Starting phenix.real_space_refine on Thu Sep 18 08:45:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxs_47297/09_2025/9dxs_47297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxs_47297/09_2025/9dxs_47297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dxs_47297/09_2025/9dxs_47297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxs_47297/09_2025/9dxs_47297.map" model { file = "/net/cci-nas-00/data/ceres_data/9dxs_47297/09_2025/9dxs_47297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxs_47297/09_2025/9dxs_47297.cif" } resolution = 3.55 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= 0.059 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 12 5.49 5 S 96 5.16 5 C 10002 2.51 5 N 2362 2.21 5 O 2818 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15294 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3532 Classifications: {'peptide': 446} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 428} Chain: "B" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3532 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "C" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3532 Classifications: {'peptide': 446} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 428} Chain: "D" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3532 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 336 Unusual residues: {'2J9': 1, 'CLR': 3, 'NAG': 1, 'POV': 4, 'SPM': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 164 Unusual residues: {'2J9': 2, 'CLR': 1, 'POV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 278 Unusual residues: {'CLR': 2, 'NAG': 1, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 176 Unusual residues: {'2J9': 1, 'CLR': 2, 'POV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 3.60, per 1000 atoms: 0.24 Number of scatterers: 15294 At special positions: 0 Unit cell: (134.435, 114.395, 141.115, 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 96 16.00 P 12 15.00 F 4 9.00 O 2818 8.00 N 2362 7.00 C 10002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS D 595 " distance=2.04 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " " BMA I 3 " - " BMA I 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1006 " - " ASN A 546 " " NAG C1006 " - " ASN C 546 " " NAG E 1 " - " ASN A 751 " " NAG F 1 " - " ASN B 546 " " NAG G 1 " - " ASN B 751 " " NAG H 1 " - " ASN C 751 " " NAG I 1 " - " ASN D 546 " " NAG J 1 " - " ASN D 751 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 470.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 20 sheets defined 51.3% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.525A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 removed outlier: 3.872A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.800A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 562 through 585 removed outlier: 3.823A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.582A pdb=" N PHE A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 665 removed outlier: 4.169A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.502A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.746A pdb=" N LYS A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 730 removed outlier: 3.811A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.846A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 788 removed outlier: 3.508A pdb=" N LEU A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 800 removed outlier: 3.673A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 850 removed outlier: 3.640A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 869 removed outlier: 4.151A pdb=" N VAL A 862 " --> pdb=" O CYS A 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.917A pdb=" N GLU B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 4.160A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.513A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.860A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 583 " --> pdb=" O PHE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 630 through 632 No H-bonds generated for 'chain 'B' and resid 630 through 632' Processing helix chain 'B' and resid 633 through 661 removed outlier: 3.652A pdb=" N GLY B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.590A pdb=" N LYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 697 removed outlier: 3.522A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.706A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.677A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 removed outlier: 4.021A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 789 removed outlier: 3.678A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 783 " --> pdb=" O THR B 779 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B 788 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 800 removed outlier: 3.517A pdb=" N ARG B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 850 removed outlier: 3.597A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 846 " --> pdb=" O PHE B 842 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 868 removed outlier: 3.774A pdb=" N MET B 861 " --> pdb=" O PHE B 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.524A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 removed outlier: 3.872A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.802A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 562 through 585 removed outlier: 3.823A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C 580 " --> pdb=" O CYS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.581A pdb=" N PHE C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 665 removed outlier: 4.169A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 676 Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.502A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.746A pdb=" N LYS C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 730 removed outlier: 3.812A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 730 " --> pdb=" O GLN C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 749 removed outlier: 3.846A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 788 removed outlier: 3.508A pdb=" N LEU C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 799 removed outlier: 3.671A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 850 removed outlier: 3.640A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 850 " --> pdb=" O SER C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 869 removed outlier: 4.152A pdb=" N VAL C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.917A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.161A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 506 " --> pdb=" O VAL D 502 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP D 507 " --> pdb=" O ARG D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.513A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 585 removed outlier: 3.861A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 589 Processing helix chain 'D' and resid 607 through 620 Processing helix chain 'D' and resid 630 through 632 No H-bonds generated for 'chain 'D' and resid 630 through 632' Processing helix chain 'D' and resid 633 through 661 removed outlier: 3.651A pdb=" N GLY D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 677 removed outlier: 3.590A pdb=" N LYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN D 677 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 697 removed outlier: 3.521A pdb=" N PHE D 694 " --> pdb=" O THR D 690 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.706A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.677A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 removed outlier: 4.021A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 789 removed outlier: 3.677A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 783 " --> pdb=" O THR D 779 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU D 788 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 800 removed outlier: 3.517A pdb=" N ARG D 800 " --> pdb=" O GLU D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 850 removed outlier: 3.597A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 846 " --> pdb=" O PHE D 842 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS D 848 " --> pdb=" O TYR D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 868 removed outlier: 3.773A pdb=" N MET D 861 " --> pdb=" O PHE D 857 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 435 Processing sheet with id=AA2, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.574A pdb=" N GLN A 497 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 540 Processing sheet with id=AA5, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.819A pdb=" N TYR A 542 " --> pdb=" O THR A 753 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 436 through 437 Processing sheet with id=AA7, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA8, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.151A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 735 through 738 removed outlier: 3.584A pdb=" N MET B 737 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 684 through 685 removed outlier: 6.324A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 433 through 435 Processing sheet with id=AB3, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.573A pdb=" N GLN C 497 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AB5, first strand: chain 'C' and resid 538 through 540 Processing sheet with id=AB6, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.818A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 436 through 437 Processing sheet with id=AB8, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AB9, first strand: chain 'D' and resid 534 through 536 removed outlier: 4.152A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 735 through 738 removed outlier: 3.585A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 684 through 685 removed outlier: 6.324A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 602 hydrogen bonds defined for protein. 1764 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: 1.93 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2360 1.31 - 1.44: 4098 1.44 - 1.57: 8964 1.57 - 1.70: 47 1.70 - 1.82: 156 Bond restraints: 15625 Sorted by residual: bond pdb=" OAA 2J9 B1001 " pdb=" SAP 2J9 B1001 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAB 2J9 B1001 " pdb=" SAP 2J9 B1001 " ideal model delta sigma weight residual 1.452 1.652 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" OAB 2J9 D1002 " pdb=" SAP 2J9 D1002 " ideal model delta sigma weight residual 1.452 1.652 -0.200 2.00e-02 2.50e+03 9.96e+01 bond pdb=" OAA 2J9 D1002 " pdb=" SAP 2J9 D1002 " ideal model delta sigma weight residual 1.452 1.651 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" OAA 2J9 A1001 " pdb=" SAP 2J9 A1001 " ideal model delta sigma weight residual 1.452 1.650 -0.198 2.00e-02 2.50e+03 9.75e+01 ... (remaining 15620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.52: 20918 6.52 - 13.03: 148 13.03 - 19.55: 0 19.55 - 26.07: 0 26.07 - 32.58: 8 Bond angle restraints: 21074 Sorted by residual: angle pdb=" CAH 2J9 B1004 " pdb=" CAN 2J9 B1004 " pdb=" NAO 2J9 B1004 " ideal model delta sigma weight residual 117.67 150.25 -32.58 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CAH 2J9 D1002 " pdb=" CAN 2J9 D1002 " pdb=" NAO 2J9 D1002 " ideal model delta sigma weight residual 117.67 150.03 -32.36 3.00e+00 1.11e-01 1.16e+02 angle pdb=" CAH 2J9 B1001 " pdb=" CAN 2J9 B1001 " pdb=" NAO 2J9 B1001 " ideal model delta sigma weight residual 117.67 149.98 -32.31 3.00e+00 1.11e-01 1.16e+02 angle pdb=" CAH 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 117.67 149.64 -31.97 3.00e+00 1.11e-01 1.14e+02 angle pdb=" CAG 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 118.82 150.19 -31.37 3.00e+00 1.11e-01 1.09e+02 ... (remaining 21069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 9600 35.97 - 71.94: 369 71.94 - 107.91: 86 107.91 - 143.88: 19 143.88 - 179.85: 6 Dihedral angle restraints: 10080 sinusoidal: 4928 harmonic: 5152 Sorted by residual: dihedral pdb=" CA GLU B 441 " pdb=" C GLU B 441 " pdb=" N PRO B 442 " pdb=" CA PRO B 442 " ideal model delta harmonic sigma weight residual 180.00 -118.46 -61.54 0 5.00e+00 4.00e-02 1.52e+02 dihedral pdb=" CA GLU D 441 " pdb=" C GLU D 441 " pdb=" N PRO D 442 " pdb=" CA PRO D 442 " ideal model delta harmonic sigma weight residual -180.00 -118.46 -61.54 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA ASN A 819 " pdb=" C ASN A 819 " pdb=" N ILE A 820 " pdb=" CA ILE A 820 " ideal model delta harmonic sigma weight residual -180.00 -126.25 -53.75 0 5.00e+00 4.00e-02 1.16e+02 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.059: 2332 1.059 - 2.119: 0 2.119 - 3.178: 4 3.178 - 4.237: 0 4.237 - 5.296: 2 Chirality restraints: 2338 Sorted by residual: chirality pdb=" C13 CLR C1005 " pdb=" C12 CLR C1005 " pdb=" C14 CLR C1005 " pdb=" C17 CLR C1005 " both_signs ideal model delta sigma weight residual False -2.93 2.36 -5.30 2.00e-01 2.50e+01 7.01e+02 chirality pdb=" C13 CLR A1005 " pdb=" C12 CLR A1005 " pdb=" C14 CLR A1005 " pdb=" C17 CLR A1005 " both_signs ideal model delta sigma weight residual False -2.93 2.36 -5.29 2.00e-01 2.50e+01 6.99e+02 chirality pdb=" CAN 2J9 B1001 " pdb=" CAG 2J9 B1001 " pdb=" CAH 2J9 B1001 " pdb=" NAO 2J9 B1001 " both_signs ideal model delta sigma weight residual True 2.32 0.00 2.32 2.00e-01 2.50e+01 1.34e+02 ... (remaining 2335 not shown) Planarity restraints: 2534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 441 " 0.051 5.00e-02 4.00e+02 7.66e-02 9.39e+00 pdb=" N PRO D 442 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 442 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 442 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 441 " -0.051 5.00e-02 4.00e+02 7.64e-02 9.34e+00 pdb=" N PRO B 442 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 442 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 442 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 515 " -0.049 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO A 516 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " -0.040 5.00e-02 4.00e+02 ... (remaining 2531 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2304 2.75 - 3.29: 13969 3.29 - 3.83: 23421 3.83 - 4.36: 27480 4.36 - 4.90: 46583 Nonbonded interactions: 113757 Sorted by model distance: nonbonded pdb=" O VAL A 716 " pdb=" OH TYR A 733 " model vdw 2.217 3.040 nonbonded pdb=" O VAL C 716 " pdb=" OH TYR C 733 " model vdw 2.217 3.040 nonbonded pdb=" ND1 HIS A 593 " pdb=" O PRO D 594 " model vdw 2.298 3.120 nonbonded pdb=" OH TYR C 590 " pdb=" OD1 ASN C 605 " model vdw 2.321 3.040 nonbonded pdb=" OH TYR A 590 " pdb=" OD1 ASN A 605 " model vdw 2.321 3.040 ... (remaining 113752 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 429 through 874 or resid 1003 or resid 1005)) selection = (chain 'B' and (resid 429 through 874 or resid 1003 or resid 1005)) selection = (chain 'C' and (resid 429 through 874 or resid 1003 or resid 1005)) selection = (chain 'D' and (resid 429 through 874 or resid 1003 or resid 1005)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.140 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.202 15648 Z= 0.541 Angle : 1.517 32.584 21138 Z= 0.656 Chirality : 0.192 5.296 2338 Planarity : 0.007 0.077 2526 Dihedral : 20.284 179.854 6761 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.04 % Favored : 88.40 % Rotamer: Outliers : 0.39 % Allowed : 6.46 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.23 % 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 aren not related in a simple way. whole: -5.80 (0.13), residues: 1776 helix: -3.91 (0.08), residues: 900 sheet: -3.78 (0.37), residues: 130 loop : -3.62 (0.19), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 866 TYR 0.027 0.003 TYR A 733 PHE 0.020 0.002 PHE B 446 TRP 0.032 0.003 TRP B 589 HIS 0.002 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.01124 (15625) covalent geometry : angle 1.46588 (21074) SS BOND : bond 0.00606 ( 5) SS BOND : angle 1.06836 ( 10) hydrogen bonds : bond 0.31418 ( 602) hydrogen bonds : angle 9.30255 ( 1764) link_BETA1-3 : bond 0.02355 ( 2) link_BETA1-3 : angle 4.17187 ( 6) link_BETA1-4 : bond 0.01894 ( 8) link_BETA1-4 : angle 6.01405 ( 24) link_NAG-ASN : bond 0.01958 ( 8) link_NAG-ASN : angle 9.99767 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 649 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8424 (mtpp) REVERT: A 528 ASP cc_start: 0.7270 (m-30) cc_final: 0.6977 (m-30) REVERT: A 549 ASN cc_start: 0.8976 (t0) cc_final: 0.8732 (t0) REVERT: A 590 TYR cc_start: 0.9078 (p90) cc_final: 0.8852 (p90) REVERT: A 605 ASN cc_start: 0.8346 (m110) cc_final: 0.7561 (m-40) REVERT: A 639 ILE cc_start: 0.9485 (tp) cc_final: 0.9270 (tp) REVERT: A 665 GLU cc_start: 0.8918 (tp30) cc_final: 0.8579 (tm-30) REVERT: A 673 ASP cc_start: 0.9305 (m-30) cc_final: 0.9069 (m-30) REVERT: A 685 VAL cc_start: 0.9262 (t) cc_final: 0.8768 (p) REVERT: A 696 LYS cc_start: 0.9621 (mttt) cc_final: 0.9405 (mmtp) REVERT: A 702 TYR cc_start: 0.9571 (m-10) cc_final: 0.9184 (m-80) REVERT: A 704 LYS cc_start: 0.9457 (ptmt) cc_final: 0.9205 (ptmm) REVERT: A 705 MET cc_start: 0.9539 (mtp) cc_final: 0.8935 (mtp) REVERT: A 708 PHE cc_start: 0.9500 (t80) cc_final: 0.8914 (t80) REVERT: A 713 ARG cc_start: 0.8960 (ttt90) cc_final: 0.8732 (mtp-110) REVERT: A 732 ASP cc_start: 0.8650 (m-30) cc_final: 0.8168 (p0) REVERT: A 775 ARG cc_start: 0.8215 (ptm160) cc_final: 0.7770 (ttp-170) REVERT: A 779 THR cc_start: 0.8600 (m) cc_final: 0.8379 (m) REVERT: A 792 HIS cc_start: 0.8931 (t70) cc_final: 0.8698 (t70) REVERT: A 818 GLN cc_start: 0.9160 (mp10) cc_final: 0.8926 (mp10) REVERT: A 864 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8317 (mt-10) REVERT: B 441 GLU cc_start: 0.8884 (tp30) cc_final: 0.8566 (tp30) REVERT: B 481 ARG cc_start: 0.7369 (ttm170) cc_final: 0.6953 (mtm-85) REVERT: B 484 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8033 (tm-30) REVERT: B 524 GLU cc_start: 0.8962 (tp30) cc_final: 0.8641 (tp30) REVERT: B 575 SER cc_start: 0.9096 (m) cc_final: 0.8682 (t) REVERT: B 588 GLU cc_start: 0.9541 (tp30) cc_final: 0.9200 (tp30) REVERT: B 589 TRP cc_start: 0.9000 (m100) cc_final: 0.8671 (m-10) REVERT: B 603 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8004 (mm-30) REVERT: B 611 SER cc_start: 0.9246 (m) cc_final: 0.8735 (m) REVERT: B 612 PHE cc_start: 0.8374 (m-80) cc_final: 0.8152 (m-80) REVERT: B 626 LEU cc_start: 0.9268 (pp) cc_final: 0.9042 (pp) REVERT: B 686 GLU cc_start: 0.8810 (tt0) cc_final: 0.8525 (tm-30) REVERT: B 722 GLU cc_start: 0.9137 (tp30) cc_final: 0.8641 (tp30) REVERT: B 779 THR cc_start: 0.9339 (m) cc_final: 0.9017 (p) REVERT: B 784 GLN cc_start: 0.9239 (tt0) cc_final: 0.8735 (tm-30) REVERT: B 787 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9230 (mm-30) REVERT: B 788 GLU cc_start: 0.8939 (mp0) cc_final: 0.8649 (mp0) REVERT: B 795 LYS cc_start: 0.9511 (tttt) cc_final: 0.9221 (tptm) REVERT: B 796 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8942 (mm-30) REVERT: B 797 LYS cc_start: 0.9724 (tttt) cc_final: 0.9295 (tttt) REVERT: B 798 TRP cc_start: 0.9218 (m100) cc_final: 0.8428 (m100) REVERT: B 847 LYS cc_start: 0.7840 (tttt) cc_final: 0.7573 (tppt) REVERT: C 465 ASP cc_start: 0.8382 (m-30) cc_final: 0.8141 (m-30) REVERT: C 478 TYR cc_start: 0.7643 (p90) cc_final: 0.7411 (p90) REVERT: C 487 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8375 (mtpp) REVERT: C 528 ASP cc_start: 0.7312 (m-30) cc_final: 0.6893 (m-30) REVERT: C 603 GLU cc_start: 0.7326 (tp30) cc_final: 0.6999 (tp30) REVERT: C 604 ASN cc_start: 0.8101 (p0) cc_final: 0.7898 (p0) REVERT: C 607 THR cc_start: 0.9339 (p) cc_final: 0.9075 (t) REVERT: C 673 ASP cc_start: 0.9402 (m-30) cc_final: 0.9198 (m-30) REVERT: C 692 THR cc_start: 0.9380 (m) cc_final: 0.9149 (p) REVERT: C 708 PHE cc_start: 0.9282 (t80) cc_final: 0.8987 (t80) REVERT: C 732 ASP cc_start: 0.8534 (m-30) cc_final: 0.8227 (t70) REVERT: C 779 THR cc_start: 0.8520 (m) cc_final: 0.8269 (m) REVERT: C 793 MET cc_start: 0.8764 (mmm) cc_final: 0.8547 (mmm) REVERT: C 842 PHE cc_start: 0.8950 (t80) cc_final: 0.8724 (t80) REVERT: D 479 GLU cc_start: 0.7440 (tt0) cc_final: 0.7139 (tm-30) REVERT: D 484 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7838 (tm-30) REVERT: D 524 GLU cc_start: 0.8922 (tp30) cc_final: 0.8652 (tp30) REVERT: D 575 SER cc_start: 0.9175 (m) cc_final: 0.8802 (t) REVERT: D 588 GLU cc_start: 0.9436 (tp30) cc_final: 0.8871 (tp30) REVERT: D 603 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8050 (mm-30) REVERT: D 625 GLU cc_start: 0.8371 (pm20) cc_final: 0.8073 (pm20) REVERT: D 673 ASP cc_start: 0.9318 (m-30) cc_final: 0.9088 (m-30) REVERT: D 686 GLU cc_start: 0.8792 (tt0) cc_final: 0.8460 (tm-30) REVERT: D 722 GLU cc_start: 0.9149 (tp30) cc_final: 0.8646 (tp30) REVERT: D 784 GLN cc_start: 0.9266 (tt0) cc_final: 0.9038 (tt0) REVERT: D 787 GLU cc_start: 0.9511 (mm-30) cc_final: 0.9263 (mm-30) REVERT: D 795 LYS cc_start: 0.9528 (tttt) cc_final: 0.9296 (tptm) REVERT: D 797 LYS cc_start: 0.9649 (tttt) cc_final: 0.9415 (ttpp) REVERT: D 798 TRP cc_start: 0.9346 (m100) cc_final: 0.8845 (m100) outliers start: 6 outliers final: 0 residues processed: 650 average time/residue: 0.1309 time to fit residues: 122.9406 Evaluate side-chains 409 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.4980 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 747 GLN A 749 ASN B 456 ASN B 495 ASN B 549 ASN B 596 ASN C 491 GLN C 605 ASN C 677 GLN C 714 GLN C 749 ASN D 495 ASN D 549 ASN D 596 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.147968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.110189 restraints weight = 26430.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.114230 restraints weight = 11940.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116805 restraints weight = 7819.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.118303 restraints weight = 6243.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119080 restraints weight = 5535.063| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15648 Z= 0.171 Angle : 1.007 32.006 21138 Z= 0.447 Chirality : 0.069 1.777 2338 Planarity : 0.006 0.078 2526 Dihedral : 21.873 167.661 3373 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.47 % Favored : 89.30 % Rotamer: Outliers : 4.33 % Allowed : 13.95 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.23 % 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 aren not related in a simple way. whole: -3.36 (0.17), residues: 1776 helix: -1.20 (0.15), residues: 932 sheet: -2.76 (0.50), residues: 100 loop : -3.53 (0.19), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 727 TYR 0.024 0.002 TYR B 590 PHE 0.024 0.002 PHE B 529 TRP 0.035 0.002 TRP D 589 HIS 0.004 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00370 (15625) covalent geometry : angle 0.96100 (21074) SS BOND : bond 0.00527 ( 5) SS BOND : angle 1.87672 ( 10) hydrogen bonds : bond 0.06570 ( 602) hydrogen bonds : angle 4.71271 ( 1764) link_BETA1-3 : bond 0.02347 ( 2) link_BETA1-3 : angle 3.74927 ( 6) link_BETA1-4 : bond 0.01776 ( 8) link_BETA1-4 : angle 4.84575 ( 24) link_NAG-ASN : bond 0.01413 ( 8) link_NAG-ASN : angle 7.30646 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 439 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ASP cc_start: 0.8642 (m-30) cc_final: 0.8414 (m-30) REVERT: A 471 SER cc_start: 0.8834 (t) cc_final: 0.8528 (p) REVERT: A 487 LYS cc_start: 0.9181 (mtpp) cc_final: 0.8772 (mtmm) REVERT: A 549 ASN cc_start: 0.8980 (t0) cc_final: 0.8763 (t0) REVERT: A 598 ASP cc_start: 0.8356 (m-30) cc_final: 0.8144 (m-30) REVERT: A 605 ASN cc_start: 0.8451 (m110) cc_final: 0.8166 (p0) REVERT: A 665 GLU cc_start: 0.8834 (tp30) cc_final: 0.8569 (tm-30) REVERT: A 673 ASP cc_start: 0.9166 (m-30) cc_final: 0.8693 (m-30) REVERT: A 705 MET cc_start: 0.9483 (mtp) cc_final: 0.9166 (mtp) REVERT: A 713 ARG cc_start: 0.8934 (ttt90) cc_final: 0.8724 (mtp-110) REVERT: A 775 ARG cc_start: 0.8234 (ptm160) cc_final: 0.7931 (ttp-170) REVERT: B 473 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8822 (mp) REVERT: B 528 ASP cc_start: 0.7754 (m-30) cc_final: 0.7483 (m-30) REVERT: B 566 TYR cc_start: 0.9063 (m-10) cc_final: 0.8728 (m-80) REVERT: B 575 SER cc_start: 0.9254 (m) cc_final: 0.8852 (t) REVERT: B 603 GLU cc_start: 0.8237 (mm-30) cc_final: 0.8003 (mm-30) REVERT: B 611 SER cc_start: 0.9372 (m) cc_final: 0.8940 (m) REVERT: B 784 GLN cc_start: 0.9106 (tt0) cc_final: 0.8643 (tm-30) REVERT: B 795 LYS cc_start: 0.9472 (tttt) cc_final: 0.9172 (tptm) REVERT: B 797 LYS cc_start: 0.9708 (tttt) cc_final: 0.9401 (tttt) REVERT: B 798 TRP cc_start: 0.9008 (m100) cc_final: 0.8502 (m100) REVERT: B 844 TYR cc_start: 0.8982 (t80) cc_final: 0.8630 (t80) REVERT: B 861 MET cc_start: 0.8097 (tpt) cc_final: 0.7847 (tpp) REVERT: C 440 GLU cc_start: 0.8271 (tp30) cc_final: 0.7830 (tp30) REVERT: C 487 LYS cc_start: 0.9089 (mtpp) cc_final: 0.8558 (mtmm) REVERT: C 488 TYR cc_start: 0.9003 (m-10) cc_final: 0.8667 (m-10) REVERT: C 590 TYR cc_start: 0.8222 (p90) cc_final: 0.7712 (p90) REVERT: C 602 VAL cc_start: 0.9093 (m) cc_final: 0.7952 (t) REVERT: C 665 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8276 (mm-30) REVERT: C 673 ASP cc_start: 0.9305 (m-30) cc_final: 0.8800 (m-30) REVERT: C 709 MET cc_start: 0.9288 (mtp) cc_final: 0.8526 (mtm) REVERT: C 748 ARG cc_start: 0.8361 (mmt90) cc_final: 0.7938 (mpt180) REVERT: D 465 ASP cc_start: 0.8884 (t0) cc_final: 0.8553 (t0) REVERT: D 575 SER cc_start: 0.9199 (m) cc_final: 0.8868 (t) REVERT: D 588 GLU cc_start: 0.9443 (tp30) cc_final: 0.9227 (tp30) REVERT: D 662 GLU cc_start: 0.7624 (tm-30) cc_final: 0.6942 (tm-30) REVERT: D 664 MET cc_start: 0.8262 (pmm) cc_final: 0.7845 (pmm) REVERT: D 668 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9198 (pp) REVERT: D 797 LYS cc_start: 0.9664 (tttt) cc_final: 0.9297 (tttm) REVERT: D 798 TRP cc_start: 0.9206 (m100) cc_final: 0.8747 (m100) outliers start: 67 outliers final: 34 residues processed: 465 average time/residue: 0.1241 time to fit residues: 87.4160 Evaluate side-chains 413 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 377 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 549 ASN Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 819 ASN Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 554 SER Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 549 ASN Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 0 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 HIS C 605 ASN C 818 GLN D 456 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.104522 restraints weight = 25990.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.108380 restraints weight = 11815.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110841 restraints weight = 7722.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112287 restraints weight = 6160.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112885 restraints weight = 5465.237| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15648 Z= 0.172 Angle : 0.949 31.698 21138 Z= 0.417 Chirality : 0.067 1.721 2338 Planarity : 0.005 0.077 2526 Dihedral : 20.211 172.200 3373 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.04 % Favored : 88.74 % Rotamer: Outliers : 4.65 % Allowed : 17.57 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.23 % 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 aren not related in a simple way. whole: -2.20 (0.19), residues: 1776 helix: -0.01 (0.17), residues: 932 sheet: -2.71 (0.50), residues: 88 loop : -3.26 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 800 TYR 0.020 0.002 TYR A 733 PHE 0.021 0.002 PHE A 708 TRP 0.031 0.001 TRP D 589 HIS 0.003 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00391 (15625) covalent geometry : angle 0.91165 (21074) SS BOND : bond 0.00244 ( 5) SS BOND : angle 1.16661 ( 10) hydrogen bonds : bond 0.04826 ( 602) hydrogen bonds : angle 4.29836 ( 1764) link_BETA1-3 : bond 0.01486 ( 2) link_BETA1-3 : angle 2.78237 ( 6) link_BETA1-4 : bond 0.01601 ( 8) link_BETA1-4 : angle 4.30596 ( 24) link_NAG-ASN : bond 0.01107 ( 8) link_NAG-ASN : angle 6.57364 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 407 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 SER cc_start: 0.8833 (t) cc_final: 0.8509 (p) REVERT: A 487 LYS cc_start: 0.9182 (mtpp) cc_final: 0.8842 (mtmm) REVERT: A 549 ASN cc_start: 0.8862 (t0) cc_final: 0.8652 (t0) REVERT: A 665 GLU cc_start: 0.8831 (tp30) cc_final: 0.8593 (tm-30) REVERT: A 672 ASP cc_start: 0.8818 (p0) cc_final: 0.8521 (p0) REVERT: A 673 ASP cc_start: 0.9022 (m-30) cc_final: 0.8758 (m-30) REVERT: A 705 MET cc_start: 0.9515 (mtp) cc_final: 0.9067 (mtp) REVERT: A 737 MET cc_start: 0.7821 (ptp) cc_final: 0.7578 (ptp) REVERT: A 867 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7680 (ttm) REVERT: B 473 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8675 (mp) REVERT: B 504 GLU cc_start: 0.7183 (mp0) cc_final: 0.6965 (mp0) REVERT: B 528 ASP cc_start: 0.7771 (m-30) cc_final: 0.7480 (m-30) REVERT: B 566 TYR cc_start: 0.9048 (m-10) cc_final: 0.8609 (m-80) REVERT: B 603 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7931 (mm-30) REVERT: B 611 SER cc_start: 0.9409 (m) cc_final: 0.8999 (m) REVERT: B 620 MET cc_start: 0.9310 (mmm) cc_final: 0.8140 (mmm) REVERT: B 632 SER cc_start: 0.9515 (t) cc_final: 0.9306 (t) REVERT: B 726 GLN cc_start: 0.8959 (mm110) cc_final: 0.8723 (mm-40) REVERT: B 738 GLU cc_start: 0.8623 (mp0) cc_final: 0.8418 (mp0) REVERT: B 793 MET cc_start: 0.9044 (mmt) cc_final: 0.8819 (mmm) REVERT: B 795 LYS cc_start: 0.9489 (tttt) cc_final: 0.9190 (tptm) REVERT: B 797 LYS cc_start: 0.9707 (tttt) cc_final: 0.9403 (tttt) REVERT: B 798 TRP cc_start: 0.9039 (m100) cc_final: 0.8494 (m100) REVERT: B 861 MET cc_start: 0.8105 (tpt) cc_final: 0.7859 (tpp) REVERT: C 440 GLU cc_start: 0.8296 (tp30) cc_final: 0.7931 (tp30) REVERT: C 457 ASP cc_start: 0.8837 (t0) cc_final: 0.8488 (t0) REVERT: C 471 SER cc_start: 0.8767 (t) cc_final: 0.8397 (p) REVERT: C 487 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8621 (mtmm) REVERT: C 488 TYR cc_start: 0.8965 (m-10) cc_final: 0.8620 (m-10) REVERT: C 498 TRP cc_start: 0.8893 (m100) cc_final: 0.8305 (m100) REVERT: C 590 TYR cc_start: 0.8492 (p90) cc_final: 0.8022 (p90) REVERT: C 593 HIS cc_start: 0.8688 (m90) cc_final: 0.8433 (m90) REVERT: C 596 ASN cc_start: 0.8492 (t0) cc_final: 0.8286 (t0) REVERT: C 665 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8328 (tp30) REVERT: C 672 ASP cc_start: 0.9024 (p0) cc_final: 0.8757 (p0) REVERT: C 673 ASP cc_start: 0.9232 (m-30) cc_final: 0.9009 (m-30) REVERT: C 709 MET cc_start: 0.9312 (mtp) cc_final: 0.9089 (mtp) REVERT: C 754 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8442 (tm-30) REVERT: C 770 MET cc_start: 0.8903 (tpp) cc_final: 0.8434 (tpp) REVERT: C 864 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7403 (mt-10) REVERT: D 504 GLU cc_start: 0.7244 (mp0) cc_final: 0.7018 (mp0) REVERT: D 575 SER cc_start: 0.9203 (m) cc_final: 0.8814 (t) REVERT: D 588 GLU cc_start: 0.9424 (tp30) cc_final: 0.9157 (tp30) REVERT: D 668 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9220 (pp) REVERT: D 726 GLN cc_start: 0.8933 (mm110) cc_final: 0.8710 (mm-40) REVERT: D 793 MET cc_start: 0.9160 (mmt) cc_final: 0.8902 (mmm) REVERT: D 797 LYS cc_start: 0.9627 (tttt) cc_final: 0.9395 (ttpp) REVERT: D 798 TRP cc_start: 0.9245 (m100) cc_final: 0.8943 (m100) outliers start: 72 outliers final: 50 residues processed: 440 average time/residue: 0.1162 time to fit residues: 78.4275 Evaluate side-chains 417 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 364 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 171 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 0.0040 chunk 23 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 ASN B 604 ASN D 456 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.141157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104189 restraints weight = 25967.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108109 restraints weight = 11774.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110605 restraints weight = 7727.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112038 restraints weight = 6196.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112767 restraints weight = 5523.808| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15648 Z= 0.147 Angle : 0.922 32.028 21138 Z= 0.398 Chirality : 0.066 1.685 2338 Planarity : 0.005 0.075 2526 Dihedral : 19.029 175.003 3373 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.47 % Favored : 89.41 % Rotamer: Outliers : 5.36 % Allowed : 18.22 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.23 % 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 aren not related in a simple way. whole: -1.63 (0.20), residues: 1776 helix: 0.52 (0.17), residues: 942 sheet: -2.67 (0.49), residues: 86 loop : -3.11 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 713 TYR 0.025 0.002 TYR B 590 PHE 0.018 0.001 PHE B 476 TRP 0.027 0.001 TRP D 799 HIS 0.007 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00330 (15625) covalent geometry : angle 0.88692 (21074) SS BOND : bond 0.00456 ( 5) SS BOND : angle 1.02240 ( 10) hydrogen bonds : bond 0.04025 ( 602) hydrogen bonds : angle 4.00457 ( 1764) link_BETA1-3 : bond 0.01336 ( 2) link_BETA1-3 : angle 2.47830 ( 6) link_BETA1-4 : bond 0.01665 ( 8) link_BETA1-4 : angle 4.31470 ( 24) link_NAG-ASN : bond 0.01029 ( 8) link_NAG-ASN : angle 6.05240 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 403 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: A 487 LYS cc_start: 0.9186 (mtpp) cc_final: 0.8901 (mtmm) REVERT: A 491 GLN cc_start: 0.9380 (tt0) cc_final: 0.9155 (tt0) REVERT: A 665 GLU cc_start: 0.8783 (tp30) cc_final: 0.8558 (tm-30) REVERT: A 672 ASP cc_start: 0.8841 (p0) cc_final: 0.8505 (p0) REVERT: A 673 ASP cc_start: 0.9003 (m-30) cc_final: 0.8770 (m-30) REVERT: A 705 MET cc_start: 0.9477 (mtp) cc_final: 0.9014 (mtp) REVERT: A 770 MET cc_start: 0.8763 (tpp) cc_final: 0.8269 (tpp) REVERT: A 867 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7700 (ttm) REVERT: A 869 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8361 (tt) REVERT: B 473 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8644 (mp) REVERT: B 603 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8078 (mm-30) REVERT: B 611 SER cc_start: 0.9426 (m) cc_final: 0.9203 (m) REVERT: B 620 MET cc_start: 0.9213 (mmm) cc_final: 0.8153 (mmm) REVERT: B 779 THR cc_start: 0.9464 (m) cc_final: 0.9262 (p) REVERT: B 797 LYS cc_start: 0.9687 (tttt) cc_final: 0.9417 (tttt) REVERT: B 861 MET cc_start: 0.8084 (tpt) cc_final: 0.7845 (tpp) REVERT: C 440 GLU cc_start: 0.8251 (tp30) cc_final: 0.7876 (tp30) REVERT: C 457 ASP cc_start: 0.8813 (t0) cc_final: 0.8492 (t0) REVERT: C 460 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: C 471 SER cc_start: 0.8745 (t) cc_final: 0.8367 (p) REVERT: C 488 TYR cc_start: 0.8886 (m-10) cc_final: 0.8629 (m-10) REVERT: C 498 TRP cc_start: 0.8914 (m100) cc_final: 0.8251 (m100) REVERT: C 590 TYR cc_start: 0.8618 (p90) cc_final: 0.8297 (p90) REVERT: C 593 HIS cc_start: 0.8657 (m90) cc_final: 0.8357 (m90) REVERT: C 596 ASN cc_start: 0.8492 (t0) cc_final: 0.8211 (t0) REVERT: C 665 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8304 (tp30) REVERT: C 709 MET cc_start: 0.9287 (mtp) cc_final: 0.9052 (mtp) REVERT: C 754 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8750 (tm-30) REVERT: C 864 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7353 (mt-10) REVERT: D 575 SER cc_start: 0.9191 (m) cc_final: 0.8781 (t) REVERT: D 588 GLU cc_start: 0.9404 (tp30) cc_final: 0.9120 (tp30) REVERT: D 603 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7779 (mm-30) REVERT: D 662 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6746 (tm-30) REVERT: D 664 MET cc_start: 0.8064 (pmm) cc_final: 0.7476 (pmm) REVERT: D 668 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9217 (pp) REVERT: D 793 MET cc_start: 0.9091 (mmt) cc_final: 0.8838 (mmm) REVERT: D 797 LYS cc_start: 0.9623 (tttt) cc_final: 0.9266 (tttp) REVERT: D 798 TRP cc_start: 0.9260 (m100) cc_final: 0.8898 (m100) outliers start: 83 outliers final: 56 residues processed: 440 average time/residue: 0.1128 time to fit residues: 77.2358 Evaluate side-chains 428 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 366 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 819 ASN Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 6 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 170 optimal weight: 0.0370 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN A 677 GLN B 456 ASN ** C 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.139446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102672 restraints weight = 25889.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106453 restraints weight = 12053.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108874 restraints weight = 8042.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110285 restraints weight = 6495.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110974 restraints weight = 5803.695| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15648 Z= 0.149 Angle : 0.924 32.197 21138 Z= 0.398 Chirality : 0.066 1.676 2338 Planarity : 0.005 0.092 2526 Dihedral : 18.269 176.309 3373 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.30 % Favored : 89.53 % Rotamer: Outliers : 5.68 % Allowed : 19.38 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.23 % 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 aren not related in a simple way. whole: -1.35 (0.20), residues: 1776 helix: 0.84 (0.17), residues: 942 sheet: -3.01 (0.39), residues: 138 loop : -2.99 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 800 TYR 0.020 0.002 TYR A 733 PHE 0.019 0.001 PHE D 476 TRP 0.020 0.001 TRP D 589 HIS 0.004 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00337 (15625) covalent geometry : angle 0.89160 (21074) SS BOND : bond 0.00582 ( 5) SS BOND : angle 1.30605 ( 10) hydrogen bonds : bond 0.03801 ( 602) hydrogen bonds : angle 3.89281 ( 1764) link_BETA1-3 : bond 0.01289 ( 2) link_BETA1-3 : angle 2.03795 ( 6) link_BETA1-4 : bond 0.01670 ( 8) link_BETA1-4 : angle 4.35102 ( 24) link_NAG-ASN : bond 0.00950 ( 8) link_NAG-ASN : angle 5.72253 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 374 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: A 471 SER cc_start: 0.8809 (t) cc_final: 0.8546 (p) REVERT: A 487 LYS cc_start: 0.9225 (mtpp) cc_final: 0.8910 (mtmm) REVERT: A 665 GLU cc_start: 0.8817 (tp30) cc_final: 0.8571 (tm-30) REVERT: A 672 ASP cc_start: 0.8886 (p0) cc_final: 0.8593 (p0) REVERT: A 673 ASP cc_start: 0.9033 (m-30) cc_final: 0.8830 (m-30) REVERT: A 691 MET cc_start: 0.8911 (ptp) cc_final: 0.8692 (ptp) REVERT: A 705 MET cc_start: 0.9487 (mtp) cc_final: 0.9063 (mtp) REVERT: A 718 VAL cc_start: 0.7442 (OUTLIER) cc_final: 0.6927 (p) REVERT: A 770 MET cc_start: 0.8755 (tpp) cc_final: 0.8305 (tpp) REVERT: A 788 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: A 867 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7712 (ttm) REVERT: A 869 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8341 (tt) REVERT: B 465 ASP cc_start: 0.8908 (m-30) cc_final: 0.8675 (m-30) REVERT: B 603 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8082 (mm-30) REVERT: B 797 LYS cc_start: 0.9684 (tttt) cc_final: 0.9427 (tttt) REVERT: B 861 MET cc_start: 0.8102 (tpt) cc_final: 0.7900 (tpp) REVERT: C 440 GLU cc_start: 0.8220 (tp30) cc_final: 0.7744 (tp30) REVERT: C 457 ASP cc_start: 0.8853 (t0) cc_final: 0.8546 (t0) REVERT: C 460 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: C 471 SER cc_start: 0.8766 (t) cc_final: 0.8376 (p) REVERT: C 542 TYR cc_start: 0.8828 (t80) cc_final: 0.8615 (t80) REVERT: C 590 TYR cc_start: 0.8648 (p90) cc_final: 0.8340 (p90) REVERT: C 593 HIS cc_start: 0.8687 (m90) cc_final: 0.8363 (m90) REVERT: C 596 ASN cc_start: 0.8557 (t0) cc_final: 0.8251 (t0) REVERT: C 603 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7249 (mm-30) REVERT: C 665 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8310 (tp30) REVERT: C 681 GLU cc_start: 0.8189 (pm20) cc_final: 0.7818 (pm20) REVERT: C 705 MET cc_start: 0.9610 (mtp) cc_final: 0.9174 (mtp) REVERT: C 709 MET cc_start: 0.9332 (mtp) cc_final: 0.9095 (mtp) REVERT: C 754 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8729 (tm-30) REVERT: C 761 SER cc_start: 0.9463 (t) cc_final: 0.9251 (t) REVERT: D 575 SER cc_start: 0.9180 (m) cc_final: 0.8797 (t) REVERT: D 590 TYR cc_start: 0.8621 (p90) cc_final: 0.8411 (p90) REVERT: D 603 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7783 (mm-30) REVERT: D 611 SER cc_start: 0.9511 (m) cc_final: 0.9220 (m) REVERT: D 662 GLU cc_start: 0.7689 (tm-30) cc_final: 0.6430 (tm-30) REVERT: D 668 ILE cc_start: 0.9475 (OUTLIER) cc_final: 0.9229 (pp) REVERT: D 687 ASP cc_start: 0.7915 (m-30) cc_final: 0.7573 (m-30) REVERT: D 793 MET cc_start: 0.9111 (mmt) cc_final: 0.8862 (mmm) REVERT: D 797 LYS cc_start: 0.9617 (tttt) cc_final: 0.9288 (tttp) REVERT: D 818 GLN cc_start: 0.9053 (pm20) cc_final: 0.8840 (pm20) outliers start: 88 outliers final: 59 residues processed: 415 average time/residue: 0.1149 time to fit residues: 74.1590 Evaluate side-chains 411 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 345 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 819 ASN Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 49 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 115 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.100072 restraints weight = 25907.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103872 restraints weight = 12236.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106261 restraints weight = 8222.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107646 restraints weight = 6677.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108263 restraints weight = 5983.194| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15648 Z= 0.191 Angle : 0.930 32.303 21138 Z= 0.403 Chirality : 0.066 1.681 2338 Planarity : 0.005 0.086 2526 Dihedral : 17.898 175.470 3373 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.75 % Favored : 89.13 % Rotamer: Outliers : 6.14 % Allowed : 19.51 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -1.14 (0.21), residues: 1776 helix: 1.05 (0.18), residues: 942 sheet: -2.98 (0.39), residues: 138 loop : -2.93 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 775 TYR 0.017 0.002 TYR A 733 PHE 0.015 0.001 PHE B 476 TRP 0.022 0.001 TRP D 589 HIS 0.005 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00442 (15625) covalent geometry : angle 0.89938 (21074) SS BOND : bond 0.00304 ( 5) SS BOND : angle 1.19142 ( 10) hydrogen bonds : bond 0.03842 ( 602) hydrogen bonds : angle 3.94317 ( 1764) link_BETA1-3 : bond 0.01222 ( 2) link_BETA1-3 : angle 1.81830 ( 6) link_BETA1-4 : bond 0.01647 ( 8) link_BETA1-4 : angle 4.45295 ( 24) link_NAG-ASN : bond 0.00857 ( 8) link_NAG-ASN : angle 5.55174 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 352 time to evaluate : 0.619 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 460 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: A 487 LYS cc_start: 0.9237 (mtpp) cc_final: 0.8909 (mtmm) REVERT: A 665 GLU cc_start: 0.8815 (tp30) cc_final: 0.8566 (tm-30) REVERT: A 672 ASP cc_start: 0.8916 (p0) cc_final: 0.8602 (p0) REVERT: A 673 ASP cc_start: 0.9056 (m-30) cc_final: 0.8844 (m-30) REVERT: A 679 LYS cc_start: 0.8683 (tmtt) cc_final: 0.8354 (tmtt) REVERT: A 705 MET cc_start: 0.9504 (mtp) cc_final: 0.9068 (mtp) REVERT: A 770 MET cc_start: 0.8770 (tpp) cc_final: 0.8347 (tpp) REVERT: A 788 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8339 (mp0) REVERT: A 869 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8379 (tt) REVERT: B 441 GLU cc_start: 0.8799 (tp30) cc_final: 0.8297 (tp30) REVERT: B 465 ASP cc_start: 0.8961 (m-30) cc_final: 0.8739 (m-30) REVERT: B 528 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7382 (t70) REVERT: B 620 MET cc_start: 0.9264 (mmm) cc_final: 0.8178 (mmm) REVERT: B 738 GLU cc_start: 0.8547 (mp0) cc_final: 0.8228 (mp0) REVERT: B 793 MET cc_start: 0.9108 (mmt) cc_final: 0.8884 (mmm) REVERT: B 797 LYS cc_start: 0.9682 (tttt) cc_final: 0.9445 (tttt) REVERT: B 861 MET cc_start: 0.8101 (tpt) cc_final: 0.7899 (tpp) REVERT: C 440 GLU cc_start: 0.8065 (tp30) cc_final: 0.7690 (tp30) REVERT: C 457 ASP cc_start: 0.8847 (t0) cc_final: 0.8560 (t0) REVERT: C 460 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: C 471 SER cc_start: 0.8752 (t) cc_final: 0.8352 (p) REVERT: C 488 TYR cc_start: 0.8890 (m-10) cc_final: 0.8581 (m-10) REVERT: C 590 TYR cc_start: 0.8657 (p90) cc_final: 0.8390 (p90) REVERT: C 593 HIS cc_start: 0.8728 (m90) cc_final: 0.8417 (m90) REVERT: C 596 ASN cc_start: 0.8569 (t0) cc_final: 0.8250 (t0) REVERT: C 603 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7268 (mm-30) REVERT: C 665 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8321 (tp30) REVERT: C 681 GLU cc_start: 0.8146 (pm20) cc_final: 0.7813 (pm20) REVERT: C 709 MET cc_start: 0.9340 (mtp) cc_final: 0.9012 (mtp) REVERT: C 754 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8750 (tm-30) REVERT: D 528 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7315 (t70) REVERT: D 575 SER cc_start: 0.9215 (m) cc_final: 0.8813 (t) REVERT: D 590 TYR cc_start: 0.8660 (p90) cc_final: 0.8352 (p90) REVERT: D 603 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7690 (mm-30) REVERT: D 611 SER cc_start: 0.9528 (m) cc_final: 0.9267 (m) REVERT: D 668 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9233 (pp) REVERT: D 793 MET cc_start: 0.9119 (mmt) cc_final: 0.8885 (mmm) REVERT: D 797 LYS cc_start: 0.9635 (tttt) cc_final: 0.9326 (tttp) outliers start: 95 outliers final: 70 residues processed: 400 average time/residue: 0.1172 time to fit residues: 73.2591 Evaluate side-chains 409 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 332 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 819 ASN Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 819 ASN Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 819 ASN Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 77 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 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 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN ** C 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.137981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.100492 restraints weight = 25836.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104306 restraints weight = 12192.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106688 restraints weight = 8213.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108074 restraints weight = 6688.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108643 restraints weight = 5997.705| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15648 Z= 0.161 Angle : 0.921 32.254 21138 Z= 0.400 Chirality : 0.066 1.677 2338 Planarity : 0.005 0.099 2526 Dihedral : 17.535 176.589 3373 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.87 % Favored : 89.02 % Rotamer: Outliers : 5.36 % Allowed : 21.06 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -0.98 (0.21), residues: 1776 helix: 1.20 (0.18), residues: 942 sheet: -2.97 (0.38), residues: 138 loop : -2.88 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 800 TYR 0.026 0.002 TYR A 590 PHE 0.013 0.001 PHE D 476 TRP 0.031 0.001 TRP B 589 HIS 0.004 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00370 (15625) covalent geometry : angle 0.89094 (21074) SS BOND : bond 0.00386 ( 5) SS BOND : angle 0.88831 ( 10) hydrogen bonds : bond 0.03678 ( 602) hydrogen bonds : angle 3.83994 ( 1764) link_BETA1-3 : bond 0.01206 ( 2) link_BETA1-3 : angle 1.66584 ( 6) link_BETA1-4 : bond 0.01659 ( 8) link_BETA1-4 : angle 4.50339 ( 24) link_NAG-ASN : bond 0.00862 ( 8) link_NAG-ASN : angle 5.35078 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 352 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: A 487 LYS cc_start: 0.9251 (mtpp) cc_final: 0.8917 (mtmm) REVERT: A 665 GLU cc_start: 0.8837 (tp30) cc_final: 0.8592 (tm-30) REVERT: A 679 LYS cc_start: 0.8707 (tmtt) cc_final: 0.8394 (tmtt) REVERT: A 691 MET cc_start: 0.8721 (ptm) cc_final: 0.8467 (ptt) REVERT: A 705 MET cc_start: 0.9511 (mtp) cc_final: 0.9111 (mtp) REVERT: A 788 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: A 869 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8391 (tt) REVERT: B 441 GLU cc_start: 0.8824 (tp30) cc_final: 0.8457 (tp30) REVERT: B 465 ASP cc_start: 0.8964 (m-30) cc_final: 0.8764 (m-30) REVERT: B 528 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7133 (t0) REVERT: B 620 MET cc_start: 0.9261 (mmm) cc_final: 0.8178 (mmm) REVERT: B 687 ASP cc_start: 0.8263 (m-30) cc_final: 0.7867 (m-30) REVERT: B 738 GLU cc_start: 0.8545 (mp0) cc_final: 0.8234 (mp0) REVERT: B 793 MET cc_start: 0.9133 (mmt) cc_final: 0.8902 (mmm) REVERT: B 797 LYS cc_start: 0.9686 (tttt) cc_final: 0.9453 (tttt) REVERT: B 861 MET cc_start: 0.8122 (tpt) cc_final: 0.7917 (tpp) REVERT: C 457 ASP cc_start: 0.8849 (t0) cc_final: 0.8556 (t0) REVERT: C 460 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: C 471 SER cc_start: 0.8760 (t) cc_final: 0.8349 (p) REVERT: C 590 TYR cc_start: 0.8685 (p90) cc_final: 0.8454 (p90) REVERT: C 593 HIS cc_start: 0.8757 (m90) cc_final: 0.8442 (m90) REVERT: C 596 ASN cc_start: 0.8626 (t0) cc_final: 0.8323 (t0) REVERT: C 603 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7271 (mm-30) REVERT: C 665 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8333 (tp30) REVERT: C 681 GLU cc_start: 0.8138 (pm20) cc_final: 0.7811 (pm20) REVERT: C 705 MET cc_start: 0.9612 (mtp) cc_final: 0.9131 (mtp) REVERT: C 709 MET cc_start: 0.9332 (mtp) cc_final: 0.9075 (mtp) REVERT: C 754 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8743 (tm-30) REVERT: D 441 GLU cc_start: 0.8506 (tp30) cc_final: 0.7903 (tp30) REVERT: D 528 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7265 (t70) REVERT: D 575 SER cc_start: 0.9216 (m) cc_final: 0.8809 (t) REVERT: D 588 GLU cc_start: 0.9411 (tp30) cc_final: 0.9090 (tp30) REVERT: D 590 TYR cc_start: 0.8679 (p90) cc_final: 0.8271 (p90) REVERT: D 603 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7713 (mm-30) REVERT: D 611 SER cc_start: 0.9532 (m) cc_final: 0.9281 (m) REVERT: D 668 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9239 (pp) REVERT: D 687 ASP cc_start: 0.7721 (m-30) cc_final: 0.7439 (m-30) REVERT: D 793 MET cc_start: 0.9115 (mmt) cc_final: 0.8877 (mmm) REVERT: D 797 LYS cc_start: 0.9638 (tttt) cc_final: 0.9329 (tttp) outliers start: 83 outliers final: 62 residues processed: 389 average time/residue: 0.1106 time to fit residues: 67.1056 Evaluate side-chains 407 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 338 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 819 ASN Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 113 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 134 optimal weight: 0.0970 chunk 152 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.137757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100929 restraints weight = 25979.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104720 restraints weight = 12194.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107093 restraints weight = 8169.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108481 restraints weight = 6619.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109178 restraints weight = 5922.855| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15648 Z= 0.165 Angle : 0.925 32.289 21138 Z= 0.402 Chirality : 0.066 1.684 2338 Planarity : 0.005 0.093 2526 Dihedral : 17.199 177.019 3373 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.87 % Favored : 89.02 % Rotamer: Outliers : 5.56 % Allowed : 21.19 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: -0.84 (0.21), residues: 1776 helix: 1.28 (0.18), residues: 946 sheet: -2.85 (0.39), residues: 138 loop : -2.80 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 800 TYR 0.017 0.002 TYR B 590 PHE 0.012 0.001 PHE B 529 TRP 0.038 0.001 TRP B 589 HIS 0.004 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00381 (15625) covalent geometry : angle 0.89595 (21074) SS BOND : bond 0.00313 ( 5) SS BOND : angle 0.99380 ( 10) hydrogen bonds : bond 0.03662 ( 602) hydrogen bonds : angle 3.84215 ( 1764) link_BETA1-3 : bond 0.01200 ( 2) link_BETA1-3 : angle 1.58436 ( 6) link_BETA1-4 : bond 0.01619 ( 8) link_BETA1-4 : angle 4.57818 ( 24) link_NAG-ASN : bond 0.00813 ( 8) link_NAG-ASN : angle 5.13656 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 349 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: A 487 LYS cc_start: 0.9272 (mtpp) cc_final: 0.8940 (mtmm) REVERT: A 665 GLU cc_start: 0.8798 (tp30) cc_final: 0.8569 (tm-30) REVERT: A 679 LYS cc_start: 0.8648 (tmtt) cc_final: 0.8350 (tmtt) REVERT: A 705 MET cc_start: 0.9493 (mtp) cc_final: 0.9105 (mtp) REVERT: A 788 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: A 869 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8394 (tt) REVERT: B 441 GLU cc_start: 0.8775 (tp30) cc_final: 0.8542 (tp30) REVERT: B 528 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7201 (t0) REVERT: B 620 MET cc_start: 0.9233 (mmm) cc_final: 0.8165 (mmm) REVERT: B 793 MET cc_start: 0.9087 (mmt) cc_final: 0.8867 (mmm) REVERT: B 797 LYS cc_start: 0.9657 (tttt) cc_final: 0.9406 (tttp) REVERT: B 861 MET cc_start: 0.8106 (tpt) cc_final: 0.7898 (tpp) REVERT: C 457 ASP cc_start: 0.8788 (t0) cc_final: 0.8537 (t0) REVERT: C 460 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: C 471 SER cc_start: 0.8779 (t) cc_final: 0.8451 (p) REVERT: C 593 HIS cc_start: 0.8746 (m90) cc_final: 0.8432 (m90) REVERT: C 603 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7251 (mm-30) REVERT: C 665 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8304 (tp30) REVERT: C 681 GLU cc_start: 0.8155 (pm20) cc_final: 0.7866 (pm20) REVERT: C 705 MET cc_start: 0.9595 (mtp) cc_final: 0.9315 (mtp) REVERT: C 709 MET cc_start: 0.9309 (mtp) cc_final: 0.9026 (mtp) REVERT: C 754 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8733 (tm-30) REVERT: D 441 GLU cc_start: 0.8570 (tp30) cc_final: 0.7937 (tp30) REVERT: D 528 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7327 (t70) REVERT: D 575 SER cc_start: 0.9219 (m) cc_final: 0.8835 (t) REVERT: D 588 GLU cc_start: 0.9422 (tp30) cc_final: 0.9114 (tp30) REVERT: D 590 TYR cc_start: 0.8682 (p90) cc_final: 0.8114 (p90) REVERT: D 602 VAL cc_start: 0.8584 (p) cc_final: 0.8313 (m) REVERT: D 603 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7631 (mm-30) REVERT: D 611 SER cc_start: 0.9539 (m) cc_final: 0.9293 (m) REVERT: D 668 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9208 (pp) REVERT: D 687 ASP cc_start: 0.8125 (m-30) cc_final: 0.7787 (m-30) REVERT: D 793 MET cc_start: 0.9092 (mmt) cc_final: 0.8856 (mmm) REVERT: D 797 LYS cc_start: 0.9641 (tttt) cc_final: 0.9366 (tttt) outliers start: 86 outliers final: 67 residues processed: 390 average time/residue: 0.1079 time to fit residues: 65.8009 Evaluate side-chains 410 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 336 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 819 ASN Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 584 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 858 CYS Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 56 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 chunk 105 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102938 restraints weight = 25610.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106679 restraints weight = 12114.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.109058 restraints weight = 8138.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110315 restraints weight = 6584.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111207 restraints weight = 5924.333| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15648 Z= 0.142 Angle : 0.923 32.431 21138 Z= 0.400 Chirality : 0.066 1.670 2338 Planarity : 0.005 0.091 2526 Dihedral : 16.945 178.183 3373 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.25 % Favored : 89.70 % Rotamer: Outliers : 5.04 % Allowed : 22.61 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: -0.78 (0.21), residues: 1776 helix: 1.29 (0.18), residues: 952 sheet: -2.71 (0.38), residues: 150 loop : -2.75 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 800 TYR 0.019 0.002 TYR B 590 PHE 0.018 0.001 PHE B 446 TRP 0.048 0.001 TRP B 589 HIS 0.004 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00324 (15625) covalent geometry : angle 0.89552 (21074) SS BOND : bond 0.00393 ( 5) SS BOND : angle 0.88601 ( 10) hydrogen bonds : bond 0.03498 ( 602) hydrogen bonds : angle 3.78255 ( 1764) link_BETA1-3 : bond 0.01176 ( 2) link_BETA1-3 : angle 1.54804 ( 6) link_BETA1-4 : bond 0.01650 ( 8) link_BETA1-4 : angle 4.60837 ( 24) link_NAG-ASN : bond 0.00872 ( 8) link_NAG-ASN : angle 4.96012 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 355 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: A 471 SER cc_start: 0.8753 (t) cc_final: 0.8484 (p) REVERT: A 665 GLU cc_start: 0.8733 (tp30) cc_final: 0.8522 (tm-30) REVERT: A 679 LYS cc_start: 0.8583 (tmtt) cc_final: 0.8289 (tmtt) REVERT: A 691 MET cc_start: 0.8699 (ptm) cc_final: 0.8365 (ptt) REVERT: A 705 MET cc_start: 0.9466 (mtp) cc_final: 0.9046 (mtp) REVERT: A 788 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: B 528 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7186 (t0) REVERT: B 588 GLU cc_start: 0.9427 (tp30) cc_final: 0.9224 (tp30) REVERT: B 620 MET cc_start: 0.9172 (mmm) cc_final: 0.8154 (mmm) REVERT: B 793 MET cc_start: 0.9060 (mmt) cc_final: 0.8844 (mmm) REVERT: B 797 LYS cc_start: 0.9646 (tttt) cc_final: 0.9410 (tttp) REVERT: B 861 MET cc_start: 0.8076 (tpt) cc_final: 0.7868 (tpp) REVERT: C 457 ASP cc_start: 0.8714 (t0) cc_final: 0.8473 (t0) REVERT: C 460 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: C 471 SER cc_start: 0.8838 (t) cc_final: 0.8441 (p) REVERT: C 593 HIS cc_start: 0.8703 (m90) cc_final: 0.8414 (m90) REVERT: C 603 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7227 (mm-30) REVERT: C 665 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8281 (tp30) REVERT: C 681 GLU cc_start: 0.8115 (pm20) cc_final: 0.7869 (pm20) REVERT: C 705 MET cc_start: 0.9556 (mtp) cc_final: 0.9328 (mtp) REVERT: C 709 MET cc_start: 0.9224 (mtp) cc_final: 0.8959 (mtp) REVERT: C 754 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8676 (tm-30) REVERT: C 864 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7475 (mt-10) REVERT: D 441 GLU cc_start: 0.8582 (tp30) cc_final: 0.7976 (tp30) REVERT: D 528 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7307 (t70) REVERT: D 575 SER cc_start: 0.9184 (m) cc_final: 0.8803 (t) REVERT: D 588 GLU cc_start: 0.9390 (tp30) cc_final: 0.9086 (tp30) REVERT: D 590 TYR cc_start: 0.8683 (p90) cc_final: 0.8047 (p90) REVERT: D 602 VAL cc_start: 0.8599 (p) cc_final: 0.8312 (m) REVERT: D 603 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 611 SER cc_start: 0.9562 (m) cc_final: 0.9323 (m) REVERT: D 793 MET cc_start: 0.9046 (mmt) cc_final: 0.8818 (mmm) REVERT: D 797 LYS cc_start: 0.9619 (tttt) cc_final: 0.9359 (tttt) REVERT: D 798 TRP cc_start: 0.9240 (m100) cc_final: 0.8868 (m100) outliers start: 78 outliers final: 57 residues processed: 394 average time/residue: 0.1123 time to fit residues: 69.4887 Evaluate side-chains 408 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 346 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 819 ASN Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 21 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 163 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 139 optimal weight: 0.0070 chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.103722 restraints weight = 25871.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.107622 restraints weight = 12047.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110071 restraints weight = 8023.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111514 restraints weight = 6478.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111836 restraints weight = 5783.820| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15648 Z= 0.139 Angle : 0.936 32.427 21138 Z= 0.407 Chirality : 0.066 1.680 2338 Planarity : 0.005 0.100 2526 Dihedral : 16.742 177.791 3373 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.25 % Favored : 89.70 % Rotamer: Outliers : 4.26 % Allowed : 23.90 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: -0.73 (0.21), residues: 1776 helix: 1.34 (0.18), residues: 950 sheet: -2.60 (0.39), residues: 150 loop : -2.77 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 866 TYR 0.022 0.001 TYR C 590 PHE 0.012 0.001 PHE D 476 TRP 0.036 0.001 TRP B 589 HIS 0.004 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00314 (15625) covalent geometry : angle 0.91001 (21074) SS BOND : bond 0.00266 ( 5) SS BOND : angle 1.03690 ( 10) hydrogen bonds : bond 0.03432 ( 602) hydrogen bonds : angle 3.76436 ( 1764) link_BETA1-3 : bond 0.01220 ( 2) link_BETA1-3 : angle 1.52911 ( 6) link_BETA1-4 : bond 0.01640 ( 8) link_BETA1-4 : angle 4.58032 ( 24) link_NAG-ASN : bond 0.00819 ( 8) link_NAG-ASN : angle 4.73973 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 363 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: A 471 SER cc_start: 0.8785 (t) cc_final: 0.8496 (p) REVERT: A 665 GLU cc_start: 0.8785 (tp30) cc_final: 0.8550 (tm-30) REVERT: A 691 MET cc_start: 0.8653 (ptm) cc_final: 0.8258 (ptt) REVERT: A 705 MET cc_start: 0.9495 (mtp) cc_final: 0.9072 (mtp) REVERT: A 788 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: B 441 GLU cc_start: 0.8358 (tp30) cc_final: 0.7883 (tp30) REVERT: B 504 GLU cc_start: 0.6816 (mp0) cc_final: 0.6578 (mp0) REVERT: B 528 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7254 (t70) REVERT: B 588 GLU cc_start: 0.9414 (tp30) cc_final: 0.9173 (tp30) REVERT: B 620 MET cc_start: 0.9202 (mmm) cc_final: 0.8181 (mmm) REVERT: B 658 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8902 (m-10) REVERT: B 793 MET cc_start: 0.9077 (mmt) cc_final: 0.8854 (mmm) REVERT: B 797 LYS cc_start: 0.9660 (tttt) cc_final: 0.9418 (tttp) REVERT: B 861 MET cc_start: 0.8046 (tpt) cc_final: 0.7840 (tpp) REVERT: C 457 ASP cc_start: 0.8790 (t0) cc_final: 0.8529 (t0) REVERT: C 460 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: C 471 SER cc_start: 0.8881 (t) cc_final: 0.8455 (p) REVERT: C 593 HIS cc_start: 0.8755 (m90) cc_final: 0.8469 (m90) REVERT: C 603 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7195 (mm-30) REVERT: C 681 GLU cc_start: 0.8188 (pm20) cc_final: 0.7920 (pm20) REVERT: C 705 MET cc_start: 0.9575 (mtp) cc_final: 0.9306 (mtp) REVERT: C 709 MET cc_start: 0.9280 (mtp) cc_final: 0.9010 (mtp) REVERT: C 754 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8581 (tm-30) REVERT: C 864 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7516 (mt-10) REVERT: D 441 GLU cc_start: 0.8529 (tp30) cc_final: 0.7922 (tp30) REVERT: D 528 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7244 (t70) REVERT: D 575 SER cc_start: 0.9173 (m) cc_final: 0.8789 (t) REVERT: D 588 GLU cc_start: 0.9393 (tp30) cc_final: 0.9117 (tp30) REVERT: D 602 VAL cc_start: 0.8586 (p) cc_final: 0.8273 (m) REVERT: D 603 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7647 (mm-30) REVERT: D 611 SER cc_start: 0.9542 (m) cc_final: 0.9308 (m) REVERT: D 687 ASP cc_start: 0.8014 (m-30) cc_final: 0.7768 (m-30) REVERT: D 793 MET cc_start: 0.9081 (mmt) cc_final: 0.8852 (mmm) REVERT: D 797 LYS cc_start: 0.9636 (tttt) cc_final: 0.9380 (tttt) REVERT: D 798 TRP cc_start: 0.9267 (m100) cc_final: 0.8904 (m100) outliers start: 66 outliers final: 56 residues processed: 397 average time/residue: 0.1096 time to fit residues: 67.7428 Evaluate side-chains 409 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 347 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 819 ASN Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 90 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.136372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099329 restraints weight = 25915.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.103018 restraints weight = 12326.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105354 restraints weight = 8343.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106730 restraints weight = 6782.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107385 restraints weight = 6074.093| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15648 Z= 0.235 Angle : 0.988 32.375 21138 Z= 0.437 Chirality : 0.068 1.671 2338 Planarity : 0.005 0.101 2526 Dihedral : 16.662 175.770 3373 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.26 % Favored : 88.68 % Rotamer: Outliers : 4.26 % Allowed : 24.61 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: -0.79 (0.21), residues: 1776 helix: 1.31 (0.18), residues: 948 sheet: -2.77 (0.40), residues: 140 loop : -2.77 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 800 TYR 0.020 0.002 TYR D 590 PHE 0.013 0.002 PHE B 529 TRP 0.040 0.002 TRP B 589 HIS 0.003 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00548 (15625) covalent geometry : angle 0.96244 (21074) SS BOND : bond 0.00359 ( 5) SS BOND : angle 1.01147 ( 10) hydrogen bonds : bond 0.03820 ( 602) hydrogen bonds : angle 4.02422 ( 1764) link_BETA1-3 : bond 0.01053 ( 2) link_BETA1-3 : angle 1.52690 ( 6) link_BETA1-4 : bond 0.01521 ( 8) link_BETA1-4 : angle 4.67354 ( 24) link_NAG-ASN : bond 0.00714 ( 8) link_NAG-ASN : angle 4.83017 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3288.22 seconds wall clock time: 57 minutes 32.96 seconds (3452.96 seconds total)