Starting phenix.real_space_refine on Wed Jul 30 02:28:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmk_38480/07_2025/8xmk_38480.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmk_38480/07_2025/8xmk_38480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmk_38480/07_2025/8xmk_38480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmk_38480/07_2025/8xmk_38480.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmk_38480/07_2025/8xmk_38480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmk_38480/07_2025/8xmk_38480.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 17 9.91 5 S 132 5.16 5 C 7232 2.51 5 N 2136 2.21 5 O 2298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11815 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 3933 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 21, 'TRANS': 500} Chain breaks: 3 Chain: "E" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3847 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 20, 'TRANS': 488} Chain breaks: 5 Chain: "F" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 3934 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 21, 'TRANS': 500} Chain breaks: 3 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 34 Unusual residues: {' CA': 6, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 33 Unusual residues: {' CA': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 34 Unusual residues: {' CA': 6, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.57, per 1000 atoms: 0.64 Number of scatterers: 11815 At special positions: 0 Unit cell: (136.96, 135.89, 101.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 17 19.99 S 132 16.00 O 2298 8.00 N 2136 7.00 C 7232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS D 487 " - pdb=" SG CYS D 521 " distance=2.03 Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 567 " distance=2.03 Simple disulfide: pdb=" SG CYS D 516 " - pdb=" SG CYS D 577 " distance=2.03 Simple disulfide: pdb=" SG CYS D 547 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS D 592 " - pdb=" SG CYS D 626 " distance=2.03 Simple disulfide: pdb=" SG CYS D 608 " - pdb=" SG CYS D 672 " distance=2.03 Simple disulfide: pdb=" SG CYS D 621 " - pdb=" SG CYS D 682 " distance=2.03 Simple disulfide: pdb=" SG CYS D 652 " - pdb=" SG CYS D 662 " distance=2.03 Simple disulfide: pdb=" SG CYS D 728 " - pdb=" SG CYS D 762 " distance=2.03 Simple disulfide: pdb=" SG CYS D 744 " - pdb=" SG CYS D 808 " distance=2.03 Simple disulfide: pdb=" SG CYS D 757 " - pdb=" SG CYS D 818 " distance=2.03 Simple disulfide: pdb=" SG CYS D 788 " - pdb=" SG CYS D 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 835 " - pdb=" SG CYS D 869 " distance=2.03 Simple disulfide: pdb=" SG CYS D 864 " - pdb=" SG CYS D 925 " distance=2.03 Simple disulfide: pdb=" SG CYS D 895 " - pdb=" SG CYS D 905 " distance=2.03 Simple disulfide: pdb=" SG CYS D 938 " - pdb=" SG CYS D 972 " distance=2.03 Simple disulfide: pdb=" SG CYS D 954 " - pdb=" SG CYS D1018 " distance=2.03 Simple disulfide: pdb=" SG CYS D 967 " - pdb=" SG CYS D1028 " distance=2.03 Simple disulfide: pdb=" SG CYS D 998 " - pdb=" SG CYS D1008 " distance=2.03 Simple disulfide: pdb=" SG CYS E 487 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 503 " - pdb=" SG CYS E 567 " distance=2.03 Simple disulfide: pdb=" SG CYS E 516 " - pdb=" SG CYS E 577 " distance=2.03 Simple disulfide: pdb=" SG CYS E 547 " - pdb=" SG CYS E 557 " distance=2.03 Simple disulfide: pdb=" SG CYS E 592 " - pdb=" SG CYS E 626 " distance=2.03 Simple disulfide: pdb=" SG CYS E 608 " - pdb=" SG CYS E 672 " distance=2.03 Simple disulfide: pdb=" SG CYS E 621 " - pdb=" SG CYS E 682 " distance=2.03 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 662 " distance=2.02 Simple disulfide: pdb=" SG CYS E 728 " - pdb=" SG CYS E 762 " distance=2.03 Simple disulfide: pdb=" SG CYS E 744 " - pdb=" SG CYS E 808 " distance=2.02 Simple disulfide: pdb=" SG CYS E 757 " - pdb=" SG CYS E 818 " distance=2.03 Simple disulfide: pdb=" SG CYS E 788 " - pdb=" SG CYS E 798 " distance=2.03 Simple disulfide: pdb=" SG CYS E 835 " - pdb=" SG CYS E 869 " distance=2.03 Simple disulfide: pdb=" SG CYS E 864 " - pdb=" SG CYS E 925 " distance=2.03 Simple disulfide: pdb=" SG CYS E 895 " - pdb=" SG CYS E 905 " distance=2.03 Simple disulfide: pdb=" SG CYS E 938 " - pdb=" SG CYS E 972 " distance=2.03 Simple disulfide: pdb=" SG CYS E 954 " - pdb=" SG CYS E1018 " distance=2.03 Simple disulfide: pdb=" SG CYS E 967 " - pdb=" SG CYS E1028 " distance=2.03 Simple disulfide: pdb=" SG CYS E 998 " - pdb=" SG CYS E1008 " distance=2.03 Simple disulfide: pdb=" SG CYS F 487 " - pdb=" SG CYS F 521 " distance=2.03 Simple disulfide: pdb=" SG CYS F 503 " - pdb=" SG CYS F 567 " distance=2.03 Simple disulfide: pdb=" SG CYS F 516 " - pdb=" SG CYS F 577 " distance=2.03 Simple disulfide: pdb=" SG CYS F 547 " - pdb=" SG CYS F 557 " distance=2.03 Simple disulfide: pdb=" SG CYS F 592 " - pdb=" SG CYS F 626 " distance=2.03 Simple disulfide: pdb=" SG CYS F 608 " - pdb=" SG CYS F 672 " distance=2.03 Simple disulfide: pdb=" SG CYS F 621 " - pdb=" SG CYS F 682 " distance=2.03 Simple disulfide: pdb=" SG CYS F 652 " - pdb=" SG CYS F 662 " distance=2.03 Simple disulfide: pdb=" SG CYS F 728 " - pdb=" SG CYS F 762 " distance=2.03 Simple disulfide: pdb=" SG CYS F 744 " - pdb=" SG CYS F 808 " distance=2.03 Simple disulfide: pdb=" SG CYS F 757 " - pdb=" SG CYS F 818 " distance=2.03 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 798 " distance=2.03 Simple disulfide: pdb=" SG CYS F 835 " - pdb=" SG CYS F 869 " distance=2.03 Simple disulfide: pdb=" SG CYS F 864 " - pdb=" SG CYS F 925 " distance=2.03 Simple disulfide: pdb=" SG CYS F 895 " - pdb=" SG CYS F 905 " distance=2.03 Simple disulfide: pdb=" SG CYS F 938 " - pdb=" SG CYS F 972 " distance=2.03 Simple disulfide: pdb=" SG CYS F 954 " - pdb=" SG CYS F1018 " distance=2.03 Simple disulfide: pdb=" SG CYS F 967 " - pdb=" SG CYS F1028 " distance=2.03 Simple disulfide: pdb=" SG CYS F 998 " - pdb=" SG CYS F1008 " 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 NAG-ASN " NAG D1101 " - " ASN D 767 " " NAG D1102 " - " ASN D1027 " " NAG E1101 " - " ASN E 767 " " NAG E1102 " - " ASN E1027 " " NAG F1101 " - " ASN F 767 " " NAG F1102 " - " ASN F1027 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.6 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2726 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 35 sheets defined 18.5% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 568 through 572 Processing helix chain 'D' and resid 613 through 624 removed outlier: 3.527A pdb=" N ALA D 617 " --> pdb=" O ASP D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 662 Processing helix chain 'D' and resid 749 through 760 removed outlier: 3.807A pdb=" N VAL D 755 " --> pdb=" O SER D 751 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL D 756 " --> pdb=" O ASP D 752 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 760 " --> pdb=" O VAL D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 813 Processing helix chain 'D' and resid 856 through 867 Processing helix chain 'D' and resid 901 through 905 removed outlier: 3.722A pdb=" N GLN D 904 " --> pdb=" O THR D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 971 Processing helix chain 'D' and resid 1019 through 1023 removed outlier: 3.615A pdb=" N ASP D1023 " --> pdb=" O HIS D1020 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 477 removed outlier: 3.633A pdb=" N ARG E 476 " --> pdb=" O SER E 473 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU E 477 " --> pdb=" O ALA E 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 473 through 477' Processing helix chain 'E' and resid 503 through 507 removed outlier: 4.082A pdb=" N PHE E 507 " --> pdb=" O ASP E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 519 Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 613 through 624 Processing helix chain 'E' and resid 749 through 760 Processing helix chain 'E' and resid 794 through 798 Processing helix chain 'E' and resid 809 through 813 removed outlier: 3.816A pdb=" N GLU E 812 " --> pdb=" O ARG E 809 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP E 813 " --> pdb=" O HIS E 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 809 through 813' Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 901 through 905 removed outlier: 3.549A pdb=" N GLN E 904 " --> pdb=" O THR E 901 " (cutoff:3.500A) Processing helix chain 'E' and resid 959 through 971 Processing helix chain 'E' and resid 1004 through 1008 Processing helix chain 'E' and resid 1019 through 1023 removed outlier: 3.560A pdb=" N ASP E1023 " --> pdb=" O HIS E1020 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 507 removed outlier: 3.992A pdb=" N PHE F 507 " --> pdb=" O ASP F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 504 through 507' Processing helix chain 'F' and resid 508 through 519 Processing helix chain 'F' and resid 553 through 557 Processing helix chain 'F' and resid 568 through 572 Processing helix chain 'F' and resid 613 through 624 Processing helix chain 'F' and resid 749 through 760 Processing helix chain 'F' and resid 809 through 813 removed outlier: 3.671A pdb=" N GLU F 812 " --> pdb=" O ARG F 809 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP F 813 " --> pdb=" O HIS F 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 809 through 813' Processing helix chain 'F' and resid 856 through 867 Processing helix chain 'F' and resid 901 through 905 removed outlier: 3.717A pdb=" N GLN F 904 " --> pdb=" O THR F 901 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 920 removed outlier: 3.606A pdb=" N GLU F 920 " --> pdb=" O PRO F 917 " (cutoff:3.500A) Processing helix chain 'F' and resid 959 through 971 removed outlier: 3.574A pdb=" N ALA F 963 " --> pdb=" O ASP F 959 " (cutoff:3.500A) Processing helix chain 'F' and resid 1019 through 1023 removed outlier: 3.589A pdb=" N GLU F1022 " --> pdb=" O GLY F1019 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP F1023 " --> pdb=" O HIS F1020 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1019 through 1023' Processing sheet with id=AA1, first strand: chain 'D' and resid 476 through 481 removed outlier: 6.242A pdb=" N GLY D 574 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE D 527 " --> pdb=" O GLY D 574 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL D 576 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 476 through 481 removed outlier: 6.298A pdb=" N VAL D 491 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE D 502 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY D 500 " --> pdb=" O VAL D 493 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR D 498 " --> pdb=" O HIS D 495 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TRP D 499 " --> pdb=" O GLN D 539 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N TRP D 541 " --> pdb=" O TRP D 499 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N SER D 501 " --> pdb=" O TRP D 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 543 through 545 removed outlier: 3.587A pdb=" N GLU D 544 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 583 through 586 removed outlier: 3.567A pdb=" N THR D 600 " --> pdb=" O ALA D 603 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 583 through 586 removed outlier: 7.151A pdb=" N ILE D 681 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 649 through 650 Processing sheet with id=AA7, first strand: chain 'D' and resid 719 through 726 removed outlier: 3.559A pdb=" N GLY D 724 " --> pdb=" O ALA D 729 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ALA D 729 " --> pdb=" O GLY D 724 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 719 through 726 removed outlier: 3.559A pdb=" N GLY D 724 " --> pdb=" O ALA D 729 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ALA D 729 " --> pdb=" O GLY D 724 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 815 " --> pdb=" O THR D 769 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 823 through 827 removed outlier: 4.197A pdb=" N TRP D 922 " --> pdb=" O ASN D 876 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 823 through 827 removed outlier: 6.242A pdb=" N LEU D 839 " --> pdb=" O VAL D 850 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP D 889 " --> pdb=" O TRP D 847 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR D 849 " --> pdb=" O TRP D 889 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 929 through 932 removed outlier: 6.258A pdb=" N VAL D 942 " --> pdb=" O VAL D 953 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 953 " --> pdb=" O VAL D 942 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N TRP D 992 " --> pdb=" O TRP D 950 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR D 952 " --> pdb=" O TRP D 992 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 929 through 932 Processing sheet with id=AB4, first strand: chain 'E' and resid 480 through 481 removed outlier: 3.780A pdb=" N THR E 498 " --> pdb=" O HIS E 495 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 480 through 481 Processing sheet with id=AB6, first strand: chain 'E' and resid 583 through 586 removed outlier: 3.620A pdb=" N THR E 600 " --> pdb=" O ALA E 603 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 583 through 586 removed outlier: 6.932A pdb=" N ILE E 681 " --> pdb=" O LEU E 630 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 649 through 650 Processing sheet with id=AB9, first strand: chain 'E' and resid 719 through 722 Processing sheet with id=AC1, first strand: chain 'E' and resid 719 through 722 removed outlier: 5.990A pdb=" N GLY E 815 " --> pdb=" O ALA E 768 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA E 768 " --> pdb=" O GLY E 815 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE E 817 " --> pdb=" O ILE E 766 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 823 through 827 removed outlier: 3.919A pdb=" N TRP E 922 " --> pdb=" O ASN E 876 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 823 through 827 removed outlier: 6.378A pdb=" N LEU E 839 " --> pdb=" O VAL E 850 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 850 " --> pdb=" O LEU E 839 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP E 889 " --> pdb=" O TRP E 847 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR E 849 " --> pdb=" O TRP E 889 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 930 through 932 removed outlier: 6.224A pdb=" N ALA E1025 " --> pdb=" O ALA E 978 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ALA E 978 " --> pdb=" O ALA E1025 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN E1027 " --> pdb=" O LEU E 976 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 930 through 932 removed outlier: 6.052A pdb=" N VAL E 942 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 953 " --> pdb=" O VAL E 942 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N TRP E 992 " --> pdb=" O TRP E 950 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR E 952 " --> pdb=" O TRP E 992 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 476 through 481 Processing sheet with id=AC7, first strand: chain 'F' and resid 476 through 481 removed outlier: 6.261A pdb=" N VAL F 491 " --> pdb=" O ILE F 502 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE F 502 " --> pdb=" O VAL F 491 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR F 498 " --> pdb=" O HIS F 495 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TRP F 541 " --> pdb=" O TRP F 499 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N SER F 501 " --> pdb=" O TRP F 541 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 543 through 545 Processing sheet with id=AC9, first strand: chain 'F' and resid 583 through 586 removed outlier: 6.737A pdb=" N ILE F 681 " --> pdb=" O LEU F 630 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 583 through 586 removed outlier: 6.334A pdb=" N VAL F 596 " --> pdb=" O LEU F 607 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TRP F 646 " --> pdb=" O TRP F 604 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER F 606 " --> pdb=" O TRP F 646 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 649 through 650 Processing sheet with id=AD3, first strand: chain 'F' and resid 719 through 722 Processing sheet with id=AD4, first strand: chain 'F' and resid 719 through 722 removed outlier: 5.926A pdb=" N GLY F 815 " --> pdb=" O ALA F 768 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA F 768 " --> pdb=" O GLY F 815 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE F 817 " --> pdb=" O ILE F 766 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 823 through 827 removed outlier: 3.785A pdb=" N TRP F 922 " --> pdb=" O ASN F 876 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 823 through 827 removed outlier: 6.469A pdb=" N LEU F 839 " --> pdb=" O VAL F 850 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP F 889 " --> pdb=" O TRP F 847 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR F 849 " --> pdb=" O TRP F 889 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 929 through 932 Processing sheet with id=AD8, first strand: chain 'F' and resid 929 through 932 removed outlier: 6.220A pdb=" N VAL F 942 " --> pdb=" O VAL F 953 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL F 953 " --> pdb=" O VAL F 942 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N TRP F 950 " --> pdb=" O ILE F 991 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N LEU F 993 " --> pdb=" O TRP F 950 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR F 952 " --> pdb=" O LEU F 993 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4053 1.35 - 1.47: 2880 1.47 - 1.59: 4987 1.59 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 12070 Sorted by residual: bond pdb=" N ASN D 807 " pdb=" CA ASN D 807 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.75e+00 bond pdb=" N ASP D 745 " pdb=" CA ASP D 745 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.33e+00 bond pdb=" N CYS D 744 " pdb=" CA CYS D 744 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.35e-02 5.49e+03 4.19e+00 bond pdb=" N LYS F 811 " pdb=" CA LYS F 811 " ideal model delta sigma weight residual 1.456 1.481 -0.024 1.31e-02 5.83e+03 3.38e+00 bond pdb=" C1 NAG D1102 " pdb=" O5 NAG D1102 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 12065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 16099 1.77 - 3.54: 240 3.54 - 5.31: 11 5.31 - 7.08: 0 7.08 - 8.85: 1 Bond angle restraints: 16351 Sorted by residual: angle pdb=" N LYS F 811 " pdb=" CA LYS F 811 " pdb=" C LYS F 811 " ideal model delta sigma weight residual 113.18 109.56 3.62 1.21e+00 6.83e-01 8.95e+00 angle pdb=" N GLY E 851 " pdb=" CA GLY E 851 " pdb=" C GLY E 851 " ideal model delta sigma weight residual 111.36 114.77 -3.41 1.17e+00 7.31e-01 8.47e+00 angle pdb=" CA ASN D 807 " pdb=" C ASN D 807 " pdb=" O ASN D 807 " ideal model delta sigma weight residual 120.51 116.64 3.87 1.43e+00 4.89e-01 7.31e+00 angle pdb=" C LYS F 811 " pdb=" CA LYS F 811 " pdb=" CB LYS F 811 " ideal model delta sigma weight residual 109.95 105.05 4.90 1.99e+00 2.53e-01 6.07e+00 angle pdb=" N GLY D 643 " pdb=" CA GLY D 643 " pdb=" C GLY D 643 " ideal model delta sigma weight residual 110.43 113.75 -3.32 1.35e+00 5.49e-01 6.06e+00 ... (remaining 16346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 6527 17.77 - 35.55: 600 35.55 - 53.32: 112 53.32 - 71.10: 19 71.10 - 88.87: 13 Dihedral angle restraints: 7271 sinusoidal: 2997 harmonic: 4274 Sorted by residual: dihedral pdb=" CB CYS D 503 " pdb=" SG CYS D 503 " pdb=" SG CYS D 567 " pdb=" CB CYS D 567 " ideal model delta sinusoidal sigma weight residual 93.00 139.90 -46.90 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CB CYS E 503 " pdb=" SG CYS E 503 " pdb=" SG CYS E 567 " pdb=" CB CYS E 567 " ideal model delta sinusoidal sigma weight residual 93.00 47.98 45.02 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" CB CYS F 503 " pdb=" SG CYS F 503 " pdb=" SG CYS F 567 " pdb=" CB CYS F 567 " ideal model delta sinusoidal sigma weight residual 93.00 48.47 44.53 1 1.00e+01 1.00e-02 2.76e+01 ... (remaining 7268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1348 0.050 - 0.099: 319 0.099 - 0.149: 64 0.149 - 0.199: 2 0.199 - 0.249: 1 Chirality restraints: 1734 Sorted by residual: chirality pdb=" CA LYS F 811 " pdb=" N LYS F 811 " pdb=" C LYS F 811 " pdb=" CB LYS F 811 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB THR F 566 " pdb=" CA THR F 566 " pdb=" OG1 THR F 566 " pdb=" CG2 THR F 566 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA PRO F 591 " pdb=" N PRO F 591 " pdb=" C PRO F 591 " pdb=" CB PRO F 591 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 1731 not shown) Planarity restraints: 2152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 903 " 0.020 2.00e-02 2.50e+03 2.38e-02 1.42e+01 pdb=" CG TRP F 903 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP F 903 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP F 903 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 903 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP F 903 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 903 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 903 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 903 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 903 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS F 810 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C HIS F 810 " 0.036 2.00e-02 2.50e+03 pdb=" O HIS F 810 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS F 811 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 898 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO F 899 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO F 899 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 899 " -0.028 5.00e-02 4.00e+02 ... (remaining 2149 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 804 2.73 - 3.27: 11689 3.27 - 3.81: 20824 3.81 - 4.36: 25400 4.36 - 4.90: 43104 Nonbonded interactions: 101821 Sorted by model distance: nonbonded pdb=" OD2 ASP D 616 " pdb="CA CA D1104 " model vdw 2.186 2.510 nonbonded pdb=" O GLY E 779 " pdb=" NE2 HIS E 810 " model vdw 2.198 3.120 nonbonded pdb=" OD1 ASP E 749 " pdb="CA CA E1106 " model vdw 2.199 2.510 nonbonded pdb=" OD2 ASP F 616 " pdb="CA CA F1103 " model vdw 2.207 2.510 nonbonded pdb=" O GLY F 779 " pdb=" NE2 HIS F 810 " model vdw 2.208 3.120 ... (remaining 101816 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 'D' and (resid 473 through 562 or resid 567 through 634 or resid 644 thro \ ugh 828 or resid 835 through 1030 or resid 1101 through 1107)) selection = (chain 'E' and (resid 473 through 691 or resid 718 through 1030 or resid 1101 th \ rough 1107)) selection = (chain 'F' and (resid 473 through 562 or resid 567 through 634 or resid 644 thro \ ugh 691 or resid 718 through 1030 or resid 1101 through 1107)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.160 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.004 0.040 12133 Z= 0.173 Angle : 0.535 8.854 16483 Z= 0.297 Chirality : 0.044 0.249 1734 Planarity : 0.004 0.049 2146 Dihedral : 13.979 88.873 4374 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.16 % Allowed : 0.31 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1525 helix: 1.53 (0.39), residues: 190 sheet: -0.83 (0.39), residues: 185 loop : -0.83 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP F 903 HIS 0.008 0.001 HIS F 495 PHE 0.009 0.001 PHE F 507 TYR 0.007 0.002 TYR F 580 ARG 0.003 0.000 ARG F 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 6) link_NAG-ASN : angle 1.31280 ( 18) hydrogen bonds : bond 0.23735 ( 338) hydrogen bonds : angle 7.99963 ( 1062) SS BOND : bond 0.00307 ( 57) SS BOND : angle 1.05532 ( 114) covalent geometry : bond 0.00382 (12070) covalent geometry : angle 0.52775 (16351) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: D 764 GLU cc_start: 0.6970 (pp20) cc_final: 0.6709 (pt0) REVERT: E 495 HIS cc_start: 0.7922 (m90) cc_final: 0.6566 (m90) REVERT: E 649 MET cc_start: 0.8869 (mtm) cc_final: 0.8629 (mtp) REVERT: E 735 TYR cc_start: 0.8968 (t80) cc_final: 0.8714 (t80) REVERT: E 820 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8089 (mt-10) REVERT: E 822 MET cc_start: 0.8953 (mtm) cc_final: 0.8692 (mtm) REVERT: E 874 LYS cc_start: 0.8111 (tttt) cc_final: 0.7790 (mptt) REVERT: E 914 LEU cc_start: 0.8325 (mm) cc_final: 0.8078 (pp) REVERT: E 1023 ASP cc_start: 0.6822 (m-30) cc_final: 0.6607 (m-30) REVERT: F 640 LYS cc_start: 0.7300 (mttp) cc_final: 0.7000 (ptmm) REVERT: F 649 MET cc_start: 0.9104 (mtm) cc_final: 0.8849 (mtm) REVERT: F 685 ASN cc_start: 0.6785 (t0) cc_final: 0.6473 (m-40) REVERT: F 811 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8393 (pttt) REVERT: F 888 MET cc_start: 0.8960 (ttm) cc_final: 0.8739 (ttm) REVERT: F 1018 CYS cc_start: 0.7832 (m) cc_final: 0.7613 (m) outliers start: 2 outliers final: 0 residues processed: 233 average time/residue: 0.2426 time to fit residues: 80.9984 Evaluate side-chains 146 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 811 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.0970 chunk 116 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 810 HIS E 676 GLN E 688 GLN E 927 ASN F 789 ASN F 797 GLN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.176696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145501 restraints weight = 13704.292| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.84 r_work: 0.3458 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12133 Z= 0.144 Angle : 0.534 11.048 16483 Z= 0.286 Chirality : 0.044 0.179 1734 Planarity : 0.004 0.048 2146 Dihedral : 5.047 36.515 1752 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.26 % Allowed : 8.11 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1525 helix: 1.84 (0.39), residues: 193 sheet: -0.80 (0.38), residues: 177 loop : -0.85 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 903 HIS 0.011 0.001 HIS F 495 PHE 0.012 0.001 PHE E 979 TYR 0.006 0.001 TYR F 580 ARG 0.006 0.001 ARG E 941 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 6) link_NAG-ASN : angle 1.66824 ( 18) hydrogen bonds : bond 0.04085 ( 338) hydrogen bonds : angle 5.03476 ( 1062) SS BOND : bond 0.00342 ( 57) SS BOND : angle 0.89763 ( 114) covalent geometry : bond 0.00338 (12070) covalent geometry : angle 0.52839 (16351) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: D 764 GLU cc_start: 0.7054 (pp20) cc_final: 0.6799 (pt0) REVERT: D 805 GLN cc_start: 0.6493 (mm110) cc_final: 0.5507 (pp30) REVERT: D 810 HIS cc_start: 0.7319 (m90) cc_final: 0.6917 (m-70) REVERT: E 649 MET cc_start: 0.8883 (mtm) cc_final: 0.8601 (mtp) REVERT: E 735 TYR cc_start: 0.9014 (t80) cc_final: 0.8724 (t80) REVERT: E 820 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8189 (mt-10) REVERT: E 874 LYS cc_start: 0.8349 (tttt) cc_final: 0.7974 (ttpt) REVERT: E 914 LEU cc_start: 0.8430 (mm) cc_final: 0.7926 (pp) REVERT: E 986 GLN cc_start: 0.6679 (tp40) cc_final: 0.6470 (tp40) REVERT: E 1023 ASP cc_start: 0.7022 (m-30) cc_final: 0.6754 (m-30) REVERT: F 541 TRP cc_start: 0.8955 (m100) cc_final: 0.8735 (m100) REVERT: F 543 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8124 (mt-10) REVERT: F 597 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8115 (mt-10) REVERT: F 640 LYS cc_start: 0.7487 (mttp) cc_final: 0.7016 (ptmm) REVERT: F 649 MET cc_start: 0.9044 (mtm) cc_final: 0.8799 (mtp) REVERT: F 685 ASN cc_start: 0.7009 (t0) cc_final: 0.6673 (m-40) REVERT: F 758 ARG cc_start: 0.8206 (ptp-110) cc_final: 0.7992 (ptp90) REVERT: F 874 LYS cc_start: 0.8463 (pttm) cc_final: 0.7992 (mttm) outliers start: 16 outliers final: 11 residues processed: 186 average time/residue: 0.2458 time to fit residues: 64.8009 Evaluate side-chains 138 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 988 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 14 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 986 GLN F 686 GLN F 810 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.173484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139353 restraints weight = 13910.512| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.97 r_work: 0.3357 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12133 Z= 0.164 Angle : 0.530 11.849 16483 Z= 0.280 Chirality : 0.044 0.256 1734 Planarity : 0.004 0.049 2146 Dihedral : 4.866 29.225 1748 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.20 % Allowed : 9.84 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1525 helix: 1.83 (0.39), residues: 193 sheet: -0.89 (0.37), residues: 177 loop : -0.86 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 910 HIS 0.009 0.001 HIS F 495 PHE 0.009 0.001 PHE E 979 TYR 0.007 0.001 TYR F 580 ARG 0.006 0.000 ARG D 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 6) link_NAG-ASN : angle 2.19760 ( 18) hydrogen bonds : bond 0.03803 ( 338) hydrogen bonds : angle 4.72189 ( 1062) SS BOND : bond 0.00372 ( 57) SS BOND : angle 0.95761 ( 114) covalent geometry : bond 0.00388 (12070) covalent geometry : angle 0.52113 (16351) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: D 810 HIS cc_start: 0.7255 (m90) cc_final: 0.6655 (m-70) REVERT: E 571 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7716 (mmm-85) REVERT: E 649 MET cc_start: 0.8924 (mtm) cc_final: 0.8623 (mtp) REVERT: E 671 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8526 (mm) REVERT: E 735 TYR cc_start: 0.9051 (t80) cc_final: 0.8828 (t80) REVERT: E 820 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8240 (mt-10) REVERT: E 914 LEU cc_start: 0.8408 (mm) cc_final: 0.7902 (pp) REVERT: E 986 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6476 (tp40) REVERT: E 1023 ASP cc_start: 0.6823 (m-30) cc_final: 0.6586 (m-30) REVERT: F 541 TRP cc_start: 0.9065 (m100) cc_final: 0.8814 (m100) REVERT: F 543 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8312 (mt-10) REVERT: F 640 LYS cc_start: 0.7439 (mttp) cc_final: 0.6973 (ptmm) REVERT: F 685 ASN cc_start: 0.7145 (t0) cc_final: 0.6710 (m-40) REVERT: F 758 ARG cc_start: 0.8294 (ptp-110) cc_final: 0.8061 (ptp90) REVERT: F 874 LYS cc_start: 0.8504 (pttm) cc_final: 0.8086 (mttm) REVERT: F 1011 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7455 (mtm110) outliers start: 28 outliers final: 17 residues processed: 166 average time/residue: 0.2525 time to fit residues: 60.8416 Evaluate side-chains 147 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 986 GLN Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 822 MET Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 996 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 128 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 810 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.169146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136743 restraints weight = 13736.240| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.93 r_work: 0.3389 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12133 Z= 0.263 Angle : 0.603 11.484 16483 Z= 0.319 Chirality : 0.047 0.233 1734 Planarity : 0.004 0.052 2146 Dihedral : 5.293 31.724 1748 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.99 % Allowed : 10.47 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1525 helix: 1.56 (0.38), residues: 193 sheet: -1.23 (0.36), residues: 169 loop : -0.98 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 910 HIS 0.009 0.001 HIS F 495 PHE 0.016 0.002 PHE E 984 TYR 0.009 0.002 TYR F 580 ARG 0.005 0.001 ARG D 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 6) link_NAG-ASN : angle 2.67846 ( 18) hydrogen bonds : bond 0.04072 ( 338) hydrogen bonds : angle 4.88171 ( 1062) SS BOND : bond 0.00575 ( 57) SS BOND : angle 1.17649 ( 114) covalent geometry : bond 0.00627 (12070) covalent geometry : angle 0.59044 (16351) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8577 (m) cc_final: 0.8149 (p) REVERT: D 675 GLU cc_start: 0.7443 (mp0) cc_final: 0.6979 (pp20) REVERT: D 810 HIS cc_start: 0.7196 (m90) cc_final: 0.6704 (m-70) REVERT: E 571 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7799 (mmm-85) REVERT: E 649 MET cc_start: 0.8915 (mtm) cc_final: 0.8580 (mtp) REVERT: E 671 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8515 (mm) REVERT: E 735 TYR cc_start: 0.9018 (t80) cc_final: 0.8807 (t80) REVERT: E 820 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8292 (mt-10) REVERT: E 874 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7967 (ttpt) REVERT: E 914 LEU cc_start: 0.8463 (mm) cc_final: 0.7957 (pp) REVERT: E 1023 ASP cc_start: 0.7009 (m-30) cc_final: 0.6759 (m-30) REVERT: F 543 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8227 (mt-10) REVERT: F 649 MET cc_start: 0.9119 (mtm) cc_final: 0.8833 (mtt) REVERT: F 685 ASN cc_start: 0.7222 (t0) cc_final: 0.6786 (m-40) REVERT: F 789 ASN cc_start: 0.8398 (t160) cc_final: 0.8108 (p0) REVERT: F 874 LYS cc_start: 0.8635 (pttm) cc_final: 0.8162 (mttm) REVERT: F 914 LEU cc_start: 0.8684 (mm) cc_final: 0.8420 (mt) outliers start: 38 outliers final: 25 residues processed: 164 average time/residue: 0.2400 time to fit residues: 57.6339 Evaluate side-chains 155 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 886 ILE Chi-restraints excluded: chain D residue 889 TRP Chi-restraints excluded: chain D residue 921 THR Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 752 ASP Chi-restraints excluded: chain E residue 874 LYS Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 996 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 115 optimal weight: 0.9990 chunk 60 optimal weight: 0.0570 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 546 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.171927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139753 restraints weight = 13759.716| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.84 r_work: 0.3345 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12133 Z= 0.141 Angle : 0.516 9.776 16483 Z= 0.274 Chirality : 0.043 0.198 1734 Planarity : 0.004 0.051 2146 Dihedral : 4.798 27.862 1748 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.76 % Allowed : 12.28 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.20), residues: 1525 helix: 1.85 (0.39), residues: 193 sheet: -1.00 (0.36), residues: 170 loop : -0.90 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 910 HIS 0.005 0.001 HIS F 495 PHE 0.017 0.001 PHE D 638 TYR 0.006 0.001 TYR F 580 ARG 0.004 0.000 ARG D 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 6) link_NAG-ASN : angle 2.30333 ( 18) hydrogen bonds : bond 0.03431 ( 338) hydrogen bonds : angle 4.51057 ( 1062) SS BOND : bond 0.00335 ( 57) SS BOND : angle 0.90268 ( 114) covalent geometry : bond 0.00333 (12070) covalent geometry : angle 0.50660 (16351) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 638 PHE cc_start: 0.7358 (m-10) cc_final: 0.7057 (m-10) REVERT: D 675 GLU cc_start: 0.7342 (mp0) cc_final: 0.6841 (pp20) REVERT: D 810 HIS cc_start: 0.6986 (m90) cc_final: 0.6715 (m-70) REVERT: E 571 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7784 (mmm-85) REVERT: E 649 MET cc_start: 0.8834 (mtm) cc_final: 0.8546 (mtp) REVERT: E 681 ILE cc_start: 0.7735 (mm) cc_final: 0.7508 (mm) REVERT: E 820 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8221 (mt-10) REVERT: E 874 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7779 (ttpt) REVERT: E 914 LEU cc_start: 0.8427 (mm) cc_final: 0.7872 (pp) REVERT: E 1023 ASP cc_start: 0.6809 (m-30) cc_final: 0.6571 (m-30) REVERT: F 543 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8311 (mt-10) REVERT: F 649 MET cc_start: 0.9133 (mtm) cc_final: 0.8826 (mtt) REVERT: F 685 ASN cc_start: 0.7109 (t0) cc_final: 0.6657 (m-40) REVERT: F 789 ASN cc_start: 0.8418 (t160) cc_final: 0.8161 (p0) REVERT: F 874 LYS cc_start: 0.8472 (pttm) cc_final: 0.8012 (mttm) REVERT: F 914 LEU cc_start: 0.8637 (mm) cc_final: 0.8341 (mt) REVERT: F 1011 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7474 (mtm110) outliers start: 35 outliers final: 28 residues processed: 169 average time/residue: 0.2527 time to fit residues: 61.8166 Evaluate side-chains 157 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 590 THR Chi-restraints excluded: chain E residue 874 LYS Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 970 LEU Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 680 VAL Chi-restraints excluded: chain F residue 822 MET Chi-restraints excluded: chain F residue 936 THR Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 996 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 115 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 103 optimal weight: 0.2980 chunk 136 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 546 GLN ** E 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 789 ASN F 810 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.172007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139427 restraints weight = 13963.525| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.86 r_work: 0.3310 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12133 Z= 0.166 Angle : 0.533 10.886 16483 Z= 0.283 Chirality : 0.044 0.198 1734 Planarity : 0.004 0.054 2146 Dihedral : 4.836 28.961 1748 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.23 % Allowed : 13.07 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.20), residues: 1525 helix: 1.81 (0.39), residues: 193 sheet: -0.97 (0.36), residues: 170 loop : -0.89 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 541 HIS 0.006 0.001 HIS F 810 PHE 0.007 0.001 PHE F 979 TYR 0.007 0.002 TYR F 580 ARG 0.008 0.000 ARG D 595 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 6) link_NAG-ASN : angle 2.22961 ( 18) hydrogen bonds : bond 0.03441 ( 338) hydrogen bonds : angle 4.48396 ( 1062) SS BOND : bond 0.00373 ( 57) SS BOND : angle 0.93083 ( 114) covalent geometry : bond 0.00394 (12070) covalent geometry : angle 0.52387 (16351) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8526 (m) cc_final: 0.8055 (p) REVERT: D 638 PHE cc_start: 0.7326 (m-10) cc_final: 0.7120 (m-10) REVERT: D 675 GLU cc_start: 0.7345 (mp0) cc_final: 0.6870 (pp20) REVERT: D 903 TRP cc_start: 0.8170 (m-10) cc_final: 0.7626 (m-10) REVERT: E 571 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7755 (mmm-85) REVERT: E 649 MET cc_start: 0.8898 (mtm) cc_final: 0.8591 (mtp) REVERT: E 671 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8142 (mm) REVERT: E 764 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7904 (mm-30) REVERT: E 794 ARG cc_start: 0.8449 (mmt-90) cc_final: 0.8187 (mmt-90) REVERT: E 820 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8180 (mt-10) REVERT: E 874 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7813 (ttpt) REVERT: E 914 LEU cc_start: 0.8407 (mm) cc_final: 0.7796 (pp) REVERT: E 1023 ASP cc_start: 0.6813 (m-30) cc_final: 0.6567 (m-30) REVERT: F 543 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8227 (mt-10) REVERT: F 649 MET cc_start: 0.9121 (mtm) cc_final: 0.8729 (mtm) REVERT: F 685 ASN cc_start: 0.7058 (t0) cc_final: 0.6761 (m-40) REVERT: F 789 ASN cc_start: 0.8473 (t0) cc_final: 0.8198 (p0) REVERT: F 874 LYS cc_start: 0.8459 (pttm) cc_final: 0.7965 (mttm) REVERT: F 914 LEU cc_start: 0.8684 (mm) cc_final: 0.8393 (mt) outliers start: 41 outliers final: 32 residues processed: 168 average time/residue: 0.2298 time to fit residues: 56.3073 Evaluate side-chains 162 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 886 ILE Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 590 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 752 ASP Chi-restraints excluded: chain E residue 874 LYS Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 680 VAL Chi-restraints excluded: chain F residue 822 MET Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1029 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 152 optimal weight: 0.0970 chunk 60 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 546 GLN ** E 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 810 HIS F 968 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.170973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138813 restraints weight = 13968.717| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.89 r_work: 0.3326 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12133 Z= 0.179 Angle : 0.541 10.540 16483 Z= 0.288 Chirality : 0.044 0.181 1734 Planarity : 0.004 0.051 2146 Dihedral : 4.900 29.032 1748 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.62 % Allowed : 13.39 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1525 helix: 1.78 (0.39), residues: 193 sheet: -1.04 (0.36), residues: 160 loop : -0.90 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 541 HIS 0.006 0.001 HIS F 495 PHE 0.008 0.001 PHE E 842 TYR 0.008 0.002 TYR F 580 ARG 0.007 0.000 ARG D 595 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 6) link_NAG-ASN : angle 2.25800 ( 18) hydrogen bonds : bond 0.03482 ( 338) hydrogen bonds : angle 4.48671 ( 1062) SS BOND : bond 0.00405 ( 57) SS BOND : angle 0.96619 ( 114) covalent geometry : bond 0.00426 (12070) covalent geometry : angle 0.53216 (16351) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8566 (m) cc_final: 0.8119 (p) REVERT: D 638 PHE cc_start: 0.7513 (m-10) cc_final: 0.7174 (m-10) REVERT: D 675 GLU cc_start: 0.7336 (mp0) cc_final: 0.6864 (pp20) REVERT: E 571 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7782 (mmm-85) REVERT: E 649 MET cc_start: 0.8898 (mtm) cc_final: 0.8590 (mtp) REVERT: E 671 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8316 (mm) REVERT: E 764 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7935 (mm-30) REVERT: E 820 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8221 (mt-10) REVERT: E 874 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7837 (ttpt) REVERT: E 914 LEU cc_start: 0.8415 (mm) cc_final: 0.7810 (pp) REVERT: E 1023 ASP cc_start: 0.6876 (m-30) cc_final: 0.6641 (m-30) REVERT: F 543 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8291 (mt-10) REVERT: F 649 MET cc_start: 0.9119 (mtm) cc_final: 0.8731 (mtm) REVERT: F 685 ASN cc_start: 0.7097 (t0) cc_final: 0.6835 (m-40) REVERT: F 789 ASN cc_start: 0.8455 (t0) cc_final: 0.8206 (p0) REVERT: F 874 LYS cc_start: 0.8498 (pttm) cc_final: 0.8050 (mttm) REVERT: F 914 LEU cc_start: 0.8715 (mm) cc_final: 0.8447 (mt) REVERT: F 1011 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7579 (mtm110) outliers start: 46 outliers final: 36 residues processed: 167 average time/residue: 0.2352 time to fit residues: 57.3666 Evaluate side-chains 165 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 782 TRP Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 886 ILE Chi-restraints excluded: chain D residue 889 TRP Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 590 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 752 ASP Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 874 LYS Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 822 MET Chi-restraints excluded: chain F residue 889 TRP Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1029 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 546 GLN ** E 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 810 HIS F 968 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.171001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138531 restraints weight = 13957.888| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.87 r_work: 0.3337 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12133 Z= 0.176 Angle : 0.544 10.252 16483 Z= 0.289 Chirality : 0.044 0.182 1734 Planarity : 0.004 0.051 2146 Dihedral : 4.903 28.812 1748 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.07 % Allowed : 14.49 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1525 helix: 1.79 (0.39), residues: 193 sheet: -0.97 (0.36), residues: 170 loop : -0.92 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 541 HIS 0.006 0.001 HIS F 495 PHE 0.008 0.001 PHE E 842 TYR 0.008 0.002 TYR E 735 ARG 0.005 0.000 ARG D 595 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 6) link_NAG-ASN : angle 2.23180 ( 18) hydrogen bonds : bond 0.03422 ( 338) hydrogen bonds : angle 4.46882 ( 1062) SS BOND : bond 0.00399 ( 57) SS BOND : angle 0.97790 ( 114) covalent geometry : bond 0.00420 (12070) covalent geometry : angle 0.53506 (16351) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8508 (m) cc_final: 0.8169 (p) REVERT: D 675 GLU cc_start: 0.7173 (mp0) cc_final: 0.6744 (pp20) REVERT: E 571 ARG cc_start: 0.8007 (mmm-85) cc_final: 0.7801 (mmm-85) REVERT: E 649 MET cc_start: 0.8904 (mtm) cc_final: 0.8599 (mtp) REVERT: E 671 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8261 (mm) REVERT: E 764 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8070 (mm-30) REVERT: E 794 ARG cc_start: 0.8554 (mmt-90) cc_final: 0.8354 (mmt-90) REVERT: E 820 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8285 (mt-10) REVERT: E 874 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7889 (ttpt) REVERT: E 914 LEU cc_start: 0.8444 (mm) cc_final: 0.7836 (pp) REVERT: E 1023 ASP cc_start: 0.6960 (m-30) cc_final: 0.6729 (m-30) REVERT: F 543 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8405 (mt-10) REVERT: F 649 MET cc_start: 0.9120 (mtm) cc_final: 0.8741 (mtm) REVERT: F 685 ASN cc_start: 0.7194 (t0) cc_final: 0.6923 (m-40) REVERT: F 789 ASN cc_start: 0.8455 (t0) cc_final: 0.8223 (p0) REVERT: F 874 LYS cc_start: 0.8560 (pttm) cc_final: 0.8157 (mttm) REVERT: F 914 LEU cc_start: 0.8693 (mm) cc_final: 0.8423 (mt) REVERT: F 1011 ARG cc_start: 0.7887 (mtm110) cc_final: 0.7548 (mtm110) outliers start: 39 outliers final: 34 residues processed: 161 average time/residue: 0.2283 time to fit residues: 53.2497 Evaluate side-chains 165 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 886 ILE Chi-restraints excluded: chain D residue 889 TRP Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 590 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 752 ASP Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 874 LYS Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 962 ASP Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 822 MET Chi-restraints excluded: chain F residue 889 TRP Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1029 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 27 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 105 optimal weight: 0.0770 chunk 97 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 29 optimal weight: 0.0470 chunk 23 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 GLN F 810 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.172909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.140386 restraints weight = 13816.260| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.92 r_work: 0.3383 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12133 Z= 0.118 Angle : 0.504 9.951 16483 Z= 0.268 Chirality : 0.042 0.163 1734 Planarity : 0.004 0.051 2146 Dihedral : 4.563 25.606 1748 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.68 % Allowed : 15.35 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1525 helix: 2.00 (0.39), residues: 193 sheet: -1.00 (0.39), residues: 147 loop : -0.85 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 541 HIS 0.005 0.001 HIS D 550 PHE 0.006 0.001 PHE D 638 TYR 0.007 0.001 TYR E 735 ARG 0.006 0.000 ARG F 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 6) link_NAG-ASN : angle 1.98110 ( 18) hydrogen bonds : bond 0.03099 ( 338) hydrogen bonds : angle 4.22400 ( 1062) SS BOND : bond 0.00272 ( 57) SS BOND : angle 0.79944 ( 114) covalent geometry : bond 0.00280 (12070) covalent geometry : angle 0.49719 (16351) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8502 (m) cc_final: 0.8075 (p) REVERT: D 638 PHE cc_start: 0.7418 (m-10) cc_final: 0.7047 (m-10) REVERT: D 675 GLU cc_start: 0.7159 (mp0) cc_final: 0.6676 (pp20) REVERT: E 571 ARG cc_start: 0.7955 (mmm-85) cc_final: 0.7752 (mmm-85) REVERT: E 649 MET cc_start: 0.8868 (mtm) cc_final: 0.8596 (mtp) REVERT: E 671 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8203 (mm) REVERT: E 794 ARG cc_start: 0.8369 (mmt-90) cc_final: 0.8161 (mmt-90) REVERT: E 874 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7754 (ttpt) REVERT: E 914 LEU cc_start: 0.8416 (mm) cc_final: 0.7831 (pp) REVERT: E 939 SER cc_start: 0.8022 (m) cc_final: 0.7566 (p) REVERT: E 1023 ASP cc_start: 0.6679 (m-30) cc_final: 0.6454 (m-30) REVERT: F 543 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8191 (mt-10) REVERT: F 649 MET cc_start: 0.9069 (mtm) cc_final: 0.8753 (mtt) REVERT: F 685 ASN cc_start: 0.6962 (t0) cc_final: 0.6662 (m-40) REVERT: F 874 LYS cc_start: 0.8345 (pttm) cc_final: 0.7927 (mttm) REVERT: F 914 LEU cc_start: 0.8525 (mm) cc_final: 0.8207 (mt) outliers start: 34 outliers final: 31 residues processed: 159 average time/residue: 0.2391 time to fit residues: 55.4224 Evaluate side-chains 161 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 782 TRP Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 886 ILE Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 590 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 874 LYS Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 822 MET Chi-restraints excluded: chain F residue 889 TRP Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1029 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 GLN F 810 HIS F 968 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.137177 restraints weight = 13774.618| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.85 r_work: 0.3198 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12133 Z= 0.230 Angle : 0.584 10.273 16483 Z= 0.310 Chirality : 0.046 0.186 1734 Planarity : 0.004 0.050 2146 Dihedral : 5.080 30.364 1748 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.91 % Allowed : 15.35 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1525 helix: 1.68 (0.38), residues: 193 sheet: -1.21 (0.34), residues: 186 loop : -0.93 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 541 HIS 0.008 0.001 HIS D 495 PHE 0.009 0.002 PHE E 842 TYR 0.009 0.002 TYR F 580 ARG 0.009 0.001 ARG F 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 6) link_NAG-ASN : angle 2.31271 ( 18) hydrogen bonds : bond 0.03652 ( 338) hydrogen bonds : angle 4.56135 ( 1062) SS BOND : bond 0.00505 ( 57) SS BOND : angle 1.11180 ( 114) covalent geometry : bond 0.00548 (12070) covalent geometry : angle 0.57340 (16351) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8592 (m) cc_final: 0.8040 (p) REVERT: D 638 PHE cc_start: 0.7705 (m-10) cc_final: 0.7218 (m-10) REVERT: D 675 GLU cc_start: 0.7160 (mp0) cc_final: 0.6689 (pp20) REVERT: E 571 ARG cc_start: 0.7902 (mmm-85) cc_final: 0.7698 (mmm-85) REVERT: E 649 MET cc_start: 0.8878 (mtm) cc_final: 0.8580 (mtp) REVERT: E 671 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8296 (mm) REVERT: E 764 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7882 (mm-30) REVERT: E 794 ARG cc_start: 0.8528 (mmt-90) cc_final: 0.8250 (mmt-90) REVERT: E 874 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7669 (ttpt) REVERT: E 914 LEU cc_start: 0.8396 (mm) cc_final: 0.7699 (pp) REVERT: E 939 SER cc_start: 0.7868 (m) cc_final: 0.7435 (p) REVERT: E 1023 ASP cc_start: 0.6743 (m-30) cc_final: 0.6492 (m-30) REVERT: F 543 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8167 (mt-10) REVERT: F 649 MET cc_start: 0.9120 (mtm) cc_final: 0.8810 (mtt) REVERT: F 685 ASN cc_start: 0.6867 (t0) cc_final: 0.6612 (m-40) REVERT: F 857 GLU cc_start: 0.8054 (tp30) cc_final: 0.7758 (tt0) REVERT: F 874 LYS cc_start: 0.8419 (pttm) cc_final: 0.7892 (mttm) REVERT: F 914 LEU cc_start: 0.8627 (mm) cc_final: 0.8299 (mt) REVERT: F 977 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7794 (mmmt) REVERT: F 1011 ARG cc_start: 0.7805 (mtm110) cc_final: 0.7518 (mtm110) outliers start: 37 outliers final: 31 residues processed: 161 average time/residue: 0.2532 time to fit residues: 58.3798 Evaluate side-chains 162 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 782 TRP Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 886 ILE Chi-restraints excluded: chain D residue 889 TRP Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 590 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 874 LYS Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 822 MET Chi-restraints excluded: chain F residue 889 TRP Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 968 GLN Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1029 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 GLN F 810 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.170958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.138393 restraints weight = 13760.777| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.86 r_work: 0.3252 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12133 Z= 0.174 Angle : 0.546 10.260 16483 Z= 0.291 Chirality : 0.044 0.186 1734 Planarity : 0.004 0.052 2146 Dihedral : 4.924 28.784 1748 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.52 % Allowed : 15.98 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1525 helix: 1.75 (0.38), residues: 193 sheet: -1.07 (0.35), residues: 176 loop : -0.93 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 541 HIS 0.007 0.001 HIS D 495 PHE 0.008 0.001 PHE D 638 TYR 0.007 0.001 TYR F 580 ARG 0.006 0.000 ARG F 913 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 6) link_NAG-ASN : angle 2.22201 ( 18) hydrogen bonds : bond 0.03398 ( 338) hydrogen bonds : angle 4.44502 ( 1062) SS BOND : bond 0.00386 ( 57) SS BOND : angle 0.96203 ( 114) covalent geometry : bond 0.00413 (12070) covalent geometry : angle 0.53702 (16351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7569.74 seconds wall clock time: 130 minutes 56.61 seconds (7856.61 seconds total)