Starting phenix.real_space_refine on Fri Jan 17 11:31:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xck_38246/01_2025/8xck_38246.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xck_38246/01_2025/8xck_38246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xck_38246/01_2025/8xck_38246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xck_38246/01_2025/8xck_38246.map" model { file = "/net/cci-nas-00/data/ceres_data/8xck_38246/01_2025/8xck_38246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xck_38246/01_2025/8xck_38246.cif" } resolution = 2.75 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= -0.000 sd= 0.052 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 42 5.16 5 C 6717 2.51 5 N 1851 2.21 5 O 2061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10671 Number of models: 1 Model: "" Number of chains: 6 Chain: "J" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2323 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain: "j" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1234 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "z" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1234 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "Z" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2323 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain: "f" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1234 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2323 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Time building chain proxies: 8.34, per 1000 atoms: 0.78 Number of scatterers: 10671 At special positions: 0 Unit cell: (93.24, 92.204, 218.596, 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 42 16.00 O 2061 8.00 N 1851 7.00 C 6717 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: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 34 sheets defined 13.8% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'J' and resid 828 through 832 removed outlier: 3.666A pdb=" N LEU J 831 " --> pdb=" O GLY J 828 " (cutoff:3.500A) Processing helix chain 'J' and resid 836 through 860 removed outlier: 3.568A pdb=" N ALA J 842 " --> pdb=" O THR J 838 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS J 858 " --> pdb=" O ASP J 854 " (cutoff:3.500A) Processing helix chain 'j' and resid 49 through 62 Processing helix chain 'j' and resid 100 through 104 removed outlier: 3.835A pdb=" N ASN j 103 " --> pdb=" O GLU j 100 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY j 104 " --> pdb=" O ALA j 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 100 through 104' Processing helix chain 'j' and resid 134 through 138 Processing helix chain 'j' and resid 155 through 164 removed outlier: 3.668A pdb=" N GLN j 164 " --> pdb=" O ASP j 160 " (cutoff:3.500A) Processing helix chain 'z' and resid 49 through 62 Processing helix chain 'z' and resid 100 through 104 removed outlier: 3.567A pdb=" N ASN z 103 " --> pdb=" O GLU z 100 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY z 104 " --> pdb=" O ALA z 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 100 through 104' Processing helix chain 'z' and resid 134 through 138 Processing helix chain 'z' and resid 155 through 164 removed outlier: 3.579A pdb=" N ALA z 159 " --> pdb=" O GLY z 155 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN z 164 " --> pdb=" O ASP z 160 " (cutoff:3.500A) Processing helix chain 'Z' and resid 834 through 861 removed outlier: 4.025A pdb=" N THR Z 838 " --> pdb=" O LYS Z 834 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU Z 839 " --> pdb=" O VAL Z 835 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP Z 857 " --> pdb=" O LYS Z 853 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS Z 858 " --> pdb=" O ASP Z 854 " (cutoff:3.500A) Processing helix chain 'f' and resid 49 through 62 Processing helix chain 'f' and resid 100 through 104 removed outlier: 3.616A pdb=" N ASN f 103 " --> pdb=" O GLU f 100 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY f 104 " --> pdb=" O ALA f 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 100 through 104' Processing helix chain 'f' and resid 134 through 138 Processing helix chain 'f' and resid 155 through 164 removed outlier: 3.744A pdb=" N GLN f 164 " --> pdb=" O ASP f 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 829 through 834 Processing helix chain 'F' and resid 836 through 861 removed outlier: 3.523A pdb=" N ALA F 842 " --> pdb=" O THR F 838 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP F 857 " --> pdb=" O LYS F 853 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS F 858 " --> pdb=" O ASP F 854 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA F 861 " --> pdb=" O ASP F 857 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 863 through 868 removed outlier: 3.688A pdb=" N GLY J 879 " --> pdb=" O LYS J 866 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU J 868 " --> pdb=" O VAL J 877 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL J 877 " --> pdb=" O GLU J 868 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 895 through 897 removed outlier: 6.214A pdb=" N PHE J 895 " --> pdb=" O ALA F 903 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE F 905 " --> pdb=" O PHE J 895 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL J 897 " --> pdb=" O ILE F 905 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 912 through 914 Processing sheet with id=AA4, first strand: chain 'J' and resid 916 through 918 Processing sheet with id=AA5, first strand: chain 'J' and resid 932 through 934 Processing sheet with id=AA6, first strand: chain 'Z' and resid 932 through 934 removed outlier: 6.563A pdb=" N THR J 937 " --> pdb=" O LEU Z 933 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU J 955 " --> pdb=" O ASP F 961 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N SER F 963 " --> pdb=" O LEU J 955 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 932 through 934 removed outlier: 6.401A pdb=" N THR Z 937 " --> pdb=" O LEU F 933 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASN F 967 " --> pdb=" O ALA J 960 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE J 962 " --> pdb=" O ASN F 967 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 966 through 967 Processing sheet with id=AA9, first strand: chain 'J' and resid 972 through 973 Processing sheet with id=AB1, first strand: chain 'J' and resid 977 through 978 removed outlier: 6.344A pdb=" N THR J 977 " --> pdb=" O LEU Z 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'J' and resid 998 through 1003 removed outlier: 5.241A pdb=" N GLN J1118 " --> pdb=" O LEU J1037 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE J1080 " --> pdb=" O PRO J1038 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR J1040 " --> pdb=" O GLN J1078 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN J1078 " --> pdb=" O THR J1040 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 998 through 1003 removed outlier: 5.241A pdb=" N GLN J1118 " --> pdb=" O LEU J1037 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 1007 through 1010 Processing sheet with id=AB5, first strand: chain 'J' and resid 1066 through 1073 removed outlier: 6.631A pdb=" N VAL J1061 " --> pdb=" O ILE J1068 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP J1070 " --> pdb=" O LEU J1059 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU J1059 " --> pdb=" O ASP J1070 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA J1072 " --> pdb=" O CYS J1057 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N CYS J1057 " --> pdb=" O ALA J1072 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 1044 through 1048 Processing sheet with id=AB7, first strand: chain 'J' and resid 1129 through 1131 removed outlier: 6.541A pdb=" N CYS Z1057 " --> pdb=" O ALA Z1072 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA Z1072 " --> pdb=" O CYS Z1057 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU Z1059 " --> pdb=" O ASP Z1070 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP Z1070 " --> pdb=" O LEU Z1059 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL Z1061 " --> pdb=" O ILE Z1068 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'j' and resid 68 through 69 removed outlier: 3.714A pdb=" N THR j 68 " --> pdb=" O ILE j 183 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU j 43 " --> pdb=" O VAL j 152 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL j 152 " --> pdb=" O GLU j 43 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE j 112 " --> pdb=" O PHE j 149 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR j 111 " --> pdb=" O ASN j 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'z' and resid 68 through 69 removed outlier: 3.737A pdb=" N THR z 68 " --> pdb=" O ILE z 183 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU z 43 " --> pdb=" O VAL z 152 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL z 152 " --> pdb=" O GLU z 43 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE z 112 " --> pdb=" O PHE z 149 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR z 111 " --> pdb=" O ASN z 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Z' and resid 863 through 868 removed outlier: 3.649A pdb=" N GLY Z 879 " --> pdb=" O LYS Z 866 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU Z 868 " --> pdb=" O VAL Z 877 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL Z 877 " --> pdb=" O GLU Z 868 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Z' and resid 912 through 914 Processing sheet with id=AC3, first strand: chain 'Z' and resid 916 through 918 Processing sheet with id=AC4, first strand: chain 'Z' and resid 977 through 978 removed outlier: 6.298A pdb=" N THR Z 977 " --> pdb=" O LEU F 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'Z' and resid 998 through 1003 removed outlier: 5.211A pdb=" N GLN Z1118 " --> pdb=" O LEU Z1037 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE Z1080 " --> pdb=" O PRO Z1038 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR Z1040 " --> pdb=" O GLN Z1078 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN Z1078 " --> pdb=" O THR Z1040 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Z' and resid 998 through 1003 removed outlier: 5.211A pdb=" N GLN Z1118 " --> pdb=" O LEU Z1037 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 1007 through 1010 Processing sheet with id=AC8, first strand: chain 'Z' and resid 1044 through 1048 Processing sheet with id=AC9, first strand: chain 'Z' and resid 1129 through 1131 removed outlier: 6.531A pdb=" N CYS F1057 " --> pdb=" O ALA F1072 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA F1072 " --> pdb=" O CYS F1057 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU F1059 " --> pdb=" O ASP F1070 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP F1070 " --> pdb=" O LEU F1059 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL F1061 " --> pdb=" O ILE F1068 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'f' and resid 68 through 69 removed outlier: 3.674A pdb=" N THR f 68 " --> pdb=" O ILE f 183 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU f 41 " --> pdb=" O VAL f 153 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE f 112 " --> pdb=" O PHE f 149 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR f 111 " --> pdb=" O ASN f 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 863 through 868 removed outlier: 3.664A pdb=" N GLY F 879 " --> pdb=" O LYS F 866 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU F 868 " --> pdb=" O VAL F 877 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL F 877 " --> pdb=" O GLU F 868 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 916 through 919 Processing sheet with id=AD4, first strand: chain 'F' and resid 998 through 1003 removed outlier: 5.257A pdb=" N GLN F1118 " --> pdb=" O LEU F1037 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE F1080 " --> pdb=" O PRO F1038 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR F1040 " --> pdb=" O GLN F1078 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN F1078 " --> pdb=" O THR F1040 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 998 through 1003 removed outlier: 5.257A pdb=" N GLN F1118 " --> pdb=" O LEU F1037 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 1007 through 1010 Processing sheet with id=AD7, first strand: chain 'F' and resid 1044 through 1048 406 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.31: 1856 1.31 - 1.46: 2782 1.46 - 1.61: 6156 1.61 - 1.76: 0 1.76 - 1.91: 78 Bond restraints: 10872 Sorted by residual: bond pdb=" CG ASP Z 961 " pdb=" OD2 ASP Z 961 " ideal model delta sigma weight residual 1.249 1.411 -0.162 1.90e-02 2.77e+03 7.29e+01 bond pdb=" C ALA Z 957 " pdb=" O ALA Z 957 " ideal model delta sigma weight residual 1.234 1.345 -0.110 1.30e-02 5.92e+03 7.19e+01 bond pdb=" C VAL J1079 " pdb=" O VAL J1079 " ideal model delta sigma weight residual 1.237 1.154 0.083 1.09e-02 8.42e+03 5.77e+01 bond pdb=" C VAL Z1079 " pdb=" O VAL Z1079 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.09e-02 8.42e+03 5.30e+01 bond pdb=" C LEU F 949 " pdb=" O LEU F 949 " ideal model delta sigma weight residual 1.236 1.154 0.081 1.14e-02 7.69e+03 5.10e+01 ... (remaining 10867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 10947 1.80 - 3.60: 3271 3.60 - 5.40: 445 5.40 - 7.20: 74 7.20 - 9.00: 11 Bond angle restraints: 14748 Sorted by residual: angle pdb=" C THR F 934 " pdb=" N ALA F 935 " pdb=" CA ALA F 935 " ideal model delta sigma weight residual 123.10 129.19 -6.09 9.60e-01 1.09e+00 4.02e+01 angle pdb=" C THR J 934 " pdb=" N ALA J 935 " pdb=" CA ALA J 935 " ideal model delta sigma weight residual 123.10 128.93 -5.83 9.60e-01 1.09e+00 3.69e+01 angle pdb=" N ASN F 967 " pdb=" CA ASN F 967 " pdb=" CB ASN F 967 " ideal model delta sigma weight residual 111.23 102.23 9.00 1.53e+00 4.27e-01 3.46e+01 angle pdb=" N PRO j 75 " pdb=" CA PRO j 75 " pdb=" CB PRO j 75 " ideal model delta sigma weight residual 103.36 108.41 -5.05 8.80e-01 1.29e+00 3.30e+01 angle pdb=" N PRO f 75 " pdb=" CA PRO f 75 " pdb=" CB PRO f 75 " ideal model delta sigma weight residual 103.36 108.36 -5.00 8.80e-01 1.29e+00 3.23e+01 ... (remaining 14743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5517 17.94 - 35.87: 740 35.87 - 53.80: 232 53.80 - 71.74: 51 71.74 - 89.67: 15 Dihedral angle restraints: 6555 sinusoidal: 2559 harmonic: 3996 Sorted by residual: dihedral pdb=" CA ASN F 943 " pdb=" C ASN F 943 " pdb=" N PRO F 944 " pdb=" CA PRO F 944 " ideal model delta harmonic sigma weight residual 180.00 96.54 83.46 0 5.00e+00 4.00e-02 2.79e+02 dihedral pdb=" CA ASN J 943 " pdb=" C ASN J 943 " pdb=" N PRO J 944 " pdb=" CA PRO J 944 " ideal model delta harmonic sigma weight residual 180.00 97.41 82.59 0 5.00e+00 4.00e-02 2.73e+02 dihedral pdb=" CA ASN Z 943 " pdb=" C ASN Z 943 " pdb=" N PRO Z 944 " pdb=" CA PRO Z 944 " ideal model delta harmonic sigma weight residual 180.00 99.51 80.49 0 5.00e+00 4.00e-02 2.59e+02 ... (remaining 6552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 953 0.077 - 0.154: 568 0.154 - 0.230: 124 0.230 - 0.307: 37 0.307 - 0.384: 10 Chirality restraints: 1692 Sorted by residual: chirality pdb=" CA ASP Z 961 " pdb=" N ASP Z 961 " pdb=" C ASP Z 961 " pdb=" CB ASP Z 961 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA GLN F1118 " pdb=" N GLN F1118 " pdb=" C GLN F1118 " pdb=" CB GLN F1118 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA ASP Z 927 " pdb=" N ASP Z 927 " pdb=" C ASP Z 927 " pdb=" CB ASP Z 927 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 1689 not shown) Planarity restraints: 1932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN Z 943 " -0.022 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C ASN Z 943 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN Z 943 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO Z 944 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN Z 943 " 0.064 5.00e-02 4.00e+02 9.78e-02 1.53e+01 pdb=" N PRO Z 944 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO Z 944 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO Z 944 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN J 943 " -0.063 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO J 944 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO J 944 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO J 944 " -0.051 5.00e-02 4.00e+02 ... (remaining 1929 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 865 2.73 - 3.28: 10047 3.28 - 3.82: 16377 3.82 - 4.36: 22633 4.36 - 4.90: 37074 Nonbonded interactions: 86996 Sorted by model distance: nonbonded pdb=" NH2 ARG Z 932 " pdb=" OE1 GLN F 919 " model vdw 2.194 3.120 nonbonded pdb=" OD2 ASP Z1085 " pdb=" NZ LYS Z1124 " model vdw 2.273 3.120 nonbonded pdb=" OE1 GLN J 919 " pdb=" NH2 ARG F 932 " model vdw 2.285 3.120 nonbonded pdb=" OG SER F1011 " pdb=" N SER F1012 " model vdw 2.286 3.120 nonbonded pdb=" O ASP j 119 " pdb=" OG SER j 122 " model vdw 2.287 3.040 ... (remaining 86991 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: 0.01 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'Z' } ncs_group { reference = chain 'f' selection = chain 'j' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.740 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 : 0.016 0.162 10872 Z= 1.026 Angle : 1.664 9.002 14748 Z= 1.163 Chirality : 0.099 0.384 1692 Planarity : 0.009 0.098 1932 Dihedral : 18.704 89.671 3975 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.51 % Allowed : 11.35 % Favored : 88.14 % Rotamer: Outliers : 5.40 % Allowed : 25.96 % Favored : 68.64 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -1.67 (0.21), residues: 1383 helix: 0.55 (0.40), residues: 150 sheet: 0.02 (0.27), residues: 351 loop : -2.01 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.006 TRP Z 859 HIS 0.010 0.003 HIS Z1028 PHE 0.043 0.012 PHE F1113 TYR 0.050 0.011 TYR j 146 ARG 0.015 0.002 ARG z 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 153 time to evaluate : 1.351 Fit side-chains REVERT: J 846 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6817 (pp20) REVERT: J 853 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.6972 (tptt) REVERT: J 862 MET cc_start: 0.8832 (tpp) cc_final: 0.8545 (tpp) REVERT: j 46 LYS cc_start: 0.8192 (mttp) cc_final: 0.7777 (tmmm) REVERT: j 156 MET cc_start: 0.7621 (tpt) cc_final: 0.7049 (tpt) REVERT: j 160 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: j 187 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6540 (ttmm) REVERT: z 58 ASP cc_start: 0.7863 (m-30) cc_final: 0.7574 (m-30) REVERT: z 98 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7877 (mptm) REVERT: z 187 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6520 (ttmp) REVERT: f 46 LYS cc_start: 0.8352 (mtmt) cc_final: 0.7689 (tttp) REVERT: f 160 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: f 187 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6771 (ttmm) REVERT: F 991 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8197 (pm20) outliers start: 63 outliers final: 30 residues processed: 200 average time/residue: 1.2911 time to fit residues: 277.4263 Evaluate side-chains 179 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 853 LYS Chi-restraints excluded: chain J residue 856 SER Chi-restraints excluded: chain J residue 925 MET Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 974 SER Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1098 THR Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain J residue 1130 SER Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain j residue 187 LYS Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain z residue 98 LYS Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 856 SER Chi-restraints excluded: chain Z residue 925 MET Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 974 SER Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 187 LYS Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain F residue 856 SER Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 974 SER Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 989 ARG Chi-restraints excluded: chain F residue 991 GLU Chi-restraints excluded: chain F residue 1100 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.4980 chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 943 ASN J1008 GLN j 30 HIS j 126 GLN z 30 HIS z 174 GLN Z 869 GLN f 30 HIS ** f 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 943 ASN F 975 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.161770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127635 restraints weight = 12677.888| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.62 r_work: 0.3223 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10872 Z= 0.248 Angle : 0.717 15.924 14748 Z= 0.373 Chirality : 0.050 0.201 1692 Planarity : 0.005 0.089 1932 Dihedral : 9.527 101.268 1547 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 5.40 % Allowed : 26.48 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -1.47 (0.22), residues: 1383 helix: 1.08 (0.43), residues: 150 sheet: -0.05 (0.27), residues: 345 loop : -1.84 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 852 HIS 0.008 0.001 HIS f 139 PHE 0.014 0.002 PHE f 128 TYR 0.018 0.001 TYR z 146 ARG 0.004 0.000 ARG J1090 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 149 time to evaluate : 1.299 Fit side-chains REVERT: j 32 LEU cc_start: 0.6626 (mm) cc_final: 0.6311 (mm) REVERT: j 46 LYS cc_start: 0.7861 (mttp) cc_final: 0.7627 (OUTLIER) REVERT: j 156 MET cc_start: 0.7729 (tpt) cc_final: 0.7072 (tpt) REVERT: j 160 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: z 160 ASP cc_start: 0.8056 (m-30) cc_final: 0.7680 (m-30) REVERT: z 187 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.5948 (ptpp) REVERT: f 187 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6694 (ttmm) outliers start: 63 outliers final: 24 residues processed: 197 average time/residue: 1.1998 time to fit residues: 255.3308 Evaluate side-chains 167 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1098 THR Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain J residue 1130 SER Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 925 MET Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain f residue 187 LYS Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1130 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN J1008 GLN ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 126 GLN z 30 HIS z 139 HIS z 174 GLN Z 922 GLN f 141 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.161829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125169 restraints weight = 12175.324| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.49 r_work: 0.3213 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10872 Z= 0.257 Angle : 0.698 15.922 14748 Z= 0.358 Chirality : 0.050 0.172 1692 Planarity : 0.006 0.089 1932 Dihedral : 8.245 78.496 1506 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 6.00 % Allowed : 26.48 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -1.55 (0.22), residues: 1383 helix: 1.11 (0.43), residues: 150 sheet: -0.07 (0.27), residues: 351 loop : -1.95 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Z 859 HIS 0.007 0.001 HIS f 139 PHE 0.013 0.002 PHE z 136 TYR 0.019 0.002 TYR z 146 ARG 0.007 0.000 ARG Z1042 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 149 time to evaluate : 1.123 Fit side-chains REVERT: j 32 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6504 (mm) REVERT: j 46 LYS cc_start: 0.7918 (mttp) cc_final: 0.7620 (tttp) REVERT: j 67 ASN cc_start: 0.8514 (t0) cc_final: 0.8231 (t0) REVERT: j 156 MET cc_start: 0.7709 (tpt) cc_final: 0.7063 (tpt) REVERT: j 160 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: z 46 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7500 (tttp) REVERT: z 187 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.6043 (ttmp) REVERT: Z 989 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7508 (mmt90) REVERT: Z 1077 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8400 (m) REVERT: Z 1085 ASP cc_start: 0.8478 (m-30) cc_final: 0.8239 (m-30) REVERT: Z 1129 ILE cc_start: 0.8748 (tt) cc_final: 0.8322 (tp) REVERT: f 46 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7608 (tttp) REVERT: f 160 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: f 161 LYS cc_start: 0.6624 (tmtt) cc_final: 0.5981 (tmtt) outliers start: 70 outliers final: 32 residues processed: 205 average time/residue: 1.1285 time to fit residues: 251.3531 Evaluate side-chains 189 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1098 THR Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain J residue 1130 SER Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain j residue 188 VAL Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 46 LYS Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 143 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 925 MET Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 988 LEU Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1013 VAL Chi-restraints excluded: chain Z residue 1053 THR Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1062 LEU Chi-restraints excluded: chain F residue 1100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 9 optimal weight: 0.0070 chunk 76 optimal weight: 0.3980 chunk 110 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN J1008 GLN ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 126 GLN z 30 HIS z 174 GLN Z 911 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.162810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127354 restraints weight = 12165.044| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.14 r_work: 0.3235 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10872 Z= 0.216 Angle : 0.676 15.482 14748 Z= 0.344 Chirality : 0.049 0.254 1692 Planarity : 0.005 0.086 1932 Dihedral : 7.941 76.874 1502 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 6.00 % Allowed : 26.91 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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 (0.22), residues: 1383 helix: 1.27 (0.43), residues: 150 sheet: 0.08 (0.27), residues: 345 loop : -1.91 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Z 859 HIS 0.006 0.001 HIS f 139 PHE 0.012 0.002 PHE f 128 TYR 0.017 0.001 TYR z 146 ARG 0.006 0.000 ARG Z1042 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 155 time to evaluate : 1.177 Fit side-chains REVERT: j 32 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6561 (mm) REVERT: j 46 LYS cc_start: 0.7907 (mttp) cc_final: 0.7613 (tttp) REVERT: j 67 ASN cc_start: 0.8604 (t0) cc_final: 0.8345 (t0) REVERT: j 156 MET cc_start: 0.7761 (tpt) cc_final: 0.7163 (tpt) REVERT: j 160 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7220 (m-30) REVERT: z 46 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7511 (tttp) REVERT: z 187 LYS cc_start: 0.6347 (OUTLIER) cc_final: 0.5970 (ttmp) REVERT: Z 989 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7433 (mmt90) REVERT: Z 1085 ASP cc_start: 0.8487 (m-30) cc_final: 0.8247 (m-30) REVERT: Z 1129 ILE cc_start: 0.8708 (tt) cc_final: 0.8320 (tp) REVERT: f 46 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7667 (tttp) REVERT: f 78 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.7385 (pp-130) REVERT: F 929 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7505 (m-80) outliers start: 70 outliers final: 29 residues processed: 206 average time/residue: 1.1372 time to fit residues: 254.2157 Evaluate side-chains 179 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1098 THR Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 138 ASP Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 46 LYS Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 143 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 925 MET Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain F residue 923 ILE Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 1098 THR Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1130 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 99 optimal weight: 0.0040 chunk 33 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 16 optimal weight: 0.0770 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.2550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN J1008 GLN ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 126 GLN z 30 HIS z 174 GLN ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.165009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129944 restraints weight = 12096.523| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.15 r_work: 0.3276 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10872 Z= 0.178 Angle : 0.651 15.424 14748 Z= 0.330 Chirality : 0.048 0.265 1692 Planarity : 0.005 0.082 1932 Dihedral : 7.603 74.390 1499 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 5.91 % Allowed : 27.51 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -1.36 (0.22), residues: 1383 helix: 1.46 (0.43), residues: 150 sheet: 0.16 (0.28), residues: 345 loop : -1.90 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Z 863 HIS 0.002 0.001 HIS Z1104 PHE 0.011 0.001 PHE f 128 TYR 0.017 0.001 TYR z 146 ARG 0.005 0.000 ARG Z1042 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 153 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: j 32 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6535 (mm) REVERT: j 46 LYS cc_start: 0.7900 (mttp) cc_final: 0.7583 (tttp) REVERT: j 156 MET cc_start: 0.7739 (tpt) cc_final: 0.7013 (tpt) REVERT: j 160 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7148 (m-30) REVERT: z 46 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7589 (tttp) REVERT: z 160 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7341 (m-30) REVERT: z 187 LYS cc_start: 0.6281 (OUTLIER) cc_final: 0.5910 (ttmp) REVERT: Z 989 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7360 (mmt90) REVERT: Z 1085 ASP cc_start: 0.8388 (m-30) cc_final: 0.8182 (m-30) REVERT: f 46 LYS cc_start: 0.8022 (mtmt) cc_final: 0.7671 (tttp) REVERT: f 78 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.7213 (pp-130) REVERT: f 161 LYS cc_start: 0.6699 (tmtt) cc_final: 0.6295 (tmtt) REVERT: F 929 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7314 (m-80) REVERT: F 1060 LYS cc_start: 0.8904 (tttt) cc_final: 0.8607 (ttmt) outliers start: 69 outliers final: 33 residues processed: 202 average time/residue: 1.2318 time to fit residues: 271.6191 Evaluate side-chains 184 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1098 THR Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain J residue 1115 SER Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain j residue 138 ASP Chi-restraints excluded: chain j residue 141 GLN Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 46 LYS Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 160 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 988 LEU Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain F residue 871 LYS Chi-restraints excluded: chain F residue 886 ASP Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 1062 LEU Chi-restraints excluded: chain F residue 1130 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 82 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 136 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN J1008 GLN ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127396 restraints weight = 12217.887| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.21 r_work: 0.3244 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10872 Z= 0.250 Angle : 0.688 15.513 14748 Z= 0.349 Chirality : 0.049 0.275 1692 Planarity : 0.005 0.086 1932 Dihedral : 7.580 76.460 1494 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 5.83 % Allowed : 28.11 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -1.38 (0.22), residues: 1383 helix: 1.39 (0.44), residues: 150 sheet: 0.15 (0.28), residues: 345 loop : -1.90 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 859 HIS 0.008 0.001 HIS z 139 PHE 0.012 0.002 PHE Z 904 TYR 0.019 0.001 TYR z 146 ARG 0.005 0.000 ARG f 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 147 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: J 989 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6745 (mmm160) REVERT: j 32 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6443 (mm) REVERT: j 46 LYS cc_start: 0.7951 (mttp) cc_final: 0.7617 (tttp) REVERT: j 156 MET cc_start: 0.7795 (tpt) cc_final: 0.7081 (tpt) REVERT: j 160 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: z 46 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7696 (tttp) REVERT: z 160 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: z 187 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5906 (ttmp) REVERT: Z 859 TRP cc_start: 0.7406 (m-10) cc_final: 0.6775 (m100) REVERT: Z 1082 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8561 (tpp-160) REVERT: f 46 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7681 (tttp) REVERT: f 78 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.7500 (pp-130) REVERT: F 929 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: F 1060 LYS cc_start: 0.8905 (tttt) cc_final: 0.8600 (ttmt) outliers start: 68 outliers final: 39 residues processed: 198 average time/residue: 1.1703 time to fit residues: 250.5086 Evaluate side-chains 192 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 929 PHE Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1098 THR Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain J residue 1115 SER Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain j residue 138 ASP Chi-restraints excluded: chain j residue 141 GLN Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 46 LYS Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain z residue 68 THR Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 160 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1082 ARG Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain F residue 850 LYS Chi-restraints excluded: chain F residue 886 ASP Chi-restraints excluded: chain F residue 923 ILE Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 1062 LEU Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1098 THR Chi-restraints excluded: chain F residue 1130 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 99 optimal weight: 0.0050 chunk 72 optimal weight: 0.7980 chunk 62 optimal weight: 0.0670 chunk 34 optimal weight: 0.0570 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 105 optimal weight: 0.0020 chunk 109 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.1458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN J1008 GLN ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 126 GLN z 30 HIS z 139 HIS z 174 GLN ** f 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.167468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.132701 restraints weight = 12358.771| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.09 r_work: 0.3322 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10872 Z= 0.161 Angle : 0.636 15.361 14748 Z= 0.322 Chirality : 0.047 0.241 1692 Planarity : 0.005 0.079 1932 Dihedral : 7.184 71.805 1494 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 4.80 % Allowed : 28.62 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -1.30 (0.22), residues: 1383 helix: 1.66 (0.43), residues: 150 sheet: 0.27 (0.26), residues: 369 loop : -1.97 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 859 HIS 0.006 0.001 HIS z 139 PHE 0.015 0.001 PHE Z 916 TYR 0.014 0.001 TYR f 146 ARG 0.005 0.000 ARG f 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 989 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6611 (mmm160) REVERT: j 32 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6401 (mm) REVERT: j 46 LYS cc_start: 0.7881 (mttp) cc_final: 0.7567 (tttp) REVERT: j 87 GLN cc_start: 0.6264 (OUTLIER) cc_final: 0.5823 (tt0) REVERT: j 156 MET cc_start: 0.7747 (tpt) cc_final: 0.7025 (tpt) REVERT: j 160 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.6953 (m-30) REVERT: z 160 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: z 187 LYS cc_start: 0.6158 (OUTLIER) cc_final: 0.5882 (ttmp) REVERT: Z 859 TRP cc_start: 0.7343 (m-10) cc_final: 0.6797 (m100) REVERT: Z 1082 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8438 (tpp-160) REVERT: Z 1129 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7387 (tp) REVERT: f 46 LYS cc_start: 0.7923 (mtmt) cc_final: 0.7670 (tttp) REVERT: F 929 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: F 1060 LYS cc_start: 0.8866 (tttt) cc_final: 0.8559 (ttmt) REVERT: F 1082 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8506 (tpp80) outliers start: 56 outliers final: 24 residues processed: 195 average time/residue: 1.2502 time to fit residues: 262.9206 Evaluate side-chains 176 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain J residue 1115 SER Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 87 GLN Chi-restraints excluded: chain j residue 138 ASP Chi-restraints excluded: chain j residue 141 GLN Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 143 ASP Chi-restraints excluded: chain z residue 160 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 831 LEU Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1082 ARG Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain F residue 850 LYS Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1082 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 104 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 99 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN J1008 GLN j 66 ASN j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN ** f 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126758 restraints weight = 12093.361| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.15 r_work: 0.3237 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10872 Z= 0.310 Angle : 0.731 15.559 14748 Z= 0.368 Chirality : 0.052 0.267 1692 Planarity : 0.006 0.087 1932 Dihedral : 7.600 78.196 1492 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 4.88 % Allowed : 28.96 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -1.35 (0.22), residues: 1383 helix: 1.39 (0.44), residues: 150 sheet: 0.19 (0.28), residues: 345 loop : -1.88 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 859 HIS 0.009 0.001 HIS z 139 PHE 0.013 0.002 PHE f 128 TYR 0.019 0.002 TYR z 146 ARG 0.004 0.000 ARG J1090 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 151 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: J 989 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6671 (mmm160) REVERT: j 32 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6406 (mm) REVERT: j 46 LYS cc_start: 0.7908 (mttp) cc_final: 0.7598 (tttp) REVERT: j 87 GLN cc_start: 0.6437 (OUTLIER) cc_final: 0.5950 (tt0) REVERT: j 156 MET cc_start: 0.7759 (tpt) cc_final: 0.7123 (tpt) REVERT: j 160 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: z 160 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: z 187 LYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5856 (ttmp) REVERT: Z 859 TRP cc_start: 0.7405 (m-10) cc_final: 0.6788 (m100) REVERT: Z 989 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7084 (mmm160) REVERT: Z 1082 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8573 (tpp-160) REVERT: f 46 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7674 (tttp) REVERT: f 78 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7372 (pp-130) REVERT: f 160 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: F 929 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7404 (m-80) outliers start: 57 outliers final: 28 residues processed: 191 average time/residue: 1.2186 time to fit residues: 251.1623 Evaluate side-chains 187 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 929 PHE Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 87 GLN Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain j residue 138 ASP Chi-restraints excluded: chain j residue 141 GLN Chi-restraints excluded: chain j residue 143 ASP Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain z residue 68 THR Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 160 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 831 LEU Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1082 ARG Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain F residue 850 LYS Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 1062 LEU Chi-restraints excluded: chain F residue 1077 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 102 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 106 optimal weight: 0.0770 chunk 41 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 119 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN J1008 GLN j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN f 67 ASN ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.163991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127464 restraints weight = 12249.337| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.35 r_work: 0.3249 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10872 Z= 0.223 Angle : 0.696 15.579 14748 Z= 0.351 Chirality : 0.050 0.270 1692 Planarity : 0.005 0.085 1932 Dihedral : 7.563 76.425 1492 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 4.54 % Allowed : 29.39 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.08 % 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: -1.35 (0.22), residues: 1383 helix: 1.41 (0.44), residues: 150 sheet: 0.23 (0.28), residues: 339 loop : -1.90 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 859 HIS 0.012 0.001 HIS f 139 PHE 0.012 0.002 PHE f 128 TYR 0.018 0.001 TYR z 146 ARG 0.004 0.000 ARG Z1042 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: J 989 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6623 (mmm160) REVERT: j 32 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6415 (mm) REVERT: j 46 LYS cc_start: 0.7907 (mttp) cc_final: 0.7578 (tttp) REVERT: j 87 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.5948 (tt0) REVERT: j 97 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7981 (pt) REVERT: j 156 MET cc_start: 0.7761 (tpt) cc_final: 0.7098 (tpt) REVERT: j 160 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6712 (m-30) REVERT: z 160 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: z 187 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5994 (ttmp) REVERT: Z 859 TRP cc_start: 0.7377 (m-10) cc_final: 0.6800 (m100) REVERT: Z 989 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7028 (mmm160) REVERT: Z 1082 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8553 (tpp-160) REVERT: Z 1127 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6412 (tp) REVERT: f 46 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7648 (tttp) REVERT: f 78 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.7293 (pp-130) REVERT: F 929 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: F 1060 LYS cc_start: 0.8912 (tttt) cc_final: 0.8602 (ttmt) outliers start: 53 outliers final: 27 residues processed: 189 average time/residue: 1.1987 time to fit residues: 244.7441 Evaluate side-chains 189 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 929 PHE Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 87 GLN Chi-restraints excluded: chain j residue 97 ILE Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain j residue 138 ASP Chi-restraints excluded: chain j residue 141 GLN Chi-restraints excluded: chain j residue 143 ASP Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 143 ASP Chi-restraints excluded: chain z residue 160 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1082 ARG Chi-restraints excluded: chain Z residue 1098 THR Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain F residue 850 LYS Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1077 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 9 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 108 optimal weight: 0.0070 chunk 30 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN J1008 GLN j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.163427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127345 restraints weight = 12160.271| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.23 r_work: 0.3244 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10872 Z= 0.250 Angle : 0.714 15.766 14748 Z= 0.360 Chirality : 0.051 0.278 1692 Planarity : 0.005 0.086 1932 Dihedral : 7.568 76.981 1492 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 4.28 % Allowed : 29.65 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.08 % 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: -1.35 (0.22), residues: 1383 helix: 1.35 (0.44), residues: 150 sheet: 0.16 (0.27), residues: 345 loop : -1.87 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 859 HIS 0.010 0.001 HIS f 139 PHE 0.013 0.002 PHE f 128 TYR 0.019 0.001 TYR z 146 ARG 0.003 0.000 ARG Z1042 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 925 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7774 (mmt) REVERT: J 929 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: J 988 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7780 (tp) REVERT: J 989 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6631 (mmm160) REVERT: J 1046 ARG cc_start: 0.6710 (mtm180) cc_final: 0.5677 (mpt-90) REVERT: j 32 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6452 (mm) REVERT: j 46 LYS cc_start: 0.7899 (mttp) cc_final: 0.7581 (tttp) REVERT: j 87 GLN cc_start: 0.6446 (OUTLIER) cc_final: 0.5965 (tt0) REVERT: j 97 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7975 (pt) REVERT: j 156 MET cc_start: 0.7787 (tpt) cc_final: 0.7227 (tpt) REVERT: j 160 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.6779 (m-30) REVERT: z 60 VAL cc_start: 0.7578 (t) cc_final: 0.7188 (t) REVERT: z 160 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: z 161 LYS cc_start: 0.6788 (tmtt) cc_final: 0.6556 (tmtt) REVERT: z 187 LYS cc_start: 0.6349 (OUTLIER) cc_final: 0.5988 (ttmp) REVERT: Z 859 TRP cc_start: 0.7397 (m-10) cc_final: 0.6812 (m100) REVERT: Z 989 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6997 (mmm160) REVERT: f 46 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7648 (tttp) REVERT: f 78 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.7282 (pp-130) REVERT: f 120 LYS cc_start: 0.7819 (mptt) cc_final: 0.7341 (mttp) REVERT: F 929 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: F 1060 LYS cc_start: 0.8906 (tttt) cc_final: 0.8595 (ttmt) REVERT: F 1099 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8551 (tp) outliers start: 50 outliers final: 28 residues processed: 186 average time/residue: 1.2923 time to fit residues: 258.7467 Evaluate side-chains 194 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 925 MET Chi-restraints excluded: chain J residue 929 PHE Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 988 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 87 GLN Chi-restraints excluded: chain j residue 97 ILE Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain j residue 138 ASP Chi-restraints excluded: chain j residue 141 GLN Chi-restraints excluded: chain j residue 143 ASP Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 160 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1098 THR Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain F residue 850 LYS Chi-restraints excluded: chain F residue 925 MET Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1099 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 108 optimal weight: 0.0060 chunk 11 optimal weight: 0.0970 chunk 129 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 0.0370 chunk 72 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.2872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1008 GLN j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN f 139 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132257 restraints weight = 12780.918| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.20 r_work: 0.3316 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10872 Z= 0.186 Angle : 0.674 15.314 14748 Z= 0.340 Chirality : 0.049 0.260 1692 Planarity : 0.005 0.083 1932 Dihedral : 7.306 73.865 1492 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 3.17 % Allowed : 30.59 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.08 % 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: -1.25 (0.22), residues: 1383 helix: 1.52 (0.43), residues: 150 sheet: 0.28 (0.26), residues: 369 loop : -1.90 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Z 863 HIS 0.010 0.001 HIS f 139 PHE 0.012 0.001 PHE Z 916 TYR 0.017 0.001 TYR z 146 ARG 0.004 0.000 ARG Z1042 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9403.68 seconds wall clock time: 166 minutes 38.81 seconds (9998.81 seconds total)