Starting phenix.real_space_refine on Mon Jul 28 22:09:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xck_38246/07_2025/8xck_38246.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xck_38246/07_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_38246/07_2025/8xck_38246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xck_38246/07_2025/8xck_38246.map" model { file = "/net/cci-nas-00/data/ceres_data/8xck_38246/07_2025/8xck_38246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xck_38246/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.13, per 1000 atoms: 0.76 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: 2.50 Conformation dependent library (CDL) restraints added in 1.2 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: 1.73 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: 3.68 Time building geometry restraints manager: 3.02 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: 212.450 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.960 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 255.550 ------------------------------------------------------------------------------- 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= 1.114 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 Details of bonding type rmsd hydrogen bonds : bond 0.18670 ( 373) hydrogen bonds : angle 7.94628 ( 1056) covalent geometry : bond 0.01560 (10872) covalent geometry : angle 1.66419 (14748) *********************** 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 : 1.119 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: 1.2312 time to fit residues: 264.6566 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 : 1.283 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.161493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127966 restraints weight = 12688.149| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.46 r_work: 0.3236 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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= 0.165 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 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 373) hydrogen bonds : angle 5.94475 ( 1056) covalent geometry : bond 0.00373 (10872) covalent geometry : angle 0.71742 (14748) *********************** 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 : 1.438 Fit side-chains REVERT: j 32 LEU cc_start: 0.6619 (mm) cc_final: 0.6307 (mm) REVERT: j 46 LYS cc_start: 0.7857 (mttp) cc_final: 0.7631 (OUTLIER) REVERT: j 156 MET cc_start: 0.7718 (tpt) cc_final: 0.7062 (tpt) REVERT: j 160 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: z 160 ASP cc_start: 0.8043 (m-30) cc_final: 0.7665 (m-30) REVERT: z 187 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.5940 (ptpp) REVERT: f 187 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6686 (ttmm) outliers start: 63 outliers final: 24 residues processed: 197 average time/residue: 1.2953 time to fit residues: 276.5535 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 : 1.152 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 z 174 GLN Z 922 GLN f 141 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.161056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124136 restraints weight = 12189.653| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.56 r_work: 0.3197 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10872 Z= 0.187 Angle : 0.714 16.064 14748 Z= 0.367 Chirality : 0.051 0.185 1692 Planarity : 0.006 0.091 1932 Dihedral : 8.354 79.452 1506 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % 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: -1.58 (0.22), residues: 1383 helix: 1.06 (0.43), residues: 150 sheet: -0.08 (0.27), residues: 351 loop : -1.96 (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 0.014 0.002 PHE z 136 TYR 0.020 0.002 TYR z 146 ARG 0.007 0.000 ARG Z1042 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 373) hydrogen bonds : angle 5.64322 ( 1056) covalent geometry : bond 0.00434 (10872) covalent geometry : angle 0.71447 (14748) *********************** 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 218 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 148 time to evaluate : 1.197 Fit side-chains REVERT: j 32 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6513 (mm) REVERT: j 46 LYS cc_start: 0.7924 (mttp) cc_final: 0.7621 (tttp) REVERT: j 67 ASN cc_start: 0.8518 (t0) cc_final: 0.8238 (t0) REVERT: j 156 MET cc_start: 0.7711 (tpt) cc_final: 0.7071 (tpt) REVERT: j 160 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: z 46 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7511 (tttp) REVERT: z 187 LYS cc_start: 0.6478 (OUTLIER) cc_final: 0.6063 (ttmp) REVERT: Z 989 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7513 (mmt90) REVERT: Z 1077 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8414 (m) REVERT: Z 1085 ASP cc_start: 0.8491 (m-30) cc_final: 0.8248 (m-30) REVERT: Z 1129 ILE cc_start: 0.8768 (tt) cc_final: 0.8352 (tp) REVERT: f 46 LYS cc_start: 0.7923 (mtmt) cc_final: 0.7578 (tttp) REVERT: f 120 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7645 (mttp) REVERT: f 160 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7111 (m-30) REVERT: f 161 LYS cc_start: 0.6635 (tmtt) cc_final: 0.6162 (tmtt) outliers start: 70 outliers final: 32 residues processed: 203 average time/residue: 1.1190 time to fit residues: 246.9033 Evaluate side-chains 187 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 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 125 SER Chi-restraints excluded: chain f residue 160 ASP 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 1062 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1130 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 80 optimal weight: 0.2980 chunk 66 optimal weight: 0.0870 chunk 31 optimal weight: 0.0470 chunk 9 optimal weight: 0.3980 chunk 76 optimal weight: 0.0980 chunk 110 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 0.1856 ------------------------------------------------------------------------------- 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 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 = 0.3895 r_free = 0.3895 target = 0.164830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129638 restraints weight = 12179.652| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.12 r_work: 0.3277 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10872 Z= 0.116 Angle : 0.649 15.436 14748 Z= 0.331 Chirality : 0.048 0.237 1692 Planarity : 0.005 0.083 1932 Dihedral : 7.719 74.732 1502 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 4.80 % Allowed : 28.02 % Favored : 67.18 % 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: -1.43 (0.22), residues: 1383 helix: 1.35 (0.43), residues: 150 sheet: -0.08 (0.25), residues: 405 loop : -1.95 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 859 HIS 0.005 0.001 HIS f 139 PHE 0.013 0.001 PHE F 916 TYR 0.014 0.001 TYR z 146 ARG 0.006 0.000 ARG Z1042 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 373) hydrogen bonds : angle 5.38954 ( 1056) covalent geometry : bond 0.00244 (10872) covalent geometry : angle 0.64910 (14748) *********************** 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 213 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 1.878 Fit side-chains REVERT: j 32 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6500 (mm) REVERT: j 46 LYS cc_start: 0.7897 (mttp) cc_final: 0.7597 (tttp) REVERT: j 67 ASN cc_start: 0.8587 (t0) cc_final: 0.8345 (t0) REVERT: j 156 MET cc_start: 0.7722 (tpt) cc_final: 0.7122 (tpt) REVERT: j 160 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7130 (m-30) REVERT: z 46 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7485 (tttp) REVERT: z 187 LYS cc_start: 0.6238 (OUTLIER) cc_final: 0.5858 (ttmp) REVERT: Z 989 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7305 (mmt90) REVERT: Z 1085 ASP cc_start: 0.8447 (m-30) cc_final: 0.8243 (m-30) REVERT: Z 1129 ILE cc_start: 0.8411 (tt) cc_final: 0.8027 (tp) REVERT: f 46 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7660 (tttp) REVERT: F 929 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7472 (m-80) outliers start: 56 outliers final: 22 residues processed: 200 average time/residue: 1.2928 time to fit residues: 279.3763 Evaluate side-chains 174 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU 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 85 THR Chi-restraints excluded: chain j residue 138 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 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 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 125 SER 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 1100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 106 optimal weight: 0.0010 chunk 72 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 80 optimal weight: 0.0060 overall best weight: 0.4202 ------------------------------------------------------------------------------- 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 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 = 0.3885 r_free = 0.3885 target = 0.163795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128404 restraints weight = 12108.160| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.06 r_work: 0.3263 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1655 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= 0.144 Angle : 0.668 15.444 14748 Z= 0.339 Chirality : 0.049 0.267 1692 Planarity : 0.005 0.084 1932 Dihedral : 7.571 75.703 1496 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 5.40 % Allowed : 27.85 % Favored : 66.75 % 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: -1.37 (0.22), residues: 1383 helix: 1.38 (0.43), residues: 150 sheet: 0.16 (0.28), residues: 345 loop : -1.89 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Z 859 HIS 0.002 0.001 HIS f 139 PHE 0.012 0.002 PHE f 128 TYR 0.020 0.001 TYR z 146 ARG 0.005 0.000 ARG Z1042 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 373) hydrogen bonds : angle 5.30023 ( 1056) covalent geometry : bond 0.00324 (10872) covalent geometry : angle 0.66805 (14748) *********************** 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 211 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 148 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: j 32 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6502 (mm) REVERT: j 46 LYS cc_start: 0.7914 (mttp) cc_final: 0.7603 (tttp) REVERT: j 156 MET cc_start: 0.7769 (tpt) cc_final: 0.7043 (tpt) REVERT: j 160 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: z 46 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7617 (tttp) REVERT: z 160 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: z 187 LYS cc_start: 0.6264 (OUTLIER) cc_final: 0.5878 (ttmp) REVERT: Z 989 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7374 (mmt90) REVERT: f 46 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7693 (tttp) REVERT: f 78 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.7378 (pp-130) REVERT: f 161 LYS cc_start: 0.6607 (tmtt) cc_final: 0.6239 (tmtt) REVERT: F 929 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: F 1060 LYS cc_start: 0.8888 (tttt) cc_final: 0.8581 (ttmt) outliers start: 63 outliers final: 32 residues processed: 193 average time/residue: 1.1686 time to fit residues: 244.6930 Evaluate side-chains 184 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 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 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 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 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 1098 THR 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: 0.0370 chunk 109 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128163 restraints weight = 12217.585| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.14 r_work: 0.3248 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1698 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= 0.151 Angle : 0.671 15.603 14748 Z= 0.341 Chirality : 0.049 0.230 1692 Planarity : 0.005 0.085 1932 Dihedral : 7.545 76.073 1494 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 5.91 % Allowed : 27.68 % Favored : 66.41 % 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: 1.38 (0.43), residues: 150 sheet: 0.14 (0.28), residues: 345 loop : -1.89 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Z 859 HIS 0.008 0.001 HIS z 139 PHE 0.012 0.002 PHE f 128 TYR 0.019 0.001 TYR z 146 ARG 0.004 0.000 ARG J1090 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 373) hydrogen bonds : angle 5.27710 ( 1056) covalent geometry : bond 0.00345 (10872) covalent geometry : angle 0.67108 (14748) *********************** 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 218 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 149 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: J 989 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6739 (mmm160) REVERT: j 32 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6460 (mm) REVERT: j 46 LYS cc_start: 0.7950 (mttp) cc_final: 0.7619 (tttp) REVERT: j 156 MET cc_start: 0.7801 (tpt) cc_final: 0.7198 (tpt) REVERT: j 160 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: z 46 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7699 (tttp) REVERT: z 160 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: z 187 LYS cc_start: 0.6244 (OUTLIER) cc_final: 0.5888 (ttmp) REVERT: Z 859 TRP cc_start: 0.7261 (m-10) cc_final: 0.6778 (m100) REVERT: Z 1082 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8551 (tpp-160) REVERT: f 46 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7687 (tttp) REVERT: f 78 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.7401 (pp-130) REVERT: F 929 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: F 1060 LYS cc_start: 0.8899 (tttt) cc_final: 0.8596 (ttmt) outliers start: 69 outliers final: 40 residues processed: 200 average time/residue: 1.1915 time to fit residues: 258.2450 Evaluate side-chains 192 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 142 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 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 32 LEU Chi-restraints excluded: chain z residue 46 LYS 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 871 LYS 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 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 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 871 LYS Chi-restraints excluded: chain F residue 886 ASP Chi-restraints excluded: chain F residue 923 ILE 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 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: 0.0470 chunk 72 optimal weight: 0.9980 chunk 62 optimal weight: 0.0970 chunk 34 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 chunk 7 optimal weight: 0.0170 chunk 105 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.0712 ------------------------------------------------------------------------------- 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 z 174 GLN f 141 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134776 restraints weight = 12372.760| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.05 r_work: 0.3360 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10872 Z= 0.108 Angle : 0.628 14.818 14748 Z= 0.318 Chirality : 0.047 0.272 1692 Planarity : 0.005 0.077 1932 Dihedral : 7.055 70.064 1494 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 3.94 % Allowed : 29.82 % Favored : 66.24 % 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: -1.33 (0.22), residues: 1383 helix: 1.71 (0.44), residues: 150 sheet: 0.17 (0.28), residues: 342 loop : -1.91 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 859 HIS 0.005 0.001 HIS z 139 PHE 0.018 0.001 PHE Z 916 TYR 0.014 0.001 TYR f 146 ARG 0.005 0.000 ARG f 142 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 373) hydrogen bonds : angle 5.09626 ( 1056) covalent geometry : bond 0.00225 (10872) covalent geometry : angle 0.62787 (14748) *********************** 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 201 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 989 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6601 (mmm160) REVERT: j 32 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6320 (mm) REVERT: j 46 LYS cc_start: 0.7847 (mttp) cc_final: 0.7537 (tttp) REVERT: z 160 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: z 187 LYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5792 (ttmp) REVERT: Z 859 TRP cc_start: 0.7101 (m-10) cc_final: 0.6821 (m100) REVERT: Z 1082 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8417 (tpp-160) REVERT: Z 1129 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7332 (tp) REVERT: F 929 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: F 1060 LYS cc_start: 0.8830 (tttt) cc_final: 0.8529 (ttmt) REVERT: F 1082 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8458 (tpp80) outliers start: 46 outliers final: 16 residues processed: 192 average time/residue: 1.4799 time to fit residues: 307.1400 Evaluate side-chains 168 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 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 138 ASP Chi-restraints excluded: chain j residue 141 GLN Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 32 LEU 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 1077 VAL 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 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP 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: 2.9990 chunk 87 optimal weight: 0.0670 chunk 3 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127926 restraints weight = 12105.371| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.23 r_work: 0.3253 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10872 Z= 0.171 Angle : 0.698 15.475 14748 Z= 0.352 Chirality : 0.050 0.274 1692 Planarity : 0.005 0.084 1932 Dihedral : 7.334 75.325 1490 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 4.37 % Allowed : 29.82 % Favored : 65.81 % 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: -1.27 (0.22), residues: 1383 helix: 1.53 (0.44), residues: 150 sheet: 0.26 (0.28), residues: 345 loop : -1.85 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 859 HIS 0.008 0.001 HIS z 139 PHE 0.012 0.002 PHE f 128 TYR 0.019 0.002 TYR z 146 ARG 0.004 0.000 ARG J1090 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 373) hydrogen bonds : angle 5.16728 ( 1056) covalent geometry : bond 0.00396 (10872) covalent geometry : angle 0.69799 (14748) *********************** 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 204 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: J 989 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6640 (mmm160) REVERT: j 32 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6411 (mm) REVERT: j 46 LYS cc_start: 0.7878 (mttp) cc_final: 0.7557 (tttp) REVERT: j 87 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.5920 (tp40) REVERT: j 143 ASP cc_start: 0.3530 (OUTLIER) cc_final: 0.3282 (t70) REVERT: j 160 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.6753 (m-30) REVERT: z 160 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: z 187 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5924 (ttmp) REVERT: Z 859 TRP cc_start: 0.7351 (m-10) cc_final: 0.6837 (m100) REVERT: Z 989 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7053 (mmm160) REVERT: Z 1082 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8554 (tpp-160) REVERT: f 78 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.7223 (pp-130) REVERT: F 929 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: F 1060 LYS cc_start: 0.8900 (tttt) cc_final: 0.8585 (ttmt) outliers start: 51 outliers final: 23 residues processed: 188 average time/residue: 1.2761 time to fit residues: 258.6352 Evaluate side-chains 184 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 925 MET Chi-restraints excluded: chain J residue 929 PHE Chi-restraints excluded: chain J residue 937 THR 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 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 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 831 LEU 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 102 optimal weight: 0.9990 chunk 7 optimal weight: 0.0670 chunk 110 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 119 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 141 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.164497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.128811 restraints weight = 12272.863| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.17 r_work: 0.3266 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1924 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= 0.148 Angle : 0.690 15.397 14748 Z= 0.348 Chirality : 0.050 0.267 1692 Planarity : 0.005 0.084 1932 Dihedral : 7.404 75.401 1490 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 4.20 % Allowed : 29.99 % Favored : 65.81 % 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: -1.27 (0.22), residues: 1383 helix: 1.50 (0.44), residues: 150 sheet: 0.24 (0.26), residues: 369 loop : -1.89 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 859 HIS 0.010 0.001 HIS f 139 PHE 0.012 0.002 PHE f 128 TYR 0.019 0.001 TYR z 146 ARG 0.004 0.000 ARG Z1042 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 373) hydrogen bonds : angle 5.16167 ( 1056) covalent geometry : bond 0.00335 (10872) covalent geometry : angle 0.68976 (14748) *********************** 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 194 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: J 989 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6596 (mmm160) REVERT: j 32 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6392 (mm) REVERT: j 46 LYS cc_start: 0.7884 (mttp) cc_final: 0.7574 (tttp) REVERT: j 87 GLN cc_start: 0.6366 (OUTLIER) cc_final: 0.5911 (tp40) REVERT: j 143 ASP cc_start: 0.3485 (OUTLIER) cc_final: 0.3238 (t70) REVERT: j 160 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6659 (m-30) REVERT: z 160 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: z 187 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5907 (ttmp) REVERT: Z 859 TRP cc_start: 0.7296 (m-10) cc_final: 0.6820 (m100) REVERT: Z 989 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6985 (mmm160) REVERT: Z 1082 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8548 (tpp-160) REVERT: Z 1127 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6523 (tp) REVERT: f 46 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7563 (tttp) REVERT: F 929 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: F 1060 LYS cc_start: 0.8889 (tttt) cc_final: 0.8579 (ttmt) outliers start: 49 outliers final: 23 residues processed: 180 average time/residue: 1.2692 time to fit residues: 246.3615 Evaluate side-chains 181 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 989 ARG Chi-restraints excluded: chain J residue 1059 LEU 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 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 53 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 989 ARG Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1082 ARG 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 871 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 9 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 108 optimal weight: 0.0970 chunk 30 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.164455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129937 restraints weight = 12744.013| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.32 r_work: 0.3293 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1940 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= 0.151 Angle : 0.694 15.526 14748 Z= 0.350 Chirality : 0.050 0.276 1692 Planarity : 0.005 0.084 1932 Dihedral : 7.392 75.797 1490 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 3.68 % Allowed : 30.59 % Favored : 65.72 % 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: -1.28 (0.22), residues: 1383 helix: 1.48 (0.44), residues: 150 sheet: 0.21 (0.26), residues: 369 loop : -1.89 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 859 HIS 0.007 0.001 HIS f 139 PHE 0.012 0.002 PHE f 128 TYR 0.019 0.001 TYR z 146 ARG 0.004 0.000 ARG Z1042 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 373) hydrogen bonds : angle 5.15496 ( 1056) covalent geometry : bond 0.00343 (10872) covalent geometry : angle 0.69443 (14748) ********************** 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 190 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: J 989 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6581 (mmm160) REVERT: J 1046 ARG cc_start: 0.6621 (mtm180) cc_final: 0.5636 (mpt-90) REVERT: j 32 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6368 (mm) REVERT: j 46 LYS cc_start: 0.7845 (mttp) cc_final: 0.7563 (tttp) REVERT: j 87 GLN cc_start: 0.6351 (OUTLIER) cc_final: 0.5901 (tp40) REVERT: j 143 ASP cc_start: 0.3518 (OUTLIER) cc_final: 0.3270 (t70) REVERT: j 160 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.6679 (m-30) REVERT: z 60 VAL cc_start: 0.7545 (t) cc_final: 0.7144 (t) REVERT: z 160 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7305 (m-30) REVERT: z 161 LYS cc_start: 0.6708 (tmtt) cc_final: 0.6460 (tmtt) REVERT: z 187 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5871 (ttmp) REVERT: Z 859 TRP cc_start: 0.7280 (m-10) cc_final: 0.6791 (m100) REVERT: Z 989 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6916 (mmm160) REVERT: f 46 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7520 (tttp) REVERT: f 120 LYS cc_start: 0.7839 (mptt) cc_final: 0.7274 (mttm) REVERT: F 929 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: F 1060 LYS cc_start: 0.8853 (tttt) cc_final: 0.8554 (ttmt) outliers start: 43 outliers final: 22 residues processed: 177 average time/residue: 1.5697 time to fit residues: 299.7274 Evaluate side-chains 181 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 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 53 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 989 ARG Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 108 optimal weight: 0.0030 chunk 11 optimal weight: 0.2980 chunk 129 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 114 optimal weight: 0.0970 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.2586 ------------------------------------------------------------------------------- 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 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.166635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132545 restraints weight = 12754.358| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.22 r_work: 0.3327 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2105 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= 0.121 Angle : 0.665 15.131 14748 Z= 0.335 Chirality : 0.049 0.264 1692 Planarity : 0.005 0.081 1932 Dihedral : 7.180 73.130 1490 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 3.17 % Allowed : 31.19 % Favored : 65.64 % 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: -1.22 (0.22), residues: 1383 helix: 1.60 (0.43), residues: 150 sheet: 0.28 (0.26), residues: 369 loop : -1.88 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 859 HIS 0.008 0.001 HIS f 139 PHE 0.010 0.001 PHE Z 916 TYR 0.016 0.001 TYR z 146 ARG 0.004 0.000 ARG Z1042 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 373) hydrogen bonds : angle 5.05374 ( 1056) covalent geometry : bond 0.00265 (10872) covalent geometry : angle 0.66505 (14748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11580.66 seconds wall clock time: 208 minutes 9.11 seconds (12489.11 seconds total)