Starting phenix.real_space_refine on Sun Oct 25 02:04:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n4r_0342/10_2026/6n4r_0342_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n4r_0342/10_2026/6n4r_0342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6n4r_0342/10_2026/6n4r_0342_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n4r_0342/10_2026/6n4r_0342_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n4r_0342/10_2026/6n4r_0342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n4r_0342/10_2026/6n4r_0342.map" } resolution = 4.2 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= 0.003 sd= 0.469 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 118 5.16 5 C 10074 2.51 5 N 2468 2.21 5 O 2784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15444 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 8, 'TRANS': 216} Chain: "C" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1984 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "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: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 213} Restraints were copied for chains: D, A, F, G, H, K, L Time building chain proxies: 4.00, per 1000 atoms: 0.26 Number of scatterers: 15444 At special positions: 0 Unit cell: (142.8, 147.6, 172.8, 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 118 16.00 O 2784 8.00 N 2468 7.00 C 10074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS C 941 " - pdb=" SG CYS A 941 " distance=2.04 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 16 " distance=2.03 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=2.03 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=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 195 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.04 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: 1.22 Conformation dependent library (CDL) restraints added in 516.1 milliseconds 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 24 sheets defined 43.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.591A pdb=" N LEU B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 removed outlier: 3.690A pdb=" N THR B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N MET B 750 " --> pdb=" O ASN B 746 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.810A pdb=" N VAL B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 786 No H-bonds generated for 'chain 'B' and resid 784 through 786' Processing helix chain 'B' and resid 789 through 794 removed outlier: 3.924A pdb=" N ASP B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 809 Processing helix chain 'B' and resid 810 through 813 removed outlier: 3.979A pdb=" N LEU B 813 " --> pdb=" O GLU B 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 813' Processing helix chain 'B' and resid 819 through 828 removed outlier: 3.598A pdb=" N LEU B 822 " --> pdb=" O LEU B 819 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER B 824 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG B 826 " --> pdb=" O ARG B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 837 removed outlier: 3.868A pdb=" N LEU B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 849 removed outlier: 4.036A pdb=" N VAL B 844 " --> pdb=" O MET B 840 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 845 " --> pdb=" O ARG B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 877 removed outlier: 3.652A pdb=" N MET B 854 " --> pdb=" O VAL B 850 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 857 " --> pdb=" O GLY B 853 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 870 " --> pdb=" O TYR B 866 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET B 871 " --> pdb=" O ILE B 867 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 875 " --> pdb=" O MET B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 885 Processing helix chain 'B' and resid 886 through 899 removed outlier: 4.889A pdb=" N TYR B 892 " --> pdb=" O GLY B 888 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B 899 " --> pdb=" O PHE B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 907 Processing helix chain 'B' and resid 918 through 930 Proline residue: B 924 - end of helix Processing helix chain 'B' and resid 932 through 944 removed outlier: 3.569A pdb=" N VAL B 937 " --> pdb=" O MET B 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 731 Processing helix chain 'C' and resid 732 through 751 Processing helix chain 'C' and resid 759 through 786 removed outlier: 3.759A pdb=" N ASN C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 767 " --> pdb=" O ASN C 763 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL C 786 " --> pdb=" O LEU C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 813 removed outlier: 3.804A pdb=" N LEU C 798 " --> pdb=" O ASP C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 828 removed outlier: 3.680A pdb=" N ARG C 823 " --> pdb=" O SER C 820 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER C 824 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 825 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG C 826 " --> pdb=" O ARG C 823 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU C 827 " --> pdb=" O SER C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 834 removed outlier: 3.938A pdb=" N LEU C 833 " --> pdb=" O ARG C 829 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 834 " --> pdb=" O VAL C 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 829 through 834' Processing helix chain 'C' and resid 837 through 849 removed outlier: 3.866A pdb=" N ARG C 841 " --> pdb=" O VAL C 837 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS C 842 " --> pdb=" O PRO C 838 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE C 843 " --> pdb=" O GLN C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 876 removed outlier: 3.833A pdb=" N MET C 854 " --> pdb=" O VAL C 850 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 859 " --> pdb=" O LEU C 855 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE C 870 " --> pdb=" O TYR C 866 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET C 871 " --> pdb=" O ILE C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 885 removed outlier: 3.832A pdb=" N PHE C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 899 removed outlier: 4.911A pdb=" N TYR C 892 " --> pdb=" O GLY C 888 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C 899 " --> pdb=" O PHE C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 912 Processing helix chain 'C' and resid 918 through 959 removed outlier: 3.723A pdb=" N ILE C 923 " --> pdb=" O TRP C 919 " (cutoff:3.500A) Proline residue: C 924 - end of helix removed outlier: 3.868A pdb=" N PHE C 927 " --> pdb=" O ILE C 923 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET C 945 " --> pdb=" O CYS C 941 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 948 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN C 949 " --> pdb=" O MET C 945 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN C 950 " --> pdb=" O ALA C 946 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN C 954 " --> pdb=" O GLN C 950 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N HIS C 955 " --> pdb=" O LYS C 951 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 731 Processing helix chain 'D' and resid 732 through 752 removed outlier: 3.690A pdb=" N THR D 736 " --> pdb=" O SER D 732 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N MET D 750 " --> pdb=" O ASN D 746 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 783 removed outlier: 3.809A pdb=" N VAL D 764 " --> pdb=" O GLU D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 786 No H-bonds generated for 'chain 'D' and resid 784 through 786' Processing helix chain 'D' and resid 789 through 794 removed outlier: 3.924A pdb=" N ASP D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 809 Processing helix chain 'D' and resid 810 through 813 removed outlier: 3.979A pdb=" N LEU D 813 " --> pdb=" O GLU D 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 810 through 813' Processing helix chain 'D' and resid 819 through 828 removed outlier: 3.597A pdb=" N LEU D 822 " --> pdb=" O LEU D 819 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER D 824 " --> pdb=" O VAL D 821 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG D 826 " --> pdb=" O ARG D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 837 removed outlier: 3.868A pdb=" N LEU D 833 " --> pdb=" O ARG D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 849 removed outlier: 4.035A pdb=" N VAL D 844 " --> pdb=" O MET D 840 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 845 " --> pdb=" O ARG D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 877 removed outlier: 3.653A pdb=" N MET D 854 " --> pdb=" O VAL D 850 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL D 857 " --> pdb=" O GLY D 853 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE D 870 " --> pdb=" O TYR D 866 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET D 871 " --> pdb=" O ILE D 867 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN D 874 " --> pdb=" O ILE D 870 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D 875 " --> pdb=" O MET D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 885 Processing helix chain 'D' and resid 886 through 899 removed outlier: 4.889A pdb=" N TYR D 892 " --> pdb=" O GLY D 888 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR D 899 " --> pdb=" O PHE D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 907 Processing helix chain 'D' and resid 918 through 930 Proline residue: D 924 - end of helix Processing helix chain 'D' and resid 932 through 944 removed outlier: 3.569A pdb=" N VAL D 937 " --> pdb=" O MET D 933 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 129 Processing helix chain 'I' and resid 184 through 188 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.852A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.786A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing helix chain 'K' and resid 122 through 129 Processing helix chain 'K' and resid 184 through 188 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.852A pdb=" N TYR L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.787A pdb=" N ASP L 90 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR L 91 " --> pdb=" O SER L 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 87 through 91' Processing helix chain 'A' and resid 721 through 731 Processing helix chain 'A' and resid 732 through 751 Processing helix chain 'A' and resid 759 through 786 removed outlier: 3.759A pdb=" N ASN A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 767 " --> pdb=" O ASN A 763 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 813 removed outlier: 3.803A pdb=" N LEU A 798 " --> pdb=" O ASP A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 828 removed outlier: 3.680A pdb=" N ARG A 823 " --> pdb=" O SER A 820 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER A 824 " --> pdb=" O VAL A 821 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 825 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 826 " --> pdb=" O ARG A 823 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU A 827 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 834 removed outlier: 3.938A pdb=" N LEU A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 829 through 834' Processing helix chain 'A' and resid 837 through 849 removed outlier: 3.866A pdb=" N ARG A 841 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A 842 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 876 removed outlier: 3.833A pdb=" N MET A 854 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET A 871 " --> pdb=" O ILE A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 885 removed outlier: 3.832A pdb=" N PHE A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 899 removed outlier: 4.911A pdb=" N TYR A 892 " --> pdb=" O GLY A 888 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 899 " --> pdb=" O PHE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 918 through 959 removed outlier: 3.723A pdb=" N ILE A 923 " --> pdb=" O TRP A 919 " (cutoff:3.500A) Proline residue: A 924 - end of helix removed outlier: 3.868A pdb=" N PHE A 927 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET A 945 " --> pdb=" O CYS A 941 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 949 " --> pdb=" O MET A 945 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 950 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 954 " --> pdb=" O GLN A 950 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N HIS A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain 'F' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'G' and resid 19 through 21 Processing sheet with id=AA4, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 7 removed outlier: 4.118A pdb=" N SER I 7 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER I 64 " --> pdb=" O THR I 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 10 through 13 removed outlier: 7.264A pdb=" N LEU I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP I 36 " --> pdb=" O TRP I 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 115 through 119 removed outlier: 5.569A pdb=" N TYR I 174 " --> pdb=" O ASN I 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 146 through 150 removed outlier: 4.005A pdb=" N ASN I 146 " --> pdb=" O THR I 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.869A pdb=" N LEU J 18 " --> pdb=" O MET J 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR J 40 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU J 45 " --> pdb=" O THR J 40 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR J 50 " --> pdb=" O TYR J 59 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR J 59 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR J 111 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 129 through 133 removed outlier: 3.861A pdb=" N GLY J 148 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR J 146 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL J 192 " --> pdb=" O THR J 146 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLY J 148 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL J 190 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU J 150 " --> pdb=" O SER J 188 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER J 188 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS J 152 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU J 186 " --> pdb=" O LYS J 152 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR J 154 " --> pdb=" O TYR J 184 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER J 189 " --> pdb=" O HIS J 173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 129 through 133 removed outlier: 3.861A pdb=" N GLY J 148 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR J 146 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL J 192 " --> pdb=" O THR J 146 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLY J 148 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL J 190 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU J 150 " --> pdb=" O SER J 188 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER J 188 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS J 152 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU J 186 " --> pdb=" O LYS J 152 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR J 154 " --> pdb=" O TYR J 184 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 160 through 163 Processing sheet with id=AB6, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.119A pdb=" N SER K 7 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER K 64 " --> pdb=" O THR K 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 10 through 13 removed outlier: 7.263A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP K 36 " --> pdb=" O TRP K 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 115 through 119 removed outlier: 5.568A pdb=" N TYR K 174 " --> pdb=" O ASN K 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 146 through 150 removed outlier: 4.005A pdb=" N ASN K 146 " --> pdb=" O THR K 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 3 through 6 removed outlier: 3.870A pdb=" N LEU L 18 " --> pdb=" O MET L 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR L 40 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU L 45 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR L 50 " --> pdb=" O TYR L 59 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR L 59 " --> pdb=" O THR L 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR L 111 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 129 through 133 removed outlier: 3.861A pdb=" N GLY L 148 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR L 146 " --> pdb=" O VAL L 192 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL L 192 " --> pdb=" O THR L 146 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLY L 148 " --> pdb=" O VAL L 190 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL L 190 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU L 150 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER L 188 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS L 152 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU L 186 " --> pdb=" O LYS L 152 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR L 154 " --> pdb=" O TYR L 184 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER L 189 " --> pdb=" O HIS L 173 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 129 through 133 removed outlier: 3.861A pdb=" N GLY L 148 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR L 146 " --> pdb=" O VAL L 192 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL L 192 " --> pdb=" O THR L 146 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLY L 148 " --> pdb=" O VAL L 190 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL L 190 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU L 150 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER L 188 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS L 152 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU L 186 " --> pdb=" O LYS L 152 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR L 154 " --> pdb=" O TYR L 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 160 through 163 712 hydrogen bonds defined for protein. 1962 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: 2.26 Time building geometry restraints manager: 1.69 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: 4563 1.34 - 1.46: 4159 1.46 - 1.58: 6942 1.58 - 1.71: 0 1.71 - 1.83: 188 Bond restraints: 15852 Sorted by residual: bond pdb=" CB VAL B 932 " pdb=" CG2 VAL B 932 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.11e+00 bond pdb=" CB VAL D 932 " pdb=" CG2 VAL D 932 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.00e+00 bond pdb=" CG LEU A 887 " pdb=" CD2 LEU A 887 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.99e+00 bond pdb=" CG LEU C 887 " pdb=" CD2 LEU C 887 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.95e+00 bond pdb=" CA ILE B 851 " pdb=" C ILE B 851 " ideal model delta sigma weight residual 1.524 1.545 -0.021 1.11e-02 8.12e+03 3.49e+00 ... (remaining 15847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 20691 2.49 - 4.98: 713 4.98 - 7.47: 111 7.47 - 9.96: 19 9.96 - 12.45: 6 Bond angle restraints: 21540 Sorted by residual: angle pdb=" C THR B 758 " pdb=" N GLU B 759 " pdb=" CA GLU B 759 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C THR D 758 " pdb=" N GLU D 759 " pdb=" CA GLU D 759 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" N ILE C 851 " pdb=" CA ILE C 851 " pdb=" C ILE C 851 " ideal model delta sigma weight residual 108.88 118.01 -9.13 2.16e+00 2.14e-01 1.79e+01 angle pdb=" N ILE A 851 " pdb=" CA ILE A 851 " pdb=" C ILE A 851 " ideal model delta sigma weight residual 108.88 117.97 -9.09 2.16e+00 2.14e-01 1.77e+01 angle pdb=" C GLY I 51 " pdb=" N THR I 52 " pdb=" CA THR I 52 " ideal model delta sigma weight residual 122.61 129.04 -6.43 1.56e+00 4.11e-01 1.70e+01 ... (remaining 21535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 8730 15.00 - 29.99: 470 29.99 - 44.99: 136 44.99 - 59.99: 5 59.99 - 74.99: 12 Dihedral angle restraints: 9353 sinusoidal: 3667 harmonic: 5686 Sorted by residual: dihedral pdb=" CB CYS C 941 " pdb=" SG CYS C 941 " pdb=" SG CYS A 941 " pdb=" CB CYS A 941 " ideal model delta sinusoidal sigma weight residual -86.00 -142.20 56.20 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CA PHE D 931 " pdb=" C PHE D 931 " pdb=" N VAL D 932 " pdb=" CA VAL D 932 " ideal model delta harmonic sigma weight residual 180.00 149.28 30.72 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA PHE B 931 " pdb=" C PHE B 931 " pdb=" N VAL B 932 " pdb=" CA VAL B 932 " ideal model delta harmonic sigma weight residual 180.00 149.28 30.72 0 5.00e+00 4.00e-02 3.77e+01 ... (remaining 9350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1750 0.055 - 0.110: 546 0.110 - 0.165: 146 0.165 - 0.220: 19 0.220 - 0.275: 5 Chirality restraints: 2466 Sorted by residual: chirality pdb=" CB VAL D 850 " pdb=" CA VAL D 850 " pdb=" CG1 VAL D 850 " pdb=" CG2 VAL D 850 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB VAL B 850 " pdb=" CA VAL B 850 " pdb=" CG1 VAL B 850 " pdb=" CG2 VAL B 850 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE L 70 " pdb=" CA ILE L 70 " pdb=" CG1 ILE L 70 " pdb=" CG2 ILE L 70 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2463 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 931 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.31e+01 pdb=" C PHE C 931 " -0.063 2.00e-02 2.50e+03 pdb=" O PHE C 931 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL C 932 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 931 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C PHE A 931 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE A 931 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 932 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 930 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C THR A 930 " 0.056 2.00e-02 2.50e+03 pdb=" O THR A 930 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE A 931 " -0.019 2.00e-02 2.50e+03 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2363 2.76 - 3.29: 14506 3.29 - 3.83: 24476 3.83 - 4.36: 26874 4.36 - 4.90: 45793 Nonbonded interactions: 114012 Sorted by model distance: nonbonded pdb=" NZ LYS L 218 " pdb=" OE2 GLU L 220 " model vdw 2.222 3.120 nonbonded pdb=" NZ LYS J 218 " pdb=" OE2 GLU J 220 " model vdw 2.222 3.120 nonbonded pdb=" OE2 GLU D 779 " pdb=" NH2 ARG D 783 " model vdw 2.270 3.120 nonbonded pdb=" OE2 GLU B 779 " pdb=" NH2 ARG B 783 " model vdw 2.270 3.120 nonbonded pdb=" O LEU B 802 " pdb=" OG1 THR B 805 " model vdw 2.297 3.040 ... (remaining 114007 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'A' } 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: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.500 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 0.077 15873 Z= 0.350 Angle : 1.075 12.449 21582 Z= 0.571 Chirality : 0.057 0.275 2466 Planarity : 0.008 0.073 2634 Dihedral : 10.265 74.986 5610 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.23 % Allowed : 3.11 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.16), residues: 1918 helix: -2.08 (0.16), residues: 676 sheet: -0.92 (0.25), residues: 402 loop : -2.83 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 879 TYR 0.026 0.003 TYR C 741 PHE 0.031 0.004 PHE A 927 TRP 0.035 0.002 TRP B 883 HIS 0.008 0.002 HIS B 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.35 (15852) covalent geometry : angle 1.07400 / 0.57 (21540) SS BOND : bond 0.00472 / 0.37 ( 21) SS BOND : angle 1.35110 / 0.93 ( 42) hydrogen bonds : bond 0.17488 / 11.80 ( 692) hydrogen bonds : angle 7.85636 / 5.41 ( 1962) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 571 time to evaluate : 0.477 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: B 765 LEU cc_start: 0.9072 (mt) cc_final: 0.8842 (mt) REVERT: B 840 MET cc_start: 0.8458 (mmt) cc_final: 0.8151 (mmt) REVERT: B 854 MET cc_start: 0.8390 (mmm) cc_final: 0.8043 (mmm) REVERT: B 874 GLN cc_start: 0.8546 (mt0) cc_final: 0.8313 (mt0) REVERT: B 889 GLU cc_start: 0.7733 (mt-10) cc_final: 0.6804 (mm-30) REVERT: B 917 TYR cc_start: 0.8965 (m-10) cc_final: 0.8609 (m-10) REVERT: C 729 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8496 (tp) REVERT: C 784 ILE cc_start: 0.8710 (pp) cc_final: 0.8370 (tt) REVERT: D 780 ILE cc_start: 0.8616 (tp) cc_final: 0.8399 (tp) REVERT: D 797 SER cc_start: 0.9035 (m) cc_final: 0.8792 (p) REVERT: D 854 MET cc_start: 0.8413 (mmm) cc_final: 0.8078 (mmm) REVERT: D 874 GLN cc_start: 0.8545 (mt0) cc_final: 0.8308 (mt0) REVERT: D 889 GLU cc_start: 0.7727 (mt-10) cc_final: 0.6776 (mm-30) REVERT: D 917 TYR cc_start: 0.8971 (m-10) cc_final: 0.8601 (m-10) REVERT: G 19 MET cc_start: 0.5686 (mtm) cc_final: 0.5373 (mtm) REVERT: I 27 LEU cc_start: 0.8977 (tp) cc_final: 0.8472 (mp) REVERT: I 28 SER cc_start: 0.7962 (t) cc_final: 0.7589 (t) REVERT: I 31 SER cc_start: 0.9351 (m) cc_final: 0.9053 (t) REVERT: I 37 TYR cc_start: 0.8714 (m-80) cc_final: 0.8341 (m-10) REVERT: I 63 PHE cc_start: 0.7958 (m-10) cc_final: 0.7741 (m-10) REVERT: I 73 SER cc_start: 0.8975 (p) cc_final: 0.8768 (t) REVERT: I 88 TYR cc_start: 0.9112 (m-80) cc_final: 0.8910 (m-10) REVERT: J 13 LYS cc_start: 0.8971 (mttp) cc_final: 0.8541 (tppt) REVERT: J 86 LEU cc_start: 0.8876 (mt) cc_final: 0.8605 (mp) REVERT: J 163 TRP cc_start: 0.3711 (m100) cc_final: 0.3279 (m100) REVERT: K 73 SER cc_start: 0.9041 (p) cc_final: 0.8748 (t) REVERT: K 91 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8473 (tm-30) REVERT: L 3 GLN cc_start: 0.7578 (mm110) cc_final: 0.7365 (mm-40) REVERT: L 13 LYS cc_start: 0.8982 (mttp) cc_final: 0.8671 (tppt) REVERT: L 86 LEU cc_start: 0.8868 (mt) cc_final: 0.8538 (mp) REVERT: L 90 ASP cc_start: 0.9029 (m-30) cc_final: 0.8816 (m-30) REVERT: L 183 LEU cc_start: 0.7650 (mt) cc_final: 0.7079 (pp) REVERT: A 729 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8450 (tp) REVERT: A 779 GLU cc_start: 0.7939 (tt0) cc_final: 0.7437 (tt0) REVERT: A 784 ILE cc_start: 0.8627 (pp) cc_final: 0.8272 (tt) REVERT: A 831 PHE cc_start: 0.8005 (m-10) cc_final: 0.7687 (t80) REVERT: A 933 MET cc_start: 0.8480 (mmt) cc_final: 0.8178 (mmm) outliers start: 4 outliers final: 0 residues processed: 571 average time/residue: 0.1246 time to fit residues: 103.3335 Evaluate side-chains 396 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 394 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 769 ASN B 896 GLN C 896 GLN D 769 ASN D 896 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN J 39 GLN J 77 ASN J 164 ASN L 164 ASN A 754 HIS A 896 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.194552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.148205 restraints weight = 25688.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144602 restraints weight = 32883.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.146310 restraints weight = 29106.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.146366 restraints weight = 16478.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.148593 restraints weight = 14098.692| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15873 Z= 0.142 Angle : 0.681 7.507 21582 Z= 0.353 Chirality : 0.043 0.168 2466 Planarity : 0.006 0.061 2634 Dihedral : 5.447 21.368 2086 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.23 % Allowed : 3.34 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.18), residues: 1918 helix: -0.64 (0.19), residues: 718 sheet: -0.53 (0.26), residues: 422 loop : -2.43 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 22 TYR 0.012 0.001 TYR I 193 PHE 0.027 0.002 PHE D 749 TRP 0.022 0.001 TRP D 883 HIS 0.007 0.001 HIS C 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (15852) covalent geometry : angle 0.67733 / 0.35 (21540) SS BOND : bond 0.00683 / 0.54 ( 21) SS BOND : angle 1.81686 / 1.44 ( 42) hydrogen bonds : bond 0.05417 / 3.64 ( 692) hydrogen bonds : angle 5.85806 / 4.06 ( 1962) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 496 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 780 ILE cc_start: 0.8260 (tp) cc_final: 0.8007 (tp) REVERT: B 840 MET cc_start: 0.8448 (mmt) cc_final: 0.8196 (mmt) REVERT: B 854 MET cc_start: 0.8188 (mmm) cc_final: 0.7900 (mmm) REVERT: B 874 GLN cc_start: 0.8558 (mt0) cc_final: 0.8185 (mt0) REVERT: B 889 GLU cc_start: 0.7682 (mt-10) cc_final: 0.6751 (mm-30) REVERT: C 722 MET cc_start: 0.8315 (pmm) cc_final: 0.7274 (pmm) REVERT: C 800 ASP cc_start: 0.8489 (m-30) cc_final: 0.8158 (m-30) REVERT: C 831 PHE cc_start: 0.8192 (m-10) cc_final: 0.7631 (t80) REVERT: C 950 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7666 (tp40) REVERT: D 854 MET cc_start: 0.8255 (mmm) cc_final: 0.7963 (mmm) REVERT: D 874 GLN cc_start: 0.8539 (mt0) cc_final: 0.8218 (mt0) REVERT: D 889 GLU cc_start: 0.7655 (mt-10) cc_final: 0.6757 (mm-30) REVERT: I 31 SER cc_start: 0.9516 (m) cc_final: 0.9210 (t) REVERT: I 37 TYR cc_start: 0.9017 (m-80) cc_final: 0.8774 (m-10) REVERT: I 59 VAL cc_start: 0.8780 (t) cc_final: 0.8336 (p) REVERT: I 91 GLN cc_start: 0.9373 (pp30) cc_final: 0.9146 (pp30) REVERT: I 176 MET cc_start: 0.6034 (ttp) cc_final: 0.5051 (ptp) REVERT: J 13 LYS cc_start: 0.8961 (mttp) cc_final: 0.8614 (tppt) REVERT: K 31 SER cc_start: 0.9521 (m) cc_final: 0.9166 (t) REVERT: K 37 TYR cc_start: 0.9061 (m-80) cc_final: 0.8861 (m-10) REVERT: K 214 GLU cc_start: 0.6993 (pp20) cc_final: 0.6498 (pp20) REVERT: L 3 GLN cc_start: 0.7747 (mm110) cc_final: 0.7496 (mm-40) REVERT: L 13 LYS cc_start: 0.9008 (mttp) cc_final: 0.8664 (tppt) REVERT: L 183 LEU cc_start: 0.7723 (mt) cc_final: 0.7043 (pp) REVERT: A 722 MET cc_start: 0.8448 (pmm) cc_final: 0.7350 (pmm) REVERT: A 773 THR cc_start: 0.9553 (p) cc_final: 0.9347 (p) REVERT: A 783 ARG cc_start: 0.8227 (mtp-110) cc_final: 0.7864 (ttp80) REVERT: A 831 PHE cc_start: 0.8288 (m-10) cc_final: 0.7675 (t80) REVERT: A 933 MET cc_start: 0.8390 (mmt) cc_final: 0.8182 (mmm) outliers start: 4 outliers final: 0 residues processed: 496 average time/residue: 0.1293 time to fit residues: 93.0182 Evaluate side-chains 375 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [2, 67, 33, 37, 168, 149, 73, 174, 15, 52, 71] chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 168 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 769 ASN C 896 GLN ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 ASN I 190 HIS J 39 GLN K 95 HIS L 39 GLN A 896 GLN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.191592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139454 restraints weight = 26100.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130208 restraints weight = 24774.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131423 restraints weight = 21903.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.132965 restraints weight = 14518.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.133529 restraints weight = 12288.343| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15873 Z= 0.211 Angle : 0.715 9.222 21582 Z= 0.372 Chirality : 0.044 0.151 2466 Planarity : 0.005 0.052 2634 Dihedral : 5.335 24.103 2086 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.18), residues: 1918 helix: -0.28 (0.19), residues: 716 sheet: -0.29 (0.26), residues: 414 loop : -2.37 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 725 TYR 0.012 0.002 TYR L 184 PHE 0.022 0.002 PHE C 792 TRP 0.026 0.002 TRP B 883 HIS 0.007 0.002 HIS B 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (15852) covalent geometry : angle 0.71293 / 0.37 (21540) SS BOND : bond 0.00468 / 0.37 ( 21) SS BOND : angle 1.52747 / 1.21 ( 42) hydrogen bonds : bond 0.05243 / 3.52 ( 692) hydrogen bonds : angle 5.54542 / 3.87 ( 1962) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 723 TYR cc_start: 0.8660 (t80) cc_final: 0.8317 (t80) REVERT: B 765 LEU cc_start: 0.9140 (mt) cc_final: 0.8865 (mt) REVERT: B 840 MET cc_start: 0.8253 (mmt) cc_final: 0.8033 (mmt) REVERT: B 874 GLN cc_start: 0.8536 (mt0) cc_final: 0.8131 (mt0) REVERT: B 889 GLU cc_start: 0.7769 (mt-10) cc_final: 0.6999 (mm-30) REVERT: C 791 PHE cc_start: 0.8239 (t80) cc_final: 0.7882 (t80) REVERT: C 800 ASP cc_start: 0.8634 (m-30) cc_final: 0.8286 (m-30) REVERT: C 841 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7920 (mpt180) REVERT: C 952 GLU cc_start: 0.9200 (pp20) cc_final: 0.8887 (pp20) REVERT: D 832 ARG cc_start: 0.7135 (ptp90) cc_final: 0.6691 (ptp90) REVERT: D 841 ARG cc_start: 0.8429 (mmm160) cc_final: 0.8210 (mmm160) REVERT: D 874 GLN cc_start: 0.8564 (mt0) cc_final: 0.8149 (mt0) REVERT: D 889 GLU cc_start: 0.7781 (mt-10) cc_final: 0.6989 (mm-30) REVERT: G 22 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6837 (mtm110) REVERT: H 6 MET cc_start: 0.8228 (mtm) cc_final: 0.7840 (mmm) REVERT: I 27 LEU cc_start: 0.8975 (tp) cc_final: 0.8454 (mt) REVERT: I 28 SER cc_start: 0.8329 (t) cc_final: 0.7836 (t) REVERT: I 31 SER cc_start: 0.9545 (m) cc_final: 0.9317 (t) REVERT: I 37 TYR cc_start: 0.9067 (m-80) cc_final: 0.8857 (m-10) REVERT: I 88 TYR cc_start: 0.9259 (m-80) cc_final: 0.8991 (m-80) REVERT: I 91 GLN cc_start: 0.9364 (pp30) cc_final: 0.8902 (pp30) REVERT: I 188 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8013 (mt-10) REVERT: J 13 LYS cc_start: 0.9011 (mttp) cc_final: 0.8536 (tppt) REVERT: J 76 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8349 (tmtt) REVERT: J 86 LEU cc_start: 0.8801 (mp) cc_final: 0.8557 (mt) REVERT: J 183 LEU cc_start: 0.8644 (mt) cc_final: 0.7994 (pp) REVERT: K 31 SER cc_start: 0.9622 (m) cc_final: 0.9316 (t) REVERT: K 106 GLU cc_start: 0.7570 (mp0) cc_final: 0.7299 (pm20) REVERT: K 109 ARG cc_start: 0.7782 (ptm160) cc_final: 0.7416 (ptp-170) REVERT: K 214 GLU cc_start: 0.6322 (pp20) cc_final: 0.5834 (pp20) REVERT: L 13 LYS cc_start: 0.9069 (mttp) cc_final: 0.8578 (tppt) REVERT: L 114 GLN cc_start: 0.7922 (tp40) cc_final: 0.7643 (tm-30) REVERT: L 163 TRP cc_start: 0.3924 (m100) cc_final: 0.3638 (m100) REVERT: L 183 LEU cc_start: 0.8043 (mt) cc_final: 0.7388 (pp) REVERT: A 792 PHE cc_start: 0.7873 (m-10) cc_final: 0.7561 (t80) REVERT: A 831 PHE cc_start: 0.8421 (m-10) cc_final: 0.7774 (t80) REVERT: A 933 MET cc_start: 0.8469 (mmt) cc_final: 0.8253 (mmm) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.1212 time to fit residues: 79.8926 Evaluate side-chains 356 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [160, 109, 149, 89, 8, 23, 28, 110, 134, 13, 127] chunk 160 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 127 optimal weight: 0.0970 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 769 ASN C 935 ASN D 769 ASN J 77 ASN L 39 GLN L 77 ASN A 935 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.193344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.143652 restraints weight = 25622.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137673 restraints weight = 25579.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.139460 restraints weight = 24342.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139539 restraints weight = 14941.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.141171 restraints weight = 12755.554| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15873 Z= 0.131 Angle : 0.640 9.490 21582 Z= 0.327 Chirality : 0.042 0.170 2466 Planarity : 0.005 0.051 2634 Dihedral : 5.024 26.365 2086 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 1918 helix: 0.12 (0.19), residues: 714 sheet: -0.17 (0.26), residues: 422 loop : -2.12 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 22 TYR 0.012 0.001 TYR K 193 PHE 0.030 0.001 PHE B 749 TRP 0.018 0.001 TRP B 883 HIS 0.006 0.001 HIS B 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15852) covalent geometry : angle 0.63831 / 0.33 (21540) SS BOND : bond 0.00591 / 0.42 ( 21) SS BOND : angle 1.12698 / 0.86 ( 42) hydrogen bonds : bond 0.04425 / 2.99 ( 692) hydrogen bonds : angle 5.25898 / 3.66 ( 1962) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 0.495 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: B 840 MET cc_start: 0.8546 (mmt) cc_final: 0.8296 (mmt) REVERT: B 854 MET cc_start: 0.8284 (mmm) cc_final: 0.8020 (mmm) REVERT: B 889 GLU cc_start: 0.7717 (mt-10) cc_final: 0.6867 (mm-30) REVERT: C 791 PHE cc_start: 0.8043 (t80) cc_final: 0.7825 (t80) REVERT: C 831 PHE cc_start: 0.8239 (m-10) cc_final: 0.7574 (t80) REVERT: C 832 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8390 (ttp80) REVERT: D 780 ILE cc_start: 0.8370 (tp) cc_final: 0.8153 (tp) REVERT: D 840 MET cc_start: 0.8727 (mmt) cc_final: 0.8473 (mmt) REVERT: D 854 MET cc_start: 0.8359 (mmm) cc_final: 0.8131 (mmm) REVERT: D 889 GLU cc_start: 0.7787 (mt-10) cc_final: 0.6916 (mm-30) REVERT: F 8 THR cc_start: 0.7134 (p) cc_final: 0.6931 (p) REVERT: I 31 SER cc_start: 0.9538 (m) cc_final: 0.9338 (t) REVERT: I 59 VAL cc_start: 0.9034 (t) cc_final: 0.8621 (p) REVERT: I 88 TYR cc_start: 0.9276 (m-80) cc_final: 0.9018 (m-80) REVERT: I 91 GLN cc_start: 0.9341 (pp30) cc_final: 0.9083 (pp30) REVERT: J 86 LEU cc_start: 0.8770 (mp) cc_final: 0.8556 (mt) REVERT: J 183 LEU cc_start: 0.8511 (mt) cc_final: 0.7794 (pp) REVERT: K 31 SER cc_start: 0.9592 (m) cc_final: 0.9293 (t) REVERT: K 91 GLN cc_start: 0.9181 (pp30) cc_final: 0.8869 (pp30) REVERT: K 106 GLU cc_start: 0.7339 (mp0) cc_final: 0.7104 (mp0) REVERT: K 109 ARG cc_start: 0.7661 (ptm160) cc_final: 0.7349 (ptp-170) REVERT: K 214 GLU cc_start: 0.6871 (pp20) cc_final: 0.6551 (pp20) REVERT: L 13 LYS cc_start: 0.9045 (mttp) cc_final: 0.8680 (tppt) REVERT: L 114 GLN cc_start: 0.7840 (tp40) cc_final: 0.7555 (tp40) REVERT: L 183 LEU cc_start: 0.7831 (mt) cc_final: 0.7098 (pp) REVERT: A 800 ASP cc_start: 0.8550 (m-30) cc_final: 0.8222 (m-30) REVERT: A 831 PHE cc_start: 0.8283 (m-10) cc_final: 0.7700 (t80) REVERT: A 901 GLU cc_start: 0.9367 (tm-30) cc_final: 0.9161 (tm-30) REVERT: A 933 MET cc_start: 0.8435 (mmt) cc_final: 0.8231 (mmm) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.1268 time to fit residues: 87.2678 Evaluate side-chains 374 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [188, 96, 134, 4, 14, 148, 159, 168, 51, 92, 28] chunk 188 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 148 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 769 ASN B 896 GLN D 769 ASN D 896 GLN E 3 GLN J 77 ASN K 95 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.190744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139266 restraints weight = 25956.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.130107 restraints weight = 23224.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131741 restraints weight = 21997.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.133038 restraints weight = 13772.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134296 restraints weight = 11826.019| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15873 Z= 0.164 Angle : 0.661 9.614 21582 Z= 0.339 Chirality : 0.043 0.161 2466 Planarity : 0.004 0.047 2634 Dihedral : 5.046 43.990 2086 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.19), residues: 1918 helix: 0.23 (0.20), residues: 716 sheet: -0.16 (0.26), residues: 422 loop : -2.17 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 783 TYR 0.013 0.001 TYR K 193 PHE 0.031 0.002 PHE B 749 TRP 0.022 0.001 TRP B 883 HIS 0.006 0.001 HIS B 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (15852) covalent geometry : angle 0.65972 / 0.34 (21540) SS BOND : bond 0.00453 / 0.34 ( 21) SS BOND : angle 1.17821 / 0.95 ( 42) hydrogen bonds : bond 0.04538 / 3.05 ( 692) hydrogen bonds : angle 5.16279 / 3.59 ( 1962) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 0.574 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: B 811 LEU cc_start: 0.9078 (mp) cc_final: 0.8436 (tp) REVERT: B 840 MET cc_start: 0.8684 (mmt) cc_final: 0.8431 (mmt) REVERT: B 889 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7016 (mm-30) REVERT: C 791 PHE cc_start: 0.8034 (t80) cc_final: 0.7821 (t80) REVERT: C 841 ARG cc_start: 0.8236 (mtt180) cc_final: 0.7960 (mpt180) REVERT: C 901 GLU cc_start: 0.9495 (tm-30) cc_final: 0.9261 (tm-30) REVERT: C 950 GLN cc_start: 0.8551 (tt0) cc_final: 0.8226 (tp-100) REVERT: D 841 ARG cc_start: 0.8541 (mmm160) cc_final: 0.8018 (mmm160) REVERT: D 854 MET cc_start: 0.8260 (mmm) cc_final: 0.8057 (mmm) REVERT: D 889 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7144 (mm-30) REVERT: D 898 MET cc_start: 0.9023 (ttp) cc_final: 0.8787 (ttt) REVERT: G 19 MET cc_start: 0.5577 (tpt) cc_final: 0.5166 (tmm) REVERT: G 24 TRP cc_start: 0.8404 (p90) cc_final: 0.7898 (p90) REVERT: H 6 MET cc_start: 0.7652 (mtp) cc_final: 0.7246 (mpp) REVERT: I 27 LEU cc_start: 0.8958 (tp) cc_final: 0.8447 (mt) REVERT: I 28 SER cc_start: 0.8091 (t) cc_final: 0.7526 (t) REVERT: I 31 SER cc_start: 0.9545 (m) cc_final: 0.9319 (t) REVERT: I 59 VAL cc_start: 0.9098 (t) cc_final: 0.8809 (p) REVERT: I 88 TYR cc_start: 0.9325 (m-80) cc_final: 0.9017 (m-80) REVERT: I 91 GLN cc_start: 0.9315 (pp30) cc_final: 0.8981 (pp30) REVERT: I 176 MET cc_start: 0.5636 (ttp) cc_final: 0.5319 (ptp) REVERT: J 3 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7785 (mm-40) REVERT: J 182 ASP cc_start: 0.8158 (m-30) cc_final: 0.7587 (t0) REVERT: J 183 LEU cc_start: 0.8618 (mt) cc_final: 0.7833 (pp) REVERT: K 31 SER cc_start: 0.9602 (m) cc_final: 0.9328 (t) REVERT: K 63 PHE cc_start: 0.8121 (m-10) cc_final: 0.7796 (m-80) REVERT: K 91 GLN cc_start: 0.9227 (pp30) cc_final: 0.8808 (pp30) REVERT: K 106 GLU cc_start: 0.7557 (mp0) cc_final: 0.7296 (mp0) REVERT: K 109 ARG cc_start: 0.7772 (ptm160) cc_final: 0.7414 (ptp-170) REVERT: L 3 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7650 (mm-40) REVERT: L 13 LYS cc_start: 0.9012 (mttp) cc_final: 0.8631 (tppt) REVERT: A 800 ASP cc_start: 0.8401 (m-30) cc_final: 0.8191 (m-30) REVERT: A 831 PHE cc_start: 0.8272 (m-10) cc_final: 0.7646 (t80) REVERT: A 952 GLU cc_start: 0.8973 (pp20) cc_final: 0.8573 (pp20) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.1202 time to fit residues: 80.1292 Evaluate side-chains 358 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [2, 19, 115, 66, 24, 136, 167, 178, 77, 9, 71] chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 115 optimal weight: 40.0000 chunk 66 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 769 ASN B 896 GLN C 896 GLN C 935 ASN D 769 ASN D 896 GLN J 39 GLN J 77 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.190493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.142264 restraints weight = 25737.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135965 restraints weight = 30513.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.137667 restraints weight = 27650.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.137397 restraints weight = 17443.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.139976 restraints weight = 14304.141| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15873 Z= 0.164 Angle : 0.656 9.820 21582 Z= 0.337 Chirality : 0.043 0.204 2466 Planarity : 0.005 0.054 2634 Dihedral : 4.978 35.385 2086 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 1918 helix: 0.35 (0.20), residues: 716 sheet: -0.13 (0.26), residues: 422 loop : -2.12 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 725 TYR 0.016 0.001 TYR C 723 PHE 0.029 0.002 PHE D 749 TRP 0.023 0.001 TRP I 164 HIS 0.006 0.001 HIS B 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (15852) covalent geometry : angle 0.65480 / 0.34 (21540) SS BOND : bond 0.00435 / 0.35 ( 21) SS BOND : angle 1.14398 / 0.88 ( 42) hydrogen bonds : bond 0.04454 / 3.01 ( 692) hydrogen bonds : angle 5.10873 / 3.54 ( 1962) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.584 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: B 780 ILE cc_start: 0.8510 (tp) cc_final: 0.8295 (tp) REVERT: B 811 LEU cc_start: 0.8909 (mp) cc_final: 0.8308 (tp) REVERT: B 840 MET cc_start: 0.8809 (mmt) cc_final: 0.8540 (mmt) REVERT: B 854 MET cc_start: 0.8253 (mmm) cc_final: 0.8004 (mmm) REVERT: B 889 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7024 (mm-30) REVERT: C 783 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7314 (ttp80) REVERT: D 840 MET cc_start: 0.8762 (mmt) cc_final: 0.8533 (mmt) REVERT: D 841 ARG cc_start: 0.8562 (mmm160) cc_final: 0.8069 (mmm160) REVERT: D 889 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7093 (mm-30) REVERT: E 19 MET cc_start: 0.6408 (tpp) cc_final: 0.6051 (mmm) REVERT: E 22 ARG cc_start: 0.8785 (mmm-85) cc_final: 0.8462 (mmp-170) REVERT: G 19 MET cc_start: 0.5229 (tpt) cc_final: 0.5021 (mmm) REVERT: H 6 MET cc_start: 0.7487 (mtp) cc_final: 0.7073 (mpp) REVERT: I 27 LEU cc_start: 0.8946 (tp) cc_final: 0.8446 (mt) REVERT: I 28 SER cc_start: 0.8002 (t) cc_final: 0.7479 (t) REVERT: I 31 SER cc_start: 0.9531 (m) cc_final: 0.9291 (t) REVERT: I 59 VAL cc_start: 0.9107 (t) cc_final: 0.8804 (p) REVERT: I 88 TYR cc_start: 0.9354 (m-80) cc_final: 0.9045 (m-80) REVERT: I 91 GLN cc_start: 0.9236 (pp30) cc_final: 0.8774 (pp30) REVERT: I 106 GLU cc_start: 0.7444 (pm20) cc_final: 0.7212 (pm20) REVERT: I 176 MET cc_start: 0.6127 (ttp) cc_final: 0.5322 (ptm) REVERT: J 3 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7705 (mm-40) REVERT: J 114 GLN cc_start: 0.8124 (tp40) cc_final: 0.7896 (tp40) REVERT: J 182 ASP cc_start: 0.8112 (m-30) cc_final: 0.7628 (t0) REVERT: K 31 SER cc_start: 0.9593 (m) cc_final: 0.9331 (t) REVERT: K 63 PHE cc_start: 0.8170 (m-10) cc_final: 0.7870 (m-80) REVERT: K 91 GLN cc_start: 0.9266 (pp30) cc_final: 0.8760 (pp30) REVERT: K 106 GLU cc_start: 0.7483 (mp0) cc_final: 0.7199 (mp0) REVERT: K 109 ARG cc_start: 0.7536 (ptm160) cc_final: 0.7333 (ptp-170) REVERT: L 3 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7800 (mm-40) REVERT: L 13 LYS cc_start: 0.9028 (mttp) cc_final: 0.8684 (tppt) REVERT: A 779 GLU cc_start: 0.7968 (tt0) cc_final: 0.7518 (tt0) REVERT: A 950 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7875 (tp-100) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.1241 time to fit residues: 79.6637 Evaluate side-chains 340 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [18, 125, 187, 179, 126, 58, 79, 128, 32, 63, 149] chunk 18 optimal weight: 0.1980 chunk 125 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 58 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 0.1980 chunk 149 optimal weight: 0.0470 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 769 ASN D 769 ASN D 896 GLN I 38 GLN J 77 ASN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.194128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143974 restraints weight = 25675.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.137869 restraints weight = 28456.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139571 restraints weight = 23208.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.139370 restraints weight = 17570.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.141037 restraints weight = 13301.984| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15873 Z= 0.118 Angle : 0.633 8.333 21582 Z= 0.320 Chirality : 0.042 0.183 2466 Planarity : 0.004 0.038 2634 Dihedral : 4.773 30.015 2086 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.19), residues: 1918 helix: 0.47 (0.20), residues: 714 sheet: 0.06 (0.26), residues: 414 loop : -2.05 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 725 TYR 0.011 0.001 TYR B 866 PHE 0.029 0.001 PHE C 791 TRP 0.017 0.001 TRP E 24 HIS 0.007 0.001 HIS K 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (15852) covalent geometry : angle 0.63124 / 0.32 (21540) SS BOND : bond 0.00382 / 0.31 ( 21) SS BOND : angle 1.10722 / 0.90 ( 42) hydrogen bonds : bond 0.03884 / 2.61 ( 692) hydrogen bonds : angle 4.93548 / 3.42 ( 1962) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.585 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: B 780 ILE cc_start: 0.8404 (tp) cc_final: 0.8142 (tt) REVERT: B 832 ARG cc_start: 0.7177 (ptp90) cc_final: 0.6874 (ptp90) REVERT: B 866 TYR cc_start: 0.8941 (t80) cc_final: 0.8555 (t80) REVERT: B 889 GLU cc_start: 0.7780 (mt-10) cc_final: 0.6881 (mm-30) REVERT: C 783 ARG cc_start: 0.7519 (ttp80) cc_final: 0.7286 (ttp80) REVERT: C 800 ASP cc_start: 0.8356 (m-30) cc_final: 0.8003 (m-30) REVERT: C 831 PHE cc_start: 0.8329 (m-10) cc_final: 0.7505 (t80) REVERT: C 841 ARG cc_start: 0.8200 (mtt180) cc_final: 0.7949 (mtm-85) REVERT: C 901 GLU cc_start: 0.9370 (tm-30) cc_final: 0.9165 (tm-30) REVERT: D 832 ARG cc_start: 0.7221 (ptp90) cc_final: 0.5923 (ptp90) REVERT: D 841 ARG cc_start: 0.8611 (mmm160) cc_final: 0.8164 (mmm160) REVERT: D 889 GLU cc_start: 0.7634 (mt-10) cc_final: 0.6777 (mm-30) REVERT: E 22 ARG cc_start: 0.8829 (mmm-85) cc_final: 0.8577 (mmp-170) REVERT: H 6 MET cc_start: 0.7584 (mtp) cc_final: 0.7143 (mpp) REVERT: I 27 LEU cc_start: 0.8905 (tp) cc_final: 0.8424 (mp) REVERT: I 28 SER cc_start: 0.8058 (t) cc_final: 0.7653 (t) REVERT: I 31 SER cc_start: 0.9515 (m) cc_final: 0.9261 (t) REVERT: I 59 VAL cc_start: 0.8982 (t) cc_final: 0.8566 (p) REVERT: I 88 TYR cc_start: 0.9327 (m-80) cc_final: 0.9047 (m-80) REVERT: I 91 GLN cc_start: 0.9207 (pp30) cc_final: 0.8966 (pp30) REVERT: J 3 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7786 (mm-40) REVERT: J 13 LYS cc_start: 0.9024 (mttp) cc_final: 0.8571 (tppt) REVERT: J 182 ASP cc_start: 0.7805 (m-30) cc_final: 0.7355 (t0) REVERT: K 11 MET cc_start: 0.8013 (tpp) cc_final: 0.7648 (ttm) REVERT: K 31 SER cc_start: 0.9574 (m) cc_final: 0.9349 (t) REVERT: K 63 PHE cc_start: 0.8103 (m-10) cc_final: 0.7695 (m-80) REVERT: K 91 GLN cc_start: 0.9261 (pp30) cc_final: 0.8855 (pp30) REVERT: K 106 GLU cc_start: 0.7343 (mp0) cc_final: 0.7061 (pm20) REVERT: K 109 ARG cc_start: 0.7565 (ptm160) cc_final: 0.7318 (ptp-170) REVERT: L 3 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7699 (mm-40) REVERT: L 163 TRP cc_start: 0.3750 (m100) cc_final: 0.3507 (m100) REVERT: A 779 GLU cc_start: 0.7938 (tt0) cc_final: 0.7722 (tt0) REVERT: A 783 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7949 (ttp80) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.1216 time to fit residues: 80.7730 Evaluate side-chains 364 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [129, 177, 112, 119, 74, 56, 149, 94, 70, 67, 86] chunk 129 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 0.0470 chunk 56 optimal weight: 0.6980 chunk 149 optimal weight: 0.0170 chunk 94 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 chunk 86 optimal weight: 5.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 769 ASN B 896 GLN C 961 GLN D 769 ASN J 77 ASN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.194951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.144220 restraints weight = 25667.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.138708 restraints weight = 30705.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.140639 restraints weight = 25993.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.141894 restraints weight = 14922.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.142508 restraints weight = 13053.336| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15873 Z= 0.121 Angle : 0.646 8.273 21582 Z= 0.325 Chirality : 0.042 0.167 2466 Planarity : 0.004 0.045 2634 Dihedral : 4.677 29.432 2086 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.06 % Allowed : 1.27 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.20), residues: 1918 helix: 0.60 (0.20), residues: 716 sheet: -0.13 (0.26), residues: 418 loop : -1.86 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 725 TYR 0.010 0.001 TYR B 866 PHE 0.025 0.001 PHE A 891 TRP 0.016 0.001 TRP E 5 HIS 0.008 0.001 HIS K 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15852) covalent geometry : angle 0.64499 / 0.32 (21540) SS BOND : bond 0.00387 / 0.30 ( 21) SS BOND : angle 1.12895 / 0.91 ( 42) hydrogen bonds : bond 0.03825 / 2.56 ( 692) hydrogen bonds : angle 4.91039 / 3.40 ( 1962) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 442 time to evaluate : 0.577 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: B 780 ILE cc_start: 0.8420 (tp) cc_final: 0.8145 (tt) REVERT: B 832 ARG cc_start: 0.7152 (ptp90) cc_final: 0.6838 (ptp90) REVERT: B 840 MET cc_start: 0.9050 (mmt) cc_final: 0.8808 (mmt) REVERT: B 866 TYR cc_start: 0.8926 (t80) cc_final: 0.8564 (t80) REVERT: B 889 GLU cc_start: 0.7645 (mt-10) cc_final: 0.6854 (mm-30) REVERT: C 800 ASP cc_start: 0.8357 (m-30) cc_final: 0.7999 (m-30) REVERT: C 831 PHE cc_start: 0.8178 (m-10) cc_final: 0.7487 (t80) REVERT: C 841 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7987 (mtt90) REVERT: C 901 GLU cc_start: 0.9402 (tm-30) cc_final: 0.9054 (tm-30) REVERT: D 780 ILE cc_start: 0.8441 (tp) cc_final: 0.8198 (tt) REVERT: D 841 ARG cc_start: 0.8579 (mmm160) cc_final: 0.8217 (mmm160) REVERT: D 883 TRP cc_start: 0.8298 (p90) cc_final: 0.7066 (p90) REVERT: D 889 GLU cc_start: 0.7680 (mt-10) cc_final: 0.6838 (mm-30) REVERT: G 19 MET cc_start: 0.4525 (tpt) cc_final: 0.4282 (tmm) REVERT: H 6 MET cc_start: 0.7481 (mtp) cc_final: 0.7049 (mpp) REVERT: I 11 MET cc_start: 0.7905 (mmm) cc_final: 0.7686 (mmm) REVERT: I 27 LEU cc_start: 0.8916 (tp) cc_final: 0.8454 (mp) REVERT: I 28 SER cc_start: 0.8062 (t) cc_final: 0.7661 (p) REVERT: I 31 SER cc_start: 0.9521 (m) cc_final: 0.9284 (t) REVERT: I 59 VAL cc_start: 0.9083 (t) cc_final: 0.8680 (p) REVERT: I 88 TYR cc_start: 0.9352 (m-80) cc_final: 0.9051 (m-80) REVERT: I 91 GLN cc_start: 0.9199 (pp30) cc_final: 0.8901 (pp30) REVERT: J 3 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7731 (mm-40) REVERT: J 13 LYS cc_start: 0.8989 (mttp) cc_final: 0.8585 (tppt) REVERT: J 182 ASP cc_start: 0.7896 (m-30) cc_final: 0.7521 (t0) REVERT: K 11 MET cc_start: 0.8073 (tpp) cc_final: 0.7585 (ttm) REVERT: K 31 SER cc_start: 0.9560 (m) cc_final: 0.9355 (t) REVERT: K 63 PHE cc_start: 0.8126 (m-10) cc_final: 0.7682 (m-80) REVERT: K 91 GLN cc_start: 0.9255 (pp30) cc_final: 0.8864 (pp30) REVERT: K 106 GLU cc_start: 0.7386 (mp0) cc_final: 0.7171 (pm20) REVERT: K 109 ARG cc_start: 0.7560 (ptm160) cc_final: 0.7355 (ptp-170) REVERT: A 779 GLU cc_start: 0.8073 (tt0) cc_final: 0.7584 (tt0) REVERT: A 783 ARG cc_start: 0.8182 (mtp-110) cc_final: 0.7970 (ttp80) REVERT: A 945 MET cc_start: 0.7906 (tpp) cc_final: 0.7673 (tpp) outliers start: 1 outliers final: 0 residues processed: 442 average time/residue: 0.1227 time to fit residues: 80.4549 Evaluate side-chains 360 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [139, 99, 17, 62, 2, 151, 16, 103, 171, 20, 149] chunk 139 optimal weight: 0.0040 chunk 99 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 151 optimal weight: 0.0470 chunk 16 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 149 optimal weight: 0.0170 overall best weight: 0.1328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 769 ASN C 754 HIS C 769 ASN D 769 ASN K 6 GLN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.196937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146809 restraints weight = 26430.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.139305 restraints weight = 25376.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.140528 restraints weight = 20540.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.140464 restraints weight = 14705.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.140855 restraints weight = 11551.871| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15873 Z= 0.116 Angle : 0.636 7.254 21582 Z= 0.319 Chirality : 0.042 0.157 2466 Planarity : 0.004 0.046 2634 Dihedral : 4.545 29.142 2086 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.12 % Allowed : 0.23 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1918 helix: 0.72 (0.20), residues: 716 sheet: 0.11 (0.26), residues: 404 loop : -1.83 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 725 TYR 0.010 0.001 TYR B 866 PHE 0.025 0.001 PHE D 749 TRP 0.021 0.001 TRP G 24 HIS 0.014 0.001 HIS D 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (15852) covalent geometry : angle 0.63456 / 0.32 (21540) SS BOND : bond 0.00484 / 0.38 ( 21) SS BOND : angle 1.11563 / 0.86 ( 42) hydrogen bonds : bond 0.03564 / 2.38 ( 692) hydrogen bonds : angle 4.83105 / 3.36 ( 1962) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 456 time to evaluate : 0.597 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: B 780 ILE cc_start: 0.8331 (tp) cc_final: 0.8113 (tt) REVERT: B 832 ARG cc_start: 0.7053 (ptp90) cc_final: 0.6728 (ptp90) REVERT: B 883 TRP cc_start: 0.8330 (p90) cc_final: 0.7605 (p90) REVERT: B 889 GLU cc_start: 0.7844 (mt-10) cc_final: 0.6947 (mm-30) REVERT: C 779 GLU cc_start: 0.8414 (pp20) cc_final: 0.8201 (pp20) REVERT: C 831 PHE cc_start: 0.8348 (m-10) cc_final: 0.7535 (t80) REVERT: C 841 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7815 (mpt180) REVERT: D 841 ARG cc_start: 0.8540 (mmm160) cc_final: 0.8125 (mmm160) REVERT: D 883 TRP cc_start: 0.8348 (p90) cc_final: 0.7582 (p90) REVERT: D 889 GLU cc_start: 0.7769 (mt-10) cc_final: 0.6937 (mm-30) REVERT: G 19 MET cc_start: 0.5685 (tpt) cc_final: 0.5371 (tmm) REVERT: G 22 ARG cc_start: 0.6858 (mtm110) cc_final: 0.5970 (ptt-90) REVERT: H 6 MET cc_start: 0.7588 (mtp) cc_final: 0.7179 (mpp) REVERT: I 11 MET cc_start: 0.7846 (mmm) cc_final: 0.7591 (mpp) REVERT: I 27 LEU cc_start: 0.8935 (tp) cc_final: 0.8514 (mp) REVERT: I 28 SER cc_start: 0.8037 (t) cc_final: 0.7662 (p) REVERT: I 31 SER cc_start: 0.9519 (m) cc_final: 0.9265 (t) REVERT: I 59 VAL cc_start: 0.9088 (t) cc_final: 0.8699 (p) REVERT: I 63 PHE cc_start: 0.8122 (m-10) cc_final: 0.7639 (m-10) REVERT: I 88 TYR cc_start: 0.9296 (m-80) cc_final: 0.8987 (m-80) REVERT: I 91 GLN cc_start: 0.9143 (pp30) cc_final: 0.8863 (pp30) REVERT: J 3 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7613 (mm-40) REVERT: J 13 LYS cc_start: 0.9008 (mttp) cc_final: 0.8594 (tppt) REVERT: J 182 ASP cc_start: 0.7796 (m-30) cc_final: 0.7405 (t0) REVERT: K 11 MET cc_start: 0.7978 (tpp) cc_final: 0.7777 (ttm) REVERT: K 63 PHE cc_start: 0.7889 (m-10) cc_final: 0.7625 (m-80) REVERT: K 91 GLN cc_start: 0.9205 (pp30) cc_final: 0.8789 (pp30) REVERT: K 109 ARG cc_start: 0.7756 (ptm160) cc_final: 0.7511 (ptp-170) REVERT: L 34 MET cc_start: 0.8751 (mmm) cc_final: 0.8358 (mmt) REVERT: L 46 GLU cc_start: 0.8467 (tt0) cc_final: 0.8230 (mt-10) REVERT: L 163 TRP cc_start: 0.3804 (m100) cc_final: 0.3448 (m100) REVERT: A 779 GLU cc_start: 0.8082 (tt0) cc_final: 0.7822 (tt0) REVERT: A 945 MET cc_start: 0.7968 (tpp) cc_final: 0.7612 (tpp) REVERT: A 952 GLU cc_start: 0.8993 (pp20) cc_final: 0.8775 (pp20) outliers start: 2 outliers final: 1 residues processed: 457 average time/residue: 0.1198 time to fit residues: 81.1627 Evaluate side-chains 357 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 356 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [164, 98, 171, 162, 61, 137, 63, 180, 24, 158, 80] chunk 164 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 180 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 769 ASN C 961 GLN D 769 ASN J 114 GLN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.191665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140330 restraints weight = 25733.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.132308 restraints weight = 28157.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134545 restraints weight = 24245.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135154 restraints weight = 15210.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.135765 restraints weight = 13806.243| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15873 Z= 0.169 Angle : 0.686 7.139 21582 Z= 0.352 Chirality : 0.044 0.174 2466 Planarity : 0.005 0.063 2634 Dihedral : 4.709 28.714 2086 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 1918 helix: 0.56 (0.20), residues: 726 sheet: 0.06 (0.26), residues: 404 loop : -1.88 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 725 TYR 0.020 0.001 TYR I 187 PHE 0.024 0.002 PHE C 891 TRP 0.018 0.001 TRP B 883 HIS 0.009 0.001 HIS K 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (15852) covalent geometry : angle 0.68514 / 0.35 (21540) SS BOND : bond 0.00369 / 0.29 ( 21) SS BOND : angle 0.89533 / 0.72 ( 42) hydrogen bonds : bond 0.04296 / 2.89 ( 692) hydrogen bonds : angle 4.90975 / 3.42 ( 1962) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.598 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: B 780 ILE cc_start: 0.8741 (tp) cc_final: 0.8540 (tt) REVERT: B 832 ARG cc_start: 0.7096 (ptp90) cc_final: 0.6793 (ptp90) REVERT: B 840 MET cc_start: 0.8961 (mmt) cc_final: 0.8632 (mmt) REVERT: B 889 GLU cc_start: 0.7888 (mt-10) cc_final: 0.6955 (mm-30) REVERT: C 779 GLU cc_start: 0.8480 (pp20) cc_final: 0.8221 (pp20) REVERT: D 840 MET cc_start: 0.9019 (mmt) cc_final: 0.8727 (mmt) REVERT: D 841 ARG cc_start: 0.8530 (mmm160) cc_final: 0.8155 (mmm160) REVERT: D 883 TRP cc_start: 0.8451 (p90) cc_final: 0.7339 (p90) REVERT: D 889 GLU cc_start: 0.7866 (mt-10) cc_final: 0.6940 (mm-30) REVERT: G 19 MET cc_start: 0.5067 (tpt) cc_final: 0.4854 (tmm) REVERT: H 6 MET cc_start: 0.7713 (mtp) cc_final: 0.7258 (mpp) REVERT: I 11 MET cc_start: 0.7895 (mmm) cc_final: 0.7633 (mpp) REVERT: I 27 LEU cc_start: 0.8952 (tp) cc_final: 0.8420 (mp) REVERT: I 28 SER cc_start: 0.8104 (t) cc_final: 0.7735 (t) REVERT: I 31 SER cc_start: 0.9567 (m) cc_final: 0.9296 (t) REVERT: I 88 TYR cc_start: 0.9346 (m-80) cc_final: 0.9046 (m-80) REVERT: I 91 GLN cc_start: 0.9182 (pp30) cc_final: 0.8700 (pp30) REVERT: J 3 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7711 (mm-40) REVERT: J 182 ASP cc_start: 0.7855 (m-30) cc_final: 0.7451 (t0) REVERT: K 91 GLN cc_start: 0.9167 (pp30) cc_final: 0.8724 (pp30) REVERT: K 109 ARG cc_start: 0.7649 (ptm160) cc_final: 0.7416 (ptp-170) REVERT: L 183 LEU cc_start: 0.7768 (mt) cc_final: 0.7007 (pp) REVERT: A 945 MET cc_start: 0.8094 (tpp) cc_final: 0.7857 (tpp) REVERT: A 952 GLU cc_start: 0.9048 (pp20) cc_final: 0.8820 (pp20) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.1165 time to fit residues: 73.1549 Evaluate side-chains 346 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: [115, 68, 131, 53, 27, 75, 32, 86, 141, 18, 162] chunk 115 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 32 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 162 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 769 ASN C 769 ASN D 769 ASN J 31 ASN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.193007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.143412 restraints weight = 25304.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.137227 restraints weight = 25746.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.137737 restraints weight = 23699.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.138157 restraints weight = 15857.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.139245 restraints weight = 12736.620| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15873 Z= 0.140 Angle : 0.663 8.100 21582 Z= 0.338 Chirality : 0.044 0.276 2466 Planarity : 0.004 0.052 2634 Dihedral : 4.668 28.543 2086 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.19), residues: 1918 helix: 0.64 (0.20), residues: 726 sheet: 0.08 (0.27), residues: 392 loop : -1.85 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 725 TYR 0.023 0.001 TYR I 193 PHE 0.022 0.002 PHE D 749 TRP 0.016 0.001 TRP E 24 HIS 0.006 0.001 HIS K 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (15852) covalent geometry : angle 0.66165 / 0.34 (21540) SS BOND : bond 0.00403 / 0.32 ( 21) SS BOND : angle 1.02892 / 0.77 ( 42) hydrogen bonds : bond 0.04083 / 2.73 ( 692) hydrogen bonds : angle 4.88500 / 3.39 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2865.10 seconds wall clock time: 50 minutes 8.79 seconds (3008.79 seconds total)