Starting phenix.real_space_refine on Fri Jul 3 03:33:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmk_38480/07_2026/8xmk_38480.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmk_38480/07_2026/8xmk_38480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmk_38480/07_2026/8xmk_38480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmk_38480/07_2026/8xmk_38480.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmk_38480/07_2026/8xmk_38480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmk_38480/07_2026/8xmk_38480.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 28 Ad-hoc single atom residues: {' CA': 6} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 6 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, 28 Ad-hoc single atom residues: {' CA': 5} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 5 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, 28 Ad-hoc single atom residues: {' CA': 6} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 6 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.30, per 1000 atoms: 0.19 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: 0.71 Conformation dependent library (CDL) restraints added in 385.0 milliseconds 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: 0.28 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: 1.77 Time building geometry restraints manager: 0.97 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 3.250 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 3.250 nonbonded pdb=" OD2 ASP F 616 " pdb="CA CA F1103 " model vdw 2.207 3.250 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 1107)) selection = (chain 'E' and (resid 473 through 691 or resid 718 through 1107)) selection = (chain 'F' and (resid 473 through 562 or resid 567 through 634 or resid 644 thro \ ugh 691 or resid 718 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: 3.010 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.270 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12133 Z= 0.173 Angle : 0.535 8.854 16483 Z= 0.297 Chirality : 0.044 0.249 1734 Planarity : 0.004 0.049 2146 Dihedral : 13.979 88.873 4374 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.44 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (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 ARG 0.003 0.000 ARG F 476 TYR 0.007 0.002 TYR F 580 PHE 0.009 0.001 PHE F 507 TRP 0.057 0.001 TRP F 903 HIS 0.008 0.001 HIS F 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (12070) covalent geometry : angle 0.52775 / 0.29 (16351) SS BOND : bond 0.00307 / 0.21 ( 57) SS BOND : angle 1.05532 / 0.80 ( 114) hydrogen bonds : bond 0.23735 / 17.04 ( 338) hydrogen bonds : angle 7.99963 / 5.68 ( 1062) link_NAG-ASN : bond 0.00130 / 0.06 ( 6) link_NAG-ASN : angle 1.31280 / 0.81 ( 18) *********************** 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 : 0.428 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: 0.0951 time to fit residues: 32.1305 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 : 0.361 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0070 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 807 ASN D 810 HIS E 688 GLN E 927 ASN F 789 ASN F 797 GLN ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.174091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141527 restraints weight = 13832.535| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.98 r_work: 0.3442 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12133 Z= 0.149 Angle : 0.538 11.024 16483 Z= 0.287 Chirality : 0.044 0.194 1734 Planarity : 0.004 0.048 2146 Dihedral : 5.070 36.275 1752 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1525 helix: 1.78 (0.39), residues: 193 sheet: -0.81 (0.38), residues: 177 loop : -0.86 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 941 TYR 0.007 0.001 TYR F 580 PHE 0.010 0.001 PHE E 979 TRP 0.017 0.001 TRP F 903 HIS 0.012 0.001 HIS F 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (12070) covalent geometry : angle 0.53151 / 0.29 (16351) SS BOND : bond 0.00356 / 0.24 ( 57) SS BOND : angle 0.92934 / 0.67 ( 114) hydrogen bonds : bond 0.04261 / 2.99 ( 338) hydrogen bonds : angle 5.05269 / 3.62 ( 1062) link_NAG-ASN : bond 0.00165 / 0.10 ( 6) link_NAG-ASN : angle 1.73451 / 0.98 ( 18) *********************** 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 190 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 764 GLU cc_start: 0.7110 (pp20) cc_final: 0.6826 (pt0) REVERT: D 810 HIS cc_start: 0.7316 (m90) cc_final: 0.7100 (m-70) REVERT: E 649 MET cc_start: 0.8875 (mtm) cc_final: 0.8600 (mtp) REVERT: E 735 TYR cc_start: 0.9028 (t80) cc_final: 0.8738 (t80) REVERT: E 820 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8230 (mt-10) REVERT: E 874 LYS cc_start: 0.8379 (tttt) cc_final: 0.8003 (ttpt) REVERT: E 914 LEU cc_start: 0.8432 (mm) cc_final: 0.7922 (pp) REVERT: E 986 GLN cc_start: 0.6667 (tp40) cc_final: 0.6454 (tp40) REVERT: E 1023 ASP cc_start: 0.7076 (m-30) cc_final: 0.6814 (m-30) REVERT: F 541 TRP cc_start: 0.8977 (m100) cc_final: 0.8742 (m100) REVERT: F 543 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8196 (mt-10) REVERT: F 597 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8133 (mt-10) REVERT: F 640 LYS cc_start: 0.7506 (mttp) cc_final: 0.7032 (ptmm) REVERT: F 649 MET cc_start: 0.9048 (mtm) cc_final: 0.8813 (mtt) REVERT: F 685 ASN cc_start: 0.7060 (t0) cc_final: 0.6752 (m-40) REVERT: F 758 ARG cc_start: 0.8245 (ptp-110) cc_final: 0.8036 (ptp90) REVERT: F 874 LYS cc_start: 0.8505 (pttm) cc_final: 0.8025 (mttm) outliers start: 17 outliers final: 12 residues processed: 184 average time/residue: 0.0935 time to fit residues: 24.8706 Evaluate side-chains 139 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 959 ASP 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 146 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 622 GLN ** E 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 686 GLN F 810 HIS ** F 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.170269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137876 restraints weight = 13941.042| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.94 r_work: 0.3307 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12133 Z= 0.232 Angle : 0.580 11.626 16483 Z= 0.307 Chirality : 0.046 0.302 1734 Planarity : 0.004 0.050 2146 Dihedral : 5.218 32.898 1748 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.52 % Allowed : 9.84 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.20), residues: 1525 helix: 1.59 (0.38), residues: 193 sheet: -1.16 (0.36), residues: 182 loop : -0.94 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 647 TYR 0.009 0.002 TYR F 580 PHE 0.011 0.002 PHE F 979 TRP 0.016 0.001 TRP D 910 HIS 0.010 0.001 HIS F 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (12070) covalent geometry : angle 0.56927 / 0.30 (16351) SS BOND : bond 0.00506 / 0.34 ( 57) SS BOND : angle 1.12334 / 0.79 ( 114) hydrogen bonds : bond 0.04178 / 2.92 ( 338) hydrogen bonds : angle 4.93760 / 3.50 ( 1062) link_NAG-ASN : bond 0.00185 / 0.10 ( 6) link_NAG-ASN : angle 2.32663 / 1.37 ( 18) *********************** 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 175 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8553 (m) cc_final: 0.8117 (p) REVERT: D 638 PHE cc_start: 0.7850 (m-80) cc_final: 0.7257 (m-80) REVERT: D 675 GLU cc_start: 0.7312 (mp0) cc_final: 0.6884 (pp20) REVERT: D 810 HIS cc_start: 0.7116 (m90) cc_final: 0.6513 (m-70) REVERT: E 571 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7701 (mmm-85) REVERT: E 649 MET cc_start: 0.8870 (mtm) cc_final: 0.8553 (mtp) REVERT: E 671 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8565 (mm) REVERT: E 735 TYR cc_start: 0.9011 (t80) cc_final: 0.8775 (t80) REVERT: E 791 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7839 (mttm) REVERT: E 820 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8226 (mt-10) REVERT: E 874 LYS cc_start: 0.8181 (tttt) cc_final: 0.7826 (ttpt) REVERT: E 914 LEU cc_start: 0.8448 (mm) cc_final: 0.7924 (pp) REVERT: E 1023 ASP cc_start: 0.6851 (m-30) cc_final: 0.6608 (m-30) REVERT: F 543 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8125 (mt-10) REVERT: F 649 MET cc_start: 0.9101 (mtm) cc_final: 0.8896 (mtt) REVERT: F 685 ASN cc_start: 0.7065 (t0) cc_final: 0.6625 (m-40) REVERT: F 758 ARG cc_start: 0.8312 (ptp-110) cc_final: 0.8054 (ptp90) REVERT: F 874 LYS cc_start: 0.8536 (pttm) cc_final: 0.8008 (mttm) outliers start: 32 outliers final: 22 residues processed: 166 average time/residue: 0.0873 time to fit residues: 21.2260 Evaluate side-chains 150 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 539 GLN Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 921 THR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 671 LEU 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 1026 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 822 MET Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 988 THR 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 59 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 98 optimal weight: 0.0050 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 810 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.174760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142486 restraints weight = 13912.430| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.92 r_work: 0.3400 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12133 Z= 0.126 Angle : 0.505 12.207 16483 Z= 0.266 Chirality : 0.043 0.231 1734 Planarity : 0.004 0.050 2146 Dihedral : 4.686 27.266 1748 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.13 % Allowed : 11.89 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.20), residues: 1525 helix: 1.90 (0.39), residues: 193 sheet: -0.95 (0.37), residues: 170 loop : -0.87 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 647 TYR 0.006 0.001 TYR E 735 PHE 0.007 0.001 PHE F 979 TRP 0.011 0.001 TRP F 541 HIS 0.007 0.001 HIS D 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12070) covalent geometry : angle 0.49644 / 0.26 (16351) SS BOND : bond 0.00292 / 0.20 ( 57) SS BOND : angle 0.80191 / 0.57 ( 114) hydrogen bonds : bond 0.03422 / 2.40 ( 338) hydrogen bonds : angle 4.49658 / 3.20 ( 1062) link_NAG-ASN : bond 0.00125 / 0.06 ( 6) link_NAG-ASN : angle 2.33178 / 1.37 ( 18) *********************** 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 179 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 638 PHE cc_start: 0.7948 (m-80) cc_final: 0.7721 (m-10) REVERT: D 675 GLU cc_start: 0.7317 (mp0) cc_final: 0.6865 (pp20) REVERT: D 810 HIS cc_start: 0.7009 (m90) cc_final: 0.6768 (m-70) REVERT: E 649 MET cc_start: 0.8785 (mtm) cc_final: 0.8503 (mtp) REVERT: E 735 TYR cc_start: 0.9050 (t80) cc_final: 0.8800 (t80) REVERT: E 820 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8173 (mt-10) REVERT: E 874 LYS cc_start: 0.8163 (tttt) cc_final: 0.7897 (ttpt) REVERT: E 914 LEU cc_start: 0.8396 (mm) cc_final: 0.7887 (pp) REVERT: E 1023 ASP cc_start: 0.6851 (m-30) cc_final: 0.6615 (m-30) REVERT: F 543 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8180 (mt-10) REVERT: F 597 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8056 (mt-10) REVERT: F 685 ASN cc_start: 0.7110 (t0) cc_final: 0.6671 (m-40) REVERT: F 758 ARG cc_start: 0.8197 (ptp-110) cc_final: 0.7963 (ptp90) REVERT: F 789 ASN cc_start: 0.8407 (t160) cc_final: 0.8138 (p0) REVERT: F 874 LYS cc_start: 0.8442 (pttm) cc_final: 0.7970 (mttm) REVERT: F 914 LEU cc_start: 0.8654 (mm) cc_final: 0.8356 (mt) outliers start: 27 outliers final: 22 residues processed: 171 average time/residue: 0.0860 time to fit residues: 21.4280 Evaluate side-chains 155 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 680 VAL Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 886 ILE Chi-restraints excluded: chain D residue 889 TRP Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 970 LEU Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 566 THR 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 Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 936 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3984 r_free = 0.3984 target = 0.173603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.140901 restraints weight = 13889.800| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.90 r_work: 0.3308 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12133 Z= 0.174 Angle : 0.532 12.289 16483 Z= 0.281 Chirality : 0.044 0.215 1734 Planarity : 0.004 0.049 2146 Dihedral : 4.830 29.614 1748 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.07 % Allowed : 12.36 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.20), residues: 1525 helix: 1.80 (0.38), residues: 193 sheet: -0.92 (0.37), residues: 170 loop : -0.90 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 647 TYR 0.008 0.002 TYR F 580 PHE 0.007 0.001 PHE E 842 TRP 0.016 0.001 TRP F 541 HIS 0.006 0.001 HIS F 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (12070) covalent geometry : angle 0.52276 / 0.28 (16351) SS BOND : bond 0.00382 / 0.26 ( 57) SS BOND : angle 0.94605 / 0.68 ( 114) hydrogen bonds : bond 0.03566 / 2.49 ( 338) hydrogen bonds : angle 4.53979 / 3.23 ( 1062) link_NAG-ASN : bond 0.00171 / 0.10 ( 6) link_NAG-ASN : angle 2.26017 / 1.33 ( 18) *********************** 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 175 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8606 (m) cc_final: 0.8145 (p) REVERT: D 593 GLU cc_start: 0.6659 (pp20) cc_final: 0.6440 (pp20) REVERT: D 638 PHE cc_start: 0.7850 (m-80) cc_final: 0.7546 (m-80) REVERT: D 675 GLU cc_start: 0.7302 (mp0) cc_final: 0.6826 (pp20) REVERT: D 810 HIS cc_start: 0.6928 (m90) cc_final: 0.6600 (m-70) REVERT: E 571 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7704 (mmm-85) REVERT: E 649 MET cc_start: 0.8840 (mtm) cc_final: 0.8545 (mtp) REVERT: E 671 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8492 (mm) REVERT: E 735 TYR cc_start: 0.9020 (t80) cc_final: 0.8816 (t80) REVERT: E 820 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8207 (mt-10) REVERT: E 874 LYS cc_start: 0.8184 (tttt) cc_final: 0.7854 (ttpt) REVERT: E 914 LEU cc_start: 0.8409 (mm) cc_final: 0.7823 (pp) REVERT: E 939 SER cc_start: 0.8084 (m) cc_final: 0.7631 (p) REVERT: E 1023 ASP cc_start: 0.6785 (m-30) cc_final: 0.6542 (m-30) REVERT: F 503 CYS cc_start: 0.8005 (t) cc_final: 0.7597 (t) REVERT: F 543 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8286 (mt-10) REVERT: F 685 ASN cc_start: 0.7069 (t0) cc_final: 0.6774 (m-40) REVERT: F 789 ASN cc_start: 0.8354 (t160) cc_final: 0.8122 (p0) REVERT: F 857 GLU cc_start: 0.8165 (tp30) cc_final: 0.7879 (tt0) REVERT: F 874 LYS cc_start: 0.8421 (pttm) cc_final: 0.7934 (mttm) REVERT: F 914 LEU cc_start: 0.8646 (mm) cc_final: 0.8368 (mt) REVERT: F 1011 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7426 (mtm110) outliers start: 39 outliers final: 29 residues processed: 165 average time/residue: 0.1018 time to fit residues: 24.4173 Evaluate side-chains 157 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 827 THR Chi-restraints excluded: chain E residue 938 CYS 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 153 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 546 GLN ** E 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 789 ASN F 810 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.171553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139596 restraints weight = 13993.077| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.87 r_work: 0.3379 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12133 Z= 0.166 Angle : 0.525 12.191 16483 Z= 0.277 Chirality : 0.044 0.205 1734 Planarity : 0.004 0.051 2146 Dihedral : 4.802 28.620 1748 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.07 % Allowed : 13.07 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.20), residues: 1525 helix: 1.86 (0.39), residues: 193 sheet: -0.96 (0.36), residues: 170 loop : -0.89 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 647 TYR 0.007 0.001 TYR F 580 PHE 0.008 0.001 PHE E 842 TRP 0.020 0.001 TRP F 541 HIS 0.006 0.001 HIS F 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (12070) covalent geometry : angle 0.51631 / 0.27 (16351) SS BOND : bond 0.00375 / 0.25 ( 57) SS BOND : angle 0.91288 / 0.67 ( 114) hydrogen bonds : bond 0.03465 / 2.41 ( 338) hydrogen bonds : angle 4.48514 / 3.20 ( 1062) link_NAG-ASN : bond 0.00188 / 0.12 ( 6) link_NAG-ASN : angle 2.21189 / 1.28 ( 18) *********************** 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 174 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8584 (m) cc_final: 0.8178 (p) REVERT: D 638 PHE cc_start: 0.7919 (m-80) cc_final: 0.7535 (m-80) REVERT: D 675 GLU cc_start: 0.7300 (mp0) cc_final: 0.6848 (pp20) REVERT: D 810 HIS cc_start: 0.6901 (m90) cc_final: 0.6698 (m-70) REVERT: D 903 TRP cc_start: 0.8166 (m-10) cc_final: 0.7627 (m-10) REVERT: E 571 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7733 (mmm-85) REVERT: E 649 MET cc_start: 0.8802 (mtm) cc_final: 0.8509 (mtp) REVERT: E 671 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8141 (mm) REVERT: E 820 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8177 (mt-10) REVERT: E 874 LYS cc_start: 0.8203 (tttt) cc_final: 0.7840 (ttpt) REVERT: E 914 LEU cc_start: 0.8425 (mm) cc_final: 0.7833 (pp) REVERT: E 939 SER cc_start: 0.8043 (m) cc_final: 0.7576 (p) REVERT: E 1023 ASP cc_start: 0.6832 (m-30) cc_final: 0.6608 (m-30) REVERT: F 543 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8283 (mt-10) REVERT: F 685 ASN cc_start: 0.7067 (t0) cc_final: 0.6779 (m-40) REVERT: F 789 ASN cc_start: 0.8399 (t0) cc_final: 0.8188 (p0) REVERT: F 857 GLU cc_start: 0.8091 (tp30) cc_final: 0.7858 (tt0) REVERT: F 874 LYS cc_start: 0.8390 (pttm) cc_final: 0.7960 (mttm) REVERT: F 914 LEU cc_start: 0.8682 (mm) cc_final: 0.8395 (mt) REVERT: F 1011 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7638 (mtm110) outliers start: 39 outliers final: 30 residues processed: 164 average time/residue: 0.0936 time to fit residues: 22.7821 Evaluate side-chains 154 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 886 ILE Chi-restraints excluded: chain D residue 889 TRP Chi-restraints excluded: chain D residue 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 901 THR Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 546 GLN E 550 HIS F 810 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.168565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135929 restraints weight = 13858.765| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.93 r_work: 0.3378 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 12133 Z= 0.275 Angle : 0.614 10.530 16483 Z= 0.325 Chirality : 0.047 0.195 1734 Planarity : 0.005 0.051 2146 Dihedral : 5.386 31.451 1748 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.15 % Allowed : 14.25 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1525 helix: 1.49 (0.38), residues: 193 sheet: -1.20 (0.36), residues: 169 loop : -1.02 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 647 TYR 0.010 0.002 TYR E 735 PHE 0.021 0.002 PHE D 638 TRP 0.023 0.002 TRP F 541 HIS 0.007 0.001 HIS D 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.27 (12070) covalent geometry : angle 0.60152 / 0.32 (16351) SS BOND : bond 0.00584 / 0.40 ( 57) SS BOND : angle 1.21778 / 0.88 ( 114) hydrogen bonds : bond 0.03958 / 2.73 ( 338) hydrogen bonds : angle 4.75790 / 3.38 ( 1062) link_NAG-ASN : bond 0.00337 / 0.21 ( 6) link_NAG-ASN : angle 2.59828 / 1.51 ( 18) *********************** 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 168 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8626 (m) cc_final: 0.8228 (p) REVERT: D 675 GLU cc_start: 0.7420 (mp0) cc_final: 0.6954 (pp20) REVERT: D 742 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7585 (m) REVERT: E 571 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7783 (mmm-85) REVERT: E 649 MET cc_start: 0.8852 (mtm) cc_final: 0.8547 (mtp) REVERT: E 671 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8294 (mm) REVERT: E 820 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8287 (mt-10) REVERT: E 874 LYS cc_start: 0.8287 (tttt) cc_final: 0.7940 (ttpt) REVERT: E 914 LEU cc_start: 0.8440 (mm) cc_final: 0.7885 (pp) REVERT: E 1023 ASP cc_start: 0.7011 (m-30) cc_final: 0.6778 (m-30) REVERT: F 543 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8353 (mt-10) REVERT: F 685 ASN cc_start: 0.7106 (t0) cc_final: 0.6864 (m-40) REVERT: F 789 ASN cc_start: 0.8399 (t0) cc_final: 0.8161 (p0) REVERT: F 874 LYS cc_start: 0.8617 (pttm) cc_final: 0.8149 (mttm) REVERT: F 912 LYS cc_start: 0.8610 (tppp) cc_final: 0.8331 (ttpt) REVERT: F 914 LEU cc_start: 0.8696 (mm) cc_final: 0.8457 (mt) outliers start: 40 outliers final: 30 residues processed: 160 average time/residue: 0.0998 time to fit residues: 23.3754 Evaluate side-chains 152 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 742 THR Chi-restraints excluded: chain D residue 782 TRP Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 886 ILE Chi-restraints excluded: chain D residue 889 TRP Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 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 901 THR Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 504 ASP Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 889 TRP Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 996 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3967 r_free = 0.3967 target = 0.172014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140180 restraints weight = 13817.691| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.88 r_work: 0.3337 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12133 Z= 0.166 Angle : 0.541 10.248 16483 Z= 0.288 Chirality : 0.044 0.189 1734 Planarity : 0.004 0.052 2146 Dihedral : 4.997 28.669 1748 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.52 % Allowed : 15.20 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.20), residues: 1525 helix: 1.70 (0.39), residues: 193 sheet: -1.17 (0.35), residues: 166 loop : -0.96 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 595 TYR 0.007 0.001 TYR F 580 PHE 0.027 0.002 PHE D 638 TRP 0.017 0.001 TRP F 541 HIS 0.008 0.001 HIS D 810 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (12070) covalent geometry : angle 0.53175 / 0.29 (16351) SS BOND : bond 0.00385 / 0.27 ( 57) SS BOND : angle 0.96128 / 0.70 ( 114) hydrogen bonds : bond 0.03462 / 2.41 ( 338) hydrogen bonds : angle 4.51090 / 3.22 ( 1062) link_NAG-ASN : bond 0.00203 / 0.13 ( 6) link_NAG-ASN : angle 2.31949 / 1.34 ( 18) *********************** 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 165 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8514 (m) cc_final: 0.8172 (p) REVERT: D 675 GLU cc_start: 0.7161 (mp0) cc_final: 0.6720 (pp20) REVERT: D 742 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7468 (m) REVERT: D 794 ARG cc_start: 0.7070 (mmt-90) cc_final: 0.6853 (mmt-90) REVERT: D 903 TRP cc_start: 0.8226 (m-10) cc_final: 0.7715 (m-10) REVERT: E 571 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7774 (mmm-85) REVERT: E 649 MET cc_start: 0.8835 (mtm) cc_final: 0.8545 (mtp) REVERT: E 671 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8224 (mm) REVERT: E 820 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8257 (mt-10) REVERT: E 874 LYS cc_start: 0.8247 (tttt) cc_final: 0.7860 (ttpt) REVERT: E 914 LEU cc_start: 0.8416 (mm) cc_final: 0.7826 (pp) REVERT: E 1023 ASP cc_start: 0.6821 (m-30) cc_final: 0.6586 (m-30) REVERT: F 543 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8234 (mt-10) REVERT: F 685 ASN cc_start: 0.7077 (t0) cc_final: 0.6808 (m-40) REVERT: F 789 ASN cc_start: 0.8372 (t0) cc_final: 0.8159 (p0) REVERT: F 874 LYS cc_start: 0.8525 (pttm) cc_final: 0.8035 (mttm) REVERT: F 914 LEU cc_start: 0.8655 (mm) cc_final: 0.8410 (mt) outliers start: 32 outliers final: 30 residues processed: 156 average time/residue: 0.1019 time to fit residues: 23.2082 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 : 0.454 ------------------------------------------------------------------------------- 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 742 THR 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 901 THR Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 504 ASP Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 889 TRP Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 996 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 49 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 546 GLN E 550 HIS F 810 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.173073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.141415 restraints weight = 13720.334| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.87 r_work: 0.3356 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12133 Z= 0.149 Angle : 0.522 9.638 16483 Z= 0.278 Chirality : 0.043 0.184 1734 Planarity : 0.004 0.051 2146 Dihedral : 4.784 27.732 1748 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1525 helix: 1.83 (0.39), residues: 193 sheet: -1.04 (0.36), residues: 160 loop : -0.91 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 913 TYR 0.007 0.001 TYR F 580 PHE 0.007 0.001 PHE F 979 TRP 0.020 0.001 TRP F 541 HIS 0.005 0.001 HIS F 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (12070) covalent geometry : angle 0.51398 / 0.28 (16351) SS BOND : bond 0.00343 / 0.24 ( 57) SS BOND : angle 0.91406 / 0.67 ( 114) hydrogen bonds : bond 0.03294 / 2.30 ( 338) hydrogen bonds : angle 4.36877 / 3.13 ( 1062) link_NAG-ASN : bond 0.00187 / 0.12 ( 6) link_NAG-ASN : angle 2.14599 / 1.24 ( 18) *********************** 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 162 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8502 (m) cc_final: 0.8165 (p) REVERT: D 675 GLU cc_start: 0.7114 (mp0) cc_final: 0.6652 (pp20) REVERT: D 742 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7448 (m) REVERT: E 571 ARG cc_start: 0.7950 (mmm-85) cc_final: 0.7732 (mmm-85) REVERT: E 649 MET cc_start: 0.8834 (mtm) cc_final: 0.8543 (mtp) REVERT: E 671 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8234 (mm) REVERT: E 820 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8219 (mt-10) REVERT: E 874 LYS cc_start: 0.8239 (tttt) cc_final: 0.7825 (ttpt) REVERT: E 914 LEU cc_start: 0.8387 (mm) cc_final: 0.7804 (pp) REVERT: E 939 SER cc_start: 0.7989 (m) cc_final: 0.7557 (p) REVERT: E 1023 ASP cc_start: 0.6842 (m-30) cc_final: 0.6600 (m-30) REVERT: F 543 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8296 (mt-10) REVERT: F 685 ASN cc_start: 0.7117 (t0) cc_final: 0.6825 (m-40) REVERT: F 874 LYS cc_start: 0.8452 (pttm) cc_final: 0.7978 (mttm) REVERT: F 1011 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7338 (mtm110) outliers start: 33 outliers final: 30 residues processed: 152 average time/residue: 0.0899 time to fit residues: 20.5601 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 : 0.358 ------------------------------------------------------------------------------- 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 742 THR Chi-restraints excluded: chain D residue 782 TRP Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 886 ILE Chi-restraints excluded: chain D residue 889 TRP Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 590 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 822 MET Chi-restraints excluded: chain F residue 889 TRP Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 996 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 106 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 93 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 139 optimal weight: 0.4980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 546 GLN E 550 HIS F 810 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.175259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143814 restraints weight = 13878.382| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.88 r_work: 0.3343 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12133 Z= 0.116 Angle : 0.499 9.517 16483 Z= 0.266 Chirality : 0.042 0.175 1734 Planarity : 0.004 0.052 2146 Dihedral : 4.543 25.559 1748 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.13 % Allowed : 16.06 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1525 helix: 1.99 (0.39), residues: 193 sheet: -1.05 (0.40), residues: 137 loop : -0.85 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 913 TYR 0.005 0.001 TYR F 580 PHE 0.006 0.001 PHE F 979 TRP 0.021 0.001 TRP F 541 HIS 0.005 0.001 HIS D 810 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (12070) covalent geometry : angle 0.49251 / 0.26 (16351) SS BOND : bond 0.00266 / 0.18 ( 57) SS BOND : angle 0.80477 / 0.59 ( 114) hydrogen bonds : bond 0.03070 / 2.15 ( 338) hydrogen bonds : angle 4.20981 / 3.02 ( 1062) link_NAG-ASN : bond 0.00171 / 0.09 ( 6) link_NAG-ASN : angle 1.94965 / 1.13 ( 18) ********************** 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 159 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 501 SER cc_start: 0.8496 (m) cc_final: 0.8116 (p) REVERT: D 675 GLU cc_start: 0.7113 (mp0) cc_final: 0.6596 (pp20) REVERT: D 742 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7312 (m) REVERT: E 550 HIS cc_start: 0.7813 (p90) cc_final: 0.7233 (p90) REVERT: E 571 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.7700 (mmm-85) REVERT: E 649 MET cc_start: 0.8829 (mtm) cc_final: 0.8534 (mtp) REVERT: E 671 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8191 (mm) REVERT: E 820 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8107 (mt-10) REVERT: E 874 LYS cc_start: 0.8144 (tttt) cc_final: 0.7673 (ttpt) REVERT: E 914 LEU cc_start: 0.8420 (mm) cc_final: 0.7831 (pp) REVERT: E 939 SER cc_start: 0.7957 (m) cc_final: 0.7480 (p) REVERT: E 1023 ASP cc_start: 0.6779 (m-30) cc_final: 0.6534 (m-30) REVERT: F 543 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8201 (mt-10) REVERT: F 685 ASN cc_start: 0.6935 (t0) cc_final: 0.6640 (m-40) REVERT: F 874 LYS cc_start: 0.8350 (pttm) cc_final: 0.7832 (mttm) REVERT: F 1011 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7276 (mtm110) outliers start: 27 outliers final: 25 residues processed: 151 average time/residue: 0.0950 time to fit residues: 21.1887 Evaluate side-chains 149 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 782 TRP Chi-restraints excluded: chain D residue 801 HIS Chi-restraints excluded: chain D residue 886 ILE Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 590 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 938 CYS Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 996 VAL Chi-restraints excluded: chain E residue 1005 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain F residue 567 CYS Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 822 MET Chi-restraints excluded: chain F residue 916 SER Chi-restraints excluded: chain F residue 996 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 56 optimal weight: 0.0070 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 8 optimal weight: 0.0050 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 overall best weight: 0.3210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4025 r_free = 0.4025 target = 0.177268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145501 restraints weight = 13777.568| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.85 r_work: 0.3361 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12133 Z= 0.102 Angle : 0.487 8.877 16483 Z= 0.259 Chirality : 0.042 0.172 1734 Planarity : 0.004 0.050 2146 Dihedral : 4.346 23.921 1748 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.97 % Allowed : 16.54 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1525 helix: 2.09 (0.40), residues: 193 sheet: -0.95 (0.39), residues: 147 loop : -0.78 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F1012 TYR 0.006 0.001 TYR E 735 PHE 0.011 0.001 PHE D 638 TRP 0.020 0.001 TRP F 541 HIS 0.007 0.001 HIS D 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (12070) covalent geometry : angle 0.48117 / 0.26 (16351) SS BOND : bond 0.00230 / 0.16 ( 57) SS BOND : angle 0.74953 / 0.55 ( 114) hydrogen bonds : bond 0.02948 / 2.06 ( 338) hydrogen bonds : angle 4.06273 / 2.92 ( 1062) link_NAG-ASN : bond 0.00169 / 0.09 ( 6) link_NAG-ASN : angle 1.78204 / 1.04 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3158.52 seconds wall clock time: 54 minutes 41.23 seconds (3281.23 seconds total)