Starting phenix.real_space_refine on Sat Jan 18 06:44:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmk_38480/01_2025/8xmk_38480.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmk_38480/01_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_38480/01_2025/8xmk_38480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmk_38480/01_2025/8xmk_38480.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmk_38480/01_2025/8xmk_38480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmk_38480/01_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-5571/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: 7.87, per 1000 atoms: 0.67 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: 2.90 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: 1.79 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: 4.28 Time building geometry restraints manager: 3.37 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: 3.310 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.630 Find NCS groups from input model: 0.630 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.190 ------------------------------------------------------------------------------- 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 12070 Z= 0.258 Angle : 0.528 8.854 16351 Z= 0.295 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 *********************** 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 : 1.526 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: 0.2567 time to fit residues: 85.2283 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 : 1.781 ------------------------------------------------------------------------------- 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: 0.0020 chunk 116 optimal weight: 0.9980 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: 0.7980 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: 0.6188 ------------------------------------------------------------------------------- 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 E 986 GLN F 789 ASN F 797 GLN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.176572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145321 restraints weight = 13701.040| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.85 r_work: 0.3458 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12070 Z= 0.233 Angle : 0.530 10.924 16351 Z= 0.285 Chirality : 0.044 0.187 1734 Planarity : 0.004 0.049 2146 Dihedral : 5.028 35.352 1752 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.34 % Allowed : 8.19 % Favored : 90.47 % 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: 1.81 (0.39), residues: 193 sheet: -0.78 (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 0.011 0.001 PHE E 979 TYR 0.006 0.001 TYR F 580 ARG 0.006 0.001 ARG E 941 *********************** 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 192 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.598 Fit side-chains revert: symmetry clash REVERT: D 764 GLU cc_start: 0.7054 (pp20) cc_final: 0.6755 (pt0) REVERT: D 805 GLN cc_start: 0.6526 (mm110) cc_final: 0.5542 (pp30) REVERT: D 810 HIS cc_start: 0.7333 (m90) cc_final: 0.6980 (m-70) REVERT: E 649 MET cc_start: 0.8887 (mtm) cc_final: 0.8602 (mtp) REVERT: E 735 TYR cc_start: 0.9015 (t80) cc_final: 0.8725 (t80) REVERT: E 820 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8185 (mt-10) REVERT: E 874 LYS cc_start: 0.8375 (tttt) cc_final: 0.8006 (ttpt) REVERT: E 888 MET cc_start: 0.8195 (ttm) cc_final: 0.7920 (ttm) REVERT: E 914 LEU cc_start: 0.8433 (mm) cc_final: 0.7935 (pp) REVERT: E 986 GLN cc_start: 0.6617 (OUTLIER) cc_final: 0.6415 (tp40) REVERT: E 1023 ASP cc_start: 0.7034 (m-30) cc_final: 0.6773 (m-30) REVERT: F 541 TRP cc_start: 0.8952 (m100) cc_final: 0.8715 (m100) REVERT: F 543 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8103 (mt-10) REVERT: F 597 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8093 (mt-10) REVERT: F 640 LYS cc_start: 0.7476 (mttp) cc_final: 0.7023 (ptmm) REVERT: F 685 ASN cc_start: 0.7015 (t0) cc_final: 0.6714 (m-40) REVERT: F 758 ARG cc_start: 0.8249 (ptp-110) cc_final: 0.8039 (ptp90) REVERT: F 810 HIS cc_start: 0.8081 (m170) cc_final: 0.7852 (m-70) REVERT: F 874 LYS cc_start: 0.8471 (pttm) cc_final: 0.7998 (mttm) outliers start: 17 outliers final: 11 residues processed: 187 average time/residue: 0.2681 time to fit residues: 70.9010 Evaluate side-chains 141 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 986 GLN 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: 1.9990 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 114 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 986 GLN F 686 GLN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.174040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.141811 restraints weight = 13937.947| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.90 r_work: 0.3414 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12070 Z= 0.213 Angle : 0.502 11.827 16351 Z= 0.267 Chirality : 0.043 0.255 1734 Planarity : 0.004 0.048 2146 Dihedral : 4.850 32.076 1748 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.57 % Allowed : 10.24 % Favored : 88.19 % 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: -0.66 (0.21), residues: 1525 helix: 1.91 (0.39), residues: 193 sheet: -0.84 (0.38), residues: 170 loop : -0.83 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 910 HIS 0.009 0.001 HIS F 495 PHE 0.009 0.001 PHE E 979 TYR 0.006 0.001 TYR F 580 ARG 0.006 0.000 ARG D 647 *********************** 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 165 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: D 764 GLU cc_start: 0.6902 (pp20) cc_final: 0.6628 (pt0) REVERT: D 810 HIS cc_start: 0.7216 (m90) cc_final: 0.6691 (m170) REVERT: D 994 ASN cc_start: 0.8054 (p0) cc_final: 0.7527 (p0) REVERT: D 1011 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7620 (ptp-110) REVERT: E 571 ARG cc_start: 0.7977 (mmm-85) cc_final: 0.7701 (mmm-85) REVERT: E 649 MET cc_start: 0.8883 (mtm) cc_final: 0.8604 (mtp) REVERT: E 735 TYR cc_start: 0.9026 (t80) cc_final: 0.8806 (t80) REVERT: E 820 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8165 (mt-10) REVERT: E 914 LEU cc_start: 0.8371 (mm) cc_final: 0.7889 (pp) REVERT: E 1023 ASP cc_start: 0.6878 (m-30) cc_final: 0.6606 (m-30) REVERT: F 541 TRP cc_start: 0.9027 (m100) cc_final: 0.8784 (m100) REVERT: F 543 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8052 (mt-10) REVERT: F 597 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8050 (mt-10) REVERT: F 640 LYS cc_start: 0.7433 (mttp) cc_final: 0.6930 (ptmm) REVERT: F 649 MET cc_start: 0.9083 (mtm) cc_final: 0.8703 (mtm) REVERT: F 685 ASN cc_start: 0.6934 (t0) cc_final: 0.6635 (m-40) REVERT: F 758 ARG cc_start: 0.8137 (ptp-110) cc_final: 0.7901 (ptp90) REVERT: F 874 LYS cc_start: 0.8400 (pttm) cc_final: 0.7967 (mttm) REVERT: F 1011 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7427 (mtm110) outliers start: 20 outliers final: 15 residues processed: 159 average time/residue: 0.2452 time to fit residues: 57.0238 Evaluate side-chains 145 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 801 HIS Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 996 VAL 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 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: 3.9990 chunk 45 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 138 optimal weight: 0.0670 chunk 7 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 8 optimal weight: 0.0570 chunk 58 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 810 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.171478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138817 restraints weight = 13794.791| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.89 r_work: 0.3216 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12070 Z= 0.320 Angle : 0.549 11.938 16351 Z= 0.292 Chirality : 0.045 0.324 1734 Planarity : 0.004 0.050 2146 Dihedral : 5.342 59.043 1748 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.99 % Allowed : 10.55 % Favored : 86.46 % 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: 1.72 (0.38), residues: 193 sheet: -1.11 (0.35), residues: 182 loop : -0.88 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 910 HIS 0.008 0.001 HIS F 810 PHE 0.009 0.002 PHE F 979 TYR 0.008 0.002 TYR F 580 ARG 0.005 0.000 ARG D 647 *********************** 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 170 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: D 638 PHE cc_start: 0.8122 (m-80) cc_final: 0.7778 (m-10) REVERT: D 675 GLU cc_start: 0.7291 (mp0) cc_final: 0.6806 (pp20) REVERT: D 810 HIS cc_start: 0.7068 (m90) cc_final: 0.6758 (m-70) REVERT: E 571 ARG cc_start: 0.7957 (mmm-85) cc_final: 0.7695 (mmm-85) REVERT: E 649 MET cc_start: 0.8890 (mtm) cc_final: 0.8570 (mtp) REVERT: E 671 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8539 (mm) REVERT: E 735 TYR cc_start: 0.8963 (t80) cc_final: 0.8761 (t80) REVERT: E 820 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8161 (mt-10) REVERT: E 874 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7822 (ttpt) REVERT: E 914 LEU cc_start: 0.8355 (mm) cc_final: 0.7806 (pp) REVERT: E 1023 ASP cc_start: 0.6742 (m-30) cc_final: 0.6482 (m-30) REVERT: F 541 TRP cc_start: 0.9082 (m100) cc_final: 0.8876 (m100) REVERT: F 543 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8256 (mt-10) REVERT: F 649 MET cc_start: 0.9112 (mtm) cc_final: 0.8715 (mtm) REVERT: F 685 ASN cc_start: 0.6976 (t0) cc_final: 0.6513 (m-40) REVERT: F 758 ARG cc_start: 0.8190 (ptp-110) cc_final: 0.7912 (ptp90) REVERT: F 857 GLU cc_start: 0.8149 (tp30) cc_final: 0.7808 (tt0) REVERT: F 874 LYS cc_start: 0.8423 (pttm) cc_final: 0.7874 (mttm) outliers start: 38 outliers final: 26 residues processed: 157 average time/residue: 0.2549 time to fit residues: 57.4882 Evaluate side-chains 154 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 498 THR 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 742 THR Chi-restraints excluded: chain D residue 801 HIS 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 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 722 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 115 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.0020 chunk 9 optimal weight: 5.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3950 r_free = 0.3950 target = 0.170362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137438 restraints weight = 13782.611| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.86 r_work: 0.3329 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12070 Z= 0.299 Angle : 0.533 11.018 16351 Z= 0.285 Chirality : 0.044 0.251 1734 Planarity : 0.004 0.065 2146 Dihedral : 5.105 46.721 1748 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.23 % Allowed : 11.34 % Favored : 85.43 % 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 (0.38), residues: 193 sheet: -1.00 (0.35), residues: 177 loop : -0.90 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 910 HIS 0.006 0.001 HIS D 495 PHE 0.008 0.001 PHE F 979 TYR 0.008 0.002 TYR F 580 ARG 0.007 0.001 ARG D 595 *********************** 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 188 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8603 (m) cc_final: 0.8287 (p) REVERT: D 569 HIS cc_start: 0.7569 (m-70) cc_final: 0.6938 (m-70) REVERT: D 675 GLU cc_start: 0.7309 (mp0) cc_final: 0.6883 (pp20) REVERT: D 810 HIS cc_start: 0.7067 (m90) cc_final: 0.6812 (m-70) REVERT: E 571 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7807 (mmm-85) REVERT: E 649 MET cc_start: 0.8845 (mtm) cc_final: 0.8556 (mtp) REVERT: E 671 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8499 (mm) REVERT: E 764 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8012 (mm-30) REVERT: E 820 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8275 (mt-10) REVERT: E 874 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7996 (ttpt) REVERT: E 914 LEU cc_start: 0.8454 (mm) cc_final: 0.7951 (pp) REVERT: E 1023 ASP cc_start: 0.6926 (m-30) cc_final: 0.6709 (m-30) REVERT: F 543 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8168 (mt-10) REVERT: F 649 MET cc_start: 0.9105 (mtm) cc_final: 0.8720 (mtm) REVERT: F 685 ASN cc_start: 0.7191 (t0) cc_final: 0.6785 (m-40) REVERT: F 789 ASN cc_start: 0.8365 (t160) cc_final: 0.8150 (p0) REVERT: F 874 LYS cc_start: 0.8538 (pttm) cc_final: 0.8121 (mttm) REVERT: F 914 LEU cc_start: 0.8683 (mm) cc_final: 0.8402 (mt) REVERT: F 1011 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7590 (mtm110) outliers start: 41 outliers final: 30 residues processed: 176 average time/residue: 0.2542 time to fit residues: 63.9331 Evaluate side-chains 160 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 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 590 THR Chi-restraints excluded: chain E residue 671 LEU 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 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 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: 0.0070 chunk 39 optimal weight: 0.9980 chunk 103 optimal weight: 0.0060 chunk 136 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 134 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 546 GLN 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 = 0.4001 r_free = 0.4001 target = 0.174849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142600 restraints weight = 13938.800| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.91 r_work: 0.3384 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12070 Z= 0.175 Angle : 0.490 10.430 16351 Z= 0.262 Chirality : 0.042 0.201 1734 Planarity : 0.004 0.050 2146 Dihedral : 4.581 25.413 1748 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.52 % Allowed : 13.39 % Favored : 84.09 % 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: -0.64 (0.20), residues: 1525 helix: 2.01 (0.39), residues: 193 sheet: -0.98 (0.39), residues: 151 loop : -0.81 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 541 HIS 0.004 0.001 HIS F 495 PHE 0.006 0.001 PHE F 979 TYR 0.006 0.001 TYR E 735 ARG 0.005 0.000 ARG D 595 *********************** 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 179 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8570 (m) cc_final: 0.8243 (p) REVERT: D 638 PHE cc_start: 0.8229 (m-10) cc_final: 0.8026 (m-10) REVERT: D 675 GLU cc_start: 0.7288 (mp0) cc_final: 0.6829 (pp20) REVERT: D 764 GLU cc_start: 0.6847 (pp20) cc_final: 0.6507 (pt0) REVERT: E 571 ARG cc_start: 0.8052 (mmm-85) cc_final: 0.7824 (mmm-85) REVERT: E 649 MET cc_start: 0.8854 (mtm) cc_final: 0.8566 (mtp) REVERT: E 671 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8194 (mm) REVERT: E 764 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8020 (mm-30) REVERT: E 794 ARG cc_start: 0.8479 (mmt-90) cc_final: 0.8256 (mmt-90) REVERT: E 820 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8219 (mt-10) REVERT: E 874 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7921 (ttpt) REVERT: E 914 LEU cc_start: 0.8492 (mm) cc_final: 0.7981 (pp) REVERT: E 939 SER cc_start: 0.8141 (m) cc_final: 0.7703 (p) REVERT: E 1023 ASP cc_start: 0.6995 (m-30) cc_final: 0.6776 (m-30) REVERT: F 543 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8126 (mt-10) REVERT: F 649 MET cc_start: 0.9098 (mtm) cc_final: 0.8731 (mtm) REVERT: F 685 ASN cc_start: 0.7134 (t0) cc_final: 0.6739 (m-40) REVERT: F 874 LYS cc_start: 0.8446 (pttm) cc_final: 0.8057 (mttm) REVERT: F 914 LEU cc_start: 0.8618 (mm) cc_final: 0.8266 (mt) REVERT: F 1011 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7549 (mtm110) outliers start: 32 outliers final: 24 residues processed: 169 average time/residue: 0.2450 time to fit residues: 60.9065 Evaluate side-chains 158 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 767 ASN 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 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 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 822 MET 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: 0.8980 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 7 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 60 optimal weight: 0.0270 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3990 r_free = 0.3990 target = 0.173894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141718 restraints weight = 13952.282| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.90 r_work: 0.3360 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12070 Z= 0.208 Angle : 0.496 10.136 16351 Z= 0.266 Chirality : 0.043 0.204 1734 Planarity : 0.004 0.049 2146 Dihedral : 4.515 26.670 1748 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.83 % Allowed : 14.09 % Favored : 83.07 % 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: -0.63 (0.20), residues: 1525 helix: 2.00 (0.39), residues: 193 sheet: -0.92 (0.39), residues: 151 loop : -0.81 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 541 HIS 0.007 0.001 HIS D 495 PHE 0.007 0.001 PHE F 979 TYR 0.007 0.001 TYR F 580 ARG 0.007 0.000 ARG F 913 *********************** 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 169 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8522 (m) cc_final: 0.8189 (p) REVERT: D 675 GLU cc_start: 0.7158 (mp0) cc_final: 0.6737 (pp20) REVERT: E 571 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7788 (mmm-85) REVERT: E 649 MET cc_start: 0.8866 (mtm) cc_final: 0.8587 (mtp) REVERT: E 671 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8184 (mm) REVERT: E 764 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7902 (mm-30) REVERT: E 794 ARG cc_start: 0.8456 (mmt-90) cc_final: 0.8186 (mmt-90) REVERT: E 820 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8089 (mt-10) REVERT: E 874 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7770 (ttpt) REVERT: E 914 LEU cc_start: 0.8466 (mm) cc_final: 0.7907 (pp) REVERT: E 939 SER cc_start: 0.8046 (m) cc_final: 0.7633 (p) REVERT: E 1023 ASP cc_start: 0.6850 (m-30) cc_final: 0.6617 (m-30) REVERT: F 543 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8245 (mt-10) REVERT: F 649 MET cc_start: 0.9095 (mtm) cc_final: 0.8708 (mtm) REVERT: F 685 ASN cc_start: 0.7067 (t0) cc_final: 0.6788 (m-40) REVERT: F 874 LYS cc_start: 0.8359 (pttm) cc_final: 0.7960 (mttm) REVERT: F 914 LEU cc_start: 0.8573 (mm) cc_final: 0.8226 (mt) REVERT: F 1011 ARG cc_start: 0.7810 (mtm110) cc_final: 0.7515 (mtm110) outliers start: 36 outliers final: 31 residues processed: 157 average time/residue: 0.2378 time to fit residues: 54.2647 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 : 1.360 ------------------------------------------------------------------------------- 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 767 ASN 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 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 968 GLN Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 996 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 51 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3962 r_free = 0.3962 target = 0.171364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139041 restraints weight = 13938.865| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.88 r_work: 0.3304 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12070 Z= 0.296 Angle : 0.536 9.816 16351 Z= 0.287 Chirality : 0.044 0.236 1734 Planarity : 0.004 0.050 2146 Dihedral : 4.772 29.530 1748 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.31 % Allowed : 14.33 % Favored : 82.36 % 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 (0.20), residues: 1525 helix: 1.83 (0.38), residues: 193 sheet: -0.92 (0.36), residues: 170 loop : -0.88 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 541 HIS 0.008 0.001 HIS D 495 PHE 0.008 0.001 PHE E 842 TYR 0.008 0.002 TYR F 580 ARG 0.011 0.001 ARG D 476 *********************** 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 174 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8610 (m) cc_final: 0.8244 (p) REVERT: D 675 GLU cc_start: 0.7266 (mp0) cc_final: 0.6807 (pp20) REVERT: D 1011 ARG cc_start: 0.8177 (mtm110) cc_final: 0.7852 (mtm-85) REVERT: E 571 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7759 (mmm-85) REVERT: E 649 MET cc_start: 0.8871 (mtm) cc_final: 0.8576 (mtp) REVERT: E 671 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8269 (mm) REVERT: E 764 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7888 (mm-30) REVERT: E 820 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8185 (mt-10) REVERT: E 874 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7788 (ttpt) REVERT: E 914 LEU cc_start: 0.8400 (mm) cc_final: 0.7759 (pp) REVERT: E 939 SER cc_start: 0.8060 (m) cc_final: 0.7591 (p) REVERT: E 1023 ASP cc_start: 0.6792 (m-30) cc_final: 0.6560 (m-30) REVERT: F 543 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8250 (mt-10) REVERT: F 649 MET cc_start: 0.9107 (mtm) cc_final: 0.8809 (mtt) REVERT: F 685 ASN cc_start: 0.7069 (t0) cc_final: 0.6770 (m-40) REVERT: F 874 LYS cc_start: 0.8422 (pttm) cc_final: 0.7982 (mttm) REVERT: F 914 LEU cc_start: 0.8607 (mm) cc_final: 0.8210 (mt) outliers start: 42 outliers final: 35 residues processed: 159 average time/residue: 0.2287 time to fit residues: 53.8085 Evaluate side-chains 168 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 586 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 721 LEU Chi-restraints excluded: chain D residue 767 ASN 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 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 916 SER Chi-restraints excluded: chain F residue 936 THR 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: 5.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 29 optimal weight: 0.0170 chunk 23 optimal weight: 0.9980 chunk 153 optimal weight: 0.0670 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3998 r_free = 0.3998 target = 0.174693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142813 restraints weight = 13875.856| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.79 r_work: 0.3356 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12070 Z= 0.181 Angle : 0.492 9.335 16351 Z= 0.264 Chirality : 0.042 0.185 1734 Planarity : 0.004 0.049 2146 Dihedral : 4.442 25.254 1748 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.60 % Allowed : 15.20 % Favored : 82.20 % 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: -0.63 (0.20), residues: 1525 helix: 2.02 (0.39), residues: 193 sheet: -0.89 (0.41), residues: 141 loop : -0.83 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 541 HIS 0.008 0.001 HIS D 495 PHE 0.006 0.001 PHE F 979 TYR 0.006 0.001 TYR E 735 ARG 0.009 0.000 ARG D 476 *********************** 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 172 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8496 (m) cc_final: 0.8182 (p) REVERT: D 675 GLU cc_start: 0.7055 (mp0) cc_final: 0.6611 (pp20) REVERT: D 1011 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7747 (mtm-85) REVERT: E 571 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7783 (mmm-85) REVERT: E 649 MET cc_start: 0.8882 (mtm) cc_final: 0.8588 (mtp) REVERT: E 671 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8212 (mm) REVERT: E 764 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7851 (mm-30) REVERT: E 874 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7741 (ttpt) REVERT: E 914 LEU cc_start: 0.8459 (mm) cc_final: 0.7873 (pp) REVERT: E 939 SER cc_start: 0.8027 (m) cc_final: 0.7561 (p) REVERT: E 1023 ASP cc_start: 0.6799 (m-30) cc_final: 0.6545 (m-30) REVERT: F 543 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8208 (mt-10) REVERT: F 649 MET cc_start: 0.9081 (mtm) cc_final: 0.8689 (mtm) REVERT: F 685 ASN cc_start: 0.6983 (t0) cc_final: 0.6691 (m-40) REVERT: F 874 LYS cc_start: 0.8322 (pttm) cc_final: 0.7903 (mttm) REVERT: F 888 MET cc_start: 0.8598 (ttp) cc_final: 0.8272 (ttp) REVERT: F 914 LEU cc_start: 0.8482 (mm) cc_final: 0.8061 (mt) REVERT: F 1011 ARG cc_start: 0.7682 (mtm110) cc_final: 0.7454 (mtm110) outliers start: 33 outliers final: 31 residues processed: 161 average time/residue: 0.2328 time to fit residues: 55.1510 Evaluate side-chains 165 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 586 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 721 LEU 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 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 822 MET 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: 1.9990 chunk 42 optimal weight: 0.6980 chunk 70 optimal weight: 0.0370 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 73 optimal weight: 0.0030 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.3668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 546 GLN F 968 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.176232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144397 restraints weight = 13782.094| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.82 r_work: 0.3358 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12070 Z= 0.170 Angle : 0.489 8.711 16351 Z= 0.263 Chirality : 0.042 0.178 1734 Planarity : 0.004 0.049 2146 Dihedral : 4.299 24.652 1748 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.60 % Allowed : 15.51 % Favored : 81.89 % 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: -0.57 (0.21), residues: 1525 helix: 2.11 (0.40), residues: 193 sheet: -0.81 (0.39), residues: 151 loop : -0.80 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 541 HIS 0.007 0.001 HIS D 495 PHE 0.006 0.001 PHE F 979 TYR 0.005 0.001 TYR F 580 ARG 0.009 0.000 ARG D 476 ********************** 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 171 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8547 (m) cc_final: 0.8106 (p) REVERT: D 764 GLU cc_start: 0.6732 (pp20) cc_final: 0.6357 (pt0) REVERT: D 1011 ARG cc_start: 0.7929 (mtm110) cc_final: 0.7625 (mtm-85) REVERT: E 550 HIS cc_start: 0.7947 (p-80) cc_final: 0.7724 (p-80) REVERT: E 571 ARG cc_start: 0.7951 (mmm-85) cc_final: 0.7738 (mmm-85) REVERT: E 649 MET cc_start: 0.8857 (mtm) cc_final: 0.8572 (mtp) REVERT: E 671 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8237 (mm) REVERT: E 764 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7892 (mm-30) REVERT: E 874 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7548 (ttpt) REVERT: E 914 LEU cc_start: 0.8426 (mm) cc_final: 0.7784 (pp) REVERT: E 939 SER cc_start: 0.7950 (m) cc_final: 0.7512 (p) REVERT: E 1023 ASP cc_start: 0.6717 (m-30) cc_final: 0.6457 (m-30) REVERT: F 543 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8195 (mt-10) REVERT: F 649 MET cc_start: 0.9073 (mtm) cc_final: 0.8691 (mtm) REVERT: F 685 ASN cc_start: 0.6908 (t0) cc_final: 0.6631 (m-40) REVERT: F 874 LYS cc_start: 0.8250 (pttm) cc_final: 0.7801 (mttm) outliers start: 33 outliers final: 30 residues processed: 158 average time/residue: 0.2417 time to fit residues: 56.6241 Evaluate side-chains 157 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 586 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 721 LEU Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 886 ILE 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 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 822 MET 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: 2.9990 chunk 23 optimal weight: 5.9990 chunk 134 optimal weight: 0.4980 chunk 103 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.173323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139959 restraints weight = 13802.805| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.91 r_work: 0.3395 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12070 Z= 0.183 Angle : 0.503 9.625 16351 Z= 0.268 Chirality : 0.043 0.422 1734 Planarity : 0.004 0.049 2146 Dihedral : 4.344 25.710 1748 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.76 % Allowed : 15.67 % Favored : 81.57 % 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: -0.56 (0.21), residues: 1525 helix: 2.09 (0.39), residues: 193 sheet: -0.75 (0.39), residues: 151 loop : -0.79 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 541 HIS 0.007 0.001 HIS D 495 PHE 0.011 0.001 PHE F 979 TYR 0.007 0.001 TYR E 735 ARG 0.009 0.000 ARG D 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7225.55 seconds wall clock time: 129 minutes 21.38 seconds (7761.38 seconds total)