Starting phenix.real_space_refine on Thu Sep 18 08:41:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n4r_0342/09_2025/6n4r_0342_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n4r_0342/09_2025/6n4r_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6n4r_0342/09_2025/6n4r_0342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n4r_0342/09_2025/6n4r_0342.map" model { file = "/net/cci-nas-00/data/ceres_data/6n4r_0342/09_2025/6n4r_0342_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n4r_0342/09_2025/6n4r_0342_neut.cif" } 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-2.0-5805/lib/python3.9/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: 3.97, 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 941 " - pdb=" SG CYS A 941 " distance=2.04 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: 1.24 Conformation dependent library (CDL) restraints added in 742.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.61 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: 2.55 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: 8704 15.00 - 29.99: 450 29.99 - 44.99: 124 44.99 - 59.99: 3 59.99 - 74.99: 12 Dihedral angle restraints: 9293 sinusoidal: 3607 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 9290 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: 2.03 - 2.60: 155 2.60 - 3.18: 12843 3.18 - 3.75: 22965 3.75 - 4.33: 29959 4.33 - 4.90: 48150 Nonbonded interactions: 114072 Sorted by model distance: nonbonded pdb=" SG CYS H 15 " pdb=" SG CYS H 25 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS F 15 " pdb=" SG CYS F 25 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS E 15 " pdb=" SG CYS E 25 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS H 9 " pdb=" SG CYS H 21 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS F 9 " pdb=" SG CYS F 21 " model vdw 2.031 3.760 ... (remaining 114067 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.390 Find NCS groups from input model: 0.110 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 15853 Z= 0.350 Angle : 1.074 12.449 21542 Z= 0.571 Chirality : 0.057 0.275 2466 Planarity : 0.008 0.073 2634 Dihedral : 10.265 74.986 5610 Min Nonbonded Distance : 2.030 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 aren 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 covalent geometry : bond 0.00806 (15852) covalent geometry : angle 1.07400 (21540) SS BOND : bond 0.00931 ( 1) SS BOND : angle 1.44294 ( 2) hydrogen bonds : bond 0.17488 ( 692) hydrogen bonds : angle 7.85636 ( 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 : 0.580 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: 0.1362 time to fit residues: 112.4787 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 : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: 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: 0.1980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 A 754 HIS A 896 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.194684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.142990 restraints weight = 25775.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.134952 restraints weight = 24307.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.137060 restraints weight = 21546.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.136620 restraints weight = 17264.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137895 restraints weight = 13020.386| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15853 Z= 0.134 Angle : 0.661 7.221 21542 Z= 0.343 Chirality : 0.042 0.162 2466 Planarity : 0.006 0.055 2634 Dihedral : 5.341 20.753 2086 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.12 % Allowed : 3.46 % 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 aren not related in a simple way. whole: -1.97 (0.18), residues: 1918 helix: -0.63 (0.19), residues: 718 sheet: -0.40 (0.26), residues: 422 loop : -2.45 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 22 TYR 0.013 0.001 TYR I 193 PHE 0.028 0.002 PHE B 749 TRP 0.021 0.001 TRP D 883 HIS 0.007 0.001 HIS C 787 Details of bonding type rmsd covalent geometry : bond 0.00273 (15852) covalent geometry : angle 0.66120 (21540) SS BOND : bond 0.00674 ( 1) SS BOND : angle 0.90421 ( 2) hydrogen bonds : bond 0.05213 ( 692) hydrogen bonds : angle 5.79095 ( 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 503 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 501 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: B 854 MET cc_start: 0.8098 (mmm) cc_final: 0.7807 (mmm) REVERT: B 874 GLN cc_start: 0.8528 (mt0) cc_final: 0.8188 (mt0) REVERT: B 889 GLU cc_start: 0.7728 (mt-10) cc_final: 0.6743 (mm-30) REVERT: C 722 MET cc_start: 0.8461 (pmm) cc_final: 0.7509 (pmm) REVERT: C 742 LEU cc_start: 0.9176 (tp) cc_final: 0.8893 (tp) REVERT: C 800 ASP cc_start: 0.8437 (m-30) cc_final: 0.8119 (m-30) REVERT: C 831 PHE cc_start: 0.8238 (m-10) cc_final: 0.7637 (t80) REVERT: C 950 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7804 (tp-100) REVERT: D 762 LYS cc_start: 0.8357 (tttt) cc_final: 0.8029 (mmtm) REVERT: D 797 SER cc_start: 0.9335 (m) cc_final: 0.9101 (p) REVERT: D 854 MET cc_start: 0.8176 (mmm) cc_final: 0.7894 (mmm) REVERT: D 874 GLN cc_start: 0.8524 (mt0) cc_final: 0.8224 (mt0) REVERT: D 889 GLU cc_start: 0.7642 (mt-10) cc_final: 0.6765 (mm-30) REVERT: G 19 MET cc_start: 0.6581 (mtm) cc_final: 0.6284 (mtm) REVERT: I 31 SER cc_start: 0.9506 (m) cc_final: 0.9252 (t) REVERT: I 59 VAL cc_start: 0.8746 (t) cc_final: 0.8308 (p) REVERT: I 91 GLN cc_start: 0.9408 (pp30) cc_final: 0.9185 (pp30) REVERT: I 176 MET cc_start: 0.5458 (ttp) cc_final: 0.4593 (ptp) REVERT: I 214 GLU cc_start: 0.7650 (pm20) cc_final: 0.7361 (pp20) REVERT: J 13 LYS cc_start: 0.8963 (mttp) cc_final: 0.8604 (tppt) REVERT: K 31 SER cc_start: 0.9519 (m) cc_final: 0.9174 (t) REVERT: K 214 GLU cc_start: 0.6642 (pp20) cc_final: 0.6222 (pp20) REVERT: L 3 GLN cc_start: 0.7715 (mm110) cc_final: 0.7484 (mm-40) REVERT: L 13 LYS cc_start: 0.9006 (mttp) cc_final: 0.8649 (tppt) REVERT: L 183 LEU cc_start: 0.7793 (mt) cc_final: 0.7168 (pp) REVERT: A 722 MET cc_start: 0.8590 (pmm) cc_final: 0.7584 (pmm) REVERT: A 773 THR cc_start: 0.9545 (p) cc_final: 0.9342 (p) REVERT: A 783 ARG cc_start: 0.8241 (mtp-110) cc_final: 0.7867 (ttp80) REVERT: A 831 PHE cc_start: 0.8313 (m-10) cc_final: 0.7655 (t80) outliers start: 2 outliers final: 0 residues processed: 501 average time/residue: 0.1367 time to fit residues: 99.1617 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 : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 168 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN C 896 GLN D 769 ASN I 190 HIS J 39 GLN J 77 ASN J 164 ASN A 896 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.192291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.141140 restraints weight = 26148.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131266 restraints weight = 23844.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.133035 restraints weight = 23113.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.134224 restraints weight = 14731.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.134463 restraints weight = 12681.813| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15853 Z= 0.171 Angle : 0.663 8.893 21542 Z= 0.342 Chirality : 0.043 0.156 2466 Planarity : 0.005 0.048 2634 Dihedral : 5.126 21.376 2086 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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 aren not related in a simple way. whole: -1.54 (0.19), residues: 1918 helix: -0.15 (0.19), residues: 716 sheet: -0.07 (0.26), residues: 414 loop : -2.38 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 725 TYR 0.013 0.001 TYR K 193 PHE 0.021 0.002 PHE C 792 TRP 0.023 0.001 TRP B 883 HIS 0.006 0.001 HIS B 755 Details of bonding type rmsd covalent geometry : bond 0.00394 (15852) covalent geometry : angle 0.66315 (21540) SS BOND : bond 0.00480 ( 1) SS BOND : angle 0.84123 ( 2) hydrogen bonds : bond 0.04904 ( 692) hydrogen bonds : angle 5.35965 ( 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 455 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.666 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: B 723 TYR cc_start: 0.8417 (t80) cc_final: 0.8195 (t80) REVERT: B 829 ARG cc_start: 0.8004 (mmt180) cc_final: 0.7773 (tpp80) REVERT: B 840 MET cc_start: 0.8575 (mmt) cc_final: 0.8362 (mmt) REVERT: B 889 GLU cc_start: 0.7781 (mt-10) cc_final: 0.6924 (mm-30) REVERT: C 791 PHE cc_start: 0.8159 (t80) cc_final: 0.7899 (t80) REVERT: C 800 ASP cc_start: 0.8583 (m-30) cc_final: 0.8224 (m-30) REVERT: C 841 ARG cc_start: 0.8210 (mtt180) cc_final: 0.7924 (mpt180) REVERT: C 874 GLN cc_start: 0.8471 (tp40) cc_final: 0.8269 (tp40) REVERT: C 952 GLU cc_start: 0.9106 (pp20) cc_final: 0.8792 (pp20) REVERT: D 780 ILE cc_start: 0.8216 (tp) cc_final: 0.8013 (tp) REVERT: D 797 SER cc_start: 0.9366 (m) cc_final: 0.9106 (p) REVERT: D 832 ARG cc_start: 0.7323 (ptp90) cc_final: 0.7015 (ptp90) REVERT: D 841 ARG cc_start: 0.8407 (mmm160) cc_final: 0.8178 (mmm160) REVERT: D 874 GLN cc_start: 0.8471 (mt0) cc_final: 0.8079 (mt0) REVERT: D 889 GLU cc_start: 0.7747 (mt-10) cc_final: 0.6954 (mm-30) REVERT: G 19 MET cc_start: 0.6324 (mtm) cc_final: 0.6024 (mtm) REVERT: H 6 MET cc_start: 0.8092 (mtm) cc_final: 0.7733 (mmm) REVERT: I 27 LEU cc_start: 0.9056 (tp) cc_final: 0.8561 (mt) REVERT: I 28 SER cc_start: 0.8285 (t) cc_final: 0.7823 (t) REVERT: I 31 SER cc_start: 0.9571 (m) cc_final: 0.9326 (t) REVERT: I 59 VAL cc_start: 0.8884 (t) cc_final: 0.8427 (p) REVERT: I 83 ASP cc_start: 0.8858 (m-30) cc_final: 0.8609 (m-30) REVERT: I 88 TYR cc_start: 0.8964 (m-80) cc_final: 0.8743 (m-10) REVERT: I 91 GLN cc_start: 0.9372 (pp30) cc_final: 0.9054 (pp30) REVERT: J 13 LYS cc_start: 0.9005 (mttp) cc_final: 0.8536 (tppt) REVERT: J 76 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8338 (tmtt) REVERT: J 86 LEU cc_start: 0.8832 (mp) cc_final: 0.8538 (mt) REVERT: J 183 LEU cc_start: 0.8637 (mt) cc_final: 0.7938 (pp) REVERT: K 31 SER cc_start: 0.9581 (m) cc_final: 0.9307 (t) REVERT: K 106 GLU cc_start: 0.6926 (mp0) cc_final: 0.6708 (mp0) REVERT: L 13 LYS cc_start: 0.9044 (mttp) cc_final: 0.8571 (tppt) REVERT: L 183 LEU cc_start: 0.7947 (mt) cc_final: 0.7228 (pp) REVERT: A 791 PHE cc_start: 0.8077 (t80) cc_final: 0.7871 (t80) REVERT: A 831 PHE cc_start: 0.8445 (m-10) cc_final: 0.7716 (t80) REVERT: A 911 LEU cc_start: 0.8897 (mt) cc_final: 0.8587 (mt) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.1369 time to fit residues: 90.4349 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 : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 ASN J 77 ASN K 95 HIS ** 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 = 0.4155 r_free = 0.4155 target = 0.193697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141838 restraints weight = 25500.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.133244 restraints weight = 21622.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.134986 restraints weight = 21848.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136338 restraints weight = 13556.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.136682 restraints weight = 11571.467| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15853 Z= 0.162 Angle : 0.640 8.023 21542 Z= 0.329 Chirality : 0.043 0.179 2466 Planarity : 0.005 0.051 2634 Dihedral : 4.973 20.439 2086 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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 aren not related in a simple way. whole: -1.28 (0.19), residues: 1918 helix: 0.09 (0.19), residues: 718 sheet: -0.01 (0.26), residues: 422 loop : -2.24 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 22 TYR 0.017 0.001 TYR J 95 PHE 0.026 0.002 PHE B 749 TRP 0.023 0.001 TRP B 883 HIS 0.006 0.001 HIS B 755 Details of bonding type rmsd covalent geometry : bond 0.00373 (15852) covalent geometry : angle 0.63980 (21540) SS BOND : bond 0.00384 ( 1) SS BOND : angle 0.66963 ( 2) hydrogen bonds : bond 0.04606 ( 692) hydrogen bonds : angle 5.13245 ( 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 472 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 0.570 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 829 ARG cc_start: 0.8079 (mmt180) cc_final: 0.7794 (tpp80) REVERT: B 840 MET cc_start: 0.8685 (mmt) cc_final: 0.8466 (mmt) REVERT: B 874 GLN cc_start: 0.8455 (mt0) cc_final: 0.8153 (mt0) REVERT: B 889 GLU cc_start: 0.7761 (mt-10) cc_final: 0.6972 (mm-30) REVERT: C 791 PHE cc_start: 0.8147 (t80) cc_final: 0.7927 (t80) REVERT: C 800 ASP cc_start: 0.8590 (m-30) cc_final: 0.8231 (m-30) REVERT: C 831 PHE cc_start: 0.8313 (m-10) cc_final: 0.7524 (t80) REVERT: C 841 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7972 (mtt180) REVERT: C 874 GLN cc_start: 0.8524 (tp40) cc_final: 0.8296 (tp40) REVERT: D 797 SER cc_start: 0.9340 (m) cc_final: 0.9066 (p) REVERT: D 840 MET cc_start: 0.8662 (mmt) cc_final: 0.8418 (mmt) REVERT: D 889 GLU cc_start: 0.7791 (mt-10) cc_final: 0.6971 (mm-30) REVERT: G 19 MET cc_start: 0.6259 (mtm) cc_final: 0.5956 (mtm) REVERT: I 27 LEU cc_start: 0.9021 (tp) cc_final: 0.8504 (mt) REVERT: I 28 SER cc_start: 0.8246 (t) cc_final: 0.7661 (t) REVERT: I 91 GLN cc_start: 0.9333 (pp30) cc_final: 0.8997 (pp30) REVERT: I 176 MET cc_start: 0.5764 (ttp) cc_final: 0.5406 (ptp) REVERT: J 3 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7586 (mm-40) REVERT: J 86 LEU cc_start: 0.8841 (mp) cc_final: 0.8625 (mt) REVERT: J 182 ASP cc_start: 0.8103 (m-30) cc_final: 0.7607 (t0) REVERT: J 183 LEU cc_start: 0.8653 (mt) cc_final: 0.7856 (pp) REVERT: K 31 SER cc_start: 0.9589 (m) cc_final: 0.9315 (t) REVERT: K 109 ARG cc_start: 0.7830 (ptm160) cc_final: 0.7451 (ptp-170) REVERT: K 214 GLU cc_start: 0.6684 (pp20) cc_final: 0.6276 (pp20) REVERT: L 13 LYS cc_start: 0.9038 (mttp) cc_final: 0.8592 (tppt) REVERT: A 791 PHE cc_start: 0.8141 (t80) cc_final: 0.7792 (t80) REVERT: A 800 ASP cc_start: 0.8545 (m-30) cc_final: 0.8196 (m-30) REVERT: A 831 PHE cc_start: 0.8303 (m-10) cc_final: 0.7707 (t80) outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 0.1392 time to fit residues: 94.8530 Evaluate side-chains 365 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 188 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 148 optimal weight: 0.1980 chunk 159 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 92 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 ASN J 39 GLN J 77 ASN ** 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 = 0.4123 r_free = 0.4123 target = 0.191238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.139416 restraints weight = 25765.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.133545 restraints weight = 27746.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.135290 restraints weight = 24452.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.136539 restraints weight = 15092.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.136954 restraints weight = 13308.402| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15853 Z= 0.149 Angle : 0.631 8.830 21542 Z= 0.325 Chirality : 0.042 0.162 2466 Planarity : 0.004 0.048 2634 Dihedral : 4.860 19.760 2086 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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 aren not related in a simple way. whole: -1.15 (0.19), residues: 1918 helix: 0.24 (0.20), residues: 716 sheet: -0.04 (0.26), residues: 422 loop : -2.15 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 783 TYR 0.013 0.001 TYR K 193 PHE 0.032 0.002 PHE D 749 TRP 0.021 0.001 TRP I 164 HIS 0.006 0.001 HIS B 755 Details of bonding type rmsd covalent geometry : bond 0.00345 (15852) covalent geometry : angle 0.63118 (21540) SS BOND : bond 0.00354 ( 1) SS BOND : angle 0.63776 ( 2) hydrogen bonds : bond 0.04364 ( 692) hydrogen bonds : angle 5.02392 ( 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 456 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 0.631 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: B 832 ARG cc_start: 0.7302 (ptp90) cc_final: 0.6890 (ptp90) REVERT: B 841 ARG cc_start: 0.8493 (mmm160) cc_final: 0.7443 (mmm-85) REVERT: B 854 MET cc_start: 0.8390 (mmm) cc_final: 0.8102 (mmm) REVERT: B 889 GLU cc_start: 0.7906 (mt-10) cc_final: 0.6983 (mm-30) REVERT: C 832 ARG cc_start: 0.8703 (ttp80) cc_final: 0.8503 (ttp80) REVERT: C 874 GLN cc_start: 0.8511 (tp40) cc_final: 0.8238 (tp40) REVERT: C 931 PHE cc_start: 0.8681 (t80) cc_final: 0.8454 (t80) REVERT: C 950 GLN cc_start: 0.8461 (tt0) cc_final: 0.8222 (tp-100) REVERT: D 780 ILE cc_start: 0.8495 (tp) cc_final: 0.8294 (tp) REVERT: D 840 MET cc_start: 0.8765 (mmt) cc_final: 0.8544 (mmt) REVERT: D 841 ARG cc_start: 0.8509 (mmm160) cc_final: 0.7983 (mmm160) REVERT: D 854 MET cc_start: 0.8406 (mmm) cc_final: 0.7976 (mmm) REVERT: D 889 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7120 (mm-30) REVERT: E 19 MET cc_start: 0.6055 (tpt) cc_final: 0.5700 (tpt) REVERT: I 59 VAL cc_start: 0.8996 (t) cc_final: 0.8674 (p) REVERT: I 91 GLN cc_start: 0.9330 (pp30) cc_final: 0.9106 (pp30) REVERT: I 176 MET cc_start: 0.6240 (ttp) cc_final: 0.5083 (ptp) REVERT: J 3 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7833 (mm-40) REVERT: J 13 LYS cc_start: 0.9024 (mttp) cc_final: 0.8592 (tppt) REVERT: J 182 ASP cc_start: 0.7947 (m-30) cc_final: 0.7513 (t0) REVERT: K 31 SER cc_start: 0.9602 (m) cc_final: 0.9337 (t) REVERT: K 63 PHE cc_start: 0.8121 (m-10) cc_final: 0.7435 (m-80) REVERT: K 109 ARG cc_start: 0.7779 (ptm160) cc_final: 0.7439 (ptp-170) REVERT: K 212 ARG cc_start: 0.7133 (mmm-85) cc_final: 0.6247 (mtp180) REVERT: L 3 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7759 (mm-40) REVERT: L 13 LYS cc_start: 0.9062 (mttp) cc_final: 0.8676 (tppt) REVERT: A 791 PHE cc_start: 0.8073 (t80) cc_final: 0.7786 (t80) REVERT: A 800 ASP cc_start: 0.8469 (m-30) cc_final: 0.8241 (m-30) REVERT: A 831 PHE cc_start: 0.8224 (m-10) cc_final: 0.7649 (t80) REVERT: A 952 GLU cc_start: 0.8942 (pp20) cc_final: 0.8535 (pp20) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.1380 time to fit residues: 91.1921 Evaluate side-chains 362 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN B 896 GLN ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.191327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141160 restraints weight = 25608.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138857 restraints weight = 27568.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.138016 restraints weight = 22506.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.138543 restraints weight = 13883.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.139341 restraints weight = 11112.802| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15853 Z= 0.144 Angle : 0.625 9.267 21542 Z= 0.322 Chirality : 0.043 0.210 2466 Planarity : 0.004 0.050 2634 Dihedral : 4.779 19.660 2086 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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 aren not related in a simple way. whole: -1.04 (0.19), residues: 1918 helix: 0.37 (0.20), residues: 714 sheet: -0.01 (0.26), residues: 420 loop : -2.09 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 725 TYR 0.010 0.001 TYR J 95 PHE 0.027 0.002 PHE D 749 TRP 0.021 0.001 TRP G 24 HIS 0.009 0.001 HIS K 95 Details of bonding type rmsd covalent geometry : bond 0.00334 (15852) covalent geometry : angle 0.62496 (21540) SS BOND : bond 0.00307 ( 1) SS BOND : angle 0.57930 ( 2) hydrogen bonds : bond 0.04225 ( 692) hydrogen bonds : angle 4.96325 ( 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 453 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.594 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: 0.8513 (tp) cc_final: 0.8280 (tp) REVERT: B 811 LEU cc_start: 0.8918 (mp) cc_final: 0.8287 (tp) REVERT: B 840 MET cc_start: 0.9090 (mmt) cc_final: 0.8866 (mmt) REVERT: B 841 ARG cc_start: 0.8522 (mmm160) cc_final: 0.7529 (mmm-85) REVERT: B 874 GLN cc_start: 0.8500 (mt0) cc_final: 0.8293 (mt0) REVERT: B 889 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7013 (mm-30) REVERT: C 783 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7502 (ttp80) REVERT: C 831 PHE cc_start: 0.8290 (m-10) cc_final: 0.7523 (t80) REVERT: C 841 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7953 (mpt180) REVERT: C 874 GLN cc_start: 0.8575 (tp40) cc_final: 0.8309 (tp40) REVERT: D 841 ARG cc_start: 0.8520 (mmm160) cc_final: 0.7991 (mmm160) REVERT: D 889 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7075 (mm-30) REVERT: E 19 MET cc_start: 0.6359 (tpt) cc_final: 0.5813 (tpt) REVERT: H 6 MET cc_start: 0.7439 (mtp) cc_final: 0.7033 (mpp) REVERT: I 59 VAL cc_start: 0.9081 (t) cc_final: 0.8641 (p) REVERT: I 91 GLN cc_start: 0.9309 (pp30) cc_final: 0.8921 (pp30) REVERT: J 3 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7785 (mm-40) REVERT: J 13 LYS cc_start: 0.9032 (mttp) cc_final: 0.8611 (tppt) REVERT: J 114 GLN cc_start: 0.8108 (tp40) cc_final: 0.7890 (tp40) REVERT: J 182 ASP cc_start: 0.7956 (m-30) cc_final: 0.7455 (t0) REVERT: K 31 SER cc_start: 0.9591 (m) cc_final: 0.9342 (t) REVERT: K 63 PHE cc_start: 0.7714 (m-10) cc_final: 0.7487 (m-80) REVERT: K 106 GLU cc_start: 0.7045 (mp0) cc_final: 0.6796 (mp0) REVERT: K 109 ARG cc_start: 0.7727 (ptm160) cc_final: 0.7394 (ptp-170) REVERT: K 212 ARG cc_start: 0.7095 (mmm-85) cc_final: 0.6208 (mtp180) REVERT: L 3 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7714 (mm-40) REVERT: A 791 PHE cc_start: 0.8016 (t80) cc_final: 0.7766 (t80) REVERT: A 831 PHE cc_start: 0.8181 (m-10) cc_final: 0.7612 (t80) REVERT: A 950 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7749 (tp-100) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.1272 time to fit residues: 83.7686 Evaluate side-chains 359 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 18 optimal weight: 0.4980 chunk 125 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 0.0270 chunk 128 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 GLN D 769 ASN J 39 GLN J 77 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.191887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.140305 restraints weight = 25776.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.136236 restraints weight = 29568.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137859 restraints weight = 24868.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.137327 restraints weight = 19515.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.139130 restraints weight = 14943.923| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15853 Z= 0.135 Angle : 0.632 9.451 21542 Z= 0.323 Chirality : 0.043 0.181 2466 Planarity : 0.004 0.052 2634 Dihedral : 4.714 21.029 2086 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % 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 aren not related in a simple way. whole: -0.92 (0.19), residues: 1918 helix: 0.48 (0.20), residues: 716 sheet: -0.00 (0.26), residues: 420 loop : -1.99 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 725 TYR 0.009 0.001 TYR J 95 PHE 0.025 0.001 PHE D 749 TRP 0.020 0.001 TRP E 24 HIS 0.006 0.001 HIS K 95 Details of bonding type rmsd covalent geometry : bond 0.00307 (15852) covalent geometry : angle 0.63157 (21540) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.45064 ( 2) hydrogen bonds : bond 0.04097 ( 692) hydrogen bonds : angle 4.93106 ( 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 452 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 0.613 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: 0.8496 (tp) cc_final: 0.8215 (tt) REVERT: B 811 LEU cc_start: 0.8918 (mp) cc_final: 0.8361 (tp) REVERT: B 832 ARG cc_start: 0.6834 (ptp90) cc_final: 0.6622 (ptp90) REVERT: B 840 MET cc_start: 0.9123 (mmt) cc_final: 0.8876 (mmt) REVERT: B 841 ARG cc_start: 0.8510 (mmm160) cc_final: 0.7518 (mmm-85) REVERT: B 854 MET cc_start: 0.8255 (mmm) cc_final: 0.8044 (mmm) REVERT: B 889 GLU cc_start: 0.7817 (mt-10) cc_final: 0.6916 (mm-30) REVERT: C 783 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7618 (ttp80) REVERT: C 800 ASP cc_start: 0.8478 (m-30) cc_final: 0.8054 (m-30) REVERT: C 841 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7925 (mpt180) REVERT: C 874 GLN cc_start: 0.8560 (tp40) cc_final: 0.8272 (tt0) REVERT: D 841 ARG cc_start: 0.8552 (mmm160) cc_final: 0.8062 (mmm160) REVERT: D 854 MET cc_start: 0.8389 (mmm) cc_final: 0.8022 (mmm) REVERT: D 889 GLU cc_start: 0.7878 (mt-10) cc_final: 0.6982 (mm-30) REVERT: E 19 MET cc_start: 0.6311 (tpt) cc_final: 0.6007 (tpp) REVERT: F 27 LYS cc_start: 0.7469 (mtpp) cc_final: 0.6985 (mmmm) REVERT: G 20 VAL cc_start: 0.7469 (t) cc_final: 0.6986 (t) REVERT: H 6 MET cc_start: 0.7561 (mtp) cc_final: 0.7131 (mpp) REVERT: I 59 VAL cc_start: 0.9113 (t) cc_final: 0.8684 (p) REVERT: I 91 GLN cc_start: 0.9278 (pp30) cc_final: 0.8890 (pp30) REVERT: J 13 LYS cc_start: 0.9016 (mttp) cc_final: 0.8555 (tppt) REVERT: J 182 ASP cc_start: 0.7876 (m-30) cc_final: 0.7447 (t0) REVERT: K 10 LEU cc_start: 0.8880 (mm) cc_final: 0.8578 (mm) REVERT: K 31 SER cc_start: 0.9583 (m) cc_final: 0.9347 (t) REVERT: K 109 ARG cc_start: 0.7700 (ptm160) cc_final: 0.7363 (ptp-170) REVERT: A 791 PHE cc_start: 0.8010 (t80) cc_final: 0.7804 (t80) REVERT: A 831 PHE cc_start: 0.8248 (m-10) cc_final: 0.7561 (t80) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.1282 time to fit residues: 85.1619 Evaluate side-chains 357 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 129 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 74 optimal weight: 0.0030 chunk 56 optimal weight: 0.0980 chunk 149 optimal weight: 0.0570 chunk 94 optimal weight: 9.9990 chunk 70 optimal weight: 0.4980 chunk 67 optimal weight: 0.0670 chunk 86 optimal weight: 2.9990 overall best weight: 0.1446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN C 763 ASN C 935 ASN D 769 ASN J 39 GLN J 77 ASN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN A 935 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.195379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144686 restraints weight = 25590.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.138490 restraints weight = 29804.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.140712 restraints weight = 25244.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.141489 restraints weight = 15209.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.142754 restraints weight = 13784.953| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15853 Z= 0.117 Angle : 0.635 8.816 21542 Z= 0.318 Chirality : 0.042 0.171 2466 Planarity : 0.004 0.052 2634 Dihedral : 4.640 36.062 2086 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.06 % Allowed : 1.21 % Favored : 98.73 % 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 aren not related in a simple way. whole: -0.69 (0.20), residues: 1918 helix: 0.71 (0.20), residues: 716 sheet: 0.21 (0.26), residues: 412 loop : -1.95 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 725 TYR 0.009 0.001 TYR C 892 PHE 0.025 0.001 PHE D 749 TRP 0.022 0.001 TRP E 24 HIS 0.007 0.001 HIS C 721 Details of bonding type rmsd covalent geometry : bond 0.00246 (15852) covalent geometry : angle 0.63519 (21540) SS BOND : bond 0.00387 ( 1) SS BOND : angle 0.75435 ( 2) hydrogen bonds : bond 0.03687 ( 692) hydrogen bonds : angle 4.80379 ( 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 464 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 463 time to evaluate : 0.609 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: 0.8396 (tp) cc_final: 0.8138 (tt) REVERT: B 832 ARG cc_start: 0.6926 (ptp90) cc_final: 0.6705 (ptp90) REVERT: B 840 MET cc_start: 0.9108 (mmt) cc_final: 0.8866 (mmt) REVERT: B 889 GLU cc_start: 0.7760 (mt-10) cc_final: 0.6960 (mm-30) REVERT: C 841 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7953 (mpt180) REVERT: C 874 GLN cc_start: 0.8582 (tp40) cc_final: 0.8311 (tp40) REVERT: D 745 LEU cc_start: 0.8936 (tt) cc_final: 0.8681 (pp) REVERT: D 780 ILE cc_start: 0.8339 (tp) cc_final: 0.8101 (tt) REVERT: D 841 ARG cc_start: 0.8580 (mmm160) cc_final: 0.8199 (mmm160) REVERT: D 883 TRP cc_start: 0.8282 (p90) cc_final: 0.7059 (p90) REVERT: D 889 GLU cc_start: 0.7841 (mt-10) cc_final: 0.6960 (mm-30) REVERT: E 19 MET cc_start: 0.6140 (tpt) cc_final: 0.5917 (tpp) REVERT: F 27 LYS cc_start: 0.7316 (mtpp) cc_final: 0.7021 (mmmm) REVERT: H 6 MET cc_start: 0.7492 (mtp) cc_final: 0.7085 (mpp) REVERT: I 59 VAL cc_start: 0.9017 (t) cc_final: 0.8644 (p) REVERT: I 91 GLN cc_start: 0.9278 (pp30) cc_final: 0.8981 (pp30) REVERT: J 13 LYS cc_start: 0.9016 (mttp) cc_final: 0.8577 (tppt) REVERT: J 46 GLU cc_start: 0.8537 (tt0) cc_final: 0.8304 (mt-10) REVERT: J 182 ASP cc_start: 0.7785 (m-30) cc_final: 0.7436 (t0) REVERT: K 31 SER cc_start: 0.9565 (m) cc_final: 0.9338 (t) REVERT: K 91 GLN cc_start: 0.9207 (pp30) cc_final: 0.8922 (pp30) REVERT: K 109 ARG cc_start: 0.7638 (ptm160) cc_final: 0.7280 (ptp-170) REVERT: L 3 GLN cc_start: 0.7832 (mm110) cc_final: 0.7621 (mm-40) REVERT: A 791 PHE cc_start: 0.7923 (t80) cc_final: 0.7695 (t80) REVERT: A 831 PHE cc_start: 0.8148 (m-10) cc_final: 0.7516 (t80) REVERT: A 945 MET cc_start: 0.7948 (tpp) cc_final: 0.7745 (tpp) outliers start: 1 outliers final: 0 residues processed: 463 average time/residue: 0.1262 time to fit residues: 85.4146 Evaluate side-chains 359 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 139 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 103 optimal weight: 0.0050 chunk 171 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 149 optimal weight: 0.0980 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN C 754 HIS C 961 GLN D 769 ASN ** K 125 GLN ** 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 = 0.4171 r_free = 0.4171 target = 0.195898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.146285 restraints weight = 25164.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141653 restraints weight = 25414.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142584 restraints weight = 24622.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.143198 restraints weight = 16733.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.144440 restraints weight = 13469.289| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15853 Z= 0.119 Angle : 0.639 8.052 21542 Z= 0.320 Chirality : 0.042 0.159 2466 Planarity : 0.004 0.044 2634 Dihedral : 4.542 30.811 2086 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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 aren not related in a simple way. whole: -0.59 (0.20), residues: 1918 helix: 0.79 (0.20), residues: 716 sheet: 0.12 (0.26), residues: 404 loop : -1.78 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 725 TYR 0.015 0.001 TYR I 193 PHE 0.024 0.001 PHE B 749 TRP 0.023 0.001 TRP E 24 HIS 0.006 0.001 HIS B 755 Details of bonding type rmsd covalent geometry : bond 0.00262 (15852) covalent geometry : angle 0.63862 (21540) SS BOND : bond 0.00502 ( 1) SS BOND : angle 1.19159 ( 2) hydrogen bonds : bond 0.03691 ( 692) hydrogen bonds : angle 4.76563 ( 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 454 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 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: B 780 ILE cc_start: 0.8423 (tp) cc_final: 0.8161 (tt) REVERT: B 829 ARG cc_start: 0.8284 (mmt90) cc_final: 0.8035 (mmt-90) REVERT: B 840 MET cc_start: 0.9089 (mmt) cc_final: 0.8793 (mmt) REVERT: B 889 GLU cc_start: 0.7799 (mt-10) cc_final: 0.6948 (mm-30) REVERT: C 783 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7563 (ttp80) REVERT: C 800 ASP cc_start: 0.8316 (m-30) cc_final: 0.7949 (m-30) REVERT: C 831 PHE cc_start: 0.8209 (m-10) cc_final: 0.7467 (t80) REVERT: C 874 GLN cc_start: 0.8578 (tp40) cc_final: 0.8288 (tp40) REVERT: D 841 ARG cc_start: 0.8565 (mmm160) cc_final: 0.8212 (mmm160) REVERT: D 883 TRP cc_start: 0.8298 (p90) cc_final: 0.7006 (p90) REVERT: D 889 GLU cc_start: 0.7800 (mt-10) cc_final: 0.6930 (mm-30) REVERT: D 898 MET cc_start: 0.8890 (ttt) cc_final: 0.8677 (ttt) REVERT: E 19 MET cc_start: 0.6197 (tpt) cc_final: 0.5957 (tpp) REVERT: H 6 MET cc_start: 0.7515 (mtp) cc_final: 0.7142 (mpp) REVERT: H 16 CYS cc_start: 0.6949 (m) cc_final: 0.6607 (m) REVERT: I 11 MET cc_start: 0.7704 (mmm) cc_final: 0.7451 (mmm) REVERT: I 59 VAL cc_start: 0.9038 (t) cc_final: 0.8633 (p) REVERT: I 76 ILE cc_start: 0.7256 (mm) cc_final: 0.7033 (mm) REVERT: I 91 GLN cc_start: 0.9295 (pp30) cc_final: 0.8984 (pp30) REVERT: I 151 ILE cc_start: 0.4321 (mt) cc_final: 0.4113 (mt) REVERT: J 46 GLU cc_start: 0.8526 (tt0) cc_final: 0.8310 (mt-10) REVERT: J 182 ASP cc_start: 0.7734 (m-30) cc_final: 0.7374 (t0) REVERT: K 31 SER cc_start: 0.9571 (m) cc_final: 0.9362 (t) REVERT: K 91 GLN cc_start: 0.9182 (pp30) cc_final: 0.8898 (pp30) REVERT: K 109 ARG cc_start: 0.7766 (ptm160) cc_final: 0.7411 (ptp-170) REVERT: L 3 GLN cc_start: 0.7781 (mm110) cc_final: 0.7559 (mm-40) REVERT: A 831 PHE cc_start: 0.8139 (m-10) cc_final: 0.7524 (t80) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.1281 time to fit residues: 85.8315 Evaluate side-chains 365 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 164 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 180 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN D 769 ASN K 95 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.191551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.137932 restraints weight = 26455.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.130730 restraints weight = 22561.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131431 restraints weight = 22900.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.130942 restraints weight = 18643.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.132816 restraints weight = 13959.031| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15853 Z= 0.158 Angle : 0.672 7.658 21542 Z= 0.342 Chirality : 0.043 0.172 2466 Planarity : 0.005 0.066 2634 Dihedral : 4.635 24.934 2086 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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 aren not related in a simple way. whole: -0.64 (0.20), residues: 1918 helix: 0.68 (0.20), residues: 728 sheet: 0.17 (0.26), residues: 392 loop : -1.79 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 13 TYR 0.025 0.001 TYR I 193 PHE 0.025 0.002 PHE B 749 TRP 0.023 0.002 TRP E 24 HIS 0.012 0.001 HIS D 755 Details of bonding type rmsd covalent geometry : bond 0.00371 (15852) covalent geometry : angle 0.67141 (21540) SS BOND : bond 0.00704 ( 1) SS BOND : angle 1.47111 ( 2) hydrogen bonds : bond 0.04146 ( 692) hydrogen bonds : angle 4.83089 ( 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 440 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 0.612 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 829 ARG cc_start: 0.8351 (mmt90) cc_final: 0.7934 (mmt-90) REVERT: B 840 MET cc_start: 0.8667 (mmt) cc_final: 0.8388 (mmt) REVERT: B 889 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7037 (mm-30) REVERT: C 783 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7706 (ttp80) REVERT: C 800 ASP cc_start: 0.8517 (m-30) cc_final: 0.8082 (m-30) REVERT: C 841 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7731 (mpt180) REVERT: C 874 GLN cc_start: 0.8526 (tp40) cc_final: 0.8228 (tp40) REVERT: D 841 ARG cc_start: 0.8590 (mmm160) cc_final: 0.8134 (mmm160) REVERT: D 883 TRP cc_start: 0.8446 (p90) cc_final: 0.7307 (p90) REVERT: D 889 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7068 (mm-30) REVERT: F 19 MET cc_start: 0.2885 (mpp) cc_final: 0.2658 (mpp) REVERT: H 6 MET cc_start: 0.7623 (mtp) cc_final: 0.7232 (mpp) REVERT: I 59 VAL cc_start: 0.9128 (t) cc_final: 0.8733 (p) REVERT: I 91 GLN cc_start: 0.9292 (pp30) cc_final: 0.8926 (pp30) REVERT: J 13 LYS cc_start: 0.9045 (mttp) cc_final: 0.8475 (tppt) REVERT: J 182 ASP cc_start: 0.7608 (m-30) cc_final: 0.7143 (t0) REVERT: K 10 LEU cc_start: 0.9085 (mt) cc_final: 0.8872 (mm) REVERT: K 31 SER cc_start: 0.9576 (m) cc_final: 0.9355 (t) REVERT: K 91 GLN cc_start: 0.9207 (pp30) cc_final: 0.8938 (pp30) REVERT: K 109 ARG cc_start: 0.8021 (ptm160) cc_final: 0.7619 (ptp-170) REVERT: L 3 GLN cc_start: 0.7816 (mm110) cc_final: 0.7594 (mm-40) REVERT: L 183 LEU cc_start: 0.7787 (mt) cc_final: 0.7109 (pp) REVERT: A 831 PHE cc_start: 0.8106 (m-10) cc_final: 0.7499 (t80) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.1315 time to fit residues: 85.0604 Evaluate side-chains 352 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 115 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN C 961 GLN D 769 ASN J 39 GLN ** K 125 GLN ** 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 = 0.4117 r_free = 0.4117 target = 0.190453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.140254 restraints weight = 25382.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.133483 restraints weight = 26337.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.134636 restraints weight = 22019.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134500 restraints weight = 16287.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.136095 restraints weight = 12583.302| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15853 Z= 0.162 Angle : 0.679 8.169 21542 Z= 0.347 Chirality : 0.044 0.274 2466 Planarity : 0.005 0.062 2634 Dihedral : 4.700 21.279 2086 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.06 % Allowed : 0.63 % Favored : 99.31 % 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 aren not related in a simple way. whole: -0.67 (0.20), residues: 1918 helix: 0.64 (0.20), residues: 726 sheet: 0.18 (0.27), residues: 392 loop : -1.79 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 13 TYR 0.015 0.001 TYR I 187 PHE 0.025 0.002 PHE B 749 TRP 0.023 0.001 TRP E 24 HIS 0.008 0.001 HIS B 755 Details of bonding type rmsd covalent geometry : bond 0.00380 (15852) covalent geometry : angle 0.67848 (21540) SS BOND : bond 0.00672 ( 1) SS BOND : angle 1.39724 ( 2) hydrogen bonds : bond 0.04279 ( 692) hydrogen bonds : angle 4.89673 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3078.05 seconds wall clock time: 54 minutes 3.18 seconds (3243.18 seconds total)