Starting phenix.real_space_refine on Fri Mar 6 04:07:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uqj_26696/03_2026/7uqj_26696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uqj_26696/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uqj_26696/03_2026/7uqj_26696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uqj_26696/03_2026/7uqj_26696.map" model { file = "/net/cci-nas-00/data/ceres_data/7uqj_26696/03_2026/7uqj_26696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uqj_26696/03_2026/7uqj_26696.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.49, per 1000 atoms: 0.23 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: 2.33 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.82 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: 5.41 Time building geometry restraints manager: 3.10 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: 16946 32.18 - 64.36: 621 64.36 - 96.54: 74 96.54 - 128.72: 5 128.72 - 160.90: 4 Dihedral angle restraints: 17650 sinusoidal: 7408 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 17647 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.910 Find NCS groups from input model: 0.790 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:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 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 : 17.027 160.904 10962 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 covalent geometry : bond 0.01039 (28523) covalent geometry : angle 1.07514 (38585) hydrogen bonds : bond 0.17152 ( 1224) hydrogen bonds : angle 6.74218 ( 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 : 1.187 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: 0.6352 time to fit residues: 620.4065 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 : 0.862 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 562 ASN B 644 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 874 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 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 Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.142943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123222 restraints weight = 40641.263| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.99 r_work: 0.3469 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3193 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= 0.183 Angle : 0.712 11.633 38585 Z= 0.359 Chirality : 0.045 0.289 4403 Planarity : 0.006 0.061 4918 Dihedral : 9.887 175.157 3865 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 3.89 % Allowed : 17.98 % Favored : 78.13 % 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: -1.50 (0.14), residues: 3457 helix: -0.66 (0.12), residues: 1741 sheet: -0.82 (0.28), residues: 330 loop : -1.30 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 640 TYR 0.033 0.002 TYR E 421 PHE 0.032 0.002 PHE D 822 TRP 0.024 0.002 TRP A 841 HIS 0.006 0.002 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00426 (28523) covalent geometry : angle 0.71189 (38585) hydrogen bonds : bond 0.04227 ( 1224) hydrogen bonds : angle 4.53882 ( 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 878 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 756 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7273 (mt0) REVERT: A 477 LYS cc_start: 0.8318 (mppt) cc_final: 0.8046 (mppt) REVERT: A 481 PHE cc_start: 0.7891 (m-80) cc_final: 0.7457 (m-80) REVERT: A 513 SER cc_start: 0.8052 (m) cc_final: 0.7822 (m) REVERT: A 549 MET cc_start: 0.2894 (mmt) cc_final: 0.1546 (mmt) REVERT: A 724 LEU cc_start: 0.7579 (mt) cc_final: 0.7210 (mp) REVERT: A 727 ASN cc_start: 0.8018 (m-40) cc_final: 0.7715 (m-40) REVERT: A 800 ASN cc_start: 0.8239 (m-40) cc_final: 0.8033 (m110) REVERT: A 902 LYS cc_start: 0.8281 (tppt) cc_final: 0.7952 (tppt) REVERT: A 907 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7978 (ttp80) REVERT: A 1319 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6708 (tt0) REVERT: A 1365 ASP cc_start: 0.7625 (p0) cc_final: 0.7415 (p0) REVERT: B 414 ASP cc_start: 0.7980 (m-30) cc_final: 0.7774 (m-30) REVERT: B 431 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7604 (tp) REVERT: B 589 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8370 (mmmm) REVERT: B 627 ARG cc_start: 0.8423 (ttt180) cc_final: 0.8198 (ttt180) REVERT: B 757 GLU cc_start: 0.6811 (mm-30) cc_final: 0.5878 (mp0) REVERT: B 1336 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7291 (tm-30) REVERT: C 604 SER cc_start: 0.8169 (m) cc_final: 0.7880 (p) REVERT: C 612 ASP cc_start: 0.7912 (m-30) cc_final: 0.7568 (m-30) REVERT: C 613 LYS cc_start: 0.8287 (tttt) cc_final: 0.8026 (tttt) REVERT: C 731 TYR cc_start: 0.8001 (m-80) cc_final: 0.7577 (m-10) REVERT: C 865 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8106 (ttmm) REVERT: C 886 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.7579 (p) REVERT: C 1327 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7613 (tp) REVERT: C 1329 LYS cc_start: 0.8185 (tttt) cc_final: 0.7913 (tttt) REVERT: C 1336 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7481 (mm-30) REVERT: C 1347 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7634 (mt-10) REVERT: D 647 ARG cc_start: 0.7669 (tpp80) cc_final: 0.7289 (mmt90) REVERT: D 661 VAL cc_start: 0.7682 (m) cc_final: 0.7376 (t) REVERT: D 798 VAL cc_start: 0.8267 (m) cc_final: 0.7981 (t) REVERT: D 821 SER cc_start: 0.8026 (t) cc_final: 0.7721 (p) REVERT: D 865 LYS cc_start: 0.7358 (mtpt) cc_final: 0.7152 (mtpp) REVERT: D 887 ASP cc_start: 0.6945 (t70) cc_final: 0.6710 (t70) REVERT: D 903 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7561 (tp30) REVERT: D 925 MET cc_start: 0.4764 (mpp) cc_final: 0.4531 (mpp) REVERT: D 928 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.6975 (ttm-80) REVERT: E 460 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6848 (ttmt) REVERT: E 873 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6704 (mt-10) REVERT: E 902 LYS cc_start: 0.7822 (mtpt) cc_final: 0.7562 (mtpp) REVERT: E 1345 GLN cc_start: 0.7469 (mt0) cc_final: 0.7258 (mt0) REVERT: F 422 ILE cc_start: 0.7273 (mt) cc_final: 0.7043 (mp) REVERT: F 463 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7495 (tpp) REVERT: F 508 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6855 (tppt) REVERT: F 612 ASP cc_start: 0.6990 (t70) cc_final: 0.6759 (t70) REVERT: F 725 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6966 (mt) REVERT: F 731 TYR cc_start: 0.6526 (m-10) cc_final: 0.6122 (m-80) REVERT: F 879 GLU cc_start: 0.6797 (tp30) cc_final: 0.6583 (tp30) REVERT: F 880 VAL cc_start: 0.7356 (OUTLIER) cc_final: 0.7104 (p) REVERT: F 1361 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7455 (ttmt) outliers start: 122 outliers final: 32 residues processed: 812 average time/residue: 0.6385 time to fit residues: 606.5637 Evaluate side-chains 713 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 671 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 497 GLU Chi-restraints excluded: chain A residue 600 ARG 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 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 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 534 ILE 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 460 LYS Chi-restraints excluded: chain E residue 607 SER Chi-restraints excluded: chain E residue 665 ASP Chi-restraints excluded: chain E residue 1340 ASN Chi-restraints excluded: chain F residue 463 MET Chi-restraints excluded: chain F residue 508 LYS 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: 0.0970 chunk 296 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 199 optimal weight: 0.5980 chunk 251 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 226 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 328 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 GLN A 780 ASN A 799 GLN A 904 ASN A1340 ASN B 535 HIS B 726 GLN B1326 GLN C 791 ASN C 874 ASN C 896 GLN D 702 ASN ** D 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 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 E1350 HIS F 511 GLN F 721 ASN F 775 ASN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 GLN G 20 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120123 restraints weight = 40496.758| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.01 r_work: 0.3411 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28523 Z= 0.159 Angle : 0.632 9.931 38585 Z= 0.319 Chirality : 0.043 0.218 4403 Planarity : 0.005 0.058 4918 Dihedral : 9.241 175.295 3840 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 3.76 % Allowed : 22.09 % Favored : 74.15 % 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: -0.71 (0.14), residues: 3457 helix: 0.08 (0.12), residues: 1760 sheet: -0.64 (0.27), residues: 371 loop : -1.02 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 858 TYR 0.016 0.001 TYR A 435 PHE 0.025 0.002 PHE D 592 TRP 0.038 0.001 TRP E 841 HIS 0.007 0.001 HIS E1350 Details of bonding type rmsd covalent geometry : bond 0.00370 (28523) covalent geometry : angle 0.63173 (38585) hydrogen bonds : bond 0.03846 ( 1224) hydrogen bonds : angle 4.21941 ( 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 877 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 759 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 LEU cc_start: 0.7804 (tt) cc_final: 0.7451 (tm) REVERT: A 424 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7652 (mt0) REVERT: A 463 MET cc_start: 0.7819 (tpp) cc_final: 0.7555 (tpp) REVERT: A 465 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7192 (mtp85) REVERT: A 477 LYS cc_start: 0.8343 (mppt) cc_final: 0.8040 (mppt) REVERT: A 481 PHE cc_start: 0.7871 (m-80) cc_final: 0.7403 (m-80) REVERT: A 506 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6993 (mm-30) REVERT: A 549 MET cc_start: 0.2914 (mmt) cc_final: 0.1833 (mmt) REVERT: A 600 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7690 (ptt180) REVERT: A 619 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7139 (mttp) REVERT: A 724 LEU cc_start: 0.7739 (mt) cc_final: 0.7515 (mp) REVERT: A 807 VAL cc_start: 0.8009 (m) cc_final: 0.7728 (t) REVERT: A 873 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6869 (mt-10) REVERT: A 902 LYS cc_start: 0.8499 (tppt) cc_final: 0.8185 (tppt) REVERT: A 907 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.7917 (mtp-110) REVERT: A 1365 ASP cc_start: 0.7603 (p0) cc_final: 0.7399 (p0) REVERT: B 414 ASP cc_start: 0.8061 (m-30) cc_final: 0.7816 (m-30) REVERT: B 502 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8548 (mm) REVERT: B 579 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8389 (mtt180) REVERT: B 598 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: B 613 LYS cc_start: 0.8144 (tttt) cc_final: 0.7764 (ttpp) REVERT: B 627 ARG cc_start: 0.8478 (ttt180) cc_final: 0.8264 (ttt180) REVERT: B 806 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7535 (mt) REVERT: B 815 GLU cc_start: 0.7579 (mp0) cc_final: 0.7276 (mp0) REVERT: C 410 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8373 (m) REVERT: C 497 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6782 (mt-10) REVERT: C 502 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8255 (tp) REVERT: C 604 SER cc_start: 0.8184 (m) cc_final: 0.7970 (p) REVERT: C 612 ASP cc_start: 0.7965 (m-30) cc_final: 0.7631 (m-30) REVERT: C 613 LYS cc_start: 0.8349 (tttt) cc_final: 0.8145 (tttt) REVERT: C 864 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7186 (mm-30) REVERT: C 879 GLU cc_start: 0.8024 (tp30) cc_final: 0.7810 (tp30) REVERT: C 1325 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7221 (tm-30) REVERT: C 1361 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7742 (ttpp) REVERT: D 429 VAL cc_start: 0.6867 (t) cc_final: 0.6653 (t) REVERT: D 450 VAL cc_start: 0.7509 (m) cc_final: 0.7138 (p) REVERT: D 463 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8156 (tpp) REVERT: D 495 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7133 (mm-30) REVERT: D 508 LYS cc_start: 0.7950 (tttt) cc_final: 0.7679 (ttmm) REVERT: D 509 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7780 (tttt) REVERT: D 647 ARG cc_start: 0.7768 (tpp80) cc_final: 0.7542 (mmt90) REVERT: D 661 VAL cc_start: 0.7884 (m) cc_final: 0.7658 (t) REVERT: D 662 LYS cc_start: 0.8474 (mmmm) cc_final: 0.8262 (mttm) REVERT: D 795 GLU cc_start: 0.7066 (pm20) cc_final: 0.6843 (pm20) REVERT: D 821 SER cc_start: 0.8468 (t) cc_final: 0.8146 (p) REVERT: D 823 MET cc_start: 0.8256 (tpp) cc_final: 0.7927 (mmm) REVERT: D 887 ASP cc_start: 0.6954 (t70) cc_final: 0.6746 (t70) REVERT: D 938 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7630 (ttpt) REVERT: D 1329 LYS cc_start: 0.7755 (tptp) cc_final: 0.7320 (tptp) REVERT: D 1355 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8154 (mttm) REVERT: E 448 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6995 (mtp-110) REVERT: E 477 LYS cc_start: 0.7690 (mmtt) cc_final: 0.7321 (mptp) REVERT: E 505 GLU cc_start: 0.6439 (mt-10) cc_final: 0.6207 (mp0) REVERT: E 593 LYS cc_start: 0.8122 (tptm) cc_final: 0.7910 (tptp) REVERT: E 667 MET cc_start: 0.7038 (mmp) cc_final: 0.6374 (mmm) REVERT: E 671 LYS cc_start: 0.7606 (mmtm) cc_final: 0.7170 (mmtm) REVERT: E 850 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8098 (mp) REVERT: E 1356 ILE cc_start: 0.8073 (mp) cc_final: 0.7834 (mt) REVERT: F 518 ASP cc_start: 0.7114 (t0) cc_final: 0.6682 (m-30) REVERT: F 601 LYS cc_start: 0.7487 (tptt) cc_final: 0.7222 (tptt) REVERT: F 612 ASP cc_start: 0.7223 (t70) cc_final: 0.6982 (t70) REVERT: F 662 LYS cc_start: 0.7567 (mptp) cc_final: 0.7345 (mptp) REVERT: F 665 ASP cc_start: 0.5784 (t0) cc_final: 0.4695 (m-30) REVERT: F 713 ILE cc_start: 0.6627 (OUTLIER) cc_final: 0.6295 (tt) REVERT: F 767 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7573 (mt) REVERT: F 798 VAL cc_start: 0.8717 (m) cc_final: 0.8416 (t) REVERT: F 858 ARG cc_start: 0.7526 (mtp180) cc_final: 0.7172 (mtp180) REVERT: F 905 ILE cc_start: 0.7445 (mm) cc_final: 0.7236 (mm) REVERT: F 1361 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7674 (ttmt) outliers start: 118 outliers final: 39 residues processed: 807 average time/residue: 0.6749 time to fit residues: 630.3701 Evaluate side-chains 762 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 705 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 538 ILE Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 729 ILE 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 415 ILE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 598 GLN 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 B residue 1348 ASP Chi-restraints excluded: chain C residue 410 VAL 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 813 THR Chi-restraints excluded: chain C residue 1361 LYS Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 801 LEU Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 1355 LYS Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 448 ARG Chi-restraints excluded: chain E residue 850 ILE Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 482 MET 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 824 GLU Chi-restraints excluded: chain F residue 910 SER 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 F residue 1376 PHE 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: 0.0270 chunk 278 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 319 optimal weight: 0.0870 chunk 281 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 336 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 HIS A 554 GLN A 780 ASN A1340 ASN B 848 ASN B 911 ASN C 727 ASN D 531 GLN D 712 ASN D 775 ASN D 780 ASN E 424 GLN ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 726 GLN E1345 GLN F 554 GLN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120131 restraints weight = 40161.272| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.02 r_work: 0.3418 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28523 Z= 0.120 Angle : 0.580 8.899 38585 Z= 0.289 Chirality : 0.042 0.232 4403 Planarity : 0.004 0.059 4918 Dihedral : 8.883 177.937 3838 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 3.76 % Allowed : 23.46 % Favored : 72.78 % 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: -0.22 (0.15), residues: 3457 helix: 0.53 (0.13), residues: 1756 sheet: -0.53 (0.28), residues: 339 loop : -0.82 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 928 TYR 0.012 0.001 TYR A 435 PHE 0.019 0.001 PHE D 442 TRP 0.020 0.001 TRP E 841 HIS 0.002 0.001 HIS E1350 Details of bonding type rmsd covalent geometry : bond 0.00286 (28523) covalent geometry : angle 0.57958 (38585) hydrogen bonds : bond 0.03252 ( 1224) hydrogen bonds : angle 3.99335 ( 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 885 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 767 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 LEU cc_start: 0.7814 (tt) cc_final: 0.7445 (tm) REVERT: A 424 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: A 451 LEU cc_start: 0.8414 (tp) cc_final: 0.8125 (tm) REVERT: A 463 MET cc_start: 0.7845 (tpp) cc_final: 0.7569 (tpp) REVERT: A 477 LYS cc_start: 0.8368 (mppt) cc_final: 0.8065 (mppt) REVERT: A 481 PHE cc_start: 0.7802 (m-80) cc_final: 0.7413 (m-80) REVERT: A 484 LYS cc_start: 0.7726 (mmmm) cc_final: 0.7458 (mmmm) REVERT: A 500 LEU cc_start: 0.7894 (mt) cc_final: 0.7516 (mp) REVERT: A 506 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7073 (mm-30) REVERT: A 549 MET cc_start: 0.2849 (mmt) cc_final: 0.1584 (mmt) REVERT: A 598 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7545 (mm110) REVERT: A 600 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7651 (ptt180) REVERT: A 619 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7419 (ptmt) REVERT: A 662 LYS cc_start: 0.8145 (mttt) cc_final: 0.7811 (mttt) REVERT: A 807 VAL cc_start: 0.8010 (m) cc_final: 0.7701 (t) REVERT: A 824 GLU cc_start: 0.8217 (tp30) cc_final: 0.8000 (mm-30) REVERT: A 863 ASN cc_start: 0.8523 (p0) cc_final: 0.8278 (p0) REVERT: A 873 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6987 (mt-10) REVERT: A 879 GLU cc_start: 0.7368 (tp30) cc_final: 0.7090 (tp30) REVERT: A 902 LYS cc_start: 0.8551 (tppt) cc_final: 0.8213 (tppt) REVERT: A 907 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.7944 (mtp-110) REVERT: A 1336 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7354 (tm-30) REVERT: A 1365 ASP cc_start: 0.7620 (p0) cc_final: 0.7382 (p0) REVERT: B 414 ASP cc_start: 0.8109 (m-30) cc_final: 0.7844 (m-30) REVERT: B 450 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8464 (t) REVERT: B 491 LYS cc_start: 0.7440 (pmtt) cc_final: 0.7189 (pmtt) REVERT: B 549 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8198 (ttp) REVERT: B 561 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8215 (t) REVERT: B 613 LYS cc_start: 0.8150 (tttt) cc_final: 0.7799 (ttpp) REVERT: B 627 ARG cc_start: 0.8482 (ttt180) cc_final: 0.8110 (ttt180) REVERT: B 806 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7624 (mt) REVERT: B 815 GLU cc_start: 0.7596 (mp0) cc_final: 0.7281 (mp0) REVERT: C 410 VAL cc_start: 0.8641 (p) cc_final: 0.8412 (m) REVERT: C 463 MET cc_start: 0.8803 (tpp) cc_final: 0.8537 (tpp) REVERT: C 502 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8247 (tp) REVERT: C 604 SER cc_start: 0.8195 (m) cc_final: 0.7965 (p) REVERT: C 612 ASP cc_start: 0.7959 (m-30) cc_final: 0.7701 (m-30) REVERT: C 653 LEU cc_start: 0.8598 (tp) cc_final: 0.8395 (tm) REVERT: C 810 SER cc_start: 0.7670 (p) cc_final: 0.7457 (m) REVERT: C 823 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8061 (mmt) REVERT: C 865 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8467 (tttp) REVERT: C 903 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7051 (tm-30) REVERT: C 1361 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7762 (ttpp) REVERT: C 1372 GLU cc_start: 0.7843 (tt0) cc_final: 0.7624 (tt0) REVERT: D 429 VAL cc_start: 0.6995 (t) cc_final: 0.6780 (t) REVERT: D 450 VAL cc_start: 0.7759 (m) cc_final: 0.7382 (p) REVERT: D 463 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8203 (tpp) REVERT: D 484 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7697 (mtmm) REVERT: D 495 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7190 (mm-30) REVERT: D 509 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7834 (ttpt) REVERT: D 518 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: D 529 SER cc_start: 0.7005 (t) cc_final: 0.6597 (p) REVERT: D 531 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7614 (mp-120) REVERT: D 661 VAL cc_start: 0.7969 (m) cc_final: 0.7761 (t) REVERT: D 662 LYS cc_start: 0.8452 (mmmm) cc_final: 0.8170 (mttp) REVERT: D 821 SER cc_start: 0.8513 (t) cc_final: 0.8203 (p) REVERT: D 823 MET cc_start: 0.8290 (tpp) cc_final: 0.7991 (mmm) REVERT: D 824 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7608 (tp30) REVERT: D 887 ASP cc_start: 0.6971 (t70) cc_final: 0.6771 (t70) REVERT: D 1329 LYS cc_start: 0.7698 (tptp) cc_final: 0.7264 (tptp) REVERT: D 1340 ASN cc_start: 0.7570 (t0) cc_final: 0.7326 (t0) REVERT: D 1355 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8179 (mttp) REVERT: E 477 LYS cc_start: 0.7942 (mmtt) cc_final: 0.7612 (mptp) REVERT: E 902 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7825 (mtpp) REVERT: E 1356 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7872 (mt) REVERT: F 518 ASP cc_start: 0.7237 (t0) cc_final: 0.6719 (m-30) REVERT: F 593 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7611 (tptt) REVERT: F 612 ASP cc_start: 0.7230 (t70) cc_final: 0.6964 (t70) REVERT: F 613 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7516 (ttpt) REVERT: F 665 ASP cc_start: 0.5591 (t0) cc_final: 0.4692 (m-30) REVERT: F 767 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7518 (mt) REVERT: F 798 VAL cc_start: 0.8720 (m) cc_final: 0.8444 (t) REVERT: F 858 ARG cc_start: 0.7663 (mtp180) cc_final: 0.7335 (mtp180) REVERT: F 895 PHE cc_start: 0.6450 (t80) cc_final: 0.6210 (t80) REVERT: F 938 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7497 (ttmm) outliers start: 118 outliers final: 41 residues processed: 816 average time/residue: 0.6799 time to fit residues: 639.6730 Evaluate side-chains 805 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 746 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 538 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 636 ILE Chi-restraints excluded: chain A residue 667 MET 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 832 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 561 THR 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 806 LEU Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 1348 ASP 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 660 LYS Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 1327 ILE Chi-restraints excluded: chain C residue 1361 LYS 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 518 ASP Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 898 HIS Chi-restraints excluded: chain D residue 1348 ASP Chi-restraints excluded: chain D residue 1355 LYS Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 795 GLU Chi-restraints excluded: chain E residue 1356 ILE Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 593 LYS Chi-restraints excluded: chain F residue 767 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: 2.9990 chunk 192 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 324 optimal weight: 0.6980 chunk 208 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 GLN A 780 ASN A 800 ASN A1340 ASN B 829 GLN B 848 ASN B 904 ASN B 911 ASN C 727 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 GLN E 639 GLN ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 726 GLN F 441 ASN F 766 GLN F 775 ASN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115446 restraints weight = 40352.684| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.97 r_work: 0.3340 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28523 Z= 0.181 Angle : 0.653 12.051 38585 Z= 0.329 Chirality : 0.044 0.264 4403 Planarity : 0.005 0.056 4918 Dihedral : 8.911 175.959 3838 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.07 % Rotamer: Outliers : 4.78 % Allowed : 23.75 % Favored : 71.47 % Cbeta Deviations : 0.03 % 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: -0.09 (0.15), residues: 3457 helix: 0.65 (0.13), residues: 1758 sheet: -0.61 (0.27), residues: 371 loop : -0.72 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 591 TYR 0.018 0.002 TYR A 435 PHE 0.036 0.002 PHE F 728 TRP 0.015 0.001 TRP A 841 HIS 0.004 0.001 HIS C1350 Details of bonding type rmsd covalent geometry : bond 0.00430 (28523) covalent geometry : angle 0.65329 (38585) hydrogen bonds : bond 0.03713 ( 1224) hydrogen bonds : angle 3.98471 ( 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 1030 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 880 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: A 437 GLU cc_start: 0.7804 (pm20) cc_final: 0.7448 (pm20) REVERT: A 463 MET cc_start: 0.8153 (tpp) cc_final: 0.7866 (tpp) REVERT: A 477 LYS cc_start: 0.8389 (mppt) cc_final: 0.8084 (mppt) REVERT: A 500 LEU cc_start: 0.8069 (mt) cc_final: 0.7714 (mp) REVERT: A 549 MET cc_start: 0.2995 (mmt) cc_final: 0.1818 (mmt) REVERT: A 598 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7974 (mm110) REVERT: A 600 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7727 (ptt180) REVERT: A 619 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7567 (ptmt) REVERT: A 627 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7610 (ttp-110) REVERT: A 667 MET cc_start: 0.7588 (mmp) cc_final: 0.7248 (mmm) REVERT: A 807 VAL cc_start: 0.8071 (m) cc_final: 0.7810 (t) REVERT: A 873 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7163 (mt-10) REVERT: A 879 GLU cc_start: 0.7450 (tp30) cc_final: 0.7119 (tp30) REVERT: A 902 LYS cc_start: 0.8566 (tppt) cc_final: 0.8242 (tppt) REVERT: A 907 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.8019 (mtp-110) REVERT: A 1319 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7223 (mt-10) REVERT: A 1336 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 1348 ASP cc_start: 0.7983 (t0) cc_final: 0.7713 (t0) REVERT: A 1365 ASP cc_start: 0.7655 (p0) cc_final: 0.7426 (p0) REVERT: B 426 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8301 (ttpt) REVERT: B 431 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 433 LEU cc_start: 0.8130 (mt) cc_final: 0.7902 (mp) REVERT: B 458 THR cc_start: 0.8326 (p) cc_final: 0.8091 (m) REVERT: B 463 MET cc_start: 0.8782 (tpt) cc_final: 0.8400 (tpt) REVERT: B 483 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7800 (mmp80) REVERT: B 484 LYS cc_start: 0.8131 (mptt) cc_final: 0.7927 (mmpt) REVERT: B 601 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7630 (tptp) REVERT: B 613 LYS cc_start: 0.8236 (tttt) cc_final: 0.7853 (ttpp) REVERT: B 616 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7729 (t80) REVERT: B 627 ARG cc_start: 0.8468 (ttt180) cc_final: 0.8101 (ttt180) REVERT: B 632 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7536 (mm-30) REVERT: B 639 GLN cc_start: 0.7768 (mt0) cc_final: 0.7505 (mt0) REVERT: B 653 LEU cc_start: 0.8159 (tp) cc_final: 0.7740 (pp) REVERT: B 686 GLN cc_start: 0.7997 (mt0) cc_final: 0.7759 (tp40) REVERT: B 792 TYR cc_start: 0.8830 (t80) cc_final: 0.8557 (t80) REVERT: B 815 GLU cc_start: 0.7721 (mp0) cc_final: 0.7389 (mp0) REVERT: B 827 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8567 (mttp) REVERT: B 863 ASN cc_start: 0.8325 (p0) cc_final: 0.8122 (p0) REVERT: C 462 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8546 (tp) REVERT: C 463 MET cc_start: 0.8787 (tpp) cc_final: 0.8582 (tpp) REVERT: C 502 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8351 (tp) REVERT: C 612 ASP cc_start: 0.8038 (m-30) cc_final: 0.7829 (m-30) REVERT: C 646 TYR cc_start: 0.8814 (m-80) cc_final: 0.8567 (m-80) REVERT: C 762 MET cc_start: 0.8386 (mmm) cc_final: 0.8156 (mmt) REVERT: C 823 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8316 (mmt) REVERT: C 858 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7810 (ptp-170) REVERT: C 864 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7290 (mm-30) REVERT: C 865 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8456 (tttt) REVERT: C 879 GLU cc_start: 0.8015 (tp30) cc_final: 0.7736 (tp30) REVERT: C 1329 LYS cc_start: 0.8236 (tttt) cc_final: 0.8031 (tttt) REVERT: C 1347 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7821 (mt-10) REVERT: C 1372 GLU cc_start: 0.7841 (tt0) cc_final: 0.7621 (tt0) REVERT: D 420 ASN cc_start: 0.8367 (t0) cc_final: 0.8023 (t0) REVERT: D 429 VAL cc_start: 0.7923 (t) cc_final: 0.7644 (t) REVERT: D 450 VAL cc_start: 0.8447 (m) cc_final: 0.8061 (p) REVERT: D 463 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8464 (tpp) REVERT: D 495 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7596 (mm-30) REVERT: D 509 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7980 (mtpp) REVERT: D 529 SER cc_start: 0.8024 (t) cc_final: 0.7662 (p) REVERT: D 530 LYS cc_start: 0.8206 (mttt) cc_final: 0.7966 (mttt) REVERT: D 589 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8381 (ttmm) REVERT: D 593 LYS cc_start: 0.8805 (tptt) cc_final: 0.8601 (tptp) REVERT: D 607 SER cc_start: 0.8267 (OUTLIER) cc_final: 0.8010 (p) REVERT: D 655 ASP cc_start: 0.7572 (t70) cc_final: 0.6947 (t70) REVERT: D 658 LYS cc_start: 0.8299 (mttt) cc_final: 0.8025 (mttt) REVERT: D 728 PHE cc_start: 0.7042 (m-10) cc_final: 0.6734 (m-80) REVERT: D 821 SER cc_start: 0.8734 (t) cc_final: 0.8430 (p) REVERT: D 823 MET cc_start: 0.8275 (tpp) cc_final: 0.8022 (mmm) REVERT: D 824 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7706 (tp30) REVERT: D 879 GLU cc_start: 0.6627 (tp30) cc_final: 0.6355 (tp30) REVERT: D 911 ASN cc_start: 0.7737 (t0) cc_final: 0.7395 (t0) REVERT: D 928 ARG cc_start: 0.7398 (ttm-80) cc_final: 0.6915 (ttm-80) REVERT: D 1329 LYS cc_start: 0.7752 (tptp) cc_final: 0.7351 (tptp) REVERT: D 1340 ASN cc_start: 0.8009 (t0) cc_final: 0.7736 (t0) REVERT: D 1355 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8490 (mttm) REVERT: E 463 MET cc_start: 0.7933 (tmm) cc_final: 0.7685 (ttp) REVERT: E 502 LEU cc_start: 0.8078 (mm) cc_final: 0.7732 (mp) REVERT: E 505 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6662 (mp0) REVERT: E 519 GLU cc_start: 0.7031 (mp0) cc_final: 0.6486 (mp0) REVERT: E 528 SER cc_start: 0.8399 (t) cc_final: 0.8185 (t) REVERT: E 530 LYS cc_start: 0.7922 (mtmm) cc_final: 0.7699 (mtmm) REVERT: E 531 GLN cc_start: 0.7936 (mm110) cc_final: 0.7630 (tp40) REVERT: E 532 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7667 (mm-30) REVERT: E 554 GLN cc_start: 0.5924 (mm-40) cc_final: 0.5664 (mp10) REVERT: E 671 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7648 (mmtm) REVERT: E 862 SER cc_start: 0.8170 (m) cc_final: 0.7828 (p) REVERT: E 873 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7044 (mt-10) REVERT: E 906 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7993 (p) REVERT: E 1345 GLN cc_start: 0.8265 (mt0) cc_final: 0.8049 (mt0) REVERT: E 1348 ASP cc_start: 0.8056 (t70) cc_final: 0.7758 (t0) REVERT: E 1358 TRP cc_start: 0.8365 (t-100) cc_final: 0.8144 (t-100) REVERT: F 463 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.8034 (tpt) REVERT: F 518 ASP cc_start: 0.7785 (t0) cc_final: 0.7133 (m-30) REVERT: F 591 ARG cc_start: 0.7667 (mtp180) cc_final: 0.7294 (mtp-110) REVERT: F 593 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7836 (tptt) REVERT: F 612 ASP cc_start: 0.7570 (t70) cc_final: 0.7281 (t70) REVERT: F 613 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7725 (ttpt) REVERT: F 665 ASP cc_start: 0.5843 (t0) cc_final: 0.5098 (m-30) REVERT: F 707 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8153 (tp) REVERT: F 728 PHE cc_start: 0.6656 (OUTLIER) cc_final: 0.6437 (m-80) REVERT: F 815 GLU cc_start: 0.7480 (mp0) cc_final: 0.7113 (mp0) REVERT: F 898 HIS cc_start: 0.7481 (m-70) cc_final: 0.7173 (m-70) REVERT: F 911 ASN cc_start: 0.8471 (t0) cc_final: 0.8248 (t0) REVERT: F 913 ILE cc_start: 0.8327 (pp) cc_final: 0.8020 (mp) REVERT: F 938 LYS cc_start: 0.8025 (ttmm) cc_final: 0.7675 (ttmm) REVERT: F 1357 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7718 (mt) outliers start: 150 outliers final: 46 residues processed: 946 average time/residue: 0.6694 time to fit residues: 732.2243 Evaluate side-chains 879 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 813 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 521 ASP 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 772 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 815 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain B residue 431 LEU 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 758 PHE Chi-restraints excluded: chain B residue 765 SER 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 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 462 LEU 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 607 SER Chi-restraints excluded: chain C residue 673 ILE 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 D residue 463 MET Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain D residue 1355 LYS Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 824 GLU Chi-restraints excluded: chain E residue 906 THR Chi-restraints excluded: chain E residue 1340 ASN Chi-restraints excluded: chain F residue 463 MET Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 579 ARG 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 728 PHE Chi-restraints excluded: chain F residue 813 THR 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: 0.9980 chunk 289 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 68 optimal weight: 0.0020 chunk 152 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 221 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 GLN B 443 ASN B 562 ASN B 727 ASN B 848 ASN B1326 GLN C 554 GLN C 727 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 ASN D 829 GLN D1339 GLN E 424 GLN ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 896 GLN F1340 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115317 restraints weight = 39875.533| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.05 r_work: 0.3330 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28523 Z= 0.151 Angle : 0.610 12.007 38585 Z= 0.300 Chirality : 0.043 0.256 4403 Planarity : 0.004 0.055 4918 Dihedral : 8.723 175.813 3836 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 3.63 % Allowed : 27.16 % Favored : 69.21 % 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: 0.09 (0.15), residues: 3457 helix: 0.80 (0.13), residues: 1779 sheet: -0.59 (0.27), residues: 369 loop : -0.66 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 498 TYR 0.015 0.001 TYR A 435 PHE 0.030 0.002 PHE E 592 TRP 0.014 0.001 TRP A 841 HIS 0.004 0.001 HIS E 898 Details of bonding type rmsd covalent geometry : bond 0.00368 (28523) covalent geometry : angle 0.61004 (38585) hydrogen bonds : bond 0.03300 ( 1224) hydrogen bonds : angle 3.92691 ( 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 963 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 849 time to evaluate : 0.891 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 421 TYR cc_start: 0.8083 (m-10) cc_final: 0.7608 (m-10) REVERT: A 424 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: A 437 GLU cc_start: 0.7840 (pm20) cc_final: 0.7583 (pm20) REVERT: A 451 LEU cc_start: 0.8593 (tp) cc_final: 0.8345 (tm) REVERT: A 463 MET cc_start: 0.8187 (tpp) cc_final: 0.7917 (tpp) REVERT: A 477 LYS cc_start: 0.8402 (mppt) cc_final: 0.8038 (mppt) REVERT: A 499 GLN cc_start: 0.8107 (mm110) cc_final: 0.7748 (mm-40) REVERT: A 500 LEU cc_start: 0.8087 (mt) cc_final: 0.7774 (mt) REVERT: A 521 ASP cc_start: 0.8198 (p0) cc_final: 0.7959 (p0) REVERT: A 549 MET cc_start: 0.2868 (mmt) cc_final: 0.1725 (mmt) REVERT: A 581 PHE cc_start: 0.7841 (m-10) cc_final: 0.7637 (m-10) REVERT: A 598 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8020 (mm110) REVERT: A 600 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7793 (ptt180) REVERT: A 619 LYS cc_start: 0.7969 (ptpt) cc_final: 0.7668 (ptmt) REVERT: A 667 MET cc_start: 0.7889 (mmp) cc_final: 0.7623 (mmm) REVERT: A 807 VAL cc_start: 0.8026 (m) cc_final: 0.7770 (t) REVERT: A 873 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7101 (mt-10) REVERT: A 879 GLU cc_start: 0.7479 (tp30) cc_final: 0.7152 (tp30) REVERT: A 902 LYS cc_start: 0.8485 (tppt) cc_final: 0.8161 (tppt) REVERT: A 907 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8091 (mtp180) REVERT: A 1319 GLU cc_start: 0.7528 (mt-10) cc_final: 0.6941 (mt-10) REVERT: A 1336 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 1348 ASP cc_start: 0.7911 (t0) cc_final: 0.7661 (t0) REVERT: A 1365 ASP cc_start: 0.7536 (p0) cc_final: 0.7300 (p0) REVERT: B 414 ASP cc_start: 0.8188 (m-30) cc_final: 0.7919 (m-30) REVERT: B 431 LEU cc_start: 0.8547 (mm) cc_final: 0.8304 (mp) REVERT: B 433 LEU cc_start: 0.8193 (mt) cc_final: 0.7985 (mp) REVERT: B 463 MET cc_start: 0.8807 (tpt) cc_final: 0.8373 (tpt) REVERT: B 483 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7864 (mmp80) REVERT: B 601 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7651 (tptp) REVERT: B 613 LYS cc_start: 0.8315 (tttt) cc_final: 0.7921 (ttpp) REVERT: B 616 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7906 (t80) REVERT: B 627 ARG cc_start: 0.8433 (ttt180) cc_final: 0.8060 (ttt180) REVERT: B 639 GLN cc_start: 0.7799 (mt0) cc_final: 0.7502 (mt0) REVERT: B 653 LEU cc_start: 0.8188 (tp) cc_final: 0.7730 (pp) REVERT: B 692 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8179 (pp) REVERT: B 792 TYR cc_start: 0.8831 (t80) cc_final: 0.8585 (t80) REVERT: B 806 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7852 (mp) REVERT: B 815 GLU cc_start: 0.7708 (mp0) cc_final: 0.7507 (mp0) REVERT: B 827 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8622 (mttp) REVERT: B 848 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8068 (t0) REVERT: B 862 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.7992 (t) REVERT: B 1336 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7862 (tm-30) REVERT: C 419 ASP cc_start: 0.8206 (m-30) cc_final: 0.7624 (m-30) REVERT: C 420 ASN cc_start: 0.8266 (m-40) cc_final: 0.7936 (m-40) REVERT: C 441 ASN cc_start: 0.8268 (t0) cc_final: 0.7937 (t0) REVERT: C 462 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8537 (tp) REVERT: C 482 MET cc_start: 0.8077 (tmm) cc_final: 0.7621 (tmm) REVERT: C 497 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7326 (mm-30) REVERT: C 502 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8387 (tp) REVERT: C 538 ILE cc_start: 0.8392 (mm) cc_final: 0.8140 (mt) REVERT: C 612 ASP cc_start: 0.7946 (m-30) cc_final: 0.7722 (m-30) REVERT: C 673 ILE cc_start: 0.8870 (mm) cc_final: 0.8623 (mp) REVERT: C 693 LYS cc_start: 0.8434 (mttm) cc_final: 0.8176 (mttp) REVERT: C 762 MET cc_start: 0.8444 (mmm) cc_final: 0.8229 (mmt) REVERT: C 823 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8367 (mmt) REVERT: C 858 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7802 (ptp-170) REVERT: C 864 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7315 (mm-30) REVERT: C 865 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8440 (tttt) REVERT: C 879 GLU cc_start: 0.7972 (tp30) cc_final: 0.7600 (tp30) REVERT: C 1372 GLU cc_start: 0.7884 (tt0) cc_final: 0.7647 (tt0) REVERT: D 419 ASP cc_start: 0.7726 (m-30) cc_final: 0.7485 (m-30) REVERT: D 429 VAL cc_start: 0.8121 (t) cc_final: 0.7852 (t) REVERT: D 437 GLU cc_start: 0.7976 (pm20) cc_final: 0.7701 (pm20) REVERT: D 484 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7862 (mttt) REVERT: D 501 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7775 (ttm-80) REVERT: D 509 LYS cc_start: 0.8283 (ttmm) cc_final: 0.8065 (mtpp) REVERT: D 529 SER cc_start: 0.7841 (t) cc_final: 0.7562 (p) REVERT: D 568 ASP cc_start: 0.7983 (t70) cc_final: 0.7713 (t70) REVERT: D 593 LYS cc_start: 0.8795 (tptt) cc_final: 0.8576 (tptm) REVERT: D 607 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8219 (p) REVERT: D 655 ASP cc_start: 0.7725 (t70) cc_final: 0.7329 (t70) REVERT: D 658 LYS cc_start: 0.8425 (mttt) cc_final: 0.8012 (mttt) REVERT: D 821 SER cc_start: 0.8752 (t) cc_final: 0.8461 (p) REVERT: D 823 MET cc_start: 0.8234 (tpp) cc_final: 0.8007 (mmm) REVERT: D 824 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7787 (tp30) REVERT: D 879 GLU cc_start: 0.6844 (tp30) cc_final: 0.6615 (tp30) REVERT: D 911 ASN cc_start: 0.7740 (t0) cc_final: 0.7412 (t0) REVERT: D 928 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.6955 (ttm-80) REVERT: D 1329 LYS cc_start: 0.7881 (tptp) cc_final: 0.7512 (tptp) REVERT: E 408 MET cc_start: 0.5229 (mmm) cc_final: 0.4913 (tmm) REVERT: E 415 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8462 (mt) REVERT: E 502 LEU cc_start: 0.8211 (mm) cc_final: 0.7888 (OUTLIER) REVERT: E 508 LYS cc_start: 0.8362 (ttmm) cc_final: 0.8077 (ttpp) REVERT: E 519 GLU cc_start: 0.7169 (mp0) cc_final: 0.6593 (mp0) REVERT: E 528 SER cc_start: 0.8541 (t) cc_final: 0.8278 (t) REVERT: E 530 LYS cc_start: 0.7966 (mtmm) cc_final: 0.7646 (mttp) REVERT: E 531 GLN cc_start: 0.7849 (mm110) cc_final: 0.7574 (tp40) REVERT: E 554 GLN cc_start: 0.6321 (mm-40) cc_final: 0.6070 (mp10) REVERT: E 589 LYS cc_start: 0.8262 (ptmm) cc_final: 0.8021 (ptpp) REVERT: E 671 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7985 (mmtm) REVERT: E 730 ASP cc_start: 0.7375 (m-30) cc_final: 0.6980 (m-30) REVERT: E 758 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7677 (p90) REVERT: E 762 MET cc_start: 0.8462 (mmm) cc_final: 0.8222 (mmm) REVERT: E 764 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7640 (mt-10) REVERT: E 778 LYS cc_start: 0.8443 (tppp) cc_final: 0.8151 (tppp) REVERT: E 902 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7972 (mtpp) REVERT: E 917 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7841 (mtmm) REVERT: E 1348 ASP cc_start: 0.8129 (t70) cc_final: 0.7766 (t0) REVERT: E 1359 LYS cc_start: 0.7932 (ttpp) cc_final: 0.7714 (ttmm) REVERT: E 1375 LYS cc_start: 0.7853 (tptp) cc_final: 0.7581 (tptp) REVERT: F 414 ASP cc_start: 0.7388 (m-30) cc_final: 0.7180 (m-30) REVERT: F 463 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7992 (tpt) REVERT: F 518 ASP cc_start: 0.7829 (t0) cc_final: 0.7172 (m-30) REVERT: F 593 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7894 (tptt) REVERT: F 612 ASP cc_start: 0.7565 (t70) cc_final: 0.7262 (t70) REVERT: F 642 PHE cc_start: 0.7702 (m-80) cc_final: 0.7482 (m-80) REVERT: F 665 ASP cc_start: 0.6156 (t0) cc_final: 0.5597 (m-30) REVERT: F 707 LEU cc_start: 0.8489 (tt) cc_final: 0.8167 (tp) REVERT: F 767 ILE cc_start: 0.8235 (pt) cc_final: 0.7876 (mt) REVERT: F 815 GLU cc_start: 0.7561 (mp0) cc_final: 0.7268 (mp0) REVERT: F 898 HIS cc_start: 0.7554 (m-70) cc_final: 0.7262 (m-70) REVERT: F 911 ASN cc_start: 0.8519 (t0) cc_final: 0.8287 (t0) REVERT: F 913 ILE cc_start: 0.8422 (pp) cc_final: 0.8183 (mp) REVERT: F 923 ILE cc_start: 0.8061 (mt) cc_final: 0.7732 (pp) REVERT: F 938 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7690 (ttmm) REVERT: F 1336 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7240 (tm-30) outliers start: 114 outliers final: 48 residues processed: 904 average time/residue: 0.6944 time to fit residues: 722.9636 Evaluate side-chains 872 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 807 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 538 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 600 ARG 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 815 GLU 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 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 673 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 765 SER Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 864 GLU 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 502 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 LEU 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 D residue 493 VAL Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 714 LYS 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 415 ILE Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 673 ILE 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 E residue 1327 ILE Chi-restraints excluded: chain E residue 1340 ASN Chi-restraints excluded: chain F residue 463 MET Chi-restraints excluded: chain F residue 543 LEU 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 710 MET Chi-restraints excluded: chain F residue 813 THR 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: 0.9990 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 209 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 GLN B 562 ASN B 727 ASN B 848 ASN C 554 GLN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 ASN D 420 ASN D 531 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 775 ASN D 829 GLN D1339 GLN ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 ASN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112920 restraints weight = 39520.402| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.99 r_work: 0.3300 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.7489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 28523 Z= 0.204 Angle : 0.657 17.587 38585 Z= 0.324 Chirality : 0.045 0.388 4403 Planarity : 0.005 0.062 4918 Dihedral : 8.822 173.015 3834 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 4.02 % Allowed : 27.70 % Favored : 68.28 % 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: 0.12 (0.15), residues: 3457 helix: 0.83 (0.13), residues: 1765 sheet: -0.59 (0.27), residues: 370 loop : -0.62 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 647 TYR 0.019 0.002 TYR A 435 PHE 0.024 0.002 PHE A 642 TRP 0.013 0.001 TRP A 841 HIS 0.005 0.001 HIS C1350 Details of bonding type rmsd covalent geometry : bond 0.00494 (28523) covalent geometry : angle 0.65749 (38585) hydrogen bonds : bond 0.03684 ( 1224) hydrogen bonds : angle 3.93851 ( 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 1000 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 874 time to evaluate : 1.104 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 421 TYR cc_start: 0.8111 (m-10) cc_final: 0.7703 (m-10) REVERT: A 424 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: A 437 GLU cc_start: 0.7999 (pm20) cc_final: 0.7579 (pm20) REVERT: A 451 LEU cc_start: 0.8682 (tp) cc_final: 0.8344 (tm) REVERT: A 463 MET cc_start: 0.8275 (tpp) cc_final: 0.7996 (tpp) REVERT: A 477 LYS cc_start: 0.8405 (mppt) cc_final: 0.8018 (mppt) REVERT: A 495 GLU cc_start: 0.7518 (tp30) cc_final: 0.6416 (tp30) REVERT: A 499 GLN cc_start: 0.8233 (mm110) cc_final: 0.8024 (mm-40) REVERT: A 500 LEU cc_start: 0.8107 (mt) cc_final: 0.7841 (mt) REVERT: A 521 ASP cc_start: 0.8189 (p0) cc_final: 0.7970 (p0) REVERT: A 549 MET cc_start: 0.2912 (mmt) cc_final: 0.1906 (mmt) REVERT: A 598 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8187 (mm-40) REVERT: A 600 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7872 (ptt180) REVERT: A 619 LYS cc_start: 0.8014 (ptpt) cc_final: 0.7720 (ptmt) REVERT: A 627 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7640 (ttp-110) REVERT: A 660 LYS cc_start: 0.7735 (tppt) cc_final: 0.7513 (tmmm) REVERT: A 667 MET cc_start: 0.7984 (mmp) cc_final: 0.7732 (mmm) REVERT: A 690 GLU cc_start: 0.7236 (tp30) cc_final: 0.7001 (tp30) REVERT: A 807 VAL cc_start: 0.8040 (m) cc_final: 0.7806 (t) REVERT: A 879 GLU cc_start: 0.7533 (tp30) cc_final: 0.7167 (tp30) REVERT: A 902 LYS cc_start: 0.8433 (tppt) cc_final: 0.8119 (tppt) REVERT: A 907 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8058 (mtp-110) REVERT: A 1319 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6822 (mt-10) REVERT: A 1336 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7804 (tm-30) REVERT: A 1348 ASP cc_start: 0.7875 (t0) cc_final: 0.7608 (t0) REVERT: A 1365 ASP cc_start: 0.7537 (p0) cc_final: 0.7297 (p0) REVERT: B 431 LEU cc_start: 0.8597 (mm) cc_final: 0.8394 (mp) REVERT: B 433 LEU cc_start: 0.8257 (mt) cc_final: 0.8030 (mp) REVERT: B 445 THR cc_start: 0.8436 (m) cc_final: 0.8233 (t) REVERT: B 478 ILE cc_start: 0.8794 (mm) cc_final: 0.8558 (mt) REVERT: B 483 ARG cc_start: 0.8159 (mmm-85) cc_final: 0.7898 (mmt-90) REVERT: B 530 LYS cc_start: 0.7972 (ptpt) cc_final: 0.7658 (ptpt) REVERT: B 613 LYS cc_start: 0.8313 (tttt) cc_final: 0.7919 (ttpp) REVERT: B 616 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7957 (t80) REVERT: B 627 ARG cc_start: 0.8429 (ttt180) cc_final: 0.8081 (ttt180) REVERT: B 632 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7288 (mm-30) REVERT: B 653 LEU cc_start: 0.8261 (tp) cc_final: 0.7808 (pp) REVERT: B 671 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8196 (tppp) REVERT: B 692 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8202 (pp) REVERT: B 714 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7954 (mmtm) REVERT: B 792 TYR cc_start: 0.8846 (t80) cc_final: 0.8559 (t80) REVERT: B 815 GLU cc_start: 0.7795 (mp0) cc_final: 0.7570 (mp0) REVERT: B 827 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8615 (mttp) REVERT: B 848 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7963 (t0) REVERT: B 1336 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7798 (tm-30) REVERT: C 419 ASP cc_start: 0.8144 (m-30) cc_final: 0.7628 (m-30) REVERT: C 420 ASN cc_start: 0.8259 (m-40) cc_final: 0.7963 (m-40) REVERT: C 433 LEU cc_start: 0.8346 (mt) cc_final: 0.8132 (mp) REVERT: C 441 ASN cc_start: 0.8324 (t0) cc_final: 0.8030 (t0) REVERT: C 462 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8523 (tp) REVERT: C 497 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7288 (mm-30) REVERT: C 502 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8376 (tp) REVERT: C 528 SER cc_start: 0.8342 (t) cc_final: 0.8068 (t) REVERT: C 538 ILE cc_start: 0.8467 (mm) cc_final: 0.8234 (mt) REVERT: C 612 ASP cc_start: 0.7864 (m-30) cc_final: 0.7648 (m-30) REVERT: C 627 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7724 (ttp-110) REVERT: C 823 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8397 (mmt) REVERT: C 858 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7807 (ptp-170) REVERT: C 864 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7312 (mm-30) REVERT: C 865 LYS cc_start: 0.8662 (ttmm) cc_final: 0.8436 (tttp) REVERT: C 879 GLU cc_start: 0.7939 (tp30) cc_final: 0.7538 (tp30) REVERT: C 911 ASN cc_start: 0.8408 (m110) cc_final: 0.8152 (m-40) REVERT: C 1372 GLU cc_start: 0.7862 (tt0) cc_final: 0.7633 (tt0) REVERT: D 419 ASP cc_start: 0.7839 (m-30) cc_final: 0.7620 (m-30) REVERT: D 431 LEU cc_start: 0.8345 (tp) cc_final: 0.7942 (tt) REVERT: D 439 TYR cc_start: 0.8449 (m-80) cc_final: 0.8072 (m-80) REVERT: D 484 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7984 (mttm) REVERT: D 501 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7811 (ttm-80) REVERT: D 529 SER cc_start: 0.8213 (t) cc_final: 0.7948 (p) REVERT: D 593 LYS cc_start: 0.8764 (tptt) cc_final: 0.8550 (tptp) REVERT: D 603 SER cc_start: 0.8832 (m) cc_final: 0.8594 (m) REVERT: D 607 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.8236 (p) REVERT: D 655 ASP cc_start: 0.7809 (t70) cc_final: 0.7332 (t0) REVERT: D 658 LYS cc_start: 0.8445 (mttt) cc_final: 0.7932 (mttt) REVERT: D 706 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8367 (mtpt) REVERT: D 762 MET cc_start: 0.8204 (mmm) cc_final: 0.7958 (mmm) REVERT: D 764 GLU cc_start: 0.7678 (pt0) cc_final: 0.7456 (pt0) REVERT: D 775 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.8015 (t0) REVERT: D 813 THR cc_start: 0.7694 (m) cc_final: 0.7460 (t) REVERT: D 821 SER cc_start: 0.8720 (t) cc_final: 0.8482 (p) REVERT: D 824 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7621 (tp30) REVERT: D 845 ILE cc_start: 0.7237 (mm) cc_final: 0.7035 (mp) REVERT: D 879 GLU cc_start: 0.6971 (tp30) cc_final: 0.6513 (tp30) REVERT: D 903 GLU cc_start: 0.7878 (tp30) cc_final: 0.7117 (tm-30) REVERT: D 907 ARG cc_start: 0.8318 (ttp80) cc_final: 0.7852 (mtp-110) REVERT: D 911 ASN cc_start: 0.7757 (t0) cc_final: 0.7436 (t0) REVERT: D 928 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7282 (ttm-80) REVERT: D 1329 LYS cc_start: 0.7949 (tptp) cc_final: 0.7594 (tptp) REVERT: E 408 MET cc_start: 0.5664 (mmm) cc_final: 0.5339 (tmm) REVERT: E 413 ASP cc_start: 0.7962 (p0) cc_final: 0.7696 (p0) REVERT: E 420 ASN cc_start: 0.8208 (t0) cc_final: 0.7903 (t0) REVERT: E 440 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7496 (mm-40) REVERT: E 502 LEU cc_start: 0.8318 (mm) cc_final: 0.8005 (OUTLIER) REVERT: E 508 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8166 (ttmm) REVERT: E 519 GLU cc_start: 0.7331 (mp0) cc_final: 0.6722 (mp0) REVERT: E 528 SER cc_start: 0.8582 (t) cc_final: 0.8322 (t) REVERT: E 530 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7776 (mttm) REVERT: E 531 GLN cc_start: 0.7943 (mm110) cc_final: 0.7656 (tp40) REVERT: E 538 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8293 (mt) REVERT: E 554 GLN cc_start: 0.6857 (mm-40) cc_final: 0.6472 (mp10) REVERT: E 589 LYS cc_start: 0.8333 (ptmm) cc_final: 0.8045 (ptpp) REVERT: E 612 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7286 (m-30) REVERT: E 652 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8234 (mm) REVERT: E 671 LYS cc_start: 0.8407 (mmtm) cc_final: 0.8167 (mmtm) REVERT: E 702 ASN cc_start: 0.7299 (t0) cc_final: 0.7034 (t0) REVERT: E 730 ASP cc_start: 0.7695 (m-30) cc_final: 0.7268 (m-30) REVERT: E 762 MET cc_start: 0.8564 (mmm) cc_final: 0.8338 (mmm) REVERT: E 764 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7654 (mt-10) REVERT: E 895 PHE cc_start: 0.8188 (t80) cc_final: 0.7906 (t80) REVERT: E 902 LYS cc_start: 0.8349 (mtpt) cc_final: 0.8092 (mtpp) REVERT: E 1336 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7259 (tm-30) REVERT: E 1348 ASP cc_start: 0.8106 (t70) cc_final: 0.7774 (t0) REVERT: E 1359 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7886 (ttmm) REVERT: E 1375 LYS cc_start: 0.8100 (tptp) cc_final: 0.7822 (tptp) REVERT: F 414 ASP cc_start: 0.7559 (m-30) cc_final: 0.7119 (m-30) REVERT: F 500 LEU cc_start: 0.7679 (mt) cc_final: 0.7456 (mp) REVERT: F 501 ARG cc_start: 0.8069 (ttm110) cc_final: 0.7749 (ttm110) REVERT: F 592 PHE cc_start: 0.8638 (t80) cc_final: 0.8272 (t80) REVERT: F 593 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7997 (mptt) REVERT: F 612 ASP cc_start: 0.7628 (t70) cc_final: 0.7354 (t70) REVERT: F 632 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7440 (mm-30) REVERT: F 665 ASP cc_start: 0.6522 (t0) cc_final: 0.6300 (t70) REVERT: F 667 MET cc_start: 0.7713 (mmp) cc_final: 0.7485 (mmm) REVERT: F 707 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8230 (tp) REVERT: F 712 ASN cc_start: 0.7355 (t0) cc_final: 0.6689 (t0) REVERT: F 725 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7254 (tp) REVERT: F 728 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6707 (t80) REVERT: F 760 GLU cc_start: 0.8009 (tp30) cc_final: 0.7691 (tp30) REVERT: F 767 ILE cc_start: 0.8377 (pt) cc_final: 0.8047 (mt) REVERT: F 815 GLU cc_start: 0.7514 (mp0) cc_final: 0.7207 (mp0) REVERT: F 898 HIS cc_start: 0.7686 (m-70) cc_final: 0.7309 (m-70) REVERT: F 911 ASN cc_start: 0.8519 (t0) cc_final: 0.8298 (t0) REVERT: F 913 ILE cc_start: 0.8640 (pp) cc_final: 0.8319 (mt) REVERT: F 938 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7751 (ttmm) REVERT: F 1336 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7670 (tm-30) outliers start: 126 outliers final: 59 residues processed: 928 average time/residue: 0.6987 time to fit residues: 747.4244 Evaluate side-chains 925 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 846 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 427 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 815 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 450 VAL 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 692 ILE Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 1348 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 673 ILE 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 880 VAL 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 710 MET 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 913 ILE Chi-restraints excluded: chain E residue 427 GLU 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 652 LEU Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 1327 ILE Chi-restraints excluded: chain F residue 520 ILE 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 710 MET Chi-restraints excluded: chain F residue 725 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 847 GLU Chi-restraints excluded: chain F residue 919 LYS Chi-restraints excluded: chain F residue 923 ILE 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: 1.9990 chunk 325 optimal weight: 0.9980 chunk 60 optimal weight: 0.0030 chunk 221 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 334 optimal weight: 0.0970 chunk 261 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 191 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN A 554 GLN B 727 ASN B 848 ASN C 727 ASN C 766 GLN D 420 ASN D 531 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 GLN ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1326 GLN F 441 ASN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 896 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114081 restraints weight = 39753.784| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.03 r_work: 0.3314 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.7681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28523 Z= 0.135 Angle : 0.623 12.684 38585 Z= 0.307 Chirality : 0.042 0.230 4403 Planarity : 0.004 0.054 4918 Dihedral : 8.623 171.390 3834 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.38 % Rotamer: Outliers : 3.22 % Allowed : 29.17 % Favored : 67.61 % 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: 0.99 (0.13), residues: 1761 sheet: -0.58 (0.27), residues: 367 loop : -0.53 (0.18), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 498 TYR 0.013 0.001 TYR A 435 PHE 0.023 0.001 PHE A 642 TRP 0.015 0.001 TRP E 841 HIS 0.003 0.001 HIS C1350 Details of bonding type rmsd covalent geometry : bond 0.00328 (28523) covalent geometry : angle 0.62342 (38585) hydrogen bonds : bond 0.03287 ( 1224) hydrogen bonds : angle 3.86247 ( 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 967 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 866 time to evaluate : 1.048 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: 0.8124 (m-10) cc_final: 0.7651 (m-10) REVERT: A 424 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: A 437 GLU cc_start: 0.7989 (pm20) cc_final: 0.7623 (pm20) REVERT: A 451 LEU cc_start: 0.8654 (tp) cc_final: 0.8331 (tm) REVERT: A 463 MET cc_start: 0.8224 (tpp) cc_final: 0.7999 (tpp) REVERT: A 477 LYS cc_start: 0.8366 (mppt) cc_final: 0.7994 (mppt) REVERT: A 495 GLU cc_start: 0.7473 (tp30) cc_final: 0.6444 (tp30) REVERT: A 499 GLN cc_start: 0.8247 (mm110) cc_final: 0.8036 (mm-40) REVERT: A 500 LEU cc_start: 0.8113 (mt) cc_final: 0.7844 (mt) REVERT: A 521 ASP cc_start: 0.8174 (p0) cc_final: 0.7961 (p0) REVERT: A 549 MET cc_start: 0.2825 (mmt) cc_final: 0.1676 (mmt) REVERT: A 558 ILE cc_start: 0.8243 (mt) cc_final: 0.8006 (mm) REVERT: A 592 PHE cc_start: 0.8798 (t80) cc_final: 0.8366 (t80) REVERT: A 619 LYS cc_start: 0.8034 (ptpt) cc_final: 0.7728 (ptmt) REVERT: A 667 MET cc_start: 0.8002 (mmp) cc_final: 0.7763 (mmm) REVERT: A 807 VAL cc_start: 0.8055 (m) cc_final: 0.7819 (t) REVERT: A 813 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8377 (t) REVERT: A 879 GLU cc_start: 0.7559 (tp30) cc_final: 0.7199 (tp30) REVERT: A 902 LYS cc_start: 0.8452 (tppt) cc_final: 0.8138 (tppt) REVERT: A 906 THR cc_start: 0.8690 (t) cc_final: 0.8447 (p) REVERT: A 1319 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6701 (mt-10) REVERT: A 1336 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 1348 ASP cc_start: 0.7870 (t0) cc_final: 0.7603 (t0) REVERT: A 1365 ASP cc_start: 0.7512 (p0) cc_final: 0.7272 (p0) REVERT: B 426 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8196 (ttpp) REVERT: B 433 LEU cc_start: 0.8227 (mt) cc_final: 0.8008 (mp) REVERT: B 445 THR cc_start: 0.8402 (m) cc_final: 0.8201 (t) REVERT: B 478 ILE cc_start: 0.8808 (mm) cc_final: 0.8580 (mt) REVERT: B 519 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7738 (mm-30) REVERT: B 530 LYS cc_start: 0.8008 (ptpt) cc_final: 0.7677 (ptpt) REVERT: B 611 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7660 (mt) REVERT: B 613 LYS cc_start: 0.8327 (tttt) cc_final: 0.7934 (ttpp) REVERT: B 616 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7970 (t80) REVERT: B 627 ARG cc_start: 0.8383 (ttt180) cc_final: 0.8030 (ttt180) REVERT: B 632 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7336 (mm-30) REVERT: B 671 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8205 (tppp) REVERT: B 692 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8171 (pp) REVERT: B 714 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7941 (mmtm) REVERT: B 762 MET cc_start: 0.8399 (mmm) cc_final: 0.8102 (tpt) REVERT: B 792 TYR cc_start: 0.8841 (t80) cc_final: 0.8565 (t80) REVERT: B 806 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7941 (mp) REVERT: B 815 GLU cc_start: 0.7805 (mp0) cc_final: 0.7572 (mp0) REVERT: B 827 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8612 (mttp) REVERT: B 847 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: B 848 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7995 (t0) REVERT: B 1336 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 420 ASN cc_start: 0.8269 (m-40) cc_final: 0.8001 (m-40) REVERT: C 441 ASN cc_start: 0.8269 (t0) cc_final: 0.8002 (t0) REVERT: C 462 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8515 (tp) REVERT: C 482 MET cc_start: 0.8137 (tmm) cc_final: 0.7705 (tmm) REVERT: C 502 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8348 (tp) REVERT: C 528 SER cc_start: 0.8311 (t) cc_final: 0.8027 (t) REVERT: C 538 ILE cc_start: 0.8465 (mm) cc_final: 0.8233 (mt) REVERT: C 612 ASP cc_start: 0.7839 (m-30) cc_final: 0.7600 (m-30) REVERT: C 627 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7727 (ttp-110) REVERT: C 650 ASP cc_start: 0.8086 (p0) cc_final: 0.7586 (p0) REVERT: C 731 TYR cc_start: 0.7985 (m-80) cc_final: 0.7370 (m-80) REVERT: C 823 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8443 (mmt) REVERT: C 858 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7782 (ptp-170) REVERT: C 864 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7319 (mm-30) REVERT: C 865 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8439 (tttp) REVERT: C 879 GLU cc_start: 0.7934 (tp30) cc_final: 0.7534 (tp30) REVERT: C 911 ASN cc_start: 0.8386 (m110) cc_final: 0.8044 (m-40) REVERT: C 1329 LYS cc_start: 0.8308 (tttt) cc_final: 0.7891 (ttmm) REVERT: C 1361 LYS cc_start: 0.8392 (ttpp) cc_final: 0.7967 (ttpt) REVERT: C 1372 GLU cc_start: 0.7833 (tt0) cc_final: 0.7603 (tt0) REVERT: D 484 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7995 (mttt) REVERT: D 495 GLU cc_start: 0.7930 (tp30) cc_final: 0.7630 (mm-30) REVERT: D 501 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7826 (ttm-80) REVERT: D 529 SER cc_start: 0.8181 (t) cc_final: 0.7919 (p) REVERT: D 593 LYS cc_start: 0.8746 (tptt) cc_final: 0.8526 (tptp) REVERT: D 603 SER cc_start: 0.8826 (m) cc_final: 0.8593 (m) REVERT: D 655 ASP cc_start: 0.7822 (t70) cc_final: 0.7388 (t0) REVERT: D 658 LYS cc_start: 0.8447 (mttt) cc_final: 0.7958 (mttt) REVERT: D 711 LEU cc_start: 0.8325 (tp) cc_final: 0.8101 (tp) REVERT: D 728 PHE cc_start: 0.7276 (m-80) cc_final: 0.6986 (m-80) REVERT: D 762 MET cc_start: 0.8216 (mmm) cc_final: 0.7952 (mmm) REVERT: D 764 GLU cc_start: 0.7657 (pt0) cc_final: 0.7425 (pt0) REVERT: D 775 ASN cc_start: 0.8042 (m-40) cc_final: 0.7707 (t0) REVERT: D 813 THR cc_start: 0.7629 (m) cc_final: 0.7413 (t) REVERT: D 821 SER cc_start: 0.8698 (t) cc_final: 0.8460 (p) REVERT: D 824 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7585 (tp30) REVERT: D 845 ILE cc_start: 0.7154 (mm) cc_final: 0.6952 (mp) REVERT: D 847 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: D 903 GLU cc_start: 0.7870 (tp30) cc_final: 0.7487 (tm-30) REVERT: D 907 ARG cc_start: 0.8289 (ttp80) cc_final: 0.8041 (mtp85) REVERT: D 911 ASN cc_start: 0.7727 (t0) cc_final: 0.7435 (t0) REVERT: D 1329 LYS cc_start: 0.7931 (tptp) cc_final: 0.7567 (tptp) REVERT: D 1348 ASP cc_start: 0.7954 (t70) cc_final: 0.7543 (t0) REVERT: E 408 MET cc_start: 0.5863 (mmm) cc_final: 0.5529 (tmm) REVERT: E 420 ASN cc_start: 0.8190 (t0) cc_final: 0.7891 (t0) REVERT: E 482 MET cc_start: 0.6956 (mmm) cc_final: 0.6678 (mmm) REVERT: E 502 LEU cc_start: 0.8316 (mm) cc_final: 0.8008 (mp) REVERT: E 508 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8118 (ttmm) REVERT: E 519 GLU cc_start: 0.7310 (mp0) cc_final: 0.6690 (mp0) REVERT: E 528 SER cc_start: 0.8624 (t) cc_final: 0.8367 (t) REVERT: E 530 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7861 (mttm) REVERT: E 531 GLN cc_start: 0.7929 (mm110) cc_final: 0.7657 (tp40) REVERT: E 538 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8277 (mt) REVERT: E 589 LYS cc_start: 0.8255 (ptmm) cc_final: 0.7983 (ptpp) REVERT: E 612 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7230 (m-30) REVERT: E 671 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8174 (mmtm) REVERT: E 702 ASN cc_start: 0.7297 (t0) cc_final: 0.7021 (t0) REVERT: E 726 GLN cc_start: 0.8500 (mm110) cc_final: 0.7791 (tp40) REVERT: E 730 ASP cc_start: 0.7741 (m-30) cc_final: 0.7332 (m-30) REVERT: E 762 MET cc_start: 0.8558 (mmm) cc_final: 0.8356 (mmm) REVERT: E 847 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7046 (tm-30) REVERT: E 895 PHE cc_start: 0.8195 (t80) cc_final: 0.7733 (t80) REVERT: E 902 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8153 (mtpp) REVERT: E 1336 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7312 (tm-30) REVERT: E 1348 ASP cc_start: 0.8113 (t70) cc_final: 0.7791 (t0) REVERT: E 1359 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7945 (ttmm) REVERT: E 1375 LYS cc_start: 0.8126 (tptp) cc_final: 0.7852 (tptp) REVERT: F 414 ASP cc_start: 0.7819 (m-30) cc_final: 0.7588 (m-30) REVERT: F 500 LEU cc_start: 0.7701 (mt) cc_final: 0.7462 (mp) REVERT: F 501 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7761 (ttm110) REVERT: F 516 PHE cc_start: 0.7787 (t80) cc_final: 0.7110 (t80) REVERT: F 518 ASP cc_start: 0.7939 (t0) cc_final: 0.7454 (m-30) REVERT: F 592 PHE cc_start: 0.8621 (t80) cc_final: 0.8337 (t80) REVERT: F 593 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8010 (mptt) REVERT: F 612 ASP cc_start: 0.7617 (t70) cc_final: 0.7359 (t70) REVERT: F 632 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7657 (mm-30) REVERT: F 667 MET cc_start: 0.7764 (mmp) cc_final: 0.7545 (mmm) REVERT: F 707 LEU cc_start: 0.8508 (tt) cc_final: 0.8270 (tp) REVERT: F 712 ASN cc_start: 0.7313 (t0) cc_final: 0.6680 (t0) REVERT: F 728 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6754 (t80) REVERT: F 760 GLU cc_start: 0.8025 (tp30) cc_final: 0.7693 (tp30) REVERT: F 767 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8020 (mt) REVERT: F 815 GLU cc_start: 0.7489 (mp0) cc_final: 0.7221 (mp0) REVERT: F 820 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7637 (mp-120) REVERT: F 913 ILE cc_start: 0.8614 (pp) cc_final: 0.8327 (mt) REVERT: F 938 LYS cc_start: 0.8070 (ttmm) cc_final: 0.7750 (ttmm) REVERT: F 1336 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7638 (tm-30) outliers start: 101 outliers final: 55 residues processed: 904 average time/residue: 0.7204 time to fit residues: 747.7435 Evaluate side-chains 914 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 837 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 772 LEU 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 815 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 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 601 LYS 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 714 LYS Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 864 GLU 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 431 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 518 ASP 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 708 ASP Chi-restraints excluded: chain C residue 778 LYS 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 880 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 562 ASN Chi-restraints excluded: chain D residue 710 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 429 VAL Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 596 GLN Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 673 ILE Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 824 GLU Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 1327 ILE Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 482 MET Chi-restraints excluded: chain F residue 579 ARG 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 728 PHE Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 820 GLN Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain F residue 1372 GLU 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: 4.9990 chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 201 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 335 optimal weight: 0.1980 chunk 97 optimal weight: 0.7980 chunk 210 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 252 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN A 533 GLN A 554 GLN B 727 ASN B 848 ASN C 727 ASN D 420 ASN D 531 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 ASN D 829 GLN E 639 GLN E 644 GLN E 766 GLN F 441 ASN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 911 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114072 restraints weight = 39803.808| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.92 r_work: 0.3311 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.7912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28523 Z= 0.155 Angle : 0.644 12.392 38585 Z= 0.316 Chirality : 0.043 0.223 4403 Planarity : 0.004 0.058 4918 Dihedral : 8.596 167.660 3834 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.76 % Favored : 96.18 % Rotamer: Outliers : 2.90 % Allowed : 29.93 % Favored : 67.17 % 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: 0.35 (0.15), residues: 3457 helix: 0.99 (0.13), residues: 1762 sheet: -0.49 (0.27), residues: 370 loop : -0.46 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 907 TYR 0.015 0.001 TYR E 435 PHE 0.030 0.001 PHE A 642 TRP 0.013 0.001 TRP E 841 HIS 0.003 0.001 HIS C1350 Details of bonding type rmsd covalent geometry : bond 0.00378 (28523) covalent geometry : angle 0.64404 (38585) hydrogen bonds : bond 0.03378 ( 1224) hydrogen bonds : angle 3.86268 ( 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 954 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 863 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ILE cc_start: 0.8077 (pt) cc_final: 0.7850 (mp) REVERT: A 421 TYR cc_start: 0.8144 (m-10) cc_final: 0.7744 (m-10) REVERT: A 424 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: A 437 GLU cc_start: 0.7889 (pm20) cc_final: 0.7518 (pm20) REVERT: A 451 LEU cc_start: 0.8659 (tp) cc_final: 0.8320 (tm) REVERT: A 477 LYS cc_start: 0.8366 (mppt) cc_final: 0.7956 (mppt) REVERT: A 499 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7976 (mm-40) REVERT: A 500 LEU cc_start: 0.8107 (mt) cc_final: 0.7867 (mt) REVERT: A 502 LEU cc_start: 0.8495 (mt) cc_final: 0.8182 (mp) REVERT: A 549 MET cc_start: 0.2890 (mmt) cc_final: 0.1852 (mmt) REVERT: A 558 ILE cc_start: 0.8278 (mt) cc_final: 0.8056 (mm) REVERT: A 578 ASP cc_start: 0.7508 (m-30) cc_final: 0.7272 (m-30) REVERT: A 592 PHE cc_start: 0.8791 (t80) cc_final: 0.8334 (t80) REVERT: A 600 ARG cc_start: 0.8158 (ttp-170) cc_final: 0.7818 (ptt180) REVERT: A 667 MET cc_start: 0.7951 (mmp) cc_final: 0.7684 (mmm) REVERT: A 729 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8029 (mp) REVERT: A 807 VAL cc_start: 0.8045 (m) cc_final: 0.7820 (t) REVERT: A 813 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8394 (t) REVERT: A 879 GLU cc_start: 0.7562 (tp30) cc_final: 0.7201 (tp30) REVERT: A 902 LYS cc_start: 0.8404 (tppt) cc_final: 0.8091 (tppt) REVERT: A 906 THR cc_start: 0.8656 (t) cc_final: 0.8439 (p) REVERT: A 907 ARG cc_start: 0.8417 (ttm-80) cc_final: 0.7982 (mtp-110) REVERT: A 1319 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6675 (mt-10) REVERT: A 1336 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7831 (tm-30) REVERT: A 1348 ASP cc_start: 0.7846 (t0) cc_final: 0.7603 (t0) REVERT: A 1365 ASP cc_start: 0.7476 (p0) cc_final: 0.7239 (p0) REVERT: B 426 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8194 (ttpp) REVERT: B 478 ILE cc_start: 0.8849 (mm) cc_final: 0.8618 (mt) REVERT: B 519 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 530 LYS cc_start: 0.7976 (ptpt) cc_final: 0.7652 (ptpt) REVERT: B 611 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7641 (mt) REVERT: B 613 LYS cc_start: 0.8355 (tttt) cc_final: 0.7987 (ttpp) REVERT: B 616 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8000 (t80) REVERT: B 627 ARG cc_start: 0.8365 (ttt180) cc_final: 0.8025 (ttt180) REVERT: B 632 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7340 (mm-30) REVERT: B 671 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8189 (tppp) REVERT: B 692 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8190 (pp) REVERT: B 714 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7957 (mmtm) REVERT: B 762 MET cc_start: 0.8431 (mmm) cc_final: 0.8142 (tpt) REVERT: B 778 LYS cc_start: 0.8074 (ttpp) cc_final: 0.7874 (ttpp) REVERT: B 792 TYR cc_start: 0.8819 (t80) cc_final: 0.8550 (t80) REVERT: B 815 GLU cc_start: 0.7797 (mp0) cc_final: 0.7586 (mp0) REVERT: B 848 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7925 (OUTLIER) REVERT: B 1336 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 420 ASN cc_start: 0.8246 (m-40) cc_final: 0.7996 (m-40) REVERT: C 441 ASN cc_start: 0.8287 (t0) cc_final: 0.8042 (t0) REVERT: C 462 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8513 (tp) REVERT: C 482 MET cc_start: 0.8108 (tmm) cc_final: 0.7702 (tmm) REVERT: C 502 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8221 (tt) REVERT: C 528 SER cc_start: 0.8342 (t) cc_final: 0.8038 (t) REVERT: C 538 ILE cc_start: 0.8403 (mm) cc_final: 0.8059 (mp) REVERT: C 612 ASP cc_start: 0.7788 (m-30) cc_final: 0.7567 (m-30) REVERT: C 627 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7690 (ttp-110) REVERT: C 703 LEU cc_start: 0.8656 (tp) cc_final: 0.8407 (tp) REVERT: C 731 TYR cc_start: 0.7931 (m-80) cc_final: 0.7228 (m-80) REVERT: C 823 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8323 (mmt) REVERT: C 858 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7766 (ptp-170) REVERT: C 864 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7314 (mm-30) REVERT: C 865 LYS cc_start: 0.8628 (ttmm) cc_final: 0.8425 (tttp) REVERT: C 879 GLU cc_start: 0.7925 (tp30) cc_final: 0.7547 (tp30) REVERT: C 911 ASN cc_start: 0.8281 (m110) cc_final: 0.7951 (m-40) REVERT: C 1361 LYS cc_start: 0.8382 (ttpp) cc_final: 0.7845 (ttpp) REVERT: D 477 LYS cc_start: 0.8033 (tptt) cc_final: 0.7793 (tptt) REVERT: D 484 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7971 (mttt) REVERT: D 495 GLU cc_start: 0.7950 (tp30) cc_final: 0.7647 (mm-30) REVERT: D 501 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7851 (ttm-80) REVERT: D 529 SER cc_start: 0.8256 (t) cc_final: 0.8021 (p) REVERT: D 589 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8211 (mtpp) REVERT: D 593 LYS cc_start: 0.8711 (tptt) cc_final: 0.8490 (tptp) REVERT: D 603 SER cc_start: 0.8799 (m) cc_final: 0.8565 (m) REVERT: D 607 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8247 (p) REVERT: D 655 ASP cc_start: 0.7842 (t70) cc_final: 0.7307 (t0) REVERT: D 658 LYS cc_start: 0.8424 (mttt) cc_final: 0.7916 (mttt) REVERT: D 706 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8334 (mtpt) REVERT: D 711 LEU cc_start: 0.8269 (tp) cc_final: 0.8047 (tp) REVERT: D 729 ILE cc_start: 0.8524 (mm) cc_final: 0.8270 (mp) REVERT: D 757 GLU cc_start: 0.5552 (mm-30) cc_final: 0.4026 (tp30) REVERT: D 762 MET cc_start: 0.8231 (mmm) cc_final: 0.8004 (mmm) REVERT: D 764 GLU cc_start: 0.7656 (pt0) cc_final: 0.7422 (pt0) REVERT: D 813 THR cc_start: 0.7586 (m) cc_final: 0.7359 (t) REVERT: D 821 SER cc_start: 0.8709 (t) cc_final: 0.8461 (p) REVERT: D 824 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7609 (tp30) REVERT: D 847 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: D 903 GLU cc_start: 0.7805 (tp30) cc_final: 0.7330 (tm-30) REVERT: D 907 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7938 (mtm180) REVERT: D 911 ASN cc_start: 0.7788 (t0) cc_final: 0.7481 (t0) REVERT: D 1329 LYS cc_start: 0.7946 (tptp) cc_final: 0.7601 (tptp) REVERT: D 1338 CYS cc_start: 0.7219 (p) cc_final: 0.6954 (m) REVERT: D 1348 ASP cc_start: 0.7899 (t70) cc_final: 0.7533 (t0) REVERT: E 408 MET cc_start: 0.5890 (mmm) cc_final: 0.5612 (tmm) REVERT: E 420 ASN cc_start: 0.8210 (t0) cc_final: 0.7800 (t0) REVERT: E 502 LEU cc_start: 0.8354 (mm) cc_final: 0.8007 (mp) REVERT: E 505 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7246 (mp0) REVERT: E 508 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8217 (ttmm) REVERT: E 519 GLU cc_start: 0.7357 (mp0) cc_final: 0.6696 (mp0) REVERT: E 528 SER cc_start: 0.8636 (t) cc_final: 0.8361 (t) REVERT: E 530 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7969 (mttm) REVERT: E 531 GLN cc_start: 0.7908 (mm110) cc_final: 0.7656 (tp40) REVERT: E 538 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (mt) REVERT: E 589 LYS cc_start: 0.8140 (ptmm) cc_final: 0.7782 (mtmm) REVERT: E 612 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: E 671 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8197 (mmtm) REVERT: E 702 ASN cc_start: 0.7471 (t0) cc_final: 0.7192 (t0) REVERT: E 730 ASP cc_start: 0.7800 (m-30) cc_final: 0.7350 (m-30) REVERT: E 800 ASN cc_start: 0.8419 (m110) cc_final: 0.8011 (m-40) REVERT: E 847 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7012 (tm-30) REVERT: E 895 PHE cc_start: 0.8246 (t80) cc_final: 0.7705 (t80) REVERT: E 902 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8126 (mtpp) REVERT: E 1336 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7351 (tm-30) REVERT: E 1348 ASP cc_start: 0.8097 (t70) cc_final: 0.7778 (t0) REVERT: E 1359 LYS cc_start: 0.8284 (ttpp) cc_final: 0.8011 (ttmm) REVERT: E 1375 LYS cc_start: 0.8231 (tptp) cc_final: 0.7963 (tptp) REVERT: F 423 ASP cc_start: 0.7855 (m-30) cc_final: 0.7624 (m-30) REVERT: F 425 LEU cc_start: 0.7857 (tt) cc_final: 0.7606 (tp) REVERT: F 500 LEU cc_start: 0.7693 (mt) cc_final: 0.7462 (mp) REVERT: F 501 ARG cc_start: 0.8057 (ttm110) cc_final: 0.7776 (ttm110) REVERT: F 592 PHE cc_start: 0.8659 (t80) cc_final: 0.8376 (t80) REVERT: F 593 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8037 (mptt) REVERT: F 612 ASP cc_start: 0.7617 (t70) cc_final: 0.7344 (t70) REVERT: F 632 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7697 (mm-30) REVERT: F 665 ASP cc_start: 0.7167 (t70) cc_final: 0.6896 (m-30) REVERT: F 667 MET cc_start: 0.7890 (mmp) cc_final: 0.7682 (mmm) REVERT: F 707 LEU cc_start: 0.8511 (tt) cc_final: 0.8309 (tp) REVERT: F 712 ASN cc_start: 0.7315 (t0) cc_final: 0.6668 (t0) REVERT: F 760 GLU cc_start: 0.8011 (tp30) cc_final: 0.7689 (tp30) REVERT: F 767 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8053 (mt) REVERT: F 815 GLU cc_start: 0.7492 (mp0) cc_final: 0.7214 (mp0) REVERT: F 820 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7610 (mp-120) REVERT: F 911 ASN cc_start: 0.8617 (t0) cc_final: 0.8376 (t0) REVERT: F 913 ILE cc_start: 0.8663 (pp) cc_final: 0.8335 (mt) REVERT: F 938 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7702 (ttmm) outliers start: 91 outliers final: 51 residues processed: 896 average time/residue: 0.7015 time to fit residues: 723.7402 Evaluate side-chains 910 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 840 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 427 GLU Chi-restraints excluded: chain A residue 561 THR 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 813 THR 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 1329 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 692 ILE Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 765 SER Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 864 GLU 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 502 LEU Chi-restraints excluded: chain C residue 518 ASP 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 813 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 858 ARG Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 562 ASN 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 913 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 549 MET Chi-restraints excluded: chain E residue 554 GLN Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 710 MET 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 482 MET 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 800 ASN Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 820 GLN 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: 0.9980 chunk 65 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 300 optimal weight: 0.8980 chunk 328 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 232 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 331 optimal weight: 0.8980 chunk 271 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN A 554 GLN B 562 ASN B 727 ASN B 848 ASN C 727 ASN D 531 GLN D 829 GLN D1345 GLN E 644 GLN F 441 ASN F 649 ASN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113376 restraints weight = 39601.456| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.96 r_work: 0.3302 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.8126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28523 Z= 0.174 Angle : 0.670 13.585 38585 Z= 0.329 Chirality : 0.044 0.201 4403 Planarity : 0.005 0.077 4918 Dihedral : 8.615 163.201 3834 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 2.71 % Allowed : 30.86 % Favored : 66.43 % 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: 0.37 (0.15), residues: 3457 helix: 0.99 (0.13), residues: 1761 sheet: -0.42 (0.27), residues: 370 loop : -0.46 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 498 TYR 0.017 0.002 TYR E 435 PHE 0.030 0.002 PHE F 895 TRP 0.012 0.001 TRP A 841 HIS 0.004 0.001 HIS C1350 Details of bonding type rmsd covalent geometry : bond 0.00423 (28523) covalent geometry : angle 0.66988 (38585) hydrogen bonds : bond 0.03473 ( 1224) hydrogen bonds : angle 3.86470 ( 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 955 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 870 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ILE cc_start: 0.8043 (pt) cc_final: 0.7813 (mp) REVERT: A 421 TYR cc_start: 0.8145 (m-10) cc_final: 0.7795 (m-10) REVERT: A 424 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: A 437 GLU cc_start: 0.7949 (pm20) cc_final: 0.7547 (pm20) REVERT: A 451 LEU cc_start: 0.8656 (tp) cc_final: 0.8298 (tm) REVERT: A 477 LYS cc_start: 0.8338 (mppt) cc_final: 0.7948 (mppt) REVERT: A 500 LEU cc_start: 0.8109 (mt) cc_final: 0.7880 (mt) REVERT: A 502 LEU cc_start: 0.8489 (mt) cc_final: 0.8155 (mp) REVERT: A 549 MET cc_start: 0.2862 (mmt) cc_final: 0.1822 (mmt) REVERT: A 558 ILE cc_start: 0.8287 (mt) cc_final: 0.8043 (mm) REVERT: A 572 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7639 (mtm180) REVERT: A 578 ASP cc_start: 0.7531 (m-30) cc_final: 0.7288 (m-30) REVERT: A 592 PHE cc_start: 0.8781 (t80) cc_final: 0.8223 (t80) REVERT: A 600 ARG cc_start: 0.8164 (ttp-170) cc_final: 0.7848 (ptt180) REVERT: A 611 ILE cc_start: 0.8235 (mt) cc_final: 0.8016 (tt) REVERT: A 667 MET cc_start: 0.7934 (mmp) cc_final: 0.7709 (mmm) REVERT: A 690 GLU cc_start: 0.7310 (tp30) cc_final: 0.7078 (tp30) REVERT: A 729 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8003 (mp) REVERT: A 807 VAL cc_start: 0.8034 (m) cc_final: 0.7817 (t) REVERT: A 813 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8390 (t) REVERT: A 879 GLU cc_start: 0.7579 (tp30) cc_final: 0.7219 (tp30) REVERT: A 902 LYS cc_start: 0.8401 (tppt) cc_final: 0.8101 (tppt) REVERT: A 907 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.8004 (mtp-110) REVERT: A 1319 GLU cc_start: 0.7571 (mt-10) cc_final: 0.6643 (mt-10) REVERT: A 1336 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7876 (tm-30) REVERT: A 1348 ASP cc_start: 0.7858 (t0) cc_final: 0.7592 (t0) REVERT: A 1365 ASP cc_start: 0.7492 (p0) cc_final: 0.7280 (p0) REVERT: B 426 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8165 (ttpp) REVERT: B 478 ILE cc_start: 0.8859 (mm) cc_final: 0.8626 (mt) REVERT: B 519 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 530 LYS cc_start: 0.8035 (ptpt) cc_final: 0.7699 (ptpt) REVERT: B 611 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7659 (mt) REVERT: B 613 LYS cc_start: 0.8371 (tttt) cc_final: 0.8008 (ttpp) REVERT: B 616 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.8001 (t80) REVERT: B 627 ARG cc_start: 0.8378 (ttt180) cc_final: 0.8039 (ttt180) REVERT: B 632 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7305 (mm-30) REVERT: B 692 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8203 (pp) REVERT: B 714 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7892 (mmtm) REVERT: B 762 MET cc_start: 0.8467 (mmm) cc_final: 0.8188 (tpt) REVERT: B 792 TYR cc_start: 0.8826 (t80) cc_final: 0.8530 (t80) REVERT: B 847 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: B 848 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7977 (t0) REVERT: B 1336 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7779 (tm-30) REVERT: C 411 ASN cc_start: 0.8111 (m110) cc_final: 0.7566 (p0) REVERT: C 419 ASP cc_start: 0.8134 (m-30) cc_final: 0.7679 (m-30) REVERT: C 420 ASN cc_start: 0.8285 (m-40) cc_final: 0.8052 (m-40) REVERT: C 441 ASN cc_start: 0.8284 (t0) cc_final: 0.8042 (t0) REVERT: C 462 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8519 (tp) REVERT: C 482 MET cc_start: 0.8209 (tmm) cc_final: 0.7790 (tmm) REVERT: C 502 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8211 (tt) REVERT: C 528 SER cc_start: 0.8382 (t) cc_final: 0.8072 (t) REVERT: C 538 ILE cc_start: 0.8426 (mm) cc_final: 0.8204 (mt) REVERT: C 610 PHE cc_start: 0.8132 (t80) cc_final: 0.7859 (t80) REVERT: C 612 ASP cc_start: 0.7813 (m-30) cc_final: 0.7598 (m-30) REVERT: C 627 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7704 (ttp-110) REVERT: C 703 LEU cc_start: 0.8632 (tp) cc_final: 0.8393 (tp) REVERT: C 731 TYR cc_start: 0.7940 (m-80) cc_final: 0.7304 (m-80) REVERT: C 807 VAL cc_start: 0.8035 (m) cc_final: 0.7524 (t) REVERT: C 823 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8341 (mmt) REVERT: C 858 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7771 (ptp-170) REVERT: C 864 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7296 (mm-30) REVERT: C 865 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8371 (tttt) REVERT: C 879 GLU cc_start: 0.7924 (tp30) cc_final: 0.7536 (tp30) REVERT: C 911 ASN cc_start: 0.8233 (m110) cc_final: 0.7903 (m-40) REVERT: C 928 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7897 (tpp80) REVERT: C 1329 LYS cc_start: 0.8322 (tttt) cc_final: 0.7893 (ttmm) REVERT: C 1361 LYS cc_start: 0.8372 (ttpp) cc_final: 0.7843 (ttpp) REVERT: D 477 LYS cc_start: 0.8094 (tptt) cc_final: 0.7820 (tptt) REVERT: D 495 GLU cc_start: 0.7922 (tp30) cc_final: 0.7517 (tp30) REVERT: D 501 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7856 (ttm-80) REVERT: D 529 SER cc_start: 0.8322 (t) cc_final: 0.8097 (p) REVERT: D 589 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8215 (mtpp) REVERT: D 593 LYS cc_start: 0.8693 (tptt) cc_final: 0.8460 (tptp) REVERT: D 603 SER cc_start: 0.8813 (m) cc_final: 0.8581 (m) REVERT: D 607 SER cc_start: 0.8481 (OUTLIER) cc_final: 0.8271 (p) REVERT: D 655 ASP cc_start: 0.7863 (t70) cc_final: 0.7326 (t0) REVERT: D 658 LYS cc_start: 0.8466 (mttt) cc_final: 0.7909 (mttt) REVERT: D 706 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8364 (mtpt) REVERT: D 729 ILE cc_start: 0.8569 (mm) cc_final: 0.8323 (mp) REVERT: D 757 GLU cc_start: 0.5481 (mm-30) cc_final: 0.4539 (tp30) REVERT: D 762 MET cc_start: 0.8312 (mmm) cc_final: 0.8081 (mmm) REVERT: D 764 GLU cc_start: 0.7700 (pt0) cc_final: 0.7463 (pt0) REVERT: D 813 THR cc_start: 0.7635 (m) cc_final: 0.7385 (t) REVERT: D 821 SER cc_start: 0.8684 (t) cc_final: 0.8439 (p) REVERT: D 824 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7571 (tp30) REVERT: D 873 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7180 (mt-10) REVERT: D 903 GLU cc_start: 0.7847 (tp30) cc_final: 0.7393 (tm-30) REVERT: D 907 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7999 (mtm110) REVERT: D 911 ASN cc_start: 0.7730 (t0) cc_final: 0.7446 (t0) REVERT: D 928 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7322 (ttm-80) REVERT: D 1329 LYS cc_start: 0.7979 (tptp) cc_final: 0.7639 (tptp) REVERT: D 1338 CYS cc_start: 0.7238 (p) cc_final: 0.7036 (m) REVERT: D 1340 ASN cc_start: 0.7884 (t0) cc_final: 0.7579 (t0) REVERT: D 1348 ASP cc_start: 0.7920 (t70) cc_final: 0.7559 (t0) REVERT: E 408 MET cc_start: 0.6000 (mmm) cc_final: 0.5717 (tmm) REVERT: E 420 ASN cc_start: 0.8195 (t0) cc_final: 0.7896 (t0) REVERT: E 502 LEU cc_start: 0.8377 (mm) cc_final: 0.8024 (OUTLIER) REVERT: E 505 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7226 (mp0) REVERT: E 508 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8249 (ttmm) REVERT: E 519 GLU cc_start: 0.7376 (mp0) cc_final: 0.6710 (mp0) REVERT: E 528 SER cc_start: 0.8627 (t) cc_final: 0.8340 (t) REVERT: E 530 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7997 (mttm) REVERT: E 589 LYS cc_start: 0.8137 (ptmm) cc_final: 0.7846 (mtmm) REVERT: E 612 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: E 660 LYS cc_start: 0.7983 (ttpt) cc_final: 0.7593 (ttpt) REVERT: E 671 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8258 (mmtm) REVERT: E 702 ASN cc_start: 0.7599 (t0) cc_final: 0.7293 (t0) REVERT: E 726 GLN cc_start: 0.8496 (mm110) cc_final: 0.7845 (tp40) REVERT: E 730 ASP cc_start: 0.7839 (m-30) cc_final: 0.7420 (m-30) REVERT: E 800 ASN cc_start: 0.8432 (m110) cc_final: 0.8061 (m-40) REVERT: E 847 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6967 (tm-30) REVERT: E 895 PHE cc_start: 0.8286 (t80) cc_final: 0.7626 (t80) REVERT: E 902 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8146 (mtpp) REVERT: E 1336 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7416 (tm-30) REVERT: E 1348 ASP cc_start: 0.8098 (t70) cc_final: 0.7781 (t0) REVERT: E 1359 LYS cc_start: 0.8356 (ttpp) cc_final: 0.8073 (ttmm) REVERT: E 1375 LYS cc_start: 0.8318 (tptp) cc_final: 0.8043 (tptp) REVERT: F 423 ASP cc_start: 0.7878 (m-30) cc_final: 0.7660 (m-30) REVERT: F 425 LEU cc_start: 0.7854 (tt) cc_final: 0.7624 (tp) REVERT: F 448 ARG cc_start: 0.7228 (mtp180) cc_final: 0.6928 (mtp85) REVERT: F 479 THR cc_start: 0.7143 (m) cc_final: 0.6777 (p) REVERT: F 501 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7794 (ttm110) REVERT: F 568 ASP cc_start: 0.7749 (t0) cc_final: 0.6607 (p0) REVERT: F 592 PHE cc_start: 0.8646 (t80) cc_final: 0.8383 (t80) REVERT: F 593 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8057 (mptt) REVERT: F 612 ASP cc_start: 0.7666 (t70) cc_final: 0.7403 (t70) REVERT: F 632 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7722 (mm-30) REVERT: F 667 MET cc_start: 0.7895 (mmp) cc_final: 0.7281 (mmm) REVERT: F 671 LYS cc_start: 0.8503 (ptpp) cc_final: 0.8143 (ptpp) REVERT: F 712 ASN cc_start: 0.7363 (t0) cc_final: 0.6820 (t0) REVERT: F 760 GLU cc_start: 0.8019 (tp30) cc_final: 0.7697 (tp30) REVERT: F 767 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8085 (mt) REVERT: F 795 GLU cc_start: 0.7560 (pm20) cc_final: 0.7311 (pm20) REVERT: F 815 GLU cc_start: 0.7503 (mp0) cc_final: 0.7215 (mp0) REVERT: F 938 LYS cc_start: 0.8131 (ttmm) cc_final: 0.7725 (ttmm) REVERT: F 1376 PHE cc_start: 0.7020 (t80) cc_final: 0.6752 (t80) outliers start: 85 outliers final: 50 residues processed: 903 average time/residue: 0.7104 time to fit residues: 737.3983 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 : 1.052 ------------------------------------------------------------------------------- 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 561 THR 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 810 SER Chi-restraints excluded: chain A residue 813 THR 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 1329 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 692 ILE Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 765 SER Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 518 ASP 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 813 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 858 ARG Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 562 ASN Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 710 MET Chi-restraints excluded: chain D residue 803 LEU 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 549 MET Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 824 GLU Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 1327 ILE Chi-restraints excluded: chain F residue 482 MET Chi-restraints excluded: chain F residue 579 ARG Chi-restraints excluded: chain F residue 593 LYS Chi-restraints excluded: chain F residue 649 ASN Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 800 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 117 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 322 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN A 554 GLN A 639 GLN B 562 ASN B 727 ASN B 848 ASN D 531 GLN D 799 GLN D 829 GLN E 420 ASN E 639 GLN E 644 GLN F 441 ASN F 639 GLN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111456 restraints weight = 39711.454| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.96 r_work: 0.3275 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.8380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 28523 Z= 0.265 Angle : 0.718 14.249 38585 Z= 0.353 Chirality : 0.047 0.206 4403 Planarity : 0.005 0.063 4918 Dihedral : 8.879 161.666 3834 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 2.58 % Allowed : 31.14 % Favored : 66.27 % 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 (0.14), residues: 3457 helix: 0.78 (0.12), residues: 1771 sheet: -0.45 (0.27), residues: 371 loop : -0.54 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 498 TYR 0.020 0.002 TYR F 792 PHE 0.035 0.002 PHE A 642 TRP 0.015 0.002 TRP B1358 HIS 0.006 0.001 HIS C1350 Details of bonding type rmsd covalent geometry : bond 0.00642 (28523) covalent geometry : angle 0.71836 (38585) hydrogen bonds : bond 0.03945 ( 1224) hydrogen bonds : angle 3.97335 ( 3549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12598.35 seconds wall clock time: 214 minutes 2.74 seconds (12842.74 seconds total)