Starting phenix.real_space_refine on Thu Sep 18 11:35:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n4q_0341/09_2025/6n4q_0341_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n4q_0341/09_2025/6n4q_0341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n4q_0341/09_2025/6n4q_0341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n4q_0341/09_2025/6n4q_0341.map" model { file = "/net/cci-nas-00/data/ceres_data/6n4q_0341/09_2025/6n4q_0341_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n4q_0341/09_2025/6n4q_0341_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 10638 2.51 5 N 2624 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16358 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2136 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 252} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2150 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 8, 'TRANS': 253} Chain: "E" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 262 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "F" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 262 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "C" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2136 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 252} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2150 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 8, 'TRANS': 253} Chain: "G" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 262 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "H" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 262 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "I" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1649 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "J" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1720 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1649 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "L" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1720 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.28, per 1000 atoms: 0.26 Number of scatterers: 16358 At special positions: 0 Unit cell: (146.4, 147.6, 201.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 2976 8.00 N 2624 7.00 C 10638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 16 " distance=2.04 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 21 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 25 " distance=2.03 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 16 " distance=2.04 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 21 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 25 " distance=2.03 Simple disulfide: pdb=" SG CYS G 2 " - pdb=" SG CYS G 16 " distance=2.04 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 21 " distance=2.03 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 25 " distance=2.03 Simple disulfide: pdb=" SG CYS H 2 " - pdb=" SG CYS H 16 " distance=2.04 Simple disulfide: pdb=" SG CYS H 9 " - pdb=" SG CYS H 21 " distance=2.03 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 25 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 149 " - pdb=" SG CYS J 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 149 " - pdb=" SG CYS L 204 " 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 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 850.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 26 sheets defined 44.2% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 732 through 752 removed outlier: 3.826A pdb=" N THR A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 785 removed outlier: 3.581A pdb=" N VAL A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 793 removed outlier: 3.729A pdb=" N PHE A 792 " --> pdb=" O ILE A 789 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 793 " --> pdb=" O SER A 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 789 through 793' Processing helix chain 'A' and resid 795 through 813 removed outlier: 3.834A pdb=" N LEU A 811 " --> pdb=" O SER A 807 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 813 " --> pdb=" O VAL A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 removed outlier: 3.971A pdb=" N LEU A 822 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 830 removed outlier: 3.558A pdb=" N VAL A 830 " --> pdb=" O LEU A 827 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 827 through 830' Processing helix chain 'A' and resid 831 through 837 removed outlier: 3.648A pdb=" N THR A 835 " --> pdb=" O PHE A 831 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 849 Processing helix chain 'A' and resid 850 through 853 Processing helix chain 'A' and resid 854 through 876 removed outlier: 3.795A pdb=" N ILE A 858 " --> pdb=" O MET A 854 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 885 removed outlier: 3.664A pdb=" N PHE A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 899 removed outlier: 3.590A pdb=" N THR A 899 " --> pdb=" O PHE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 912 removed outlier: 3.593A pdb=" N LEU A 911 " --> pdb=" O ILE A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 945 Proline residue: A 924 - end of helix removed outlier: 3.535A pdb=" N PHE A 927 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 930 " --> pdb=" O ILE A 926 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 977 removed outlier: 3.714A pdb=" N GLU A 959 " --> pdb=" O HIS A 955 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 967 " --> pdb=" O HIS A 963 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN A 969 " --> pdb=" O ASP A 965 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU A 970 " --> pdb=" O ASN A 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 731 Processing helix chain 'B' and resid 732 through 752 removed outlier: 3.801A pdb=" N THR B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B 737 " --> pdb=" O SER B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 787 removed outlier: 4.000A pdb=" N ILE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 786 " --> pdb=" O LEU B 782 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS B 787 " --> pdb=" O ARG B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 813 Processing helix chain 'B' and resid 821 through 828 removed outlier: 4.045A pdb=" N PHE B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 836 removed outlier: 3.673A pdb=" N THR B 835 " --> pdb=" O PHE B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 849 removed outlier: 3.504A pdb=" N SER B 849 " --> pdb=" O SER B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 877 removed outlier: 3.828A pdb=" N ILE B 858 " --> pdb=" O MET B 854 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 875 " --> pdb=" O MET B 871 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 876 " --> pdb=" O ALA B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 899 removed outlier: 5.046A pdb=" N TYR B 892 " --> pdb=" O GLY B 888 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 899 " --> pdb=" O PHE B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 965 removed outlier: 3.694A pdb=" N PHE B 922 " --> pdb=" O ALA B 918 " (cutoff:3.500A) Proline residue: B 924 - end of helix removed outlier: 3.673A pdb=" N THR B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE B 931 " --> pdb=" O PHE B 927 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 940 " --> pdb=" O LEU B 936 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN B 954 " --> pdb=" O GLN B 950 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE B 956 " --> pdb=" O GLU B 952 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 957 " --> pdb=" O GLU B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 978 removed outlier: 3.852A pdb=" N GLU B 970 " --> pdb=" O ASN B 966 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 977 " --> pdb=" O LYS B 973 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 730 Processing helix chain 'C' and resid 732 through 752 removed outlier: 3.772A pdb=" N THR C 736 " --> pdb=" O SER C 732 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N MET C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 785 removed outlier: 3.541A pdb=" N VAL C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 793 removed outlier: 3.636A pdb=" N PHE C 792 " --> pdb=" O ILE C 789 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 793 " --> pdb=" O SER C 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 789 through 793' Processing helix chain 'C' and resid 795 through 813 removed outlier: 3.799A pdb=" N LEU C 811 " --> pdb=" O SER C 807 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE C 812 " --> pdb=" O LEU C 808 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 813 " --> pdb=" O VAL C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 826 removed outlier: 3.927A pdb=" N LEU C 822 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 834 removed outlier: 3.621A pdb=" N VAL C 830 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG C 832 " --> pdb=" O ARG C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 849 Processing helix chain 'C' and resid 850 through 853 Processing helix chain 'C' and resid 854 through 876 removed outlier: 3.784A pdb=" N ILE C 858 " --> pdb=" O MET C 854 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 885 removed outlier: 3.627A pdb=" N PHE C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 899 removed outlier: 3.647A pdb=" N THR C 899 " --> pdb=" O PHE C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 912 removed outlier: 3.594A pdb=" N LEU C 911 " --> pdb=" O ILE C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 945 Proline residue: C 924 - end of helix removed outlier: 3.503A pdb=" N PHE C 927 " --> pdb=" O ILE C 923 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR C 930 " --> pdb=" O ILE C 926 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE C 940 " --> pdb=" O LEU C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 977 removed outlier: 3.763A pdb=" N GLU C 959 " --> pdb=" O HIS C 955 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE C 967 " --> pdb=" O HIS C 963 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN C 968 " --> pdb=" O GLU C 964 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN C 969 " --> pdb=" O ASP C 965 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU C 970 " --> pdb=" O ASN C 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 731 Processing helix chain 'D' and resid 732 through 752 removed outlier: 3.860A pdb=" N THR D 736 " --> pdb=" O SER D 732 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 787 removed outlier: 4.004A pdb=" N ILE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL D 786 " --> pdb=" O LEU D 782 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS D 787 " --> pdb=" O ARG D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 813 Processing helix chain 'D' and resid 823 through 828 removed outlier: 3.743A pdb=" N LEU D 827 " --> pdb=" O ARG D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 836 removed outlier: 3.651A pdb=" N THR D 835 " --> pdb=" O PHE D 831 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 849 Processing helix chain 'D' and resid 854 through 877 removed outlier: 3.817A pdb=" N ILE D 858 " --> pdb=" O MET D 854 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN D 874 " --> pdb=" O ILE D 870 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU D 875 " --> pdb=" O MET D 871 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE D 876 " --> pdb=" O ALA D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 899 removed outlier: 5.083A pdb=" N TYR D 892 " --> pdb=" O GLY D 888 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR D 899 " --> pdb=" O PHE D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 978 removed outlier: 3.672A pdb=" N PHE D 922 " --> pdb=" O ALA D 918 " (cutoff:3.500A) Proline residue: D 924 - end of helix removed outlier: 3.677A pdb=" N THR D 930 " --> pdb=" O ILE D 926 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE D 931 " --> pdb=" O PHE D 927 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 940 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN D 954 " --> pdb=" O GLN D 950 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS D 955 " --> pdb=" O LYS D 951 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE D 956 " --> pdb=" O GLU D 952 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE D 957 " --> pdb=" O GLU D 953 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN D 966 " --> pdb=" O SER D 962 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE D 967 " --> pdb=" O HIS D 963 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN D 969 " --> pdb=" O ASP D 965 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 970 " --> pdb=" O ASN D 966 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS D 973 " --> pdb=" O ASN D 969 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 977 " --> pdb=" O LYS D 973 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE D 978 " --> pdb=" O LEU D 974 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 3.673A pdb=" N LEU I 126 " --> pdb=" O SER I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 removed outlier: 3.669A pdb=" N GLU I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.914A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 65 removed outlier: 3.725A pdb=" N VAL J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS J 65 " --> pdb=" O ASP J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 65' Processing helix chain 'J' and resid 138 through 142 removed outlier: 3.561A pdb=" N THR J 141 " --> pdb=" O GLY J 138 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY J 142 " --> pdb=" O ASP J 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 138 through 142' Processing helix chain 'K' and resid 122 through 128 removed outlier: 3.672A pdb=" N LEU K 126 " --> pdb=" O SER K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 189 removed outlier: 3.669A pdb=" N GLU K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.914A pdb=" N TYR L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 removed outlier: 3.724A pdb=" N VAL L 64 " --> pdb=" O PRO L 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS L 65 " --> pdb=" O ASP L 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 61 through 65' Processing helix chain 'L' and resid 138 through 142 removed outlier: 3.560A pdb=" N THR L 141 " --> pdb=" O GLY L 138 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY L 142 " --> pdb=" O ASP L 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 138 through 142' Processing sheet with id=AA1, first strand: chain 'E' and resid 20 through 21 removed outlier: 3.590A pdb=" N LYS E 26 " --> pdb=" O VAL E 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 20 through 21 removed outlier: 3.590A pdb=" N LYS F 26 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 20 through 21 removed outlier: 3.590A pdb=" N LYS G 26 " --> pdb=" O VAL G 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.590A pdb=" N LYS H 26 " --> pdb=" O VAL H 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.575A pdb=" N SER I 7 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU I 74 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR I 72 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.504A pdb=" N MET I 11 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU I 106 " --> pdb=" O MET I 11 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N TYR I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP I 36 " --> pdb=" O TRP I 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.504A pdb=" N MET I 11 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU I 106 " --> pdb=" O MET I 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 115 through 119 removed outlier: 3.573A pdb=" N THR I 115 " --> pdb=" O ASN I 138 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR I 174 " --> pdb=" O ASN I 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 154 through 155 removed outlier: 3.686A pdb=" N LYS I 148 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR I 193 " --> pdb=" O PHE I 210 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE I 210 " --> pdb=" O TYR I 193 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS I 195 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS I 208 " --> pdb=" O CYS I 195 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA I 197 " --> pdb=" O ILE I 206 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE I 206 " --> pdb=" O ALA I 197 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS I 199 " --> pdb=" O SER I 204 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER I 204 " --> pdb=" O HIS I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.849A pdb=" N SER J 7 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU J 18 " --> pdb=" O MET J 83 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU J 81 " --> pdb=" O LEU J 20 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP J 73 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR J 80 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.078A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR J 116 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N MET J 34 " --> pdb=" O THR J 50 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG J 44 " --> pdb=" O THR J 40 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR J 50 " --> pdb=" O TYR J 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.078A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR J 116 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR J 111 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 129 through 133 removed outlier: 3.904A pdb=" N GLY J 148 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR J 184 " --> pdb=" O GLY J 153 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER J 189 " --> pdb=" O HIS J 173 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 129 through 133 removed outlier: 3.904A pdb=" N GLY J 148 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR J 184 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 160 through 163 Processing sheet with id=AB7, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.575A pdb=" N SER K 7 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU K 74 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR K 72 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.505A pdb=" N MET K 11 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU K 106 " --> pdb=" O MET K 11 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP K 36 " --> pdb=" O TRP K 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.505A pdb=" N MET K 11 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU K 106 " --> pdb=" O MET K 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 115 through 119 removed outlier: 3.574A pdb=" N THR K 115 " --> pdb=" O ASN K 138 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR K 174 " --> pdb=" O ASN K 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 154 through 155 removed outlier: 3.687A pdb=" N LYS K 148 " --> pdb=" O GLU K 196 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR K 193 " --> pdb=" O PHE K 210 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE K 210 " --> pdb=" O TYR K 193 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS K 195 " --> pdb=" O LYS K 208 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS K 208 " --> pdb=" O CYS K 195 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA K 197 " --> pdb=" O ILE K 206 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE K 206 " --> pdb=" O ALA K 197 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS K 199 " --> pdb=" O SER K 204 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER K 204 " --> pdb=" O HIS K 199 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 3 through 7 removed outlier: 3.849A pdb=" N SER L 7 " --> pdb=" O SER L 21 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER L 21 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU L 18 " --> pdb=" O MET L 83 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU L 81 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER L 78 " --> pdb=" O ASP L 73 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP L 73 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR L 80 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER L 71 " --> pdb=" O TYR L 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.078A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 116 " --> pdb=" O TYR L 94 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N MET L 34 " --> pdb=" O THR L 50 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG L 44 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR L 50 " --> pdb=" O TYR L 59 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.078A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 116 " --> pdb=" O TYR L 94 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR L 111 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 129 through 133 removed outlier: 3.904A pdb=" N GLY L 148 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR L 184 " --> pdb=" O GLY L 153 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER L 189 " --> pdb=" O HIS L 173 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 129 through 133 removed outlier: 3.904A pdb=" N GLY L 148 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR L 184 " --> pdb=" O GLY L 153 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 160 through 163 792 hydrogen bonds defined for protein. 2217 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: 3.08 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4844 1.34 - 1.46: 4358 1.46 - 1.58: 7378 1.58 - 1.71: 0 1.71 - 1.83: 192 Bond restraints: 16772 Sorted by residual: bond pdb=" CA SER C 849 " pdb=" C SER C 849 " ideal model delta sigma weight residual 1.523 1.552 -0.028 1.34e-02 5.57e+03 4.49e+00 bond pdb=" CG LEU B 833 " pdb=" CD2 LEU B 833 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.79e+00 bond pdb=" CG LEU D 833 " pdb=" CD2 LEU D 833 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.68e+00 bond pdb=" CG LEU A 887 " pdb=" CD2 LEU A 887 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.48e+00 bond pdb=" CG LEU C 887 " pdb=" CD2 LEU C 887 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.45e+00 ... (remaining 16767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 21435 1.92 - 3.83: 1072 3.83 - 5.75: 180 5.75 - 7.66: 69 7.66 - 9.58: 24 Bond angle restraints: 22780 Sorted by residual: angle pdb=" C GLY I 51 " pdb=" N THR I 52 " pdb=" CA THR I 52 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C GLY K 51 " pdb=" N THR K 52 " pdb=" CA THR K 52 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C PRO B 756 " pdb=" N MET B 757 " pdb=" CA MET B 757 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C PRO D 756 " pdb=" N MET D 757 " pdb=" CA MET D 757 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C THR J 140 " pdb=" N THR J 141 " pdb=" CA THR J 141 " ideal model delta sigma weight residual 122.82 128.79 -5.97 1.42e+00 4.96e-01 1.77e+01 ... (remaining 22775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 9349 15.02 - 30.04: 445 30.04 - 45.07: 122 45.07 - 60.09: 6 60.09 - 75.11: 16 Dihedral angle restraints: 9938 sinusoidal: 3922 harmonic: 6016 Sorted by residual: dihedral pdb=" CA PHE A 792 " pdb=" C PHE A 792 " pdb=" N LYS A 793 " pdb=" CA LYS A 793 " ideal model delta harmonic sigma weight residual 180.00 148.43 31.57 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA PHE C 792 " pdb=" C PHE C 792 " pdb=" N LYS C 793 " pdb=" CA LYS C 793 " ideal model delta harmonic sigma weight residual 180.00 148.84 31.16 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA GLU B 753 " pdb=" C GLU B 753 " pdb=" N HIS B 754 " pdb=" CA HIS B 754 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 9935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2332 0.087 - 0.173: 259 0.173 - 0.260: 19 0.260 - 0.347: 0 0.347 - 0.433: 2 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CB ILE B 851 " pdb=" CA ILE B 851 " pdb=" CG1 ILE B 851 " pdb=" CG2 ILE B 851 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CB ILE D 851 " pdb=" CA ILE D 851 " pdb=" CG1 ILE D 851 " pdb=" CG2 ILE D 851 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA HIS D 755 " pdb=" N HIS D 755 " pdb=" C HIS D 755 " pdb=" CB HIS D 755 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2609 not shown) Planarity restraints: 2802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 909 " -0.058 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO A 910 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 910 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 910 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 909 " 0.058 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO B 910 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 910 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 910 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 909 " -0.055 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO D 910 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 910 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 910 " -0.046 5.00e-02 4.00e+02 ... (remaining 2799 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4466 2.81 - 3.33: 14652 3.33 - 3.86: 25536 3.86 - 4.38: 27144 4.38 - 4.90: 47800 Nonbonded interactions: 119598 Sorted by model distance: nonbonded pdb=" O SER K 7 " pdb=" OG1 THR K 22 " model vdw 2.288 3.040 nonbonded pdb=" O SER I 7 " pdb=" OG1 THR I 22 " model vdw 2.289 3.040 nonbonded pdb=" OE2 GLU B 760 " pdb=" ND2 ASN B 763 " model vdw 2.294 3.120 nonbonded pdb=" O TYR A 723 " pdb=" OG1 THR A 727 " model vdw 2.306 3.040 nonbonded pdb=" OG SER I 7 " pdb=" OG1 THR I 22 " model vdw 2.313 3.040 ... (remaining 119593 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.020 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 : 0.008 0.079 16792 Z= 0.330 Angle : 1.033 9.580 22820 Z= 0.559 Chirality : 0.055 0.433 2612 Planarity : 0.009 0.088 2802 Dihedral : 10.165 75.110 5978 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.11 % Allowed : 1.57 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.41 (0.16), residues: 2028 helix: -1.73 (0.15), residues: 786 sheet: -1.58 (0.25), residues: 376 loop : -3.04 (0.17), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 832 TYR 0.027 0.003 TYR C 741 PHE 0.040 0.004 PHE B 865 TRP 0.025 0.003 TRP L 36 HIS 0.012 0.003 HIS C 955 Details of bonding type rmsd covalent geometry : bond 0.00756 (16772) covalent geometry : angle 1.03314 (22780) SS BOND : bond 0.00449 ( 20) SS BOND : angle 1.17979 ( 40) hydrogen bonds : bond 0.22937 ( 752) hydrogen bonds : angle 8.50277 ( 2217) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 538 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 800 ASP cc_start: 0.8682 (t0) cc_final: 0.8423 (t0) REVERT: A 840 MET cc_start: 0.8748 (mmt) cc_final: 0.8523 (mmp) REVERT: A 866 TYR cc_start: 0.8442 (t80) cc_final: 0.8169 (t80) REVERT: A 889 GLU cc_start: 0.5694 (mm-30) cc_final: 0.4731 (mm-30) REVERT: A 933 MET cc_start: 0.8346 (mmm) cc_final: 0.7778 (ttp) REVERT: A 945 MET cc_start: 0.8632 (mtp) cc_final: 0.8366 (mtp) REVERT: A 947 ILE cc_start: 0.7342 (mt) cc_final: 0.7091 (pt) REVERT: A 957 ILE cc_start: 0.8262 (mt) cc_final: 0.7948 (pt) REVERT: B 825 PHE cc_start: 0.8790 (m-80) cc_final: 0.8278 (m-80) REVERT: B 873 THR cc_start: 0.8829 (m) cc_final: 0.8574 (m) REVERT: B 945 MET cc_start: 0.7649 (mmt) cc_final: 0.7346 (mmt) REVERT: E 24 TRP cc_start: 0.7703 (p90) cc_final: 0.7347 (p90) REVERT: F 6 MET cc_start: 0.7193 (mmp) cc_final: 0.6534 (ptt) REVERT: F 10 ASP cc_start: 0.6937 (p0) cc_final: 0.6508 (p0) REVERT: F 24 TRP cc_start: 0.7632 (p90) cc_final: 0.7160 (p-90) REVERT: C 763 ASN cc_start: 0.8564 (m110) cc_final: 0.7893 (t0) REVERT: C 784 ILE cc_start: 0.8563 (tt) cc_final: 0.8324 (tp) REVERT: C 861 MET cc_start: 0.7193 (ttp) cc_final: 0.6805 (ttp) REVERT: C 889 GLU cc_start: 0.5171 (mm-30) cc_final: 0.4648 (mm-30) REVERT: C 901 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8596 (tm-30) REVERT: C 917 TYR cc_start: 0.8857 (m-80) cc_final: 0.8613 (m-80) REVERT: C 947 ILE cc_start: 0.7205 (mt) cc_final: 0.6991 (pt) REVERT: C 966 ASN cc_start: 0.8706 (m-40) cc_final: 0.8455 (m110) REVERT: D 742 LEU cc_start: 0.9222 (tp) cc_final: 0.9000 (tp) REVERT: D 750 MET cc_start: 0.7436 (ttp) cc_final: 0.7100 (ttp) REVERT: D 772 PHE cc_start: 0.8455 (m-80) cc_final: 0.8244 (m-80) REVERT: D 804 VAL cc_start: 0.8771 (t) cc_final: 0.8525 (p) REVERT: D 825 PHE cc_start: 0.8831 (m-80) cc_final: 0.8290 (m-80) REVERT: D 840 MET cc_start: 0.8803 (mmt) cc_final: 0.8574 (mmp) REVERT: D 874 GLN cc_start: 0.8761 (mt0) cc_final: 0.8512 (mt0) REVERT: D 917 TYR cc_start: 0.8779 (m-80) cc_final: 0.8486 (m-80) REVERT: G 24 TRP cc_start: 0.7646 (p90) cc_final: 0.7232 (p90) REVERT: H 6 MET cc_start: 0.8168 (mmp) cc_final: 0.7446 (ptt) REVERT: I 11 MET cc_start: 0.4870 (ttp) cc_final: 0.4553 (ttm) REVERT: I 29 ILE cc_start: 0.5889 (mt) cc_final: 0.5444 (pt) REVERT: I 91 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7713 (tm-30) REVERT: I 98 THR cc_start: 0.8371 (m) cc_final: 0.7820 (p) REVERT: I 164 TRP cc_start: 0.7593 (m-90) cc_final: 0.7104 (m-90) REVERT: I 176 MET cc_start: 0.5371 (tmm) cc_final: 0.4853 (tmm) REVERT: J 13 LYS cc_start: 0.6015 (mttp) cc_final: 0.5796 (mmtt) REVERT: J 74 ASN cc_start: 0.7783 (m-40) cc_final: 0.7497 (m-40) REVERT: J 76 LYS cc_start: 0.8217 (mttp) cc_final: 0.7837 (tttt) REVERT: J 95 TYR cc_start: 0.6375 (m-80) cc_final: 0.4729 (m-80) REVERT: J 114 GLN cc_start: 0.7364 (pt0) cc_final: 0.7140 (pm20) REVERT: J 154 TYR cc_start: 0.7788 (p90) cc_final: 0.7251 (p90) REVERT: K 11 MET cc_start: 0.5450 (ttp) cc_final: 0.4834 (ttp) REVERT: K 29 ILE cc_start: 0.6240 (mt) cc_final: 0.5798 (pt) REVERT: K 91 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7619 (tm-30) REVERT: K 98 THR cc_start: 0.8591 (m) cc_final: 0.8006 (p) REVERT: K 164 TRP cc_start: 0.7754 (m-90) cc_final: 0.7338 (m-90) REVERT: K 176 MET cc_start: 0.5840 (tmm) cc_final: 0.5423 (tmm) REVERT: L 95 TYR cc_start: 0.6146 (m-80) cc_final: 0.5208 (m-80) REVERT: L 111 TYR cc_start: 0.7291 (t80) cc_final: 0.6556 (t80) REVERT: L 114 GLN cc_start: 0.7010 (pt0) cc_final: 0.6780 (pm20) REVERT: L 154 TYR cc_start: 0.6967 (p90) cc_final: 0.6402 (p90) REVERT: L 181 SER cc_start: 0.8959 (m) cc_final: 0.8606 (m) outliers start: 2 outliers final: 0 residues processed: 540 average time/residue: 0.1471 time to fit residues: 115.5641 Evaluate side-chains 374 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 30.0000 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 GLN A 896 GLN A 935 ASN A 961 GLN B 746 ASN B 874 GLN B 896 GLN C 754 HIS C 896 GLN C 935 ASN ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 966 ASN D 746 ASN D 896 GLN I 39 GLN I 95 HIS I 167 GLN I 213 ASN J 82 GLN J 99 HIS J 164 ASN K 39 GLN K 95 HIS K 167 GLN K 213 ASN L 99 HIS L 164 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.221966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.142759 restraints weight = 26053.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137911 restraints weight = 13438.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139001 restraints weight = 9631.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139605 restraints weight = 8154.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139780 restraints weight = 7573.504| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16792 Z= 0.174 Angle : 0.694 8.196 22820 Z= 0.370 Chirality : 0.044 0.200 2612 Planarity : 0.005 0.063 2802 Dihedral : 5.555 29.066 2198 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.93 % Allowed : 9.23 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -1.99 (0.18), residues: 2028 helix: -0.05 (0.18), residues: 796 sheet: -1.15 (0.27), residues: 376 loop : -2.64 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 832 TYR 0.019 0.001 TYR J 95 PHE 0.022 0.002 PHE C 761 TRP 0.015 0.001 TRP H 24 HIS 0.009 0.001 HIS C 963 Details of bonding type rmsd covalent geometry : bond 0.00373 (16772) covalent geometry : angle 0.69091 (22780) SS BOND : bond 0.00419 ( 20) SS BOND : angle 1.76614 ( 40) hydrogen bonds : bond 0.07683 ( 752) hydrogen bonds : angle 6.13741 ( 2217) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 422 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 866 TYR cc_start: 0.8547 (t80) cc_final: 0.8291 (t80) REVERT: A 945 MET cc_start: 0.8383 (mtp) cc_final: 0.7838 (mtp) REVERT: B 757 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6661 (tmm) REVERT: B 873 THR cc_start: 0.8712 (m) cc_final: 0.8455 (m) REVERT: B 945 MET cc_start: 0.8055 (mmt) cc_final: 0.7664 (mmt) REVERT: B 950 GLN cc_start: 0.8278 (mm110) cc_final: 0.7762 (pp30) REVERT: E 13 ARG cc_start: 0.8745 (mtp180) cc_final: 0.8521 (mtp-110) REVERT: F 6 MET cc_start: 0.7108 (mmp) cc_final: 0.6571 (mmp) REVERT: F 23 LEU cc_start: 0.6443 (tp) cc_final: 0.6133 (tp) REVERT: F 24 TRP cc_start: 0.7714 (p90) cc_final: 0.7467 (p-90) REVERT: C 726 ILE cc_start: 0.9713 (mt) cc_final: 0.9490 (tt) REVERT: C 791 PHE cc_start: 0.7621 (t80) cc_final: 0.7032 (t80) REVERT: C 819 LEU cc_start: 0.3676 (OUTLIER) cc_final: 0.3263 (pp) REVERT: C 861 MET cc_start: 0.7208 (ttp) cc_final: 0.6843 (ttp) REVERT: C 889 GLU cc_start: 0.4827 (mm-30) cc_final: 0.4312 (mm-30) REVERT: C 917 TYR cc_start: 0.8773 (m-80) cc_final: 0.8490 (m-80) REVERT: C 945 MET cc_start: 0.8602 (mtp) cc_final: 0.8159 (mtp) REVERT: C 966 ASN cc_start: 0.8585 (m110) cc_final: 0.8272 (m110) REVERT: D 742 LEU cc_start: 0.9261 (tp) cc_final: 0.8892 (tp) REVERT: D 825 PHE cc_start: 0.8725 (m-80) cc_final: 0.8204 (m-80) REVERT: D 832 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8222 (ttt-90) REVERT: D 845 SER cc_start: 0.8991 (t) cc_final: 0.8748 (p) REVERT: D 861 MET cc_start: 0.8591 (tpp) cc_final: 0.7472 (ttp) REVERT: D 917 TYR cc_start: 0.8684 (m-80) cc_final: 0.8415 (m-80) REVERT: H 6 MET cc_start: 0.7990 (mmp) cc_final: 0.7673 (mtm) REVERT: H 19 MET cc_start: 0.5539 (mtm) cc_final: 0.5102 (mmt) REVERT: H 24 TRP cc_start: 0.6919 (p90) cc_final: 0.6471 (p-90) REVERT: I 29 ILE cc_start: 0.6255 (mt) cc_final: 0.5804 (pt) REVERT: I 91 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7557 (tm-30) REVERT: I 164 TRP cc_start: 0.7434 (m-90) cc_final: 0.6936 (m-90) REVERT: I 176 MET cc_start: 0.4760 (tmm) cc_final: 0.4393 (tmm) REVERT: J 82 GLN cc_start: 0.4245 (OUTLIER) cc_final: 0.3769 (mm-40) REVERT: J 93 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7432 (ptm) REVERT: J 95 TYR cc_start: 0.6219 (m-80) cc_final: 0.5688 (m-80) REVERT: J 114 GLN cc_start: 0.7327 (pt0) cc_final: 0.6968 (pm20) REVERT: J 154 TYR cc_start: 0.7731 (p90) cc_final: 0.7368 (p90) REVERT: J 183 LEU cc_start: 0.8206 (mt) cc_final: 0.7992 (mp) REVERT: K 29 ILE cc_start: 0.6598 (mt) cc_final: 0.6097 (pt) REVERT: K 91 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8022 (tm-30) REVERT: K 98 THR cc_start: 0.8087 (m) cc_final: 0.7484 (p) REVERT: K 164 TRP cc_start: 0.7578 (m-90) cc_final: 0.7204 (m-90) REVERT: L 154 TYR cc_start: 0.7022 (p90) cc_final: 0.6486 (p90) outliers start: 54 outliers final: 34 residues processed: 446 average time/residue: 0.1298 time to fit residues: 87.9177 Evaluate side-chains 395 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 356 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 826 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 739 ILE Chi-restraints excluded: chain D residue 744 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain D residue 832 ARG Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 136 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 195 optimal weight: 0.1980 chunk 74 optimal weight: 0.0980 chunk 199 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 GLN A 935 ASN B 874 GLN B 896 GLN C 746 ASN C 935 ASN ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 874 GLN I 39 GLN J 39 GLN L 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.222460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.135309 restraints weight = 26340.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135103 restraints weight = 14761.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137681 restraints weight = 8213.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137528 restraints weight = 6280.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.137716 restraints weight = 6571.086| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16792 Z= 0.144 Angle : 0.660 9.846 22820 Z= 0.340 Chirality : 0.043 0.197 2612 Planarity : 0.004 0.055 2802 Dihedral : 5.164 37.558 2198 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.61 % Allowed : 10.86 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.18), residues: 2028 helix: 0.66 (0.18), residues: 810 sheet: -0.88 (0.27), residues: 384 loop : -2.63 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 829 TYR 0.012 0.001 TYR J 95 PHE 0.021 0.001 PHE C 761 TRP 0.017 0.001 TRP G 24 HIS 0.010 0.001 HIS D 955 Details of bonding type rmsd covalent geometry : bond 0.00305 (16772) covalent geometry : angle 0.65363 (22780) SS BOND : bond 0.00310 ( 20) SS BOND : angle 2.32122 ( 40) hydrogen bonds : bond 0.05968 ( 752) hydrogen bonds : angle 5.29507 ( 2217) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 387 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 MET cc_start: 0.8766 (mmp) cc_final: 0.8108 (mmp) REVERT: A 866 TYR cc_start: 0.8464 (t80) cc_final: 0.8200 (t80) REVERT: A 917 TYR cc_start: 0.8653 (m-80) cc_final: 0.8331 (m-80) REVERT: B 757 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6190 (tmm) REVERT: B 761 PHE cc_start: 0.6989 (m-10) cc_final: 0.6740 (m-10) REVERT: B 775 ILE cc_start: 0.8870 (mt) cc_final: 0.8651 (pt) REVERT: B 791 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.6184 (t80) REVERT: B 873 THR cc_start: 0.8577 (m) cc_final: 0.8331 (m) REVERT: B 950 GLN cc_start: 0.8063 (mm110) cc_final: 0.7673 (tm-30) REVERT: E 24 TRP cc_start: 0.7481 (p90) cc_final: 0.6961 (p90) REVERT: F 6 MET cc_start: 0.7206 (mmp) cc_final: 0.6534 (mmp) REVERT: C 819 LEU cc_start: 0.3209 (OUTLIER) cc_final: 0.2886 (pp) REVERT: C 861 MET cc_start: 0.6991 (ttp) cc_final: 0.6557 (ttp) REVERT: C 889 GLU cc_start: 0.4808 (mm-30) cc_final: 0.4228 (mm-30) REVERT: C 917 TYR cc_start: 0.8820 (m-80) cc_final: 0.8511 (m-80) REVERT: D 825 PHE cc_start: 0.8775 (m-80) cc_final: 0.8237 (m-80) REVERT: D 845 SER cc_start: 0.8990 (t) cc_final: 0.8739 (p) REVERT: D 945 MET cc_start: 0.7357 (mmt) cc_final: 0.6827 (mmt) REVERT: D 952 GLU cc_start: 0.8815 (tp30) cc_final: 0.8516 (tp30) REVERT: G 23 LEU cc_start: 0.8277 (mm) cc_final: 0.7828 (tt) REVERT: H 6 MET cc_start: 0.8120 (mmp) cc_final: 0.7776 (mtm) REVERT: H 24 TRP cc_start: 0.7079 (p90) cc_final: 0.6572 (p-90) REVERT: I 29 ILE cc_start: 0.6559 (mt) cc_final: 0.6199 (pt) REVERT: I 98 THR cc_start: 0.7841 (m) cc_final: 0.7375 (p) REVERT: I 164 TRP cc_start: 0.7364 (m-90) cc_final: 0.6864 (m-90) REVERT: I 176 MET cc_start: 0.4750 (tmm) cc_final: 0.4367 (tmm) REVERT: J 95 TYR cc_start: 0.6201 (m-80) cc_final: 0.5878 (m-80) REVERT: J 114 GLN cc_start: 0.7381 (pt0) cc_final: 0.7015 (pm20) REVERT: K 11 MET cc_start: 0.5079 (ttp) cc_final: 0.4800 (ttm) REVERT: K 29 ILE cc_start: 0.6624 (mt) cc_final: 0.6164 (pt) REVERT: K 98 THR cc_start: 0.7831 (m) cc_final: 0.7354 (p) REVERT: K 164 TRP cc_start: 0.7488 (m-90) cc_final: 0.7139 (m-90) REVERT: K 176 MET cc_start: 0.4497 (tmm) cc_final: 0.4105 (tmm) REVERT: L 114 GLN cc_start: 0.6321 (pm20) cc_final: 0.6075 (pm20) outliers start: 48 outliers final: 30 residues processed: 418 average time/residue: 0.1251 time to fit residues: 79.6987 Evaluate side-chains 385 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 352 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 963 HIS Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 136 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 134 optimal weight: 9.9990 chunk 11 optimal weight: 0.0670 chunk 165 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 177 optimal weight: 0.0040 overall best weight: 0.5932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 GLN A 935 ASN B 874 GLN ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 874 GLN D 955 HIS J 82 GLN L 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.221345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130732 restraints weight = 25790.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134983 restraints weight = 10683.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.137415 restraints weight = 6680.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138589 restraints weight = 5369.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138917 restraints weight = 4906.826| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16792 Z= 0.154 Angle : 0.649 13.086 22820 Z= 0.331 Chirality : 0.043 0.197 2612 Planarity : 0.004 0.043 2802 Dihedral : 5.004 31.534 2198 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.66 % Allowed : 12.16 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.18), residues: 2028 helix: 0.97 (0.18), residues: 812 sheet: -0.70 (0.27), residues: 380 loop : -2.49 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 829 TYR 0.018 0.001 TYR J 184 PHE 0.015 0.001 PHE C 761 TRP 0.021 0.001 TRP G 5 HIS 0.010 0.001 HIS C 963 Details of bonding type rmsd covalent geometry : bond 0.00346 (16772) covalent geometry : angle 0.64403 (22780) SS BOND : bond 0.00324 ( 20) SS BOND : angle 2.00751 ( 40) hydrogen bonds : bond 0.05607 ( 752) hydrogen bonds : angle 5.04810 ( 2217) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 361 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 LYS cc_start: 0.7488 (ttpp) cc_final: 0.7287 (ttmm) REVERT: A 840 MET cc_start: 0.8786 (mmp) cc_final: 0.8169 (mmp) REVERT: B 735 PHE cc_start: 0.8207 (t80) cc_final: 0.7856 (t80) REVERT: B 757 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5906 (tmm) REVERT: B 761 PHE cc_start: 0.7112 (m-10) cc_final: 0.6786 (m-10) REVERT: B 791 PHE cc_start: 0.6844 (OUTLIER) cc_final: 0.6402 (t80) REVERT: B 873 THR cc_start: 0.8589 (m) cc_final: 0.8333 (m) REVERT: B 950 GLN cc_start: 0.7951 (mm110) cc_final: 0.7661 (tm-30) REVERT: F 6 MET cc_start: 0.7061 (mmp) cc_final: 0.6160 (mtm) REVERT: F 26 LYS cc_start: 0.4847 (mmtm) cc_final: 0.4193 (tppt) REVERT: C 819 LEU cc_start: 0.3465 (OUTLIER) cc_final: 0.3203 (pp) REVERT: C 861 MET cc_start: 0.7059 (ttp) cc_final: 0.6595 (ttp) REVERT: C 917 TYR cc_start: 0.8837 (m-80) cc_final: 0.8522 (m-80) REVERT: C 965 ASP cc_start: 0.9372 (p0) cc_final: 0.9162 (p0) REVERT: D 735 PHE cc_start: 0.8197 (t80) cc_final: 0.7925 (t80) REVERT: D 772 PHE cc_start: 0.8818 (m-80) cc_final: 0.8594 (m-80) REVERT: D 825 PHE cc_start: 0.8756 (m-80) cc_final: 0.8246 (m-80) REVERT: D 845 SER cc_start: 0.9003 (t) cc_final: 0.8754 (p) REVERT: D 952 GLU cc_start: 0.8875 (tp30) cc_final: 0.8492 (tm-30) REVERT: G 23 LEU cc_start: 0.8535 (mm) cc_final: 0.8070 (tt) REVERT: H 24 TRP cc_start: 0.7400 (p90) cc_final: 0.6812 (p-90) REVERT: I 29 ILE cc_start: 0.6647 (mt) cc_final: 0.6281 (pt) REVERT: I 98 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7382 (p) REVERT: I 164 TRP cc_start: 0.7368 (m-90) cc_final: 0.6945 (m-90) REVERT: I 176 MET cc_start: 0.4695 (tmm) cc_final: 0.4290 (tmm) REVERT: J 83 MET cc_start: 0.3948 (mtt) cc_final: 0.3737 (mtt) REVERT: J 89 GLU cc_start: 0.7330 (tp30) cc_final: 0.6829 (tp30) REVERT: J 95 TYR cc_start: 0.6368 (m-80) cc_final: 0.6042 (m-80) REVERT: J 114 GLN cc_start: 0.7334 (pt0) cc_final: 0.6807 (pm20) REVERT: J 154 TYR cc_start: 0.7382 (p90) cc_final: 0.6965 (p90) REVERT: K 11 MET cc_start: 0.5442 (ttp) cc_final: 0.5097 (ttm) REVERT: K 29 ILE cc_start: 0.6926 (mt) cc_final: 0.6365 (pt) REVERT: K 98 THR cc_start: 0.7867 (m) cc_final: 0.7367 (p) REVERT: K 164 TRP cc_start: 0.7481 (m-90) cc_final: 0.7195 (m-90) REVERT: K 176 MET cc_start: 0.4747 (tmm) cc_final: 0.4443 (tmm) REVERT: L 83 MET cc_start: 0.4722 (mtt) cc_final: 0.4385 (mtt) outliers start: 49 outliers final: 32 residues processed: 388 average time/residue: 0.1219 time to fit residues: 72.7198 Evaluate side-chains 377 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 341 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 826 ARG Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain L residue 136 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 7 optimal weight: 0.0870 chunk 80 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 174 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 GLN A 935 ASN C 763 ASN C 961 GLN ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 874 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.221674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.139768 restraints weight = 25918.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138192 restraints weight = 13323.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138512 restraints weight = 8699.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139114 restraints weight = 8973.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139313 restraints weight = 7279.417| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16792 Z= 0.138 Angle : 0.637 10.148 22820 Z= 0.322 Chirality : 0.042 0.225 2612 Planarity : 0.004 0.044 2802 Dihedral : 4.825 26.284 2198 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.77 % Allowed : 13.95 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -0.77 (0.19), residues: 2028 helix: 1.22 (0.19), residues: 812 sheet: -0.43 (0.28), residues: 376 loop : -2.39 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 13 TYR 0.010 0.001 TYR L 111 PHE 0.016 0.001 PHE C 761 TRP 0.012 0.001 TRP E 5 HIS 0.007 0.001 HIS C 963 Details of bonding type rmsd covalent geometry : bond 0.00307 (16772) covalent geometry : angle 0.63208 (22780) SS BOND : bond 0.00322 ( 20) SS BOND : angle 1.91029 ( 40) hydrogen bonds : bond 0.05194 ( 752) hydrogen bonds : angle 4.77488 ( 2217) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 368 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 MET cc_start: 0.8751 (mmp) cc_final: 0.8119 (mmp) REVERT: A 945 MET cc_start: 0.8933 (ttm) cc_final: 0.8381 (ttm) REVERT: A 959 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7968 (tp30) REVERT: B 757 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.5834 (tmm) REVERT: B 761 PHE cc_start: 0.7068 (m-10) cc_final: 0.6800 (m-10) REVERT: B 791 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.6393 (t80) REVERT: B 873 THR cc_start: 0.8581 (m) cc_final: 0.8330 (m) REVERT: B 950 GLN cc_start: 0.8030 (mm110) cc_final: 0.7727 (tm-30) REVERT: F 6 MET cc_start: 0.7374 (mmp) cc_final: 0.6228 (mtm) REVERT: F 24 TRP cc_start: 0.7677 (p90) cc_final: 0.7441 (p90) REVERT: F 26 LYS cc_start: 0.3963 (mmtm) cc_final: 0.2902 (mmtt) REVERT: C 861 MET cc_start: 0.7113 (ttp) cc_final: 0.6649 (ttp) REVERT: C 965 ASP cc_start: 0.9488 (p0) cc_final: 0.9274 (p0) REVERT: D 735 PHE cc_start: 0.8312 (t80) cc_final: 0.7971 (t80) REVERT: D 757 MET cc_start: 0.4734 (tpp) cc_final: 0.4357 (tmm) REVERT: D 772 PHE cc_start: 0.8711 (m-80) cc_final: 0.8440 (m-80) REVERT: D 825 PHE cc_start: 0.8751 (m-80) cc_final: 0.8256 (m-80) REVERT: D 845 SER cc_start: 0.9004 (t) cc_final: 0.8780 (p) REVERT: D 945 MET cc_start: 0.8225 (mmm) cc_final: 0.7738 (mmm) REVERT: D 952 GLU cc_start: 0.8783 (tp30) cc_final: 0.8557 (tm-30) REVERT: G 23 LEU cc_start: 0.8461 (mm) cc_final: 0.8131 (tt) REVERT: H 19 MET cc_start: 0.4714 (mmt) cc_final: 0.4291 (mtm) REVERT: I 98 THR cc_start: 0.7885 (m) cc_final: 0.7328 (p) REVERT: I 164 TRP cc_start: 0.7396 (m-90) cc_final: 0.6969 (m-90) REVERT: I 176 MET cc_start: 0.4721 (tmm) cc_final: 0.4339 (tmm) REVERT: J 89 GLU cc_start: 0.7316 (tp30) cc_final: 0.6713 (tp30) REVERT: J 95 TYR cc_start: 0.6469 (m-80) cc_final: 0.6091 (m-80) REVERT: J 114 GLN cc_start: 0.7472 (pt0) cc_final: 0.7000 (pm20) REVERT: J 154 TYR cc_start: 0.7426 (p90) cc_final: 0.7050 (p90) REVERT: K 11 MET cc_start: 0.5446 (ttp) cc_final: 0.5109 (ttm) REVERT: K 29 ILE cc_start: 0.6952 (mt) cc_final: 0.6418 (pt) REVERT: K 98 THR cc_start: 0.7856 (m) cc_final: 0.7382 (p) REVERT: K 164 TRP cc_start: 0.7450 (m-90) cc_final: 0.7167 (m-90) REVERT: K 176 MET cc_start: 0.4653 (tmm) cc_final: 0.4442 (tmm) REVERT: L 83 MET cc_start: 0.4708 (mtt) cc_final: 0.4491 (mtt) REVERT: L 154 TYR cc_start: 0.6440 (p90) cc_final: 0.5776 (p90) outliers start: 51 outliers final: 39 residues processed: 397 average time/residue: 0.1239 time to fit residues: 74.9325 Evaluate side-chains 390 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 349 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 739 ILE Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 72 optimal weight: 0.9980 chunk 100 optimal weight: 0.0060 chunk 57 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 194 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN B 954 GLN ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.221076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138764 restraints weight = 25788.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.138677 restraints weight = 12668.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137755 restraints weight = 8638.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138859 restraints weight = 9178.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139539 restraints weight = 7432.013| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16792 Z= 0.147 Angle : 0.642 10.809 22820 Z= 0.327 Chirality : 0.042 0.212 2612 Planarity : 0.004 0.055 2802 Dihedral : 4.741 24.516 2198 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.82 % Allowed : 14.93 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -0.60 (0.19), residues: 2028 helix: 1.32 (0.19), residues: 812 sheet: -0.23 (0.28), residues: 366 loop : -2.27 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 829 TYR 0.011 0.001 TYR A 866 PHE 0.018 0.001 PHE C 761 TRP 0.015 0.001 TRP H 24 HIS 0.006 0.001 HIS C 963 Details of bonding type rmsd covalent geometry : bond 0.00330 (16772) covalent geometry : angle 0.63733 (22780) SS BOND : bond 0.00246 ( 20) SS BOND : angle 1.94640 ( 40) hydrogen bonds : bond 0.05050 ( 752) hydrogen bonds : angle 4.69555 ( 2217) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 359 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 TRP cc_start: 0.7563 (m100) cc_final: 0.7024 (m100) REVERT: A 917 TYR cc_start: 0.8677 (m-80) cc_final: 0.8426 (m-80) REVERT: A 933 MET cc_start: 0.6766 (ttp) cc_final: 0.6433 (mtp) REVERT: A 945 MET cc_start: 0.8752 (ttm) cc_final: 0.8394 (ttm) REVERT: A 959 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7949 (tp30) REVERT: B 757 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.5762 (tmm) REVERT: B 761 PHE cc_start: 0.7099 (m-10) cc_final: 0.6847 (m-10) REVERT: B 791 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6407 (t80) REVERT: B 873 THR cc_start: 0.8603 (m) cc_final: 0.8356 (m) REVERT: B 950 GLN cc_start: 0.8011 (mm110) cc_final: 0.7563 (tm-30) REVERT: F 6 MET cc_start: 0.7347 (mmp) cc_final: 0.6117 (mtm) REVERT: F 24 TRP cc_start: 0.7695 (p90) cc_final: 0.7389 (p90) REVERT: F 26 LYS cc_start: 0.4082 (mmtm) cc_final: 0.3045 (mmtt) REVERT: C 861 MET cc_start: 0.7185 (ttp) cc_final: 0.6717 (ttp) REVERT: C 933 MET cc_start: 0.6617 (ttp) cc_final: 0.6208 (mtp) REVERT: C 959 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8002 (mm-30) REVERT: C 965 ASP cc_start: 0.9450 (p0) cc_final: 0.9247 (p0) REVERT: D 735 PHE cc_start: 0.8348 (t80) cc_final: 0.7976 (t80) REVERT: D 757 MET cc_start: 0.5128 (tpp) cc_final: 0.4700 (tmm) REVERT: D 825 PHE cc_start: 0.8754 (m-80) cc_final: 0.8241 (m-80) REVERT: D 845 SER cc_start: 0.8992 (t) cc_final: 0.8787 (p) REVERT: D 913 GLU cc_start: 0.8380 (tt0) cc_final: 0.8065 (tm-30) REVERT: D 945 MET cc_start: 0.8138 (mmm) cc_final: 0.7523 (mmm) REVERT: G 13 ARG cc_start: 0.8846 (mtp180) cc_final: 0.8326 (mtp85) REVERT: G 23 LEU cc_start: 0.8837 (mm) cc_final: 0.8287 (tt) REVERT: H 19 MET cc_start: 0.4513 (mmt) cc_final: 0.4142 (mtm) REVERT: I 164 TRP cc_start: 0.7421 (m-90) cc_final: 0.7027 (m-90) REVERT: I 176 MET cc_start: 0.4811 (tmm) cc_final: 0.4459 (tmm) REVERT: J 43 LYS cc_start: 0.5016 (mmmt) cc_final: 0.3893 (pttt) REVERT: J 89 GLU cc_start: 0.7385 (tp30) cc_final: 0.6698 (tp30) REVERT: J 95 TYR cc_start: 0.6535 (m-80) cc_final: 0.6249 (m-80) REVERT: J 114 GLN cc_start: 0.7409 (pt0) cc_final: 0.6960 (pm20) REVERT: J 154 TYR cc_start: 0.7262 (p90) cc_final: 0.6846 (p90) REVERT: J 183 LEU cc_start: 0.8444 (mt) cc_final: 0.7619 (pp) REVERT: K 29 ILE cc_start: 0.6789 (mt) cc_final: 0.6300 (pt) REVERT: K 98 THR cc_start: 0.7882 (m) cc_final: 0.7421 (p) REVERT: K 164 TRP cc_start: 0.7435 (m-90) cc_final: 0.7199 (m-90) REVERT: L 154 TYR cc_start: 0.6455 (p90) cc_final: 0.5749 (p90) outliers start: 52 outliers final: 42 residues processed: 388 average time/residue: 0.1173 time to fit residues: 69.6769 Evaluate side-chains 392 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 348 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 739 ILE Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 97 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 ASN B 954 GLN C 961 GLN ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 ASN D 961 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.218416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132509 restraints weight = 25917.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132783 restraints weight = 14209.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133564 restraints weight = 8575.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134032 restraints weight = 7956.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134049 restraints weight = 7099.158| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16792 Z= 0.203 Angle : 0.691 11.905 22820 Z= 0.351 Chirality : 0.044 0.236 2612 Planarity : 0.004 0.047 2802 Dihedral : 4.855 26.339 2198 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.31 % Allowed : 15.47 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -0.65 (0.19), residues: 2028 helix: 1.14 (0.18), residues: 830 sheet: -0.22 (0.28), residues: 366 loop : -2.22 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 829 TYR 0.015 0.001 TYR J 184 PHE 0.020 0.002 PHE C 761 TRP 0.022 0.001 TRP H 24 HIS 0.005 0.001 HIS C 963 Details of bonding type rmsd covalent geometry : bond 0.00484 (16772) covalent geometry : angle 0.68970 (22780) SS BOND : bond 0.00259 ( 20) SS BOND : angle 1.24986 ( 40) hydrogen bonds : bond 0.05445 ( 752) hydrogen bonds : angle 4.80999 ( 2217) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 352 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 TRP cc_start: 0.7393 (m100) cc_final: 0.6983 (m100) REVERT: A 889 GLU cc_start: 0.5352 (mm-30) cc_final: 0.4401 (mm-30) REVERT: A 917 TYR cc_start: 0.8786 (m-80) cc_final: 0.8532 (m-80) REVERT: A 945 MET cc_start: 0.8671 (ttm) cc_final: 0.8304 (ttm) REVERT: B 757 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5266 (tmm) REVERT: B 761 PHE cc_start: 0.7062 (m-10) cc_final: 0.6850 (m-10) REVERT: B 791 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6577 (t80) REVERT: B 873 THR cc_start: 0.8707 (m) cc_final: 0.8473 (m) REVERT: B 950 GLN cc_start: 0.7787 (mm110) cc_final: 0.7414 (tm-30) REVERT: F 6 MET cc_start: 0.7462 (mmp) cc_final: 0.6253 (mmp) REVERT: F 26 LYS cc_start: 0.4010 (mmtm) cc_final: 0.3175 (mmtt) REVERT: C 861 MET cc_start: 0.7328 (ttp) cc_final: 0.6883 (ttp) REVERT: C 889 GLU cc_start: 0.5143 (mm-30) cc_final: 0.4451 (mm-30) REVERT: C 959 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8028 (mm-30) REVERT: D 735 PHE cc_start: 0.8477 (t80) cc_final: 0.8048 (t80) REVERT: D 757 MET cc_start: 0.5064 (tpp) cc_final: 0.4699 (tmm) REVERT: D 825 PHE cc_start: 0.8766 (m-80) cc_final: 0.8274 (m-80) REVERT: D 842 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8244 (mtpp) REVERT: D 845 SER cc_start: 0.9036 (t) cc_final: 0.8816 (p) REVERT: D 945 MET cc_start: 0.7989 (mmm) cc_final: 0.7594 (mmm) REVERT: G 13 ARG cc_start: 0.8812 (mtp180) cc_final: 0.8280 (mtp-110) REVERT: G 19 MET cc_start: 0.6532 (tpt) cc_final: 0.5600 (tpt) REVERT: G 23 LEU cc_start: 0.8717 (mm) cc_final: 0.8228 (tt) REVERT: H 19 MET cc_start: 0.4495 (mmt) cc_final: 0.4116 (mtm) REVERT: H 24 TRP cc_start: 0.7689 (p90) cc_final: 0.6893 (p-90) REVERT: I 164 TRP cc_start: 0.7400 (m-90) cc_final: 0.7021 (m-90) REVERT: I 176 MET cc_start: 0.4896 (tmm) cc_final: 0.4454 (tmm) REVERT: J 95 TYR cc_start: 0.6492 (m-80) cc_final: 0.6052 (m-80) REVERT: J 114 GLN cc_start: 0.7305 (pt0) cc_final: 0.6861 (pm20) REVERT: J 154 TYR cc_start: 0.7202 (p90) cc_final: 0.6767 (p90) REVERT: J 183 LEU cc_start: 0.8429 (mt) cc_final: 0.7496 (pp) REVERT: K 29 ILE cc_start: 0.6814 (mt) cc_final: 0.6312 (pt) REVERT: K 98 THR cc_start: 0.7925 (m) cc_final: 0.7389 (p) REVERT: K 164 TRP cc_start: 0.7432 (m-90) cc_final: 0.7156 (m-90) REVERT: L 114 GLN cc_start: 0.6168 (pm20) cc_final: 0.5936 (pm20) REVERT: L 183 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7301 (pp) outliers start: 61 outliers final: 50 residues processed: 390 average time/residue: 0.1214 time to fit residues: 73.0442 Evaluate side-chains 396 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 342 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain C residue 961 GLN Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 739 ILE Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 183 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 139 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 131 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 166 optimal weight: 0.7980 chunk 195 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 954 GLN C 961 GLN ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.219306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137922 restraints weight = 25990.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134354 restraints weight = 14469.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134832 restraints weight = 9580.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135410 restraints weight = 9121.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135666 restraints weight = 7831.024| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16792 Z= 0.168 Angle : 0.694 12.662 22820 Z= 0.350 Chirality : 0.044 0.249 2612 Planarity : 0.004 0.047 2802 Dihedral : 4.822 25.751 2198 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.26 % Allowed : 16.18 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -0.62 (0.19), residues: 2028 helix: 1.11 (0.18), residues: 842 sheet: -0.17 (0.28), residues: 366 loop : -2.20 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 829 TYR 0.014 0.001 TYR J 95 PHE 0.022 0.001 PHE A 791 TRP 0.022 0.001 TRP F 24 HIS 0.006 0.001 HIS C 963 Details of bonding type rmsd covalent geometry : bond 0.00391 (16772) covalent geometry : angle 0.69232 (22780) SS BOND : bond 0.00535 ( 20) SS BOND : angle 1.40905 ( 40) hydrogen bonds : bond 0.05306 ( 752) hydrogen bonds : angle 4.72286 ( 2217) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 353 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 783 ARG cc_start: 0.8881 (tpp80) cc_final: 0.8541 (mtp180) REVERT: A 796 TRP cc_start: 0.7385 (m100) cc_final: 0.7004 (m100) REVERT: A 889 GLU cc_start: 0.5264 (mm-30) cc_final: 0.4338 (mm-30) REVERT: A 917 TYR cc_start: 0.8766 (m-80) cc_final: 0.8511 (m-80) REVERT: A 945 MET cc_start: 0.8516 (ttm) cc_final: 0.8108 (ttm) REVERT: A 959 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8080 (tp30) REVERT: B 757 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.5319 (tmm) REVERT: B 791 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6635 (t80) REVERT: B 873 THR cc_start: 0.8682 (m) cc_final: 0.8451 (m) REVERT: B 950 GLN cc_start: 0.7689 (mm110) cc_final: 0.7451 (tm-30) REVERT: F 6 MET cc_start: 0.7250 (mmp) cc_final: 0.6452 (mmp) REVERT: F 26 LYS cc_start: 0.3848 (mmtm) cc_final: 0.3606 (mmtt) REVERT: C 861 MET cc_start: 0.7326 (ttp) cc_final: 0.6876 (ttp) REVERT: C 889 GLU cc_start: 0.5018 (mm-30) cc_final: 0.4356 (mm-30) REVERT: C 959 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8035 (mm-30) REVERT: D 735 PHE cc_start: 0.8486 (t80) cc_final: 0.8057 (t80) REVERT: D 757 MET cc_start: 0.5038 (tpp) cc_final: 0.4691 (tmm) REVERT: D 825 PHE cc_start: 0.8685 (m-80) cc_final: 0.8180 (m-80) REVERT: D 842 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8279 (mtpp) REVERT: D 845 SER cc_start: 0.9037 (t) cc_final: 0.8819 (p) REVERT: D 861 MET cc_start: 0.8634 (tpp) cc_final: 0.7578 (ttp) REVERT: G 23 LEU cc_start: 0.8667 (mm) cc_final: 0.8223 (tt) REVERT: H 24 TRP cc_start: 0.7721 (p90) cc_final: 0.6942 (p-90) REVERT: H 27 LYS cc_start: 0.6373 (mttt) cc_final: 0.5820 (mmmt) REVERT: I 164 TRP cc_start: 0.7380 (m-90) cc_final: 0.7011 (m-90) REVERT: I 176 MET cc_start: 0.4974 (tmm) cc_final: 0.4541 (tmm) REVERT: J 89 GLU cc_start: 0.7365 (tp30) cc_final: 0.6900 (mt-10) REVERT: J 95 TYR cc_start: 0.6504 (m-80) cc_final: 0.6220 (m-80) REVERT: J 114 GLN cc_start: 0.7269 (pt0) cc_final: 0.6849 (pm20) REVERT: J 154 TYR cc_start: 0.7261 (p90) cc_final: 0.6794 (p90) REVERT: J 183 LEU cc_start: 0.8500 (mt) cc_final: 0.7615 (pp) REVERT: K 29 ILE cc_start: 0.6810 (mt) cc_final: 0.6317 (pt) REVERT: K 98 THR cc_start: 0.7894 (m) cc_final: 0.7376 (p) REVERT: K 164 TRP cc_start: 0.7394 (m-90) cc_final: 0.7127 (m-90) REVERT: L 114 GLN cc_start: 0.6009 (pm20) cc_final: 0.5799 (pm20) REVERT: L 183 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7366 (pp) outliers start: 60 outliers final: 51 residues processed: 389 average time/residue: 0.1165 time to fit residues: 69.3947 Evaluate side-chains 398 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 343 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 933 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain C residue 961 GLN Chi-restraints excluded: chain C residue 966 ASN Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 739 ILE Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 183 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 184 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 174 optimal weight: 8.9990 chunk 14 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 185 optimal weight: 0.8980 chunk 144 optimal weight: 0.0670 chunk 42 optimal weight: 0.0670 chunk 154 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 954 GLN C 961 GLN ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.220740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139624 restraints weight = 25762.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136297 restraints weight = 14990.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136477 restraints weight = 9958.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137117 restraints weight = 8471.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.137404 restraints weight = 7787.345| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16792 Z= 0.137 Angle : 0.699 13.408 22820 Z= 0.351 Chirality : 0.043 0.254 2612 Planarity : 0.004 0.083 2802 Dihedral : 4.744 25.374 2198 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.77 % Allowed : 17.26 % Favored : 79.97 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -0.47 (0.19), residues: 2028 helix: 1.29 (0.19), residues: 830 sheet: -0.16 (0.28), residues: 376 loop : -2.14 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 975 TYR 0.014 0.001 TYR A 866 PHE 0.024 0.001 PHE B 761 TRP 0.021 0.001 TRP F 24 HIS 0.006 0.001 HIS D 963 Details of bonding type rmsd covalent geometry : bond 0.00295 (16772) covalent geometry : angle 0.69803 (22780) SS BOND : bond 0.00400 ( 20) SS BOND : angle 1.16268 ( 40) hydrogen bonds : bond 0.04929 ( 752) hydrogen bonds : angle 4.57128 ( 2217) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 358 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 TRP cc_start: 0.7250 (m100) cc_final: 0.6942 (m100) REVERT: A 933 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6447 (mtp) REVERT: A 945 MET cc_start: 0.8228 (ttm) cc_final: 0.7997 (ttp) REVERT: A 959 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8069 (tp30) REVERT: B 757 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5273 (tmm) REVERT: B 791 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6612 (t80) REVERT: B 873 THR cc_start: 0.8537 (m) cc_final: 0.8309 (m) REVERT: F 6 MET cc_start: 0.7166 (mmp) cc_final: 0.6294 (mmp) REVERT: F 26 LYS cc_start: 0.4321 (mmtm) cc_final: 0.3789 (mmtt) REVERT: C 861 MET cc_start: 0.7095 (ttp) cc_final: 0.6639 (ttp) REVERT: C 889 GLU cc_start: 0.4887 (mm-30) cc_final: 0.4286 (mm-30) REVERT: C 959 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8055 (mm-30) REVERT: D 735 PHE cc_start: 0.8427 (t80) cc_final: 0.8047 (t80) REVERT: D 757 MET cc_start: 0.5085 (tpp) cc_final: 0.4806 (tmm) REVERT: D 825 PHE cc_start: 0.8649 (m-80) cc_final: 0.8098 (m-80) REVERT: D 842 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8262 (mtpp) REVERT: D 845 SER cc_start: 0.8986 (t) cc_final: 0.8784 (p) REVERT: D 861 MET cc_start: 0.8610 (tpp) cc_final: 0.7558 (ttp) REVERT: G 19 MET cc_start: 0.6850 (tpt) cc_final: 0.5876 (tpt) REVERT: G 23 LEU cc_start: 0.8693 (mm) cc_final: 0.8195 (tt) REVERT: H 19 MET cc_start: 0.5865 (mtm) cc_final: 0.4927 (mmt) REVERT: H 24 TRP cc_start: 0.7836 (p90) cc_final: 0.7175 (p-90) REVERT: H 27 LYS cc_start: 0.6635 (mttt) cc_final: 0.5914 (mttt) REVERT: I 164 TRP cc_start: 0.7393 (m-90) cc_final: 0.7054 (m-90) REVERT: I 176 MET cc_start: 0.4996 (tmm) cc_final: 0.4584 (tmm) REVERT: J 89 GLU cc_start: 0.7416 (tp30) cc_final: 0.6917 (mt-10) REVERT: J 95 TYR cc_start: 0.6528 (m-80) cc_final: 0.6210 (m-80) REVERT: J 114 GLN cc_start: 0.7387 (pt0) cc_final: 0.6603 (pm20) REVERT: J 154 TYR cc_start: 0.7245 (p90) cc_final: 0.6780 (p90) REVERT: J 183 LEU cc_start: 0.8552 (mt) cc_final: 0.7594 (pp) REVERT: K 98 THR cc_start: 0.7811 (m) cc_final: 0.7310 (p) REVERT: K 164 TRP cc_start: 0.7055 (m-90) cc_final: 0.6831 (m-90) REVERT: L 114 GLN cc_start: 0.6116 (pm20) cc_final: 0.5892 (pm20) REVERT: L 183 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7503 (pp) outliers start: 51 outliers final: 41 residues processed: 390 average time/residue: 0.1209 time to fit residues: 72.0267 Evaluate side-chains 393 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 347 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 933 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain C residue 961 GLN Chi-restraints excluded: chain C residue 966 ASN Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 739 ILE Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 167 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 177 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 68 optimal weight: 0.0060 chunk 188 optimal weight: 0.1980 chunk 44 optimal weight: 0.0770 chunk 119 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 ASN B 954 GLN C 961 GLN ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.221342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141130 restraints weight = 25718.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138136 restraints weight = 13496.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139043 restraints weight = 9880.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139638 restraints weight = 8984.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139963 restraints weight = 7725.426| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16792 Z= 0.135 Angle : 0.699 14.904 22820 Z= 0.350 Chirality : 0.043 0.259 2612 Planarity : 0.004 0.050 2802 Dihedral : 4.689 24.207 2198 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.55 % Allowed : 17.70 % Favored : 79.75 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -0.40 (0.19), residues: 2028 helix: 1.41 (0.19), residues: 824 sheet: -0.12 (0.27), residues: 376 loop : -2.15 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 13 TYR 0.021 0.001 TYR J 184 PHE 0.025 0.001 PHE B 761 TRP 0.024 0.001 TRP F 24 HIS 0.006 0.001 HIS D 963 Details of bonding type rmsd covalent geometry : bond 0.00294 (16772) covalent geometry : angle 0.69778 (22780) SS BOND : bond 0.00343 ( 20) SS BOND : angle 1.03958 ( 40) hydrogen bonds : bond 0.04805 ( 752) hydrogen bonds : angle 4.53176 ( 2217) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 351 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 TRP cc_start: 0.7300 (m100) cc_final: 0.6957 (m100) REVERT: A 933 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6444 (mtp) REVERT: A 959 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8067 (tp30) REVERT: B 757 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5180 (tmm) REVERT: B 791 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.6564 (t80) REVERT: B 873 THR cc_start: 0.8492 (m) cc_final: 0.8266 (m) REVERT: F 6 MET cc_start: 0.7094 (mmp) cc_final: 0.6262 (mmp) REVERT: F 26 LYS cc_start: 0.4176 (mmtm) cc_final: 0.3781 (mmtt) REVERT: C 861 MET cc_start: 0.7099 (ttp) cc_final: 0.6648 (ttp) REVERT: C 889 GLU cc_start: 0.4854 (mm-30) cc_final: 0.4270 (mm-30) REVERT: C 933 MET cc_start: 0.6630 (ttp) cc_final: 0.6241 (mtp) REVERT: C 959 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7941 (mm-30) REVERT: D 735 PHE cc_start: 0.8400 (t80) cc_final: 0.8146 (t80) REVERT: D 757 MET cc_start: 0.5065 (tpp) cc_final: 0.4788 (tmm) REVERT: D 825 PHE cc_start: 0.8655 (m-80) cc_final: 0.8110 (m-80) REVERT: D 842 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8258 (mtpp) REVERT: D 845 SER cc_start: 0.8984 (t) cc_final: 0.8782 (p) REVERT: D 861 MET cc_start: 0.8609 (tpp) cc_final: 0.7528 (ttp) REVERT: G 14 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8496 (tmtt) REVERT: G 19 MET cc_start: 0.6726 (tpt) cc_final: 0.5990 (tpp) REVERT: G 23 LEU cc_start: 0.8691 (mm) cc_final: 0.8197 (tt) REVERT: H 19 MET cc_start: 0.5859 (mtm) cc_final: 0.4826 (mmt) REVERT: H 24 TRP cc_start: 0.7921 (p90) cc_final: 0.7258 (p-90) REVERT: H 27 LYS cc_start: 0.6700 (mttt) cc_final: 0.6015 (mttt) REVERT: I 164 TRP cc_start: 0.7369 (m-90) cc_final: 0.7011 (m-90) REVERT: I 176 MET cc_start: 0.4907 (tmm) cc_final: 0.4520 (tmm) REVERT: J 89 GLU cc_start: 0.7371 (tp30) cc_final: 0.6860 (mt-10) REVERT: J 95 TYR cc_start: 0.6550 (m-80) cc_final: 0.6258 (m-80) REVERT: J 114 GLN cc_start: 0.7343 (pt0) cc_final: 0.6854 (tp40) REVERT: J 154 TYR cc_start: 0.7237 (p90) cc_final: 0.6782 (p90) REVERT: J 183 LEU cc_start: 0.8581 (mt) cc_final: 0.7614 (pp) REVERT: K 164 TRP cc_start: 0.7026 (m-90) cc_final: 0.6817 (m-90) REVERT: L 114 GLN cc_start: 0.6082 (pm20) cc_final: 0.5860 (pm20) REVERT: L 183 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7429 (pp) outliers start: 47 outliers final: 39 residues processed: 379 average time/residue: 0.1188 time to fit residues: 69.8387 Evaluate side-chains 387 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 342 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 933 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 739 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain C residue 961 GLN Chi-restraints excluded: chain C residue 966 ASN Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 739 ILE Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 102 optimal weight: 0.2980 chunk 165 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 159 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 961 GLN ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 968 ASN G 3 GLN ** J 180 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 = 0.4503 r_free = 0.4503 target = 0.221328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134073 restraints weight = 25775.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136042 restraints weight = 13547.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137857 restraints weight = 7338.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138157 restraints weight = 6346.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138167 restraints weight = 5976.256| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16792 Z= 0.140 Angle : 0.701 13.485 22820 Z= 0.351 Chirality : 0.043 0.259 2612 Planarity : 0.004 0.042 2802 Dihedral : 4.642 24.084 2198 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.44 % Allowed : 18.35 % Favored : 79.21 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -0.39 (0.19), residues: 2028 helix: 1.42 (0.19), residues: 824 sheet: -0.11 (0.27), residues: 376 loop : -2.14 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 975 TYR 0.017 0.001 TYR A 723 PHE 0.025 0.001 PHE B 761 TRP 0.026 0.001 TRP H 5 HIS 0.006 0.001 HIS D 963 Details of bonding type rmsd covalent geometry : bond 0.00314 (16772) covalent geometry : angle 0.70009 (22780) SS BOND : bond 0.00337 ( 20) SS BOND : angle 0.97567 ( 40) hydrogen bonds : bond 0.04773 ( 752) hydrogen bonds : angle 4.49561 ( 2217) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4083.26 seconds wall clock time: 70 minutes 47.88 seconds (4247.88 seconds total)