Starting phenix.real_space_refine on Fri Sep 27 08:33:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/09_2024/6n4r_0342_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/09_2024/6n4r_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/09_2024/6n4r_0342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/09_2024/6n4r_0342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/09_2024/6n4r_0342_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/09_2024/6n4r_0342_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: "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} Chain: "A" 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 Restraints were copied for chains: C, D, L, G, F, H, K Time building chain proxies: 10.46, per 1000 atoms: 0.68 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=0, symmetry=0 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: 3.77 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.03 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: 4.96 Time building geometry restraints manager: 4.46 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: 0 59.99 - 74.99: 12 Dihedral angle restraints: 9290 sinusoidal: 3604 harmonic: 5686 Sorted by residual: 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 dihedral pdb=" CA ALA A 814 " pdb=" C ALA A 814 " pdb=" N ASP A 815 " pdb=" CA ASP A 815 " ideal model delta harmonic sigma weight residual -180.00 -153.00 -27.00 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 9287 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: 156 2.60 - 3.18: 12845 3.18 - 3.75: 22965 3.75 - 4.33: 29959 4.33 - 4.90: 48150 Nonbonded interactions: 114075 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 114070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 720 through 944) selection = (chain 'B' and (resid 720 through 736 or (resid 737 and (name N or name CA or na \ me C or name O or name CB )) or resid 738 through 944)) selection = (chain 'C' and resid 720 through 944) selection = (chain 'D' and (resid 720 through 736 or (resid 737 and (name N or name CA or na \ me C or name O or name CB )) or resid 738 through 944)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 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: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 38.330 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.020 ------------------------------------------------------------------------------- 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 15852 Z= 0.511 Angle : 1.074 12.449 21540 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 : 4.60 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.035 0.002 TRP B 883 HIS 0.008 0.002 HIS B 721 PHE 0.031 0.004 PHE A 927 TYR 0.026 0.003 TYR C 741 ARG 0.011 0.001 ARG A 879 *********************** 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 fitting. rotamer outliers: 4 poor density : 571 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 765 LEU cc_start: 0.9072 (mt) cc_final: 0.8842 (mt) REVERT: B 840 MET cc_start: 0.8458 (mmt) cc_final: 0.8150 (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: 0.8608 (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: 0.8404 (tp) REVERT: D 797 SER cc_start: 0.9035 (m) cc_final: 0.8791 (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: 0.8309 (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: 0.8340 (m-10) REVERT: I 63 PHE cc_start: 0.7958 (m-10) cc_final: 0.7739 (m-10) REVERT: I 73 SER cc_start: 0.8975 (p) cc_final: 0.8774 (t) REVERT: J 13 LYS cc_start: 0.8971 (mttp) cc_final: 0.8539 (tppt) REVERT: J 86 LEU cc_start: 0.8876 (mt) cc_final: 0.8598 (mp) REVERT: J 163 TRP cc_start: 0.3711 (m100) cc_final: 0.3277 (m100) REVERT: K 73 SER cc_start: 0.9041 (p) cc_final: 0.8749 (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: 0.8817 (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: 0.7688 (t80) REVERT: A 933 MET cc_start: 0.8480 (mmt) cc_final: 0.8177 (mmm) outliers start: 4 outliers final: 0 residues processed: 571 average time/residue: 0.2864 time to fit residues: 233.1563 Evaluate side-chains 397 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 395 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 49 optimal weight: 0.0270 chunk 97 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 GLN D 769 ASN ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN J 39 GLN J 77 ASN L 39 GLN A 754 HIS A 896 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15852 Z= 0.284 Angle : 0.707 8.192 21540 Z= 0.370 Chirality : 0.044 0.163 2466 Planarity : 0.006 0.052 2634 Dihedral : 5.523 25.666 2086 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.12 % Allowed : 3.86 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.18), residues: 1918 helix: -0.63 (0.19), residues: 712 sheet: -0.50 (0.26), residues: 418 loop : -2.49 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 883 HIS 0.006 0.001 HIS C 787 PHE 0.027 0.002 PHE B 749 TYR 0.012 0.001 TYR C 723 ARG 0.010 0.001 ARG B 832 *********************** 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 476 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 474 time to evaluate : 1.803 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 765 LEU cc_start: 0.9076 (mt) cc_final: 0.8779 (mt) REVERT: B 780 ILE cc_start: 0.8546 (tp) cc_final: 0.8267 (tp) REVERT: B 840 MET cc_start: 0.8523 (mmt) cc_final: 0.8291 (mmt) REVERT: B 854 MET cc_start: 0.8079 (mmm) cc_final: 0.7843 (mmm) REVERT: B 874 GLN cc_start: 0.8638 (mt0) cc_final: 0.8361 (mt0) REVERT: B 889 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7034 (mm-30) REVERT: C 722 MET cc_start: 0.8324 (pmm) cc_final: 0.7347 (pmm) REVERT: C 773 THR cc_start: 0.9500 (p) cc_final: 0.9282 (p) REVERT: C 784 ILE cc_start: 0.8760 (pt) cc_final: 0.8516 (tt) REVERT: C 800 ASP cc_start: 0.8529 (m-30) cc_final: 0.8159 (m-30) REVERT: C 831 PHE cc_start: 0.7927 (m-10) cc_final: 0.7462 (t80) REVERT: C 950 GLN cc_start: 0.7927 (tp-100) cc_final: 0.7561 (tp40) REVERT: C 952 GLU cc_start: 0.8749 (pp20) cc_final: 0.8413 (pp20) REVERT: D 780 ILE cc_start: 0.8703 (tp) cc_final: 0.8494 (tp) REVERT: D 840 MET cc_start: 0.8465 (mmt) cc_final: 0.8242 (mmt) REVERT: D 854 MET cc_start: 0.8168 (mmm) cc_final: 0.7909 (mmm) REVERT: D 874 GLN cc_start: 0.8620 (mt0) cc_final: 0.8369 (mt0) REVERT: D 889 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7052 (mm-30) REVERT: I 27 LEU cc_start: 0.9053 (tp) cc_final: 0.8528 (mt) REVERT: I 28 SER cc_start: 0.8104 (t) cc_final: 0.7652 (t) REVERT: I 31 SER cc_start: 0.9467 (m) cc_final: 0.9174 (t) REVERT: I 37 TYR cc_start: 0.8938 (m-80) cc_final: 0.8646 (m-10) REVERT: I 59 VAL cc_start: 0.8887 (t) cc_final: 0.8586 (p) REVERT: I 91 GLN cc_start: 0.9461 (pp30) cc_final: 0.9221 (pp30) REVERT: I 176 MET cc_start: 0.6352 (ttp) cc_final: 0.5266 (ptp) REVERT: J 13 LYS cc_start: 0.8929 (mttp) cc_final: 0.8656 (tppt) REVERT: J 83 MET cc_start: 0.8119 (mtm) cc_final: 0.7655 (mtm) REVERT: J 163 TRP cc_start: 0.3284 (m100) cc_final: 0.2970 (m100) REVERT: K 31 SER cc_start: 0.9553 (m) cc_final: 0.9231 (t) REVERT: K 91 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8502 (tm-30) REVERT: K 214 GLU cc_start: 0.7065 (pp20) cc_final: 0.6557 (pp20) REVERT: L 13 LYS cc_start: 0.8948 (mttp) cc_final: 0.8722 (tppt) REVERT: L 183 LEU cc_start: 0.7759 (mt) cc_final: 0.7027 (pp) REVERT: A 722 MET cc_start: 0.8496 (pmm) cc_final: 0.7438 (pmm) REVERT: A 773 THR cc_start: 0.9532 (p) cc_final: 0.9295 (p) REVERT: A 831 PHE cc_start: 0.7845 (m-10) cc_final: 0.7611 (t80) outliers start: 2 outliers final: 0 residues processed: 474 average time/residue: 0.2901 time to fit residues: 195.8998 Evaluate side-chains 377 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.0000 chunk 53 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 117 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 186 optimal weight: 0.4980 chunk 153 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 overall best weight: 0.4182 ------------------------------------------------------------------------------- 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 D 769 ASN D 896 GLN I 190 HIS J 164 ASN L 3 GLN A 935 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15852 Z= 0.179 Angle : 0.639 10.240 21540 Z= 0.328 Chirality : 0.042 0.147 2466 Planarity : 0.005 0.052 2634 Dihedral : 5.079 21.395 2086 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 1918 helix: -0.08 (0.19), residues: 716 sheet: -0.18 (0.26), residues: 422 loop : -2.23 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 883 HIS 0.006 0.001 HIS D 755 PHE 0.020 0.001 PHE D 749 TYR 0.015 0.001 TYR J 95 ARG 0.009 0.001 ARG A 725 *********************** 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 478 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 1.699 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 780 ILE cc_start: 0.8522 (tp) cc_final: 0.8273 (tp) REVERT: B 874 GLN cc_start: 0.8435 (mt0) cc_final: 0.8017 (mt0) REVERT: B 889 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6912 (mm-30) REVERT: C 742 LEU cc_start: 0.9075 (tp) cc_final: 0.8821 (tp) REVERT: C 800 ASP cc_start: 0.8419 (m-30) cc_final: 0.8099 (m-30) REVERT: C 831 PHE cc_start: 0.7858 (m-10) cc_final: 0.7197 (t80) REVERT: C 841 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7772 (mpt180) REVERT: D 780 ILE cc_start: 0.8563 (tp) cc_final: 0.8362 (tp) REVERT: D 840 MET cc_start: 0.8482 (mmt) cc_final: 0.8237 (mmt) REVERT: D 841 ARG cc_start: 0.8392 (mmm160) cc_final: 0.8144 (mmm160) REVERT: D 874 GLN cc_start: 0.8451 (mt0) cc_final: 0.8001 (mt0) REVERT: D 889 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6913 (mm-30) REVERT: E 13 ARG cc_start: 0.7313 (mtm-85) cc_final: 0.7033 (mtm110) REVERT: I 27 LEU cc_start: 0.9050 (tp) cc_final: 0.8537 (mt) REVERT: I 28 SER cc_start: 0.8192 (t) cc_final: 0.7748 (t) REVERT: I 31 SER cc_start: 0.9484 (m) cc_final: 0.9216 (t) REVERT: I 37 TYR cc_start: 0.8955 (m-80) cc_final: 0.8695 (m-10) REVERT: I 59 VAL cc_start: 0.8901 (t) cc_final: 0.8589 (p) REVERT: I 91 GLN cc_start: 0.9363 (pp30) cc_final: 0.9083 (pp30) REVERT: I 176 MET cc_start: 0.6459 (ttp) cc_final: 0.5465 (ptp) REVERT: J 163 TRP cc_start: 0.3287 (m100) cc_final: 0.2892 (m100) REVERT: J 183 LEU cc_start: 0.8405 (mt) cc_final: 0.7696 (pp) REVERT: K 31 SER cc_start: 0.9544 (m) cc_final: 0.9223 (t) REVERT: K 212 ARG cc_start: 0.6690 (mmm-85) cc_final: 0.6273 (mtp180) REVERT: L 3 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7639 (mm-40) REVERT: L 13 LYS cc_start: 0.8950 (mttp) cc_final: 0.8748 (tppt) REVERT: L 46 GLU cc_start: 0.8289 (tt0) cc_final: 0.8046 (tt0) REVERT: L 183 LEU cc_start: 0.7730 (mt) cc_final: 0.7014 (pp) REVERT: A 831 PHE cc_start: 0.7833 (m-10) cc_final: 0.7460 (t80) outliers start: 0 outliers final: 0 residues processed: 478 average time/residue: 0.3009 time to fit residues: 209.5977 Evaluate side-chains 379 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 0.0770 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- 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 J 39 GLN J 77 ASN K 95 HIS ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 15852 Z= 0.301 Angle : 0.682 10.100 21540 Z= 0.353 Chirality : 0.044 0.183 2466 Planarity : 0.005 0.048 2634 Dihedral : 5.104 25.430 2086 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1918 helix: 0.07 (0.19), residues: 718 sheet: 0.04 (0.26), residues: 414 loop : -2.27 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 883 HIS 0.006 0.001 HIS B 755 PHE 0.029 0.002 PHE B 749 TYR 0.016 0.001 TYR L 95 ARG 0.009 0.001 ARG H 22 *********************** 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 458 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 1.852 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 765 LEU cc_start: 0.9052 (mt) cc_final: 0.8817 (mt) REVERT: B 780 ILE cc_start: 0.8732 (tp) cc_final: 0.8531 (tp) REVERT: B 840 MET cc_start: 0.8783 (mmt) cc_final: 0.8572 (mmt) REVERT: B 854 MET cc_start: 0.8180 (mmm) cc_final: 0.7927 (mmm) REVERT: B 889 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7091 (mm-30) REVERT: C 791 PHE cc_start: 0.7936 (t80) cc_final: 0.7676 (t80) REVERT: C 874 GLN cc_start: 0.8519 (tt0) cc_final: 0.8158 (tm-30) REVERT: D 840 MET cc_start: 0.8829 (mmt) cc_final: 0.8529 (mmt) REVERT: D 841 ARG cc_start: 0.8515 (mmm160) cc_final: 0.8258 (mmm160) REVERT: D 854 MET cc_start: 0.8271 (mmm) cc_final: 0.7952 (mmm) REVERT: D 889 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7098 (mm-30) REVERT: H 6 MET cc_start: 0.7302 (mtp) cc_final: 0.6943 (mpp) REVERT: I 27 LEU cc_start: 0.9041 (tp) cc_final: 0.8532 (mt) REVERT: I 28 SER cc_start: 0.8039 (t) cc_final: 0.7473 (t) REVERT: I 31 SER cc_start: 0.9501 (m) cc_final: 0.9236 (t) REVERT: I 37 TYR cc_start: 0.8909 (m-80) cc_final: 0.8634 (m-10) REVERT: I 59 VAL cc_start: 0.9103 (t) cc_final: 0.8777 (p) REVERT: I 91 GLN cc_start: 0.9309 (pp30) cc_final: 0.9015 (pp30) REVERT: I 164 TRP cc_start: 0.7207 (m-90) cc_final: 0.6893 (m-90) REVERT: I 176 MET cc_start: 0.6475 (ttp) cc_final: 0.5400 (ptp) REVERT: J 3 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7605 (mm-40) REVERT: J 76 LYS cc_start: 0.8649 (ttpt) cc_final: 0.8340 (tmtt) REVERT: J 163 TRP cc_start: 0.3313 (m100) cc_final: 0.2939 (m100) REVERT: J 183 LEU cc_start: 0.8434 (mt) cc_final: 0.7744 (pp) REVERT: K 31 SER cc_start: 0.9569 (m) cc_final: 0.9248 (t) REVERT: K 63 PHE cc_start: 0.8119 (m-10) cc_final: 0.7917 (m-80) REVERT: K 91 GLN cc_start: 0.9243 (pp30) cc_final: 0.9018 (pp30) REVERT: K 212 ARG cc_start: 0.6712 (mmm-85) cc_final: 0.6271 (mtp180) REVERT: L 13 LYS cc_start: 0.9024 (mttp) cc_final: 0.8819 (tppt) REVERT: L 114 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7397 (tm-30) REVERT: A 791 PHE cc_start: 0.8409 (t80) cc_final: 0.8166 (t80) REVERT: A 800 ASP cc_start: 0.8441 (m-30) cc_final: 0.8068 (m-30) REVERT: A 874 GLN cc_start: 0.8579 (tt0) cc_final: 0.8317 (tm-30) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.2875 time to fit residues: 189.1144 Evaluate side-chains 368 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 0.0070 chunk 156 optimal weight: 8.9990 chunk 126 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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 L 39 GLN L 77 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 15852 Z= 0.210 Angle : 0.638 9.809 21540 Z= 0.326 Chirality : 0.042 0.161 2466 Planarity : 0.005 0.056 2634 Dihedral : 4.880 21.621 2086 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1918 helix: 0.23 (0.20), residues: 714 sheet: -0.08 (0.26), residues: 422 loop : -2.07 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 883 HIS 0.006 0.001 HIS B 755 PHE 0.030 0.001 PHE B 749 TYR 0.015 0.001 TYR C 723 ARG 0.013 0.001 ARG A 725 *********************** 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 469 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 468 time to evaluate : 1.726 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 841 ARG cc_start: 0.8409 (mmm160) cc_final: 0.7469 (mmm-85) REVERT: B 889 GLU cc_start: 0.7626 (mt-10) cc_final: 0.6954 (mm-30) REVERT: C 783 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7311 (ttp80) REVERT: C 831 PHE cc_start: 0.8020 (m-10) cc_final: 0.7369 (t80) REVERT: C 841 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7837 (mpt180) REVERT: C 874 GLN cc_start: 0.8488 (tt0) cc_final: 0.8154 (tm-30) REVERT: D 840 MET cc_start: 0.8840 (mmt) cc_final: 0.8537 (mmt) REVERT: D 854 MET cc_start: 0.8119 (mmm) cc_final: 0.7901 (mmm) REVERT: D 866 TYR cc_start: 0.8995 (t80) cc_final: 0.8673 (t80) REVERT: D 889 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6929 (mm-30) REVERT: G 19 MET cc_start: 0.4584 (tpt) cc_final: 0.4289 (tmm) REVERT: H 6 MET cc_start: 0.7335 (mtp) cc_final: 0.6928 (mpp) REVERT: I 31 SER cc_start: 0.9483 (m) cc_final: 0.9226 (t) REVERT: I 37 TYR cc_start: 0.8865 (m-80) cc_final: 0.8513 (m-10) REVERT: I 59 VAL cc_start: 0.9097 (t) cc_final: 0.8838 (p) REVERT: I 91 GLN cc_start: 0.9307 (pp30) cc_final: 0.8980 (pp30) REVERT: I 176 MET cc_start: 0.6403 (ttp) cc_final: 0.5918 (ptp) REVERT: J 3 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7717 (mm-40) REVERT: J 163 TRP cc_start: 0.3349 (m100) cc_final: 0.2888 (m100) REVERT: J 182 ASP cc_start: 0.8105 (m-30) cc_final: 0.7720 (t0) REVERT: K 31 SER cc_start: 0.9541 (m) cc_final: 0.9233 (t) REVERT: K 55 LEU cc_start: 0.8958 (mt) cc_final: 0.8750 (mm) REVERT: K 63 PHE cc_start: 0.8046 (m-10) cc_final: 0.7600 (m-80) REVERT: K 91 GLN cc_start: 0.9334 (pp30) cc_final: 0.8883 (pp30) REVERT: K 212 ARG cc_start: 0.6689 (mmm-85) cc_final: 0.6263 (mtp180) REVERT: K 214 GLU cc_start: 0.7322 (pp20) cc_final: 0.6829 (pp20) REVERT: L 13 LYS cc_start: 0.8991 (mttp) cc_final: 0.8767 (tppt) REVERT: A 779 GLU cc_start: 0.7833 (tt0) cc_final: 0.7289 (tt0) REVERT: A 791 PHE cc_start: 0.8221 (t80) cc_final: 0.7860 (t80) REVERT: A 874 GLN cc_start: 0.8542 (tt0) cc_final: 0.8263 (tm-30) outliers start: 1 outliers final: 0 residues processed: 469 average time/residue: 0.2834 time to fit residues: 192.1823 Evaluate side-chains 368 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 45 optimal weight: 0.0670 chunk 183 optimal weight: 0.4980 chunk 152 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 J 39 GLN J 77 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 190 HIS ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15852 Z= 0.209 Angle : 0.636 9.304 21540 Z= 0.325 Chirality : 0.042 0.207 2466 Planarity : 0.004 0.048 2634 Dihedral : 4.782 24.374 2086 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.06 % Allowed : 1.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 1918 helix: 0.38 (0.20), residues: 714 sheet: -0.05 (0.26), residues: 420 loop : -2.08 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 164 HIS 0.006 0.001 HIS B 755 PHE 0.030 0.002 PHE D 749 TYR 0.013 0.001 TYR E 1 ARG 0.019 0.001 ARG C 725 *********************** 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 473 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 472 time to evaluate : 1.792 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: 0.8711 (tp) cc_final: 0.8505 (tp) REVERT: B 840 MET cc_start: 0.9149 (mmt) cc_final: 0.8932 (mmt) REVERT: B 841 ARG cc_start: 0.8445 (mmm160) cc_final: 0.7569 (mmm-85) REVERT: B 889 GLU cc_start: 0.7567 (mt-10) cc_final: 0.6887 (mm-30) REVERT: C 874 GLN cc_start: 0.8396 (tt0) cc_final: 0.8061 (tm-30) REVERT: D 840 MET cc_start: 0.8829 (mmt) cc_final: 0.8622 (mmt) REVERT: D 841 ARG cc_start: 0.8515 (mmm160) cc_final: 0.7286 (mmm160) REVERT: D 889 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6854 (mm-30) REVERT: E 19 MET cc_start: 0.4962 (tpt) cc_final: 0.3793 (mmm) REVERT: E 24 TRP cc_start: 0.8283 (p90) cc_final: 0.7988 (p90) REVERT: G 19 MET cc_start: 0.4201 (tpt) cc_final: 0.3957 (tmm) REVERT: G 20 VAL cc_start: 0.6531 (t) cc_final: 0.6236 (t) REVERT: H 6 MET cc_start: 0.7315 (mtp) cc_final: 0.6917 (mpp) REVERT: I 31 SER cc_start: 0.9522 (m) cc_final: 0.9235 (t) REVERT: I 37 TYR cc_start: 0.8933 (m-80) cc_final: 0.8584 (m-10) REVERT: I 59 VAL cc_start: 0.9136 (t) cc_final: 0.8886 (p) REVERT: I 91 GLN cc_start: 0.9251 (pp30) cc_final: 0.8964 (pp30) REVERT: I 176 MET cc_start: 0.6516 (ttp) cc_final: 0.5599 (ptm) REVERT: J 13 LYS cc_start: 0.8993 (mttp) cc_final: 0.8644 (tppt) REVERT: J 163 TRP cc_start: 0.3377 (m100) cc_final: 0.2925 (m100) REVERT: J 182 ASP cc_start: 0.8096 (m-30) cc_final: 0.7675 (t0) REVERT: K 31 SER cc_start: 0.9523 (m) cc_final: 0.9227 (t) REVERT: K 63 PHE cc_start: 0.8003 (m-10) cc_final: 0.7718 (m-80) REVERT: K 91 GLN cc_start: 0.9310 (pp30) cc_final: 0.8754 (pp30) REVERT: K 212 ARG cc_start: 0.6685 (mmm-85) cc_final: 0.6207 (mtp180) REVERT: K 214 GLU cc_start: 0.7289 (pp20) cc_final: 0.6686 (pp20) REVERT: L 13 LYS cc_start: 0.8992 (mttp) cc_final: 0.8761 (tppt) REVERT: A 779 GLU cc_start: 0.7710 (tt0) cc_final: 0.7334 (tt0) REVERT: A 791 PHE cc_start: 0.8183 (t80) cc_final: 0.7916 (t80) REVERT: A 874 GLN cc_start: 0.8612 (tt0) cc_final: 0.8277 (tm-30) REVERT: A 952 GLU cc_start: 0.8837 (pp20) cc_final: 0.8424 (pp20) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.2656 time to fit residues: 182.9785 Evaluate side-chains 363 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.0470 chunk 20 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 183 optimal weight: 0.4980 chunk 114 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 113 optimal weight: 5.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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** C 961 GLN D 769 ASN D 896 GLN J 39 GLN J 77 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15852 Z= 0.194 Angle : 0.639 8.243 21540 Z= 0.323 Chirality : 0.043 0.180 2466 Planarity : 0.004 0.044 2634 Dihedral : 4.682 18.513 2086 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 1918 helix: 0.46 (0.20), residues: 714 sheet: -0.02 (0.26), residues: 420 loop : -2.07 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 24 HIS 0.006 0.001 HIS B 755 PHE 0.029 0.001 PHE D 749 TYR 0.010 0.001 TYR J 95 ARG 0.009 0.001 ARG A 725 *********************** 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 463 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 1.886 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: 0.8692 (tp) cc_final: 0.8423 (tt) REVERT: B 840 MET cc_start: 0.9170 (mmt) cc_final: 0.8929 (mmt) REVERT: B 889 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6833 (mm-30) REVERT: C 800 ASP cc_start: 0.8218 (m-30) cc_final: 0.7870 (m-30) REVERT: C 831 PHE cc_start: 0.7907 (m-10) cc_final: 0.7343 (t80) REVERT: C 841 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7798 (mtm-85) REVERT: C 874 GLN cc_start: 0.8354 (tt0) cc_final: 0.8046 (tm-30) REVERT: C 945 MET cc_start: 0.7751 (tpp) cc_final: 0.7551 (tpp) REVERT: D 841 ARG cc_start: 0.8498 (mmm160) cc_final: 0.8093 (mmm160) REVERT: D 854 MET cc_start: 0.8130 (mmm) cc_final: 0.7851 (mmm) REVERT: D 889 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6793 (mm-30) REVERT: E 19 MET cc_start: 0.5171 (tpt) cc_final: 0.4198 (mmm) REVERT: E 24 TRP cc_start: 0.8367 (p90) cc_final: 0.8011 (p90) REVERT: F 27 LYS cc_start: 0.7342 (mtpp) cc_final: 0.7040 (mmmm) REVERT: H 6 MET cc_start: 0.7391 (mtp) cc_final: 0.6976 (mpp) REVERT: I 31 SER cc_start: 0.9520 (m) cc_final: 0.9247 (t) REVERT: I 59 VAL cc_start: 0.9038 (t) cc_final: 0.8783 (p) REVERT: I 91 GLN cc_start: 0.9252 (pp30) cc_final: 0.8949 (pp30) REVERT: J 3 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7434 (mm-40) REVERT: J 13 LYS cc_start: 0.8982 (mttp) cc_final: 0.8637 (tppt) REVERT: J 93 MET cc_start: 0.8115 (tpt) cc_final: 0.7678 (tpt) REVERT: J 182 ASP cc_start: 0.7955 (m-30) cc_final: 0.7629 (t0) REVERT: K 27 LEU cc_start: 0.9005 (tp) cc_final: 0.8365 (mp) REVERT: K 28 SER cc_start: 0.8026 (p) cc_final: 0.7726 (p) REVERT: K 31 SER cc_start: 0.9506 (m) cc_final: 0.9238 (t) REVERT: K 63 PHE cc_start: 0.7993 (m-10) cc_final: 0.7599 (m-80) REVERT: K 91 GLN cc_start: 0.9314 (pp30) cc_final: 0.8739 (pp30) REVERT: K 212 ARG cc_start: 0.6638 (mmm-85) cc_final: 0.6171 (mtp180) REVERT: A 791 PHE cc_start: 0.8155 (t80) cc_final: 0.7765 (t80) REVERT: A 829 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7843 (ttp-170) REVERT: A 874 GLN cc_start: 0.8588 (tt0) cc_final: 0.8286 (tm-30) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.2745 time to fit residues: 184.9036 Evaluate side-chains 364 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.5980 chunk 109 optimal weight: 0.4980 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 143 optimal weight: 30.0000 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 ASN D 896 GLN J 39 GLN J 77 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15852 Z= 0.233 Angle : 0.667 8.091 21540 Z= 0.342 Chirality : 0.043 0.176 2466 Planarity : 0.005 0.058 2634 Dihedral : 4.721 20.230 2086 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 1918 helix: 0.42 (0.20), residues: 726 sheet: -0.03 (0.26), residues: 420 loop : -2.05 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 164 HIS 0.010 0.001 HIS D 755 PHE 0.027 0.002 PHE D 749 TYR 0.010 0.001 TYR I 187 ARG 0.015 0.001 ARG A 725 *********************** 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 445 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 1.817 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 780 ILE cc_start: 0.8885 (tp) cc_final: 0.8660 (tt) REVERT: B 811 LEU cc_start: 0.8754 (mp) cc_final: 0.8163 (tp) REVERT: B 824 SER cc_start: 0.9042 (t) cc_final: 0.8817 (t) REVERT: B 832 ARG cc_start: 0.6989 (ptp90) cc_final: 0.6735 (ptp90) REVERT: B 840 MET cc_start: 0.9136 (mmt) cc_final: 0.8889 (mmt) REVERT: B 889 GLU cc_start: 0.7714 (mt-10) cc_final: 0.6953 (mm-30) REVERT: C 779 GLU cc_start: 0.8186 (pp20) cc_final: 0.7851 (pp20) REVERT: C 800 ASP cc_start: 0.8219 (m-30) cc_final: 0.7811 (m-30) REVERT: C 874 GLN cc_start: 0.8528 (tt0) cc_final: 0.8157 (tm-30) REVERT: D 832 ARG cc_start: 0.7229 (ptp90) cc_final: 0.5841 (ptp90) REVERT: D 840 MET cc_start: 0.9126 (mmt) cc_final: 0.8841 (mmt) REVERT: D 841 ARG cc_start: 0.8537 (mmm160) cc_final: 0.8136 (mmm160) REVERT: D 889 GLU cc_start: 0.7657 (mt-10) cc_final: 0.6906 (mm-30) REVERT: E 24 TRP cc_start: 0.8315 (p90) cc_final: 0.8040 (p90) REVERT: H 6 MET cc_start: 0.7569 (mtp) cc_final: 0.7106 (mpp) REVERT: I 31 SER cc_start: 0.9504 (m) cc_final: 0.9250 (t) REVERT: I 59 VAL cc_start: 0.9123 (t) cc_final: 0.8887 (p) REVERT: I 91 GLN cc_start: 0.9241 (pp30) cc_final: 0.8959 (pp30) REVERT: J 3 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7464 (mm-40) REVERT: J 13 LYS cc_start: 0.8988 (mttp) cc_final: 0.8659 (mmtm) REVERT: J 182 ASP cc_start: 0.7950 (m-30) cc_final: 0.7596 (t0) REVERT: K 31 SER cc_start: 0.9505 (m) cc_final: 0.9233 (t) REVERT: K 63 PHE cc_start: 0.7976 (m-10) cc_final: 0.7534 (m-80) REVERT: K 91 GLN cc_start: 0.9312 (pp30) cc_final: 0.8799 (pp30) REVERT: K 93 SER cc_start: 0.8229 (p) cc_final: 0.7954 (p) REVERT: K 212 ARG cc_start: 0.6553 (mmm-85) cc_final: 0.6130 (mtp180) REVERT: A 791 PHE cc_start: 0.8039 (t80) cc_final: 0.7761 (t80) REVERT: A 813 LEU cc_start: 0.8780 (tp) cc_final: 0.8422 (tp) REVERT: A 874 GLN cc_start: 0.8546 (tt0) cc_final: 0.8187 (tm-30) REVERT: A 945 MET cc_start: 0.7903 (tpp) cc_final: 0.7592 (tpp) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.2767 time to fit residues: 178.0553 Evaluate side-chains 363 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 175 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 0.0870 chunk 154 optimal weight: 0.5980 chunk 161 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 180 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 D 896 GLN J 39 GLN J 77 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 GLN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15852 Z= 0.195 Angle : 0.646 8.287 21540 Z= 0.329 Chirality : 0.043 0.168 2466 Planarity : 0.004 0.053 2634 Dihedral : 4.618 19.129 2086 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1918 helix: 0.59 (0.20), residues: 714 sheet: 0.06 (0.26), residues: 420 loop : -2.00 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 24 HIS 0.006 0.001 HIS D 755 PHE 0.026 0.002 PHE D 749 TYR 0.009 0.001 TYR C 892 ARG 0.013 0.001 ARG A 725 *********************** 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 450 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 1.734 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 780 ILE cc_start: 0.8864 (tp) cc_final: 0.8634 (tt) REVERT: B 840 MET cc_start: 0.9085 (mmt) cc_final: 0.8719 (mmt) REVERT: B 874 GLN cc_start: 0.8436 (mt0) cc_final: 0.8094 (mm-40) REVERT: B 889 GLU cc_start: 0.7601 (mt-10) cc_final: 0.6821 (mm-30) REVERT: C 779 GLU cc_start: 0.8203 (pp20) cc_final: 0.7816 (pp20) REVERT: C 800 ASP cc_start: 0.8232 (m-30) cc_final: 0.7816 (m-30) REVERT: C 841 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7723 (mpt180) REVERT: C 874 GLN cc_start: 0.8559 (tt0) cc_final: 0.7894 (tp40) REVERT: D 832 ARG cc_start: 0.7096 (ptp90) cc_final: 0.5757 (ptp90) REVERT: D 840 MET cc_start: 0.9089 (mmt) cc_final: 0.8829 (mmt) REVERT: D 841 ARG cc_start: 0.8519 (mmm160) cc_final: 0.8148 (mmm160) REVERT: D 883 TRP cc_start: 0.8558 (p90) cc_final: 0.7356 (p90) REVERT: D 889 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6836 (mm-30) REVERT: E 24 TRP cc_start: 0.8386 (p90) cc_final: 0.8006 (p90) REVERT: H 6 MET cc_start: 0.7618 (mtp) cc_final: 0.7161 (mpp) REVERT: I 31 SER cc_start: 0.9501 (m) cc_final: 0.9280 (t) REVERT: I 59 VAL cc_start: 0.9096 (t) cc_final: 0.8872 (p) REVERT: I 83 ASP cc_start: 0.8829 (m-30) cc_final: 0.8593 (m-30) REVERT: I 91 GLN cc_start: 0.9240 (pp30) cc_final: 0.8968 (pp30) REVERT: J 13 LYS cc_start: 0.8986 (mttp) cc_final: 0.8677 (mmtm) REVERT: J 182 ASP cc_start: 0.7841 (m-30) cc_final: 0.7519 (t0) REVERT: K 31 SER cc_start: 0.9501 (m) cc_final: 0.9229 (t) REVERT: K 63 PHE cc_start: 0.7974 (m-10) cc_final: 0.7622 (m-80) REVERT: K 91 GLN cc_start: 0.9300 (pp30) cc_final: 0.8789 (pp30) REVERT: K 93 SER cc_start: 0.8131 (p) cc_final: 0.7859 (p) REVERT: K 176 MET cc_start: 0.6560 (ptt) cc_final: 0.6214 (ptm) REVERT: K 212 ARG cc_start: 0.6664 (mmm-85) cc_final: 0.6345 (mtp180) REVERT: A 779 GLU cc_start: 0.8318 (tt0) cc_final: 0.8099 (tt0) REVERT: A 783 ARG cc_start: 0.8184 (mtp-110) cc_final: 0.7936 (ttp80) REVERT: A 791 PHE cc_start: 0.8169 (t80) cc_final: 0.7733 (t80) REVERT: A 874 GLN cc_start: 0.8635 (tt0) cc_final: 0.8319 (tm-30) REVERT: A 945 MET cc_start: 0.7887 (tpp) cc_final: 0.7656 (tpp) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.2707 time to fit residues: 178.0974 Evaluate side-chains 365 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 189 optimal weight: 0.3980 chunk 174 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 116 optimal weight: 0.0570 chunk 92 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 896 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15852 Z= 0.210 Angle : 0.663 7.146 21540 Z= 0.337 Chirality : 0.043 0.197 2466 Planarity : 0.005 0.052 2634 Dihedral : 4.670 23.398 2086 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.06 % Allowed : 0.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1918 helix: 0.66 (0.20), residues: 714 sheet: 0.04 (0.26), residues: 420 loop : -1.96 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 883 HIS 0.005 0.001 HIS D 755 PHE 0.025 0.002 PHE D 749 TYR 0.011 0.001 TYR C 892 ARG 0.012 0.001 ARG A 725 ********************** 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 434 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 433 time to evaluate : 1.900 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: 0.8872 (tp) cc_final: 0.8658 (tt) REVERT: B 823 ARG cc_start: 0.8224 (ptp-170) cc_final: 0.7975 (ptp-170) REVERT: B 832 ARG cc_start: 0.7170 (ptp90) cc_final: 0.6909 (ptp90) REVERT: B 840 MET cc_start: 0.9032 (mmt) cc_final: 0.8733 (mmt) REVERT: B 889 GLU cc_start: 0.7657 (mt-10) cc_final: 0.6865 (mm-30) REVERT: C 800 ASP cc_start: 0.8196 (m-30) cc_final: 0.7783 (m-30) REVERT: C 841 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7694 (mtm-85) REVERT: C 874 GLN cc_start: 0.8557 (tt0) cc_final: 0.7893 (tp40) REVERT: D 823 ARG cc_start: 0.8464 (ptp-170) cc_final: 0.8094 (mtt180) REVERT: D 840 MET cc_start: 0.9096 (mmt) cc_final: 0.8855 (mmt) REVERT: D 841 ARG cc_start: 0.8512 (mmm160) cc_final: 0.8219 (mmm160) REVERT: D 883 TRP cc_start: 0.8590 (p90) cc_final: 0.7365 (p90) REVERT: D 889 GLU cc_start: 0.7587 (mt-10) cc_final: 0.6851 (mm-30) REVERT: E 23 LEU cc_start: 0.8706 (tp) cc_final: 0.8475 (tt) REVERT: H 6 MET cc_start: 0.7625 (mtp) cc_final: 0.7174 (mpp) REVERT: I 59 VAL cc_start: 0.9125 (t) cc_final: 0.8897 (p) REVERT: I 83 ASP cc_start: 0.8805 (m-30) cc_final: 0.8586 (m-30) REVERT: J 13 LYS cc_start: 0.8996 (mttp) cc_final: 0.8690 (mmtm) REVERT: J 182 ASP cc_start: 0.7822 (m-30) cc_final: 0.7504 (t0) REVERT: K 27 LEU cc_start: 0.9007 (tp) cc_final: 0.8352 (mp) REVERT: K 31 SER cc_start: 0.9523 (m) cc_final: 0.9282 (t) REVERT: K 63 PHE cc_start: 0.7892 (m-10) cc_final: 0.7451 (m-80) REVERT: K 91 GLN cc_start: 0.9309 (pp30) cc_final: 0.8793 (pp30) REVERT: K 93 SER cc_start: 0.8162 (p) cc_final: 0.7943 (p) REVERT: K 176 MET cc_start: 0.6609 (ptt) cc_final: 0.6253 (ptm) REVERT: K 212 ARG cc_start: 0.6493 (mmm-85) cc_final: 0.6176 (mtp180) REVERT: L 93 MET cc_start: 0.7240 (tpt) cc_final: 0.6841 (tpt) REVERT: A 779 GLU cc_start: 0.8318 (tt0) cc_final: 0.8093 (tt0) REVERT: A 791 PHE cc_start: 0.8008 (t80) cc_final: 0.7727 (t80) REVERT: A 874 GLN cc_start: 0.8649 (tt0) cc_final: 0.8315 (tm-30) REVERT: A 945 MET cc_start: 0.7915 (tpp) cc_final: 0.7658 (tpp) outliers start: 1 outliers final: 0 residues processed: 433 average time/residue: 0.2697 time to fit residues: 170.8338 Evaluate side-chains 354 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 150 optimal weight: 0.4980 chunk 63 optimal weight: 0.0970 chunk 155 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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** C 961 GLN ** D 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.192617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141536 restraints weight = 25441.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137305 restraints weight = 29284.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.139855 restraints weight = 25251.643| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15852 Z= 0.189 Angle : 0.652 7.652 21540 Z= 0.329 Chirality : 0.043 0.271 2466 Planarity : 0.004 0.046 2634 Dihedral : 4.592 19.294 2086 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1918 helix: 0.82 (0.20), residues: 714 sheet: 0.15 (0.26), residues: 392 loop : -1.86 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 883 HIS 0.006 0.001 HIS D 755 PHE 0.024 0.001 PHE D 749 TYR 0.011 0.001 TYR C 892 ARG 0.010 0.001 ARG E 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3987.14 seconds wall clock time: 71 minutes 34.61 seconds (4294.61 seconds total)