978 (m-40) REVERT: C 433 LEU cc_start: 0.8259 (mt) cc_final: 0.8002 (mp) REVERT: C 441 ASN cc_start: 0.8274 (t0) cc_final: 0.7987 (t0) REVERT: C 462 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8549 (tp) REVERT: C 463 MET cc_start: 0.8851 (tpp) cc_final: 0.8447 (tpp) REVERT: C 482 MET cc_start: 0.8113 (tmm) cc_final: 0.7749 (tmm) REVERT: C 528 SER cc_start: 0.8408 (t) cc_final: 0.8153 (t) REVERT: C 538 ILE cc_start: 0.8437 (mm) cc_final: 0.8217 (mt) REVERT: C 546 MET cc_start: 0.8280 (mtp) cc_final: 0.7967 (mtt) REVERT: C 612 ASP cc_start: 0.7886 (m-30) cc_final: 0.7682 (m-30) REVERT: C 650 ASP cc_start: 0.8040 (p0) cc_final: 0.7516 (p0) REVERT: C 671 LYS cc_start: 0.8278 (mtpt) cc_final: 0.8063 (mtpt) REVERT: C 708 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7730 (p0) REVERT: C 759 PHE cc_start: 0.8122 (m-80) cc_final: 0.7887 (m-10) REVERT: C 762 MET cc_start: 0.8484 (mmm) cc_final: 0.8244 (mmt) REVERT: C 807 VAL cc_start: 0.8080 (m) cc_final: 0.7634 (t) REVERT: C 823 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8449 (mmt) REVERT: C 864 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7722 (mm-30) REVERT: C 865 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8549 (tttt) REVERT: C 911 ASN cc_start: 0.8547 (m110) cc_final: 0.8201 (m110) REVERT: C 938 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8402 (mtpp) REVERT: C 1329 LYS cc_start: 0.8137 (tttt) cc_final: 0.7898 (ttmm) REVERT: C 1372 GLU cc_start: 0.7862 (tt0) cc_final: 0.7659 (tt0) REVERT: D 419 ASP cc_start: 0.7825 (m-30) cc_final: 0.7589 (m-30) REVERT: D 437 GLU cc_start: 0.8086 (pm20) cc_final: 0.7686 (pm20) REVERT: D 450 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8385 (t) REVERT: D 484 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7724 (mttt) REVERT: D 497 GLU cc_start: 0.7915 (mp0) cc_final: 0.7284 (mp0) REVERT: D 501 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7711 (ttm-80) REVERT: D 529 SER cc_start: 0.8151 (m) cc_final: 0.7855 (p) REVERT: D 589 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8102 (mtpp) REVERT: D 607 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8227 (p) REVERT: D 655 ASP cc_start: 0.7776 (t70) cc_final: 0.7311 (t0) REVERT: D 658 LYS cc_start: 0.8456 (mttt) cc_final: 0.7939 (mttt) REVERT: D 662 LYS cc_start: 0.8525 (mttp) cc_final: 0.8303 (mtpp) REVERT: D 704 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8221 (mttm) REVERT: D 706 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8369 (mtpt) REVERT: D 728 PHE cc_start: 0.7459 (m-10) cc_final: 0.7218 (m-80) REVERT: D 762 MET cc_start: 0.8175 (mmm) cc_final: 0.7908 (mmm) REVERT: D 775 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7982 (t0) REVERT: D 821 SER cc_start: 0.8708 (t) cc_final: 0.8421 (p) REVERT: D 823 MET cc_start: 0.8590 (tpp) cc_final: 0.8120 (mmm) REVERT: D 857 PHE cc_start: 0.8714 (m-80) cc_final: 0.8382 (m-80) REVERT: D 903 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7479 (tm-30) REVERT: D 928 ARG cc_start: 0.7571 (ttm-80) cc_final: 0.7036 (ttm-80) REVERT: D 937 GLN cc_start: 0.7466 (tm-30) cc_final: 0.7192 (tm-30) REVERT: D 1329 LYS cc_start: 0.7948 (tptp) cc_final: 0.7591 (tptp) REVERT: D 1342 THR cc_start: 0.8484 (t) cc_final: 0.8174 (p) REVERT: D 1375 LYS cc_start: 0.8165 (tttm) cc_final: 0.7959 (tttm) REVERT: E 408 MET cc_start: 0.5434 (mmm) cc_final: 0.5099 (tmm) REVERT: E 420 ASN cc_start: 0.8239 (t0) cc_final: 0.7916 (t0) REVERT: E 440 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7472 (mm-40) REVERT: E 463 MET cc_start: 0.8405 (tpp) cc_final: 0.7910 (ttp) REVERT: E 502 LEU cc_start: 0.8291 (mm) cc_final: 0.7965 (mp) REVERT: E 508 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8126 (ttpp) REVERT: E 518 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7228 (t70) REVERT: E 519 GLU cc_start: 0.7408 (mp0) cc_final: 0.6482 (mp0) REVERT: E 528 SER cc_start: 0.8573 (t) cc_final: 0.8354 (t) REVERT: E 530 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7705 (mttm) REVERT: E 531 GLN cc_start: 0.7942 (mm110) cc_final: 0.7650 (tp40) REVERT: E 538 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8253 (mt) REVERT: E 554 GLN cc_start: 0.6845 (mm-40) cc_final: 0.6461 (mp10) REVERT: E 612 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7230 (m-30) REVERT: E 671 LYS cc_start: 0.8403 (mmtm) cc_final: 0.8153 (mmtm) REVERT: E 730 ASP cc_start: 0.7717 (m-30) cc_final: 0.7317 (m-30) REVERT: E 758 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7718 (p90) REVERT: E 762 MET cc_start: 0.8577 (mmm) cc_final: 0.8351 (mmm) REVERT: E 764 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7662 (mt-10) REVERT: E 1336 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7354 (tm-30) REVERT: E 1348 ASP cc_start: 0.8154 (t70) cc_final: 0.7812 (t0) REVERT: E 1375 LYS cc_start: 0.8129 (tptp) cc_final: 0.7833 (tptp) REVERT: F 414 ASP cc_start: 0.7953 (m-30) cc_final: 0.7655 (m-30) REVERT: F 498 ARG cc_start: 0.7227 (ttp80) cc_final: 0.6938 (ttp80) REVERT: F 518 ASP cc_start: 0.7881 (t0) cc_final: 0.7243 (m-30) REVERT: F 540 SER cc_start: 0.8376 (t) cc_final: 0.8174 (t) REVERT: F 593 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7976 (mptt) REVERT: F 601 LYS cc_start: 0.7961 (tptp) cc_final: 0.7542 (tptt) REVERT: F 612 ASP cc_start: 0.7599 (t70) cc_final: 0.7186 (t70) REVERT: F 616 PHE cc_start: 0.7312 (m-80) cc_final: 0.7046 (m-80) REVERT: F 632 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7673 (mm-30) REVERT: F 662 LYS cc_start: 0.7609 (mptp) cc_final: 0.7361 (mptp) REVERT: F 667 MET cc_start: 0.7810 (mmp) cc_final: 0.7589 (mmm) REVERT: F 707 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8292 (tp) REVERT: F 712 ASN cc_start: 0.7206 (t0) cc_final: 0.6587 (t0) REVERT: F 760 GLU cc_start: 0.8052 (tp30) cc_final: 0.7731 (tp30) REVERT: F 767 ILE cc_start: 0.8340 (pt) cc_final: 0.7945 (mt) REVERT: F 815 GLU cc_start: 0.7585 (mp0) cc_final: 0.7299 (mp0) REVERT: F 827 LYS cc_start: 0.8477 (tttp) cc_final: 0.8243 (ttpp) REVERT: F 845 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7398 (mp) REVERT: F 879 GLU cc_start: 0.7453 (tp30) cc_final: 0.7031 (tp30) REVERT: F 898 HIS cc_start: 0.7756 (m-70) cc_final: 0.7421 (m-70) REVERT: F 911 ASN cc_start: 0.8517 (t0) cc_final: 0.8242 (t0) REVERT: F 913 ILE cc_start: 0.8543 (pp) cc_final: 0.8271 (mt) REVERT: F 914 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7792 (tm-30) REVERT: F 938 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7567 (ttmm) REVERT: F 1336 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7667 (tm-30) REVERT: F 1359 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7679 (ttpt) outliers start: 132 outliers final: 54 residues processed: 923 average time/residue: 0.6270 time to fit residues: 670.0287 Evaluate side-chains 920 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 839 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 616 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain B residue 1348 ASP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 811 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 1327 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 704 LYS Chi-restraints excluded: chain D residue 710 MET Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 775 ASN Chi-restraints excluded: chain D residue 847 GLU Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 758 PHE Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 824 GLU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 482 MET Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 593 LYS Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 728 PHE Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 845 ILE Chi-restraints excluded: chain F residue 847 GLU Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 172 optimal weight: 0.9980 chunk 334 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 274 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 305 optimal weight: 0.9980 chunk 232 optimal weight: 0.0980 chunk 209 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 533 GLN A 554 GLN A 699 GLN B 727 ASN C 554 GLN C 727 ASN C 766 GLN D 420 ASN D 829 GLN E 644 GLN F 441 ASN ** F 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 649 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.133286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113504 restraints weight = 39596.992| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.97 r_work: 0.3309 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.7729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28523 Z= 0.152 Angle : 0.601 11.482 38585 Z= 0.297 Chirality : 0.043 0.221 4403 Planarity : 0.005 0.061 4918 Dihedral : 7.718 175.716 3780 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 4.08 % Allowed : 28.02 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 0.30 (0.15), residues: 3457 helix: 0.94 (0.13), residues: 1771 sheet: -0.52 (0.27), residues: 370 loop : -0.47 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 498 TYR 0.016 0.001 TYR D 435 PHE 0.029 0.002 PHE A 642 TRP 0.015 0.001 TRP E 841 HIS 0.003 0.001 HIS C1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (28523) covalent geometry : angle 0.60081 / 0.30 (38585) hydrogen bonds : bond 0.03337 / 2.21 ( 1224) hydrogen bonds : angle 3.87964 / 2.70 ( 3549) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 861 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7002 (mt) REVERT: A 421 TYR cc_start: 0.8107 (m-10) cc_final: 0.7713 (m-10) REVERT: A 424 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: A 437 GLU cc_start: 0.7952 (pm20) cc_final: 0.7339 (pm20) REVERT: A 451 LEU cc_start: 0.8651 (tp) cc_final: 0.8294 (tm) REVERT: A 463 MET cc_start: 0.8191 (tpp) cc_final: 0.7940 (tpp) REVERT: A 465 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7841 (mtp-110) REVERT: A 477 LYS cc_start: 0.8327 (mppt) cc_final: 0.7953 (mppt) REVERT: A 500 LEU cc_start: 0.8110 (mt) cc_final: 0.7809 (mt) REVERT: A 509 LYS cc_start: 0.7870 (tptp) cc_final: 0.7643 (tppp) REVERT: A 549 MET cc_start: 0.2803 (mmt) cc_final: 0.1916 (mmt) REVERT: A 598 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8186 (mm-40) REVERT: A 667 MET cc_start: 0.8041 (mmp) cc_final: 0.7761 (mmm) REVERT: A 672 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7604 (ttmm) REVERT: A 813 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8288 (t) REVERT: A 824 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: A 879 GLU cc_start: 0.7539 (tp30) cc_final: 0.7199 (tp30) REVERT: A 902 LYS cc_start: 0.8419 (tppt) cc_final: 0.8077 (tppt) REVERT: A 906 THR cc_start: 0.8693 (t) cc_final: 0.8456 (p) REVERT: A 1319 GLU cc_start: 0.7867 (mt-10) cc_final: 0.6216 (tt0) REVERT: A 1336 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7872 (tm-30) REVERT: A 1348 ASP cc_start: 0.7806 (t0) cc_final: 0.7549 (t0) REVERT: A 1365 ASP cc_start: 0.7507 (p0) cc_final: 0.7272 (p0) REVERT: B 414 ASP cc_start: 0.8042 (m-30) cc_final: 0.7830 (m-30) REVERT: B 426 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8264 (ttpp) REVERT: B 445 THR cc_start: 0.8435 (m) cc_final: 0.8231 (t) REVERT: B 467 LEU cc_start: 0.8810 (tp) cc_final: 0.8534 (tp) REVERT: B 519 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 530 LYS cc_start: 0.7939 (ptpt) cc_final: 0.7636 (ptpt) REVERT: B 611 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7712 (mt) REVERT: B 616 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7972 (t80) REVERT: B 647 ARG cc_start: 0.8477 (mtp85) cc_final: 0.8261 (mtp85) REVERT: B 671 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8237 (tppp) REVERT: B 672 LYS cc_start: 0.8571 (ptpt) cc_final: 0.8311 (pttp) REVERT: B 692 ILE cc_start: 0.8407 (pt) cc_final: 0.8185 (pp) REVERT: B 762 MET cc_start: 0.8436 (mmm) cc_final: 0.8143 (tpt) REVERT: B 778 LYS cc_start: 0.8096 (ttpp) cc_final: 0.7891 (ttpp) REVERT: B 815 GLU cc_start: 0.7703 (mp0) cc_final: 0.7364 (mp0) REVERT: B 827 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8593 (mttp) REVERT: B 847 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8030 (mt-10) REVERT: B 868 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8414 (tp) REVERT: B 1336 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7720 (tm-30) REVERT: C 420 ASN cc_start: 0.8275 (m-40) cc_final: 0.8024 (m110) REVERT: C 441 ASN cc_start: 0.8251 (t0) cc_final: 0.7995 (t0) REVERT: C 462 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8555 (tp) REVERT: C 482 MET cc_start: 0.8078 (tmm) cc_final: 0.7690 (tmm) REVERT: C 505 GLU cc_start: 0.8007 (tt0) cc_final: 0.7632 (tt0) REVERT: C 506 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: C 528 SER cc_start: 0.8473 (t) cc_final: 0.8210 (t) REVERT: C 538 ILE cc_start: 0.8401 (mm) cc_final: 0.8180 (mt) REVERT: C 546 MET cc_start: 0.8251 (mtp) cc_final: 0.7942 (mtt) REVERT: C 612 ASP cc_start: 0.7821 (m-30) cc_final: 0.7613 (m-30) REVERT: C 650 ASP cc_start: 0.8034 (p0) cc_final: 0.7571 (p0) REVERT: C 690 GLU cc_start: 0.7217 (tp30) cc_final: 0.6994 (mp0) REVERT: C 703 LEU cc_start: 0.8624 (tp) cc_final: 0.8414 (tp) REVERT: C 708 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7673 (p0) REVERT: C 731 TYR cc_start: 0.7948 (m-80) cc_final: 0.7269 (m-80) REVERT: C 762 MET cc_start: 0.8516 (mmm) cc_final: 0.8265 (mmt) REVERT: C 858 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7796 (ptp-170) REVERT: C 864 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7648 (mm-30) REVERT: C 865 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8527 (tttt) REVERT: C 911 ASN cc_start: 0.8452 (m110) cc_final: 0.8111 (m-40) REVERT: C 1329 LYS cc_start: 0.8113 (tttt) cc_final: 0.7895 (ttmm) REVERT: C 1361 LYS cc_start: 0.8357 (ttpp) cc_final: 0.7829 (ttpp) REVERT: C 1372 GLU cc_start: 0.7835 (tt0) cc_final: 0.7617 (tt0) REVERT: D 437 GLU cc_start: 0.8056 (pm20) cc_final: 0.7578 (pm20) REVERT: D 440 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: D 450 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8278 (p) REVERT: D 477 LYS cc_start: 0.8047 (tptt) cc_final: 0.7803 (tptt) REVERT: D 484 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7795 (mttm) REVERT: D 497 GLU cc_start: 0.7910 (mp0) cc_final: 0.7216 (mp0) REVERT: D 501 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7741 (ttm-80) REVERT: D 529 SER cc_start: 0.8253 (m) cc_final: 0.7995 (p) REVERT: D 589 LYS cc_start: 0.8384 (ttmm) cc_final: 0.8081 (mtpp) REVERT: D 607 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8218 (p) REVERT: D 655 ASP cc_start: 0.7784 (t70) cc_final: 0.7241 (t0) REVERT: D 658 LYS cc_start: 0.8428 (mttt) cc_final: 0.7953 (mttt) REVERT: D 662 LYS cc_start: 0.8481 (mttp) cc_final: 0.8280 (mtpp) REVERT: D 706 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8380 (mtpt) REVERT: D 762 MET cc_start: 0.8244 (mmm) cc_final: 0.8035 (mmm) REVERT: D 821 SER cc_start: 0.8687 (t) cc_final: 0.8413 (p) REVERT: D 823 MET cc_start: 0.8491 (tpp) cc_final: 0.8042 (mmm) REVERT: D 847 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: D 857 PHE cc_start: 0.8767 (m-80) cc_final: 0.8387 (m-80) REVERT: D 903 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7125 (tm-30) REVERT: D 907 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7754 (mtp-110) REVERT: D 928 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.7326 (ttm-80) REVERT: D 937 GLN cc_start: 0.7458 (tm-30) cc_final: 0.7257 (tm-30) REVERT: D 1329 LYS cc_start: 0.7950 (tptp) cc_final: 0.7600 (tptp) REVERT: D 1348 ASP cc_start: 0.7909 (t70) cc_final: 0.7529 (t0) REVERT: D 1375 LYS cc_start: 0.8187 (tttm) cc_final: 0.7983 (tttm) REVERT: E 408 MET cc_start: 0.5561 (mmm) cc_final: 0.5218 (tmm) REVERT: E 413 ASP cc_start: 0.7817 (p0) cc_final: 0.7603 (p0) REVERT: E 420 ASN cc_start: 0.8226 (t0) cc_final: 0.7917 (t0) REVERT: E 463 MET cc_start: 0.8418 (tpp) cc_final: 0.8053 (ttp) REVERT: E 502 LEU cc_start: 0.8354 (mm) cc_final: 0.8033 (OUTLIER) REVERT: E 508 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8213 (ttpp) REVERT: E 518 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7175 (t70) REVERT: E 519 GLU cc_start: 0.7397 (mp0) cc_final: 0.6458 (mp0) REVERT: E 528 SER cc_start: 0.8636 (t) cc_final: 0.8410 (t) REVERT: E 530 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7861 (mttm) REVERT: E 531 GLN cc_start: 0.7939 (mm110) cc_final: 0.7673 (tp40) REVERT: E 538 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8242 (mt) REVERT: E 554 GLN cc_start: 0.6975 (mm-40) cc_final: 0.6592 (mp10) REVERT: E 601 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8254 (mtmt) REVERT: E 612 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: E 671 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8165 (mmtm) REVERT: E 702 ASN cc_start: 0.7381 (t0) cc_final: 0.7020 (t0) REVERT: E 730 ASP cc_start: 0.7757 (m-30) cc_final: 0.7381 (m-30) REVERT: E 764 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7631 (mt-10) REVERT: E 827 LYS cc_start: 0.8328 (ptpt) cc_final: 0.8011 (ptpt) REVERT: E 847 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7069 (tm-30) REVERT: E 1336 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7322 (tm-30) REVERT: E 1348 ASP cc_start: 0.8117 (t70) cc_final: 0.7796 (t0) REVERT: E 1375 LYS cc_start: 0.8085 (tptp) cc_final: 0.7784 (tptp) REVERT: F 414 ASP cc_start: 0.7987 (m-30) cc_final: 0.7654 (m-30) REVERT: F 498 ARG cc_start: 0.7231 (ttp80) cc_final: 0.6917 (ttp80) REVERT: F 501 ARG cc_start: 0.8046 (ttm110) cc_final: 0.7725 (ttm110) REVERT: F 508 LYS cc_start: 0.8124 (tppt) cc_final: 0.7697 (mtpp) REVERT: F 516 PHE cc_start: 0.7744 (t80) cc_final: 0.6551 (t80) REVERT: F 518 ASP cc_start: 0.7899 (t0) cc_final: 0.7245 (m-30) REVERT: F 593 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7955 (mptt) REVERT: F 597 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8030 (pt) REVERT: F 601 LYS cc_start: 0.7918 (tptp) cc_final: 0.7532 (tptt) REVERT: F 606 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7941 (mt) REVERT: F 612 ASP cc_start: 0.7610 (t70) cc_final: 0.7205 (t70) REVERT: F 616 PHE cc_start: 0.7289 (m-80) cc_final: 0.7039 (m-80) REVERT: F 632 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7636 (mm-30) REVERT: F 640 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8299 (ttp80) REVERT: F 654 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8384 (t) REVERT: F 662 LYS cc_start: 0.7694 (mptp) cc_final: 0.7234 (mptp) REVERT: F 667 MET cc_start: 0.7923 (mmp) cc_final: 0.7679 (mmm) REVERT: F 712 ASN cc_start: 0.7216 (t0) cc_final: 0.6586 (t0) REVERT: F 760 GLU cc_start: 0.7983 (tp30) cc_final: 0.7663 (tp30) REVERT: F 767 ILE cc_start: 0.8361 (pt) cc_final: 0.8012 (mt) REVERT: F 815 GLU cc_start: 0.7504 (mp0) cc_final: 0.7186 (mp0) REVERT: F 827 LYS cc_start: 0.8467 (tttp) cc_final: 0.8244 (ttpp) REVERT: F 845 ILE cc_start: 0.7721 (mm) cc_final: 0.7421 (mp) REVERT: F 879 GLU cc_start: 0.7464 (tp30) cc_final: 0.6867 (tp30) REVERT: F 913 ILE cc_start: 0.8579 (pp) cc_final: 0.8303 (mt) REVERT: F 938 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7528 (ttmm) REVERT: F 1336 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7674 (tm-30) outliers start: 128 outliers final: 63 residues processed: 918 average time/residue: 0.6383 time to fit residues: 679.4449 Evaluate side-chains 930 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 841 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 616 PHE Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain B residue 1348 ASP Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 858 ARG Chi-restraints excluded: chain C residue 1327 ILE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 440 GLN Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 518 ASP Chi-restraints excluded: chain D residue 549 MET Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 847 GLU Chi-restraints excluded: chain D residue 898 HIS Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 549 MET Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 824 GLU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 862 SER Chi-restraints excluded: chain E residue 1327 ILE Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 593 LYS Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 691 LEU Chi-restraints excluded: chain F residue 728 PHE Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 847 GLU Chi-restraints excluded: chain F residue 919 LYS Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 112 optimal weight: 0.5980 chunk 325 optimal weight: 0.0070 chunk 60 optimal weight: 0.6980 chunk 221 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 334 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 191 optimal weight: 0.0060 chunk 103 optimal weight: 0.6980 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 GLN A 554 GLN A 699 GLN B 727 ASN C 727 ASN D 420 ASN D 775 ASN D 829 GLN D 911 ASN E 644 GLN E1326 GLN F 441 ASN F 911 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114152 restraints weight = 39686.894| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.06 r_work: 0.3312 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.7902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28523 Z= 0.122 Angle : 0.593 9.979 38585 Z= 0.291 Chirality : 0.042 0.232 4403 Planarity : 0.004 0.068 4918 Dihedral : 7.539 171.558 3780 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 3.86 % Allowed : 29.14 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 0.49 (0.15), residues: 3457 helix: 1.09 (0.13), residues: 1771 sheet: -0.47 (0.27), residues: 368 loop : -0.36 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 498 TYR 0.015 0.001 TYR E 435 PHE 0.030 0.001 PHE A 642 TRP 0.015 0.001 TRP E 841 HIS 0.003 0.001 HIS D1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (28523) covalent geometry : angle 0.59309 / 0.29 (38585) hydrogen bonds : bond 0.03078 / 2.03 ( 1224) hydrogen bonds : angle 3.84642 / 2.68 ( 3549) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 866 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ILE cc_start: 0.8008 (pt) cc_final: 0.7774 (mp) REVERT: A 421 TYR cc_start: 0.8154 (m-10) cc_final: 0.7700 (m-10) REVERT: A 424 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8034 (mt0) REVERT: A 437 GLU cc_start: 0.7935 (pm20) cc_final: 0.7281 (pm20) REVERT: A 451 LEU cc_start: 0.8639 (tp) cc_final: 0.8316 (tm) REVERT: A 463 MET cc_start: 0.8214 (tpp) cc_final: 0.7952 (tpp) REVERT: A 477 LYS cc_start: 0.8315 (mppt) cc_final: 0.7926 (mppt) REVERT: A 498 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7327 (ttt-90) REVERT: A 500 LEU cc_start: 0.8096 (mt) cc_final: 0.7822 (mt) REVERT: A 509 LYS cc_start: 0.7858 (tptp) cc_final: 0.7632 (tppp) REVERT: A 549 MET cc_start: 0.2706 (mmt) cc_final: 0.1852 (mmt) REVERT: A 600 ARG cc_start: 0.8153 (ttp-170) cc_final: 0.7795 (ptt180) REVERT: A 627 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7526 (ttp-110) REVERT: A 642 PHE cc_start: 0.8201 (m-10) cc_final: 0.7987 (m-10) REVERT: A 662 LYS cc_start: 0.8334 (mttm) cc_final: 0.8060 (mttt) REVERT: A 672 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7615 (ttmm) REVERT: A 726 GLN cc_start: 0.8245 (tp40) cc_final: 0.7832 (mm-40) REVERT: A 729 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8033 (mp) REVERT: A 813 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8253 (t) REVERT: A 824 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: A 879 GLU cc_start: 0.7552 (tp30) cc_final: 0.7205 (tp30) REVERT: A 902 LYS cc_start: 0.8381 (tppt) cc_final: 0.8066 (tppt) REVERT: A 906 THR cc_start: 0.8656 (t) cc_final: 0.8430 (p) REVERT: A 907 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8041 (mtp-110) REVERT: A 1319 GLU cc_start: 0.7845 (mt-10) cc_final: 0.5925 (mt-10) REVERT: A 1336 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 1348 ASP cc_start: 0.7849 (t0) cc_final: 0.7590 (t0) REVERT: A 1365 ASP cc_start: 0.7491 (p0) cc_final: 0.7286 (p0) REVERT: B 414 ASP cc_start: 0.8109 (m-30) cc_final: 0.7886 (m-30) REVERT: B 445 THR cc_start: 0.8419 (m) cc_final: 0.8211 (t) REVERT: B 519 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7672 (mm-30) REVERT: B 530 LYS cc_start: 0.7965 (ptpt) cc_final: 0.7649 (ptpt) REVERT: B 611 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7692 (mt) REVERT: B 616 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7988 (t80) REVERT: B 647 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8225 (mtp85) REVERT: B 671 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8259 (tppp) REVERT: B 672 LYS cc_start: 0.8601 (ptpt) cc_final: 0.8363 (pttp) REVERT: B 692 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8168 (pp) REVERT: B 762 MET cc_start: 0.8440 (mmm) cc_final: 0.8165 (tpt) REVERT: B 778 LYS cc_start: 0.8109 (ttpp) cc_final: 0.7904 (ttpp) REVERT: B 806 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7891 (mp) REVERT: B 815 GLU cc_start: 0.7885 (mp0) cc_final: 0.7639 (mp0) REVERT: B 847 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7970 (mt-10) REVERT: B 868 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8397 (tp) REVERT: B 1336 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7800 (tm-30) REVERT: C 411 ASN cc_start: 0.8194 (m110) cc_final: 0.7650 (p0) REVERT: C 420 ASN cc_start: 0.8241 (m-40) cc_final: 0.7981 (m-40) REVERT: C 441 ASN cc_start: 0.8198 (t0) cc_final: 0.7973 (t0) REVERT: C 482 MET cc_start: 0.8106 (tmm) cc_final: 0.7713 (tmm) REVERT: C 505 GLU cc_start: 0.8040 (tt0) cc_final: 0.7676 (tt0) REVERT: C 506 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: C 528 SER cc_start: 0.8471 (t) cc_final: 0.8211 (t) REVERT: C 538 ILE cc_start: 0.8406 (mm) cc_final: 0.8195 (mt) REVERT: C 546 MET cc_start: 0.8316 (mtp) cc_final: 0.8028 (mtt) REVERT: C 610 PHE cc_start: 0.8117 (t80) cc_final: 0.7875 (t80) REVERT: C 612 ASP cc_start: 0.7830 (m-30) cc_final: 0.7622 (m-30) REVERT: C 690 GLU cc_start: 0.7245 (tp30) cc_final: 0.7026 (mp0) REVERT: C 708 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7729 (p0) REVERT: C 731 TYR cc_start: 0.7950 (m-80) cc_final: 0.7102 (m-80) REVERT: C 762 MET cc_start: 0.8494 (mmm) cc_final: 0.8285 (mmt) REVERT: C 858 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7958 (ptp-170) REVERT: C 864 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7479 (mm-30) REVERT: C 865 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8490 (tttt) REVERT: C 879 GLU cc_start: 0.8045 (tp30) cc_final: 0.7670 (tp30) REVERT: C 911 ASN cc_start: 0.8389 (m110) cc_final: 0.8043 (m-40) REVERT: C 1329 LYS cc_start: 0.8123 (tttt) cc_final: 0.7893 (ttmm) REVERT: C 1361 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7940 (ttpt) REVERT: D 423 ASP cc_start: 0.8280 (m-30) cc_final: 0.8075 (m-30) REVERT: D 427 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: D 437 GLU cc_start: 0.8060 (pm20) cc_final: 0.7727 (pm20) REVERT: D 440 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7694 (mt0) REVERT: D 450 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8387 (t) REVERT: D 477 LYS cc_start: 0.8038 (tptt) cc_final: 0.7793 (tptt) REVERT: D 484 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7814 (mttm) REVERT: D 501 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7773 (ttm-80) REVERT: D 529 SER cc_start: 0.8267 (m) cc_final: 0.8011 (p) REVERT: D 589 LYS cc_start: 0.8413 (ttmm) cc_final: 0.8101 (mtpp) REVERT: D 607 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.8243 (p) REVERT: D 655 ASP cc_start: 0.7844 (t70) cc_final: 0.7295 (t0) REVERT: D 658 LYS cc_start: 0.8414 (mttt) cc_final: 0.7910 (mttt) REVERT: D 706 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8394 (mtpt) REVERT: D 728 PHE cc_start: 0.7434 (m-80) cc_final: 0.7178 (m-80) REVERT: D 729 ILE cc_start: 0.8502 (mm) cc_final: 0.8242 (mp) REVERT: D 762 MET cc_start: 0.8253 (mmm) cc_final: 0.8044 (mmm) REVERT: D 764 GLU cc_start: 0.7630 (pt0) cc_final: 0.7321 (pt0) REVERT: D 821 SER cc_start: 0.8688 (t) cc_final: 0.8415 (p) REVERT: D 823 MET cc_start: 0.8487 (tpp) cc_final: 0.8061 (mmm) REVERT: D 847 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: D 857 PHE cc_start: 0.8776 (m-80) cc_final: 0.8409 (m-80) REVERT: D 879 GLU cc_start: 0.6987 (tp30) cc_final: 0.6691 (tp30) REVERT: D 903 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7629 (tm-30) REVERT: D 928 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.7303 (ttm-80) REVERT: D 1329 LYS cc_start: 0.7937 (tptp) cc_final: 0.7590 (tptp) REVERT: D 1348 ASP cc_start: 0.7936 (t70) cc_final: 0.7546 (t0) REVERT: E 408 MET cc_start: 0.5722 (mmm) cc_final: 0.5381 (tmm) REVERT: E 413 ASP cc_start: 0.7862 (p0) cc_final: 0.7629 (p0) REVERT: E 420 ASN cc_start: 0.8175 (t0) cc_final: 0.7855 (t0) REVERT: E 463 MET cc_start: 0.8382 (tpp) cc_final: 0.8081 (ttp) REVERT: E 502 LEU cc_start: 0.8373 (mm) cc_final: 0.8010 (mp) REVERT: E 505 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7261 (mp0) REVERT: E 508 LYS cc_start: 0.8431 (ttmm) cc_final: 0.8176 (ttpp) REVERT: E 518 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7187 (t70) REVERT: E 519 GLU cc_start: 0.7421 (mp0) cc_final: 0.6463 (mp0) REVERT: E 528 SER cc_start: 0.8653 (t) cc_final: 0.8445 (t) REVERT: E 530 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7916 (mttm) REVERT: E 531 GLN cc_start: 0.7968 (mm110) cc_final: 0.7706 (tp40) REVERT: E 612 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7236 (m-30) REVERT: E 671 LYS cc_start: 0.8429 (mmtm) cc_final: 0.8189 (mmtm) REVERT: E 702 ASN cc_start: 0.7512 (t0) cc_final: 0.7151 (t0) REVERT: E 730 ASP cc_start: 0.7811 (m-30) cc_final: 0.7388 (m-30) REVERT: E 800 ASN cc_start: 0.8455 (m110) cc_final: 0.8018 (m-40) REVERT: E 827 LYS cc_start: 0.8353 (ptpt) cc_final: 0.8032 (ptpt) REVERT: E 845 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7768 (tt) REVERT: E 847 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7049 (tm-30) REVERT: E 895 PHE cc_start: 0.8045 (t80) cc_final: 0.7278 (t80) REVERT: E 1336 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7389 (tm-30) REVERT: E 1348 ASP cc_start: 0.8115 (t70) cc_final: 0.7808 (t0) REVERT: E 1375 LYS cc_start: 0.8106 (tptp) cc_final: 0.7803 (tptp) REVERT: F 414 ASP cc_start: 0.7964 (m-30) cc_final: 0.7665 (m-30) REVERT: F 425 LEU cc_start: 0.7827 (tt) cc_final: 0.7581 (tp) REVERT: F 448 ARG cc_start: 0.7090 (mtp180) cc_final: 0.6798 (mtp85) REVERT: F 498 ARG cc_start: 0.7208 (ttp80) cc_final: 0.6899 (ttp80) REVERT: F 501 ARG cc_start: 0.8038 (ttm110) cc_final: 0.7796 (ttm110) REVERT: F 508 LYS cc_start: 0.8129 (tppt) cc_final: 0.7732 (mtpp) REVERT: F 516 PHE cc_start: 0.7728 (t80) cc_final: 0.7005 (t80) REVERT: F 518 ASP cc_start: 0.7930 (t0) cc_final: 0.7487 (m-30) REVERT: F 593 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8006 (mptt) REVERT: F 597 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8104 (pt) REVERT: F 601 LYS cc_start: 0.7925 (tptp) cc_final: 0.7548 (tptt) REVERT: F 612 ASP cc_start: 0.7585 (t70) cc_final: 0.7305 (t70) REVERT: F 632 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7630 (mm-30) REVERT: F 640 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8309 (ttp80) REVERT: F 662 LYS cc_start: 0.7733 (mptp) cc_final: 0.7217 (mptp) REVERT: F 667 MET cc_start: 0.7954 (mmp) cc_final: 0.7722 (mmm) REVERT: F 712 ASN cc_start: 0.7201 (t0) cc_final: 0.6568 (t0) REVERT: F 760 GLU cc_start: 0.8011 (tp30) cc_final: 0.7685 (tp30) REVERT: F 767 ILE cc_start: 0.8337 (pt) cc_final: 0.8005 (mt) REVERT: F 815 GLU cc_start: 0.7516 (mp0) cc_final: 0.7218 (mp0) REVERT: F 827 LYS cc_start: 0.8520 (tttp) cc_final: 0.8288 (ttpp) REVERT: F 845 ILE cc_start: 0.7747 (mm) cc_final: 0.7437 (mp) REVERT: F 879 GLU cc_start: 0.7496 (tp30) cc_final: 0.6855 (tp30) REVERT: F 894 ILE cc_start: 0.8693 (mm) cc_final: 0.8457 (mm) REVERT: F 913 ILE cc_start: 0.8618 (pp) cc_final: 0.8350 (mt) REVERT: F 938 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7515 (ttmm) outliers start: 121 outliers final: 56 residues processed: 916 average time/residue: 0.6535 time to fit residues: 692.6548 Evaluate side-chains 928 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 848 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 616 PHE Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 858 ARG Chi-restraints excluded: chain C residue 1377 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 440 GLN Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 847 GLU Chi-restraints excluded: chain D residue 898 HIS Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 448 ARG Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 549 MET Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 824 GLU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain F residue 593 LYS Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 691 LEU Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 728 PHE Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 326 optimal weight: 0.0010 chunk 125 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 201 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 335 optimal weight: 0.0570 chunk 97 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 overall best weight: 0.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 GLN A 554 GLN A 639 GLN B 727 ASN B 848 ASN C 727 ASN D 420 ASN D 511 GLN D 829 GLN E 639 GLN E 644 GLN F 441 ASN F 649 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113738 restraints weight = 39770.091| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.12 r_work: 0.3309 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.8023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28523 Z= 0.133 Angle : 0.602 10.009 38585 Z= 0.296 Chirality : 0.042 0.196 4403 Planarity : 0.005 0.056 4918 Dihedral : 7.499 168.480 3780 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 3.22 % Allowed : 29.84 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 0.57 (0.15), residues: 3457 helix: 1.17 (0.13), residues: 1761 sheet: -0.45 (0.27), residues: 369 loop : -0.33 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 498 TYR 0.014 0.001 TYR E 435 PHE 0.026 0.001 PHE A 642 TRP 0.014 0.001 TRP E 841 HIS 0.003 0.001 HIS C1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (28523) covalent geometry : angle 0.60158 / 0.30 (38585) hydrogen bonds : bond 0.03122 / 2.06 ( 1224) hydrogen bonds : angle 3.81376 / 2.65 ( 3549) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 863 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7755 (mp) REVERT: A 421 TYR cc_start: 0.8147 (m-10) cc_final: 0.7697 (m-10) REVERT: A 424 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: A 437 GLU cc_start: 0.7962 (pm20) cc_final: 0.7323 (pm20) REVERT: A 451 LEU cc_start: 0.8639 (tp) cc_final: 0.8304 (tm) REVERT: A 463 MET cc_start: 0.8236 (tpp) cc_final: 0.7998 (tpp) REVERT: A 477 LYS cc_start: 0.8312 (mppt) cc_final: 0.7933 (mppt) REVERT: A 498 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.7269 (ttt-90) REVERT: A 500 LEU cc_start: 0.8066 (mt) cc_final: 0.7800 (mt) REVERT: A 502 LEU cc_start: 0.8481 (mt) cc_final: 0.8158 (mp) REVERT: A 509 LYS cc_start: 0.7852 (tptp) cc_final: 0.7632 (tppp) REVERT: A 518 ASP cc_start: 0.7176 (t0) cc_final: 0.6889 (m-30) REVERT: A 549 MET cc_start: 0.2744 (mmt) cc_final: 0.1710 (mmt) REVERT: A 592 PHE cc_start: 0.8758 (t80) cc_final: 0.8275 (t80) REVERT: A 600 ARG cc_start: 0.8154 (ttp-170) cc_final: 0.7800 (ptt180) REVERT: A 611 ILE cc_start: 0.8240 (mt) cc_final: 0.8039 (tt) REVERT: A 642 PHE cc_start: 0.8250 (m-10) cc_final: 0.7997 (m-10) REVERT: A 662 LYS cc_start: 0.8337 (mttm) cc_final: 0.8074 (mttt) REVERT: A 672 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7650 (ttmm) REVERT: A 726 GLN cc_start: 0.8246 (tp40) cc_final: 0.7829 (mm-40) REVERT: A 729 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 813 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8253 (t) REVERT: A 824 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: A 879 GLU cc_start: 0.7583 (tp30) cc_final: 0.7233 (tp30) REVERT: A 902 LYS cc_start: 0.8435 (tppt) cc_final: 0.8134 (tppt) REVERT: A 906 THR cc_start: 0.8676 (t) cc_final: 0.8439 (p) REVERT: A 907 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8118 (mtp-110) REVERT: A 1319 GLU cc_start: 0.7856 (mt-10) cc_final: 0.6251 (tt0) REVERT: A 1336 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7907 (tm-30) REVERT: A 1348 ASP cc_start: 0.7878 (t0) cc_final: 0.7625 (t0) REVERT: A 1365 ASP cc_start: 0.7473 (p0) cc_final: 0.7263 (p0) REVERT: B 414 ASP cc_start: 0.8121 (m-30) cc_final: 0.7880 (m-30) REVERT: B 445 THR cc_start: 0.8444 (m) cc_final: 0.8241 (t) REVERT: B 519 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7695 (mm-30) REVERT: B 530 LYS cc_start: 0.7990 (ptpt) cc_final: 0.7667 (ptpt) REVERT: B 611 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7680 (mt) REVERT: B 616 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.8014 (t80) REVERT: B 627 ARG cc_start: 0.8398 (ttt180) cc_final: 0.8132 (ttt180) REVERT: B 647 ARG cc_start: 0.8470 (mtp85) cc_final: 0.8212 (mtp85) REVERT: B 671 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8265 (tppp) REVERT: B 672 LYS cc_start: 0.8638 (ptpt) cc_final: 0.8385 (pttp) REVERT: B 692 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8177 (pp) REVERT: B 730 ASP cc_start: 0.6997 (p0) cc_final: 0.6416 (p0) REVERT: B 731 TYR cc_start: 0.8219 (m-10) cc_final: 0.8001 (m-10) REVERT: B 762 MET cc_start: 0.8475 (mmm) cc_final: 0.8203 (tpt) REVERT: B 778 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7917 (ttpp) REVERT: B 806 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7940 (mp) REVERT: B 815 GLU cc_start: 0.7927 (mp0) cc_final: 0.7674 (mp0) REVERT: B 847 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8014 (mt-10) REVERT: B 868 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8401 (tp) REVERT: B 1336 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7771 (tm-30) REVERT: C 411 ASN cc_start: 0.8175 (m110) cc_final: 0.7642 (p0) REVERT: C 414 ASP cc_start: 0.8358 (m-30) cc_final: 0.7902 (m-30) REVERT: C 420 ASN cc_start: 0.8241 (m-40) cc_final: 0.7990 (m-40) REVERT: C 441 ASN cc_start: 0.8217 (t0) cc_final: 0.8007 (t0) REVERT: C 482 MET cc_start: 0.8125 (tmm) cc_final: 0.7729 (tmm) REVERT: C 502 LEU cc_start: 0.8357 (tp) cc_final: 0.7739 (tt) REVERT: C 506 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: C 528 SER cc_start: 0.8513 (t) cc_final: 0.8246 (t) REVERT: C 538 ILE cc_start: 0.8428 (mm) cc_final: 0.8217 (mt) REVERT: C 546 MET cc_start: 0.8257 (mtp) cc_final: 0.7967 (mtt) REVERT: C 612 ASP cc_start: 0.7835 (m-30) cc_final: 0.7625 (m-30) REVERT: C 627 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7753 (ttp-110) REVERT: C 690 GLU cc_start: 0.7253 (tp30) cc_final: 0.7030 (mp0) REVERT: C 703 LEU cc_start: 0.8635 (tp) cc_final: 0.8391 (tp) REVERT: C 708 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7708 (p0) REVERT: C 731 TYR cc_start: 0.7974 (m-80) cc_final: 0.7051 (m-80) REVERT: C 845 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.6923 (tt) REVERT: C 864 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7500 (mm-30) REVERT: C 865 LYS cc_start: 0.8819 (ttmt) cc_final: 0.8532 (tttt) REVERT: C 879 GLU cc_start: 0.8015 (tp30) cc_final: 0.7646 (tp30) REVERT: C 911 ASN cc_start: 0.8353 (m110) cc_final: 0.8008 (m-40) REVERT: C 1361 LYS cc_start: 0.8378 (ttpp) cc_final: 0.7851 (ttpp) REVERT: D 437 GLU cc_start: 0.8070 (pm20) cc_final: 0.7493 (pm20) REVERT: D 440 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7573 (mt0) REVERT: D 450 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8400 (t) REVERT: D 477 LYS cc_start: 0.8042 (tptt) cc_final: 0.7766 (tptt) REVERT: D 484 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7809 (mttm) REVERT: D 501 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7788 (ttm-80) REVERT: D 529 SER cc_start: 0.8332 (m) cc_final: 0.8073 (p) REVERT: D 589 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8106 (mtpp) REVERT: D 607 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8252 (p) REVERT: D 632 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7715 (mm-30) REVERT: D 655 ASP cc_start: 0.7875 (t70) cc_final: 0.7304 (t0) REVERT: D 658 LYS cc_start: 0.8458 (mttt) cc_final: 0.7877 (mttt) REVERT: D 706 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8411 (mtpt) REVERT: D 729 ILE cc_start: 0.8509 (mm) cc_final: 0.8262 (mp) REVERT: D 757 GLU cc_start: 0.6309 (tp30) cc_final: 0.5315 (mm-30) REVERT: D 764 GLU cc_start: 0.7686 (pt0) cc_final: 0.7339 (pt0) REVERT: D 821 SER cc_start: 0.8682 (t) cc_final: 0.8411 (p) REVERT: D 823 MET cc_start: 0.8502 (tpp) cc_final: 0.8082 (mmm) REVERT: D 847 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: D 857 PHE cc_start: 0.8807 (m-80) cc_final: 0.8393 (m-80) REVERT: D 903 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7171 (tm-30) REVERT: D 907 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7804 (mtp-110) REVERT: D 928 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7289 (ttm-80) REVERT: D 1329 LYS cc_start: 0.7956 (tptp) cc_final: 0.7607 (tptp) REVERT: D 1348 ASP cc_start: 0.7957 (t70) cc_final: 0.7572 (t0) REVERT: E 408 MET cc_start: 0.5781 (mmm) cc_final: 0.5430 (tmm) REVERT: E 420 ASN cc_start: 0.8184 (t0) cc_final: 0.7625 (t0) REVERT: E 424 GLN cc_start: 0.8526 (mt0) cc_final: 0.8247 (mt0) REVERT: E 463 MET cc_start: 0.8392 (tpp) cc_final: 0.8094 (ttp) REVERT: E 502 LEU cc_start: 0.8372 (mm) cc_final: 0.8005 (mp) REVERT: E 505 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7245 (mp0) REVERT: E 508 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8177 (ttpp) REVERT: E 518 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7235 (t0) REVERT: E 519 GLU cc_start: 0.7422 (mp0) cc_final: 0.6787 (mp0) REVERT: E 528 SER cc_start: 0.8691 (t) cc_final: 0.8483 (t) REVERT: E 530 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7948 (mttm) REVERT: E 531 GLN cc_start: 0.7950 (mm110) cc_final: 0.7669 (tp40) REVERT: E 612 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: E 671 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8210 (mmtm) REVERT: E 726 GLN cc_start: 0.8510 (tp40) cc_final: 0.7923 (tp40) REVERT: E 730 ASP cc_start: 0.7814 (m-30) cc_final: 0.7325 (m-30) REVERT: E 800 ASN cc_start: 0.8446 (m110) cc_final: 0.8122 (m-40) REVERT: E 827 LYS cc_start: 0.8371 (ptpt) cc_final: 0.8040 (ptpt) REVERT: E 845 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7800 (tt) REVERT: E 895 PHE cc_start: 0.8066 (t80) cc_final: 0.7780 (t80) REVERT: E 1336 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7409 (tm-30) REVERT: E 1348 ASP cc_start: 0.8106 (t70) cc_final: 0.7804 (t0) REVERT: E 1375 LYS cc_start: 0.8184 (tptp) cc_final: 0.7866 (tptp) REVERT: F 414 ASP cc_start: 0.7959 (m-30) cc_final: 0.7667 (m-30) REVERT: F 425 LEU cc_start: 0.7827 (tt) cc_final: 0.7586 (tp) REVERT: F 448 ARG cc_start: 0.7137 (mtp180) cc_final: 0.6844 (mtp85) REVERT: F 479 THR cc_start: 0.7107 (m) cc_final: 0.6760 (p) REVERT: F 498 ARG cc_start: 0.7269 (ttp80) cc_final: 0.6949 (ttp80) REVERT: F 501 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7819 (ttm110) REVERT: F 502 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7751 (tt) REVERT: F 508 LYS cc_start: 0.8142 (tppt) cc_final: 0.7752 (mtpp) REVERT: F 516 PHE cc_start: 0.7726 (t80) cc_final: 0.7003 (t80) REVERT: F 518 ASP cc_start: 0.7945 (t0) cc_final: 0.7484 (m-30) REVERT: F 593 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8008 (mptt) REVERT: F 597 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8084 (pt) REVERT: F 601 LYS cc_start: 0.7957 (tptp) cc_final: 0.7572 (tptt) REVERT: F 612 ASP cc_start: 0.7596 (t70) cc_final: 0.7309 (t70) REVERT: F 628 SER cc_start: 0.8294 (m) cc_final: 0.7959 (t) REVERT: F 640 ARG cc_start: 0.8558 (ttp80) cc_final: 0.8340 (ttp80) REVERT: F 662 LYS cc_start: 0.7787 (mptp) cc_final: 0.7230 (mptp) REVERT: F 667 MET cc_start: 0.7951 (mmp) cc_final: 0.7343 (mmm) REVERT: F 671 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8218 (ptpp) REVERT: F 712 ASN cc_start: 0.7243 (t0) cc_final: 0.6594 (t0) REVERT: F 760 GLU cc_start: 0.8023 (tp30) cc_final: 0.7707 (tp30) REVERT: F 767 ILE cc_start: 0.8324 (pt) cc_final: 0.8016 (mt) REVERT: F 815 GLU cc_start: 0.7532 (mp0) cc_final: 0.7239 (mp0) REVERT: F 827 LYS cc_start: 0.8548 (tttp) cc_final: 0.8315 (ttpp) REVERT: F 845 ILE cc_start: 0.7780 (mm) cc_final: 0.7482 (mp) REVERT: F 879 GLU cc_start: 0.7554 (tp30) cc_final: 0.6852 (tp30) REVERT: F 913 ILE cc_start: 0.8666 (pp) cc_final: 0.8343 (mt) REVERT: F 938 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7534 (ttmm) outliers start: 101 outliers final: 56 residues processed: 905 average time/residue: 0.7054 time to fit residues: 736.8033 Evaluate side-chains 932 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 850 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 616 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 839 ASP Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 440 GLN Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 518 ASP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 660 LYS Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 847 GLU Chi-restraints excluded: chain D residue 898 HIS Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 448 ARG Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 549 MET Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 824 GLU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 1327 ILE Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 593 LYS Chi-restraints excluded: chain F residue 597 ILE Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 691 LEU Chi-restraints excluded: chain F residue 710 MET Chi-restraints excluded: chain F residue 728 PHE Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 824 GLU Chi-restraints excluded: chain F residue 847 GLU Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 317 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 328 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 146 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 331 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 GLN A 554 GLN A 699 GLN B 727 ASN B 848 ASN C 554 GLN C 727 ASN D 420 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 ASN D 829 GLN E 639 GLN E 644 GLN F 441 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.111174 restraints weight = 39550.885| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.01 r_work: 0.3283 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.8263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28523 Z= 0.202 Angle : 0.651 12.166 38585 Z= 0.320 Chirality : 0.045 0.178 4403 Planarity : 0.005 0.059 4918 Dihedral : 7.668 162.065 3780 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 2.96 % Allowed : 30.00 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 0.47 (0.15), residues: 3457 helix: 1.05 (0.13), residues: 1764 sheet: -0.48 (0.27), residues: 372 loop : -0.34 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 498 TYR 0.019 0.002 TYR F 792 PHE 0.029 0.002 PHE A 642 TRP 0.013 0.001 TRP A 841 HIS 0.006 0.001 HIS C1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (28523) covalent geometry : angle 0.65108 / 0.32 (38585) hydrogen bonds : bond 0.03535 / 2.33 ( 1224) hydrogen bonds : angle 3.85968 / 2.68 ( 3549) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 877 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ILE cc_start: 0.8034 (pt) cc_final: 0.7795 (mp) REVERT: A 418 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7131 (mt) REVERT: A 421 TYR cc_start: 0.8179 (m-10) cc_final: 0.7769 (m-10) REVERT: A 424 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8117 (mt0) REVERT: A 437 GLU cc_start: 0.7967 (pm20) cc_final: 0.7430 (pm20) REVERT: A 451 LEU cc_start: 0.8700 (tp) cc_final: 0.8333 (tm) REVERT: A 477 LYS cc_start: 0.8314 (mppt) cc_final: 0.7931 (mppt) REVERT: A 498 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7330 (ttt-90) REVERT: A 500 LEU cc_start: 0.8131 (mt) cc_final: 0.7891 (mt) REVERT: A 502 LEU cc_start: 0.8500 (mt) cc_final: 0.8173 (mp) REVERT: A 509 LYS cc_start: 0.7884 (tptp) cc_final: 0.7665 (tppp) REVERT: A 549 MET cc_start: 0.2835 (mmt) cc_final: 0.1696 (mmt) REVERT: A 558 ILE cc_start: 0.8327 (mt) cc_final: 0.7996 (mm) REVERT: A 592 PHE cc_start: 0.8761 (t80) cc_final: 0.8184 (t80) REVERT: A 600 ARG cc_start: 0.8144 (ttp-170) cc_final: 0.7806 (ptt180) REVERT: A 611 ILE cc_start: 0.8290 (mt) cc_final: 0.8088 (tt) REVERT: A 642 PHE cc_start: 0.8287 (m-10) cc_final: 0.8014 (m-10) REVERT: A 672 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7782 (ttmm) REVERT: A 690 GLU cc_start: 0.7397 (tp30) cc_final: 0.7178 (tp30) REVERT: A 729 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8044 (mp) REVERT: A 813 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8367 (t) REVERT: A 824 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: A 879 GLU cc_start: 0.7578 (tp30) cc_final: 0.7231 (tp30) REVERT: A 902 LYS cc_start: 0.8378 (tppt) cc_final: 0.8111 (tppt) REVERT: A 907 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.8087 (mtp-110) REVERT: A 1319 GLU cc_start: 0.7883 (mt-10) cc_final: 0.6218 (tt0) REVERT: A 1336 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 1348 ASP cc_start: 0.7866 (t0) cc_final: 0.7622 (t0) REVERT: A 1365 ASP cc_start: 0.7452 (p0) cc_final: 0.7244 (p0) REVERT: B 414 ASP cc_start: 0.8106 (m-30) cc_final: 0.7858 (m-30) REVERT: B 519 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7746 (mm-30) REVERT: B 530 LYS cc_start: 0.8026 (ptpt) cc_final: 0.7706 (ptpt) REVERT: B 611 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7740 (mt) REVERT: B 616 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8007 (t80) REVERT: B 627 ARG cc_start: 0.8410 (ttt180) cc_final: 0.7978 (ttt180) REVERT: B 660 LYS cc_start: 0.7821 (ptmm) cc_final: 0.7600 (ptmm) REVERT: B 671 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8296 (tppp) REVERT: B 672 LYS cc_start: 0.8743 (ptpt) cc_final: 0.8432 (pttp) REVERT: B 692 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8194 (pp) REVERT: B 730 ASP cc_start: 0.7072 (p0) cc_final: 0.6467 (p0) REVERT: B 731 TYR cc_start: 0.8325 (m-10) cc_final: 0.8076 (m-10) REVERT: B 762 MET cc_start: 0.8495 (mmm) cc_final: 0.8221 (tpt) REVERT: B 778 LYS cc_start: 0.8145 (ttpp) cc_final: 0.7907 (ttpp) REVERT: B 815 GLU cc_start: 0.7901 (mp0) cc_final: 0.7629 (mp0) REVERT: B 840 ILE cc_start: 0.8468 (pt) cc_final: 0.8244 (pt) REVERT: B 847 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8021 (mt-10) REVERT: B 868 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8472 (tp) REVERT: B 1336 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7821 (tm-30) REVERT: C 411 ASN cc_start: 0.8162 (m110) cc_final: 0.7627 (p0) REVERT: C 414 ASP cc_start: 0.8367 (m-30) cc_final: 0.7890 (m-30) REVERT: C 420 ASN cc_start: 0.8273 (m-40) cc_final: 0.8062 (m-40) REVERT: C 441 ASN cc_start: 0.8269 (t0) cc_final: 0.8067 (t0) REVERT: C 482 MET cc_start: 0.8140 (tmm) cc_final: 0.7764 (tmm) REVERT: C 502 LEU cc_start: 0.8367 (tp) cc_final: 0.8157 (tt) REVERT: C 528 SER cc_start: 0.8562 (t) cc_final: 0.8279 (t) REVERT: C 538 ILE cc_start: 0.8524 (mm) cc_final: 0.8316 (mt) REVERT: C 546 MET cc_start: 0.8225 (mtp) cc_final: 0.7913 (mtt) REVERT: C 612 ASP cc_start: 0.7803 (m-30) cc_final: 0.7595 (m-30) REVERT: C 627 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7718 (ttp-110) REVERT: C 690 GLU cc_start: 0.7344 (tp30) cc_final: 0.7105 (mp0) REVERT: C 703 LEU cc_start: 0.8595 (tp) cc_final: 0.8378 (tp) REVERT: C 708 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7655 (p0) REVERT: C 731 TYR cc_start: 0.8004 (m-80) cc_final: 0.7107 (m-80) REVERT: C 828 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7312 (mmm-85) REVERT: C 864 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7399 (mm-30) REVERT: C 865 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8450 (tttt) REVERT: C 879 GLU cc_start: 0.7986 (tp30) cc_final: 0.7601 (tp30) REVERT: C 911 ASN cc_start: 0.8318 (m110) cc_final: 0.7982 (m-40) REVERT: C 1329 LYS cc_start: 0.8150 (tttt) cc_final: 0.7908 (ttmm) REVERT: C 1361 LYS cc_start: 0.8385 (ttpp) cc_final: 0.8155 (ttpp) REVERT: D 419 ASP cc_start: 0.7757 (m-30) cc_final: 0.7464 (m-30) REVERT: D 427 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: D 439 TYR cc_start: 0.8637 (m-80) cc_final: 0.8427 (m-80) REVERT: D 440 GLN cc_start: 0.7980 (mt0) cc_final: 0.7584 (mt0) REVERT: D 450 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8394 (t) REVERT: D 477 LYS cc_start: 0.8008 (tptt) cc_final: 0.7722 (tptt) REVERT: D 495 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7548 (tp30) REVERT: D 501 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7775 (ttm-80) REVERT: D 505 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7849 (mm-30) REVERT: D 529 SER cc_start: 0.8443 (m) cc_final: 0.8210 (p) REVERT: D 589 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8111 (mtpp) REVERT: D 655 ASP cc_start: 0.7868 (t70) cc_final: 0.7338 (t0) REVERT: D 658 LYS cc_start: 0.8444 (mttt) cc_final: 0.7902 (mttt) REVERT: D 667 MET cc_start: 0.8441 (mmt) cc_final: 0.8212 (mmt) REVERT: D 706 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8426 (mtpt) REVERT: D 729 ILE cc_start: 0.8655 (mm) cc_final: 0.8414 (mp) REVERT: D 821 SER cc_start: 0.8664 (t) cc_final: 0.8410 (p) REVERT: D 823 MET cc_start: 0.8477 (tpp) cc_final: 0.8043 (mmm) REVERT: D 847 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: D 857 PHE cc_start: 0.8830 (m-80) cc_final: 0.8474 (m-80) REVERT: D 873 GLU cc_start: 0.7247 (mt-10) cc_final: 0.7014 (mp0) REVERT: D 903 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7611 (tm-30) REVERT: D 928 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.7293 (ttm-80) REVERT: D 1329 LYS cc_start: 0.7990 (tptp) cc_final: 0.7672 (tptp) REVERT: D 1338 CYS cc_start: 0.7364 (p) cc_final: 0.7086 (m) REVERT: D 1340 ASN cc_start: 0.7931 (t0) cc_final: 0.7612 (t0) REVERT: D 1342 THR cc_start: 0.8458 (t) cc_final: 0.8237 (p) REVERT: E 408 MET cc_start: 0.5818 (mmm) cc_final: 0.5496 (tmm) REVERT: E 420 ASN cc_start: 0.8217 (t0) cc_final: 0.7599 (t0) REVERT: E 424 GLN cc_start: 0.8565 (mt0) cc_final: 0.8235 (mt0) REVERT: E 463 MET cc_start: 0.8402 (tpp) cc_final: 0.8124 (ttp) REVERT: E 502 LEU cc_start: 0.8395 (mm) cc_final: 0.8030 (mp) REVERT: E 505 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7184 (mp0) REVERT: E 508 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8179 (ttpp) REVERT: E 518 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7243 (t70) REVERT: E 519 GLU cc_start: 0.7463 (mp0) cc_final: 0.6515 (mp0) REVERT: E 528 SER cc_start: 0.8725 (t) cc_final: 0.8502 (t) REVERT: E 530 LYS cc_start: 0.8299 (mtmm) cc_final: 0.8011 (mttp) REVERT: E 660 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7540 (ttpt) REVERT: E 702 ASN cc_start: 0.7887 (t0) cc_final: 0.7488 (t0) REVERT: E 726 GLN cc_start: 0.8501 (tp40) cc_final: 0.7904 (tp40) REVERT: E 730 ASP cc_start: 0.7861 (m-30) cc_final: 0.7448 (m-30) REVERT: E 800 ASN cc_start: 0.8436 (m110) cc_final: 0.8066 (m-40) REVERT: E 827 LYS cc_start: 0.8373 (ptpt) cc_final: 0.8040 (ptpt) REVERT: E 906 THR cc_start: 0.8419 (p) cc_final: 0.8197 (t) REVERT: E 917 LYS cc_start: 0.8248 (mtpp) cc_final: 0.8017 (mtpt) REVERT: E 1336 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7449 (tm-30) REVERT: E 1348 ASP cc_start: 0.8054 (t70) cc_final: 0.7752 (t0) REVERT: E 1375 LYS cc_start: 0.8293 (tptp) cc_final: 0.8005 (tptp) REVERT: F 414 ASP cc_start: 0.7977 (m-30) cc_final: 0.7690 (m-30) REVERT: F 425 LEU cc_start: 0.7834 (tt) cc_final: 0.7596 (tp) REVERT: F 448 ARG cc_start: 0.7252 (mtp180) cc_final: 0.6948 (mtp85) REVERT: F 479 THR cc_start: 0.7235 (m) cc_final: 0.6894 (p) REVERT: F 484 LYS cc_start: 0.7814 (mtmm) cc_final: 0.7429 (mtmm) REVERT: F 498 ARG cc_start: 0.7319 (ttp80) cc_final: 0.6984 (ttp80) REVERT: F 501 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7876 (ttm110) REVERT: F 502 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7818 (tt) REVERT: F 508 LYS cc_start: 0.8241 (tppt) cc_final: 0.7840 (mtpp) REVERT: F 516 PHE cc_start: 0.7773 (t80) cc_final: 0.6525 (t80) REVERT: F 518 ASP cc_start: 0.7974 (t0) cc_final: 0.7305 (m-30) REVERT: F 593 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8037 (mptt) REVERT: F 601 LYS cc_start: 0.8122 (tptp) cc_final: 0.7702 (tptt) REVERT: F 612 ASP cc_start: 0.7635 (t70) cc_final: 0.7369 (t70) REVERT: F 628 SER cc_start: 0.8342 (m) cc_final: 0.8050 (t) REVERT: F 642 PHE cc_start: 0.8134 (m-80) cc_final: 0.7902 (m-80) REVERT: F 712 ASN cc_start: 0.7342 (t0) cc_final: 0.6794 (t0) REVERT: F 760 GLU cc_start: 0.7968 (tp30) cc_final: 0.7655 (tp30) REVERT: F 767 ILE cc_start: 0.8391 (pt) cc_final: 0.8171 (mt) REVERT: F 795 GLU cc_start: 0.7536 (pm20) cc_final: 0.7304 (pm20) REVERT: F 815 GLU cc_start: 0.7479 (mp0) cc_final: 0.7198 (mp0) REVERT: F 845 ILE cc_start: 0.7871 (mm) cc_final: 0.7610 (mp) REVERT: F 879 GLU cc_start: 0.7573 (tp30) cc_final: 0.7043 (tp30) REVERT: F 938 LYS cc_start: 0.8067 (ttmm) cc_final: 0.7599 (ttmm) outliers start: 93 outliers final: 48 residues processed: 916 average time/residue: 0.6482 time to fit residues: 686.3214 Evaluate side-chains 913 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 846 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 616 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 549 MET Chi-restraints excluded: chain D residue 847 GLU Chi-restraints excluded: chain D residue 898 HIS Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 448 ARG Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 824 GLU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 1327 ILE Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 593 LYS Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 691 LEU Chi-restraints excluded: chain F residue 728 PHE Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 824 GLU Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 117 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 170 optimal weight: 0.6980 chunk 322 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 294 optimal weight: 0.0670 chunk 154 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 GLN A 554 GLN A 562 ASN A 699 GLN B 727 ASN B 848 ASN C 554 GLN C 727 ASN D 420 ASN D 531 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 GLN E 639 GLN E 644 GLN F 441 ASN ** F 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 649 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.133045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.113416 restraints weight = 39586.057| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.97 r_work: 0.3306 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.8377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28523 Z= 0.135 Angle : 0.616 13.779 38585 Z= 0.303 Chirality : 0.043 0.227 4403 Planarity : 0.005 0.060 4918 Dihedral : 7.522 157.743 3780 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 2.81 % Allowed : 30.83 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 0.58 (0.15), residues: 3457 helix: 1.13 (0.13), residues: 1773 sheet: -0.45 (0.27), residues: 371 loop : -0.26 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 498 TYR 0.016 0.001 TYR E 435 PHE 0.026 0.001 PHE F1376 TRP 0.014 0.001 TRP A 841 HIS 0.003 0.001 HIS F1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (28523) covalent geometry : angle 0.61552 / 0.30 (38585) hydrogen bonds : bond 0.03188 / 2.10 ( 1224) hydrogen bonds : angle 3.80865 / 2.65 ( 3549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12128.94 seconds wall clock time: 206 minutes 26.12 seconds (12386.12 seconds total)