Starting phenix.real_space_refine on Sat Oct 11 02:02:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xck_38246/10_2025/8xck_38246.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xck_38246/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xck_38246/10_2025/8xck_38246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xck_38246/10_2025/8xck_38246.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xck_38246/10_2025/8xck_38246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xck_38246/10_2025/8xck_38246.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.60, per 1000 atoms: 0.24 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: 1.03 Conformation dependent library (CDL) restraints added in 358.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.47 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: 2.03 Time building geometry restraints manager: 1.35 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: 9.010 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.130 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.070 ------------------------------------------------------------------------------- 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 : 9.25 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (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 ARG 0.015 0.002 ARG z 72 TYR 0.050 0.011 TYR j 146 PHE 0.043 0.012 PHE F1113 TRP 0.020 0.006 TRP Z 859 HIS 0.010 0.003 HIS Z1028 Details of bonding type rmsd covalent geometry : bond 0.01560 (10872) covalent geometry : angle 1.66419 (14748) hydrogen bonds : bond 0.18670 ( 373) hydrogen bonds : angle 7.94628 ( 1056) *********************** 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 : 0.450 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: 0.6224 time to fit residues: 133.4919 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 : 0.421 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 126 GLN z 30 HIS z 174 GLN Z 869 GLN Z 911 ASN ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 943 ASN f 30 HIS ** f 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 943 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.162095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128581 restraints weight = 12728.545| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.42 r_work: 0.3248 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10872 Z= 0.156 Angle : 0.709 15.903 14748 Z= 0.369 Chirality : 0.049 0.196 1692 Planarity : 0.005 0.088 1932 Dihedral : 9.470 100.725 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 : 26.39 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.22), residues: 1383 helix: 1.11 (0.43), residues: 150 sheet: -0.04 (0.27), residues: 345 loop : -1.83 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J1090 TYR 0.017 0.001 TYR z 146 PHE 0.013 0.002 PHE J 916 TRP 0.005 0.001 TRP J 852 HIS 0.008 0.001 HIS f 139 Details of bonding type rmsd covalent geometry : bond 0.00345 (10872) covalent geometry : angle 0.70949 (14748) hydrogen bonds : bond 0.04736 ( 373) hydrogen bonds : angle 5.95687 ( 1056) *********************** 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 : 0.433 Fit side-chains REVERT: j 32 LEU cc_start: 0.6609 (mm) cc_final: 0.6290 (mm) REVERT: j 46 LYS cc_start: 0.7862 (mttp) cc_final: 0.7632 (OUTLIER) REVERT: j 160 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: z 160 ASP cc_start: 0.8017 (m-30) cc_final: 0.7658 (m-30) REVERT: z 187 LYS cc_start: 0.6475 (OUTLIER) cc_final: 0.5921 (ptpp) REVERT: f 143 ASP cc_start: 0.4665 (OUTLIER) cc_final: 0.4413 (t70) REVERT: f 187 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6653 (ttmm) outliers start: 63 outliers final: 23 residues processed: 198 average time/residue: 0.5645 time to fit residues: 120.6970 Evaluate side-chains 168 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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 143 ASP 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 66 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 90 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 123 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN J1008 GLN ** j 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 126 GLN z 30 HIS z 139 HIS z 174 GLN Z 922 GLN f 141 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.161817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125107 restraints weight = 12183.585| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.52 r_work: 0.3209 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10872 Z= 0.168 Angle : 0.700 16.011 14748 Z= 0.359 Chirality : 0.050 0.221 1692 Planarity : 0.006 0.089 1932 Dihedral : 8.241 78.464 1506 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 5.83 % Allowed : 26.56 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.22), residues: 1383 helix: 1.14 (0.43), residues: 150 sheet: 0.03 (0.27), residues: 345 loop : -1.90 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z1042 TYR 0.019 0.002 TYR z 146 PHE 0.013 0.002 PHE z 136 TRP 0.004 0.001 TRP Z 859 HIS 0.007 0.001 HIS f 139 Details of bonding type rmsd covalent geometry : bond 0.00384 (10872) covalent geometry : angle 0.69953 (14748) hydrogen bonds : bond 0.04390 ( 373) hydrogen bonds : angle 5.63007 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 151 time to evaluate : 0.409 Fit side-chains REVERT: j 32 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6433 (mm) REVERT: j 46 LYS cc_start: 0.7921 (mttp) cc_final: 0.7623 (tttp) REVERT: j 67 ASN cc_start: 0.8521 (t0) cc_final: 0.8236 (t0) REVERT: j 156 MET cc_start: 0.7715 (tpt) cc_final: 0.7081 (tpt) REVERT: j 160 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7164 (m-30) REVERT: z 46 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7499 (tttp) REVERT: z 187 LYS cc_start: 0.6433 (OUTLIER) cc_final: 0.6037 (ttmp) REVERT: Z 989 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7503 (mmt90) REVERT: Z 1077 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8397 (m) REVERT: Z 1085 ASP cc_start: 0.8485 (m-30) cc_final: 0.8245 (m-30) REVERT: Z 1129 ILE cc_start: 0.8747 (tt) cc_final: 0.8325 (tp) REVERT: f 46 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7606 (tttp) REVERT: f 160 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7111 (m-30) outliers start: 68 outliers final: 32 residues processed: 204 average time/residue: 0.5385 time to fit residues: 118.9349 Evaluate side-chains 186 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 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 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 1077 VAL 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 160 ASP Chi-restraints excluded: chain F residue 925 MET Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 989 ARG Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1062 LEU Chi-restraints excluded: chain F residue 1100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 89 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124620 restraints weight = 12272.596| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.54 r_work: 0.3207 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10872 Z= 0.177 Angle : 0.703 15.785 14748 Z= 0.359 Chirality : 0.050 0.179 1692 Planarity : 0.006 0.090 1932 Dihedral : 8.135 78.550 1502 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.34 % Favored : 89.59 % Rotamer: Outliers : 6.43 % Allowed : 26.65 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.22), residues: 1383 helix: 1.16 (0.43), residues: 150 sheet: 0.00 (0.27), residues: 345 loop : -1.93 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z1042 TYR 0.019 0.002 TYR z 146 PHE 0.014 0.002 PHE f 136 TRP 0.004 0.001 TRP Z 859 HIS 0.006 0.001 HIS f 139 Details of bonding type rmsd covalent geometry : bond 0.00407 (10872) covalent geometry : angle 0.70269 (14748) hydrogen bonds : bond 0.04209 ( 373) hydrogen bonds : angle 5.49895 ( 1056) *********************** 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 226 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 151 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: J 1125 GLN cc_start: 0.8947 (tp-100) cc_final: 0.8693 (tp-100) REVERT: j 32 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6531 (mm) REVERT: j 46 LYS cc_start: 0.7934 (mttp) cc_final: 0.7630 (tttp) REVERT: j 67 ASN cc_start: 0.8609 (t0) cc_final: 0.8358 (t0) REVERT: j 160 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7249 (m-30) REVERT: z 46 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7540 (tttp) REVERT: z 187 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6034 (ttmp) REVERT: Z 989 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7490 (mmt90) REVERT: Z 1085 ASP cc_start: 0.8516 (m-30) cc_final: 0.8272 (m-30) REVERT: Z 1129 ILE cc_start: 0.8787 (tt) cc_final: 0.8381 (tp) REVERT: f 46 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7615 (tttp) REVERT: f 160 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7106 (m-30) REVERT: F 929 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: F 1129 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8161 (tp) outliers start: 75 outliers final: 36 residues processed: 205 average time/residue: 0.5680 time to fit residues: 125.7945 Evaluate side-chains 191 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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 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 923 ILE 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 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 923 ILE Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 989 ARG Chi-restraints excluded: chain F residue 1062 LEU Chi-restraints excluded: chain F residue 1098 THR Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1129 ILE Chi-restraints excluded: chain F residue 1130 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 123 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 40 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.162229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126200 restraints weight = 12143.375| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.27 r_work: 0.3223 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1556 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= 0.158 Angle : 0.690 15.876 14748 Z= 0.350 Chirality : 0.050 0.272 1692 Planarity : 0.006 0.088 1932 Dihedral : 7.983 77.641 1501 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.14 % Favored : 88.79 % Rotamer: Outliers : 7.28 % Allowed : 26.05 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.22), residues: 1383 helix: 1.24 (0.43), residues: 150 sheet: 0.02 (0.27), residues: 345 loop : -1.94 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z1042 TYR 0.019 0.001 TYR z 146 PHE 0.012 0.002 PHE f 128 TRP 0.003 0.001 TRP F 859 HIS 0.002 0.001 HIS f 139 Details of bonding type rmsd covalent geometry : bond 0.00359 (10872) covalent geometry : angle 0.68969 (14748) hydrogen bonds : bond 0.03996 ( 373) hydrogen bonds : angle 5.39186 ( 1056) *********************** 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 237 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 152 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: J 988 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7876 (tp) REVERT: J 1125 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8665 (tp-100) REVERT: j 32 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6647 (mm) REVERT: j 46 LYS cc_start: 0.7973 (mttp) cc_final: 0.7641 (tttp) REVERT: j 156 MET cc_start: 0.7668 (tpt) cc_final: 0.7013 (tpt) REVERT: j 160 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7245 (m-30) REVERT: z 46 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7543 (tttp) REVERT: z 160 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7411 (m-30) REVERT: z 187 LYS cc_start: 0.6395 (OUTLIER) cc_final: 0.5991 (ttmp) REVERT: Z 989 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7376 (mmt90) REVERT: Z 1129 ILE cc_start: 0.8742 (tt) cc_final: 0.8542 (tp) REVERT: f 46 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7651 (tttp) REVERT: f 78 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.7402 (pp-130) REVERT: f 160 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: F 929 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: F 1129 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8120 (tp) outliers start: 85 outliers final: 42 residues processed: 217 average time/residue: 0.5337 time to fit residues: 125.7792 Evaluate side-chains 202 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 148 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 973 LEU Chi-restraints excluded: chain J residue 988 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 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 831 LEU Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 925 MET Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 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 57 VAL Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain f residue 160 ASP 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 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP 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 1129 ILE 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 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 67 optimal weight: 0.0050 chunk 2 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN J1008 GLN j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.162124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126190 restraints weight = 12337.122| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.24 r_work: 0.3226 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10872 Z= 0.172 Angle : 0.700 15.907 14748 Z= 0.355 Chirality : 0.050 0.278 1692 Planarity : 0.006 0.089 1932 Dihedral : 7.945 78.065 1499 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.92 % Favored : 89.01 % Rotamer: Outliers : 6.51 % Allowed : 26.82 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.22), residues: 1383 helix: 1.21 (0.43), residues: 150 sheet: 0.01 (0.27), residues: 345 loop : -1.94 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J1090 TYR 0.019 0.002 TYR z 146 PHE 0.013 0.002 PHE f 128 TRP 0.021 0.001 TRP Z 859 HIS 0.009 0.001 HIS z 139 Details of bonding type rmsd covalent geometry : bond 0.00395 (10872) covalent geometry : angle 0.69990 (14748) hydrogen bonds : bond 0.04033 ( 373) hydrogen bonds : angle 5.36109 ( 1056) *********************** 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 228 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 152 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: J 1125 GLN cc_start: 0.8939 (tp-100) cc_final: 0.8669 (tp-100) REVERT: j 32 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6626 (mm) REVERT: j 46 LYS cc_start: 0.7974 (mttp) cc_final: 0.7635 (tttp) REVERT: j 87 GLN cc_start: 0.6384 (OUTLIER) cc_final: 0.5937 (tt0) REVERT: j 156 MET cc_start: 0.7663 (tpt) cc_final: 0.7004 (tpt) REVERT: j 160 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: z 160 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7399 (m-30) REVERT: z 187 LYS cc_start: 0.6353 (OUTLIER) cc_final: 0.5935 (ttmp) REVERT: Z 859 TRP cc_start: 0.7295 (m-10) cc_final: 0.6755 (m100) REVERT: Z 1082 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8568 (tpp-160) REVERT: Z 1129 ILE cc_start: 0.8754 (tt) cc_final: 0.8469 (tp) REVERT: f 46 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7677 (tttp) REVERT: f 160 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7058 (m-30) REVERT: F 929 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: F 1060 LYS cc_start: 0.8903 (tttt) cc_final: 0.8595 (ttmt) REVERT: F 1099 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8607 (tp) REVERT: F 1129 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8112 (tp) outliers start: 76 outliers final: 48 residues processed: 211 average time/residue: 0.5656 time to fit residues: 129.0288 Evaluate side-chains 205 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 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 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 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 831 LEU Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 925 MET Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 988 LEU Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1053 THR Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1082 ARG Chi-restraints excluded: chain Z residue 1098 THR Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain F residue 850 LYS Chi-restraints excluded: chain F residue 871 LYS Chi-restraints excluded: chain F residue 886 ASP Chi-restraints excluded: chain F residue 923 ILE Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 1053 THR 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 1099 LEU Chi-restraints excluded: chain F residue 1129 ILE 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 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 9 optimal weight: 0.0270 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127646 restraints weight = 12100.097| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.13 r_work: 0.3229 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1697 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= 0.159 Angle : 0.696 15.967 14748 Z= 0.353 Chirality : 0.049 0.246 1692 Planarity : 0.006 0.089 1932 Dihedral : 7.911 77.427 1498 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 6.26 % Allowed : 27.68 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.22), residues: 1383 helix: 1.29 (0.43), residues: 150 sheet: 0.01 (0.27), residues: 345 loop : -1.92 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 142 TYR 0.018 0.001 TYR z 146 PHE 0.013 0.002 PHE Z 904 TRP 0.016 0.001 TRP Z 859 HIS 0.009 0.001 HIS z 139 Details of bonding type rmsd covalent geometry : bond 0.00363 (10872) covalent geometry : angle 0.69596 (14748) hydrogen bonds : bond 0.03921 ( 373) hydrogen bonds : angle 5.31970 ( 1056) *********************** 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 225 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 152 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: J 988 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7867 (tp) REVERT: J 1125 GLN cc_start: 0.8923 (tp-100) cc_final: 0.8669 (tp-100) REVERT: j 32 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6525 (mm) REVERT: j 46 LYS cc_start: 0.7974 (mttp) cc_final: 0.7640 (tttp) REVERT: j 87 GLN cc_start: 0.6366 (OUTLIER) cc_final: 0.5919 (tt0) REVERT: j 160 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7173 (m-30) REVERT: z 160 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: z 187 LYS cc_start: 0.6346 (OUTLIER) cc_final: 0.5948 (ttmp) REVERT: Z 859 TRP cc_start: 0.7335 (m-10) cc_final: 0.6786 (m100) REVERT: Z 1082 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8563 (tpp-160) REVERT: f 46 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7678 (tttp) REVERT: f 78 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.7398 (pp-130) REVERT: f 160 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: F 929 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7372 (m-80) REVERT: F 1060 LYS cc_start: 0.8914 (tttt) cc_final: 0.8612 (ttmt) REVERT: F 1099 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8610 (tp) REVERT: F 1129 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8091 (tp) outliers start: 73 outliers final: 43 residues processed: 204 average time/residue: 0.5452 time to fit residues: 120.5607 Evaluate side-chains 204 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 148 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 973 LEU Chi-restraints excluded: chain J residue 988 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 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 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 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 57 VAL Chi-restraints excluded: chain z residue 68 THR Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 160 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 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 1053 THR 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 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 160 ASP 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 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 1053 THR 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 1099 LEU Chi-restraints excluded: chain F residue 1129 ILE Chi-restraints excluded: chain F residue 1130 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 46 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 55 optimal weight: 0.0050 chunk 68 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 overall best weight: 0.2394 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.165230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130922 restraints weight = 12725.208| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.22 r_work: 0.3303 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10872 Z= 0.119 Angle : 0.660 15.643 14748 Z= 0.334 Chirality : 0.048 0.249 1692 Planarity : 0.005 0.085 1932 Dihedral : 7.574 74.020 1497 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 4.88 % Allowed : 29.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.22), residues: 1383 helix: 1.50 (0.43), residues: 150 sheet: 0.15 (0.26), residues: 369 loop : -1.95 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z1042 TYR 0.016 0.001 TYR z 146 PHE 0.011 0.001 PHE f 128 TRP 0.012 0.001 TRP Z 859 HIS 0.008 0.001 HIS z 139 Details of bonding type rmsd covalent geometry : bond 0.00260 (10872) covalent geometry : angle 0.65961 (14748) hydrogen bonds : bond 0.03550 ( 373) hydrogen bonds : angle 5.17725 ( 1056) *********************** 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 213 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 156 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 989 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6470 (mmm160) REVERT: J 1098 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8749 (m) REVERT: j 32 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6427 (mm) REVERT: j 46 LYS cc_start: 0.7852 (mttp) cc_final: 0.7556 (tttp) REVERT: j 87 GLN cc_start: 0.6281 (OUTLIER) cc_final: 0.5818 (tt0) REVERT: j 160 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7071 (m-30) REVERT: z 160 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: z 187 LYS cc_start: 0.6240 (OUTLIER) cc_final: 0.5940 (ttmp) REVERT: Z 859 TRP cc_start: 0.7222 (m-10) cc_final: 0.6751 (m100) REVERT: Z 989 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6906 (mmm160) REVERT: Z 1082 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8502 (tpp-160) REVERT: f 46 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7620 (tttp) REVERT: f 160 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.6923 (m-30) REVERT: F 929 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: F 1060 LYS cc_start: 0.8846 (tttt) cc_final: 0.8552 (ttmt) REVERT: F 1099 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8590 (tp) outliers start: 57 outliers final: 30 residues processed: 197 average time/residue: 0.5747 time to fit residues: 122.0181 Evaluate side-chains 188 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1098 THR Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain J residue 1115 SER Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 87 GLN Chi-restraints excluded: chain j residue 138 ASP Chi-restraints excluded: chain j residue 141 GLN Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 68 THR Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 143 ASP Chi-restraints excluded: chain z residue 160 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 831 LEU Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 871 LYS Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1082 ARG Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain 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 850 LYS Chi-restraints excluded: chain F residue 871 LYS Chi-restraints excluded: chain F residue 886 ASP Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1099 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.0670 chunk 79 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 0.0020 chunk 131 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 44 optimal weight: 0.0060 overall best weight: 0.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN J1008 GLN j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN f 139 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.166228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132838 restraints weight = 12714.511| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.25 r_work: 0.3312 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10872 Z= 0.120 Angle : 0.660 15.305 14748 Z= 0.334 Chirality : 0.048 0.267 1692 Planarity : 0.005 0.083 1932 Dihedral : 7.332 72.985 1493 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 4.37 % Allowed : 30.25 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.22), residues: 1383 helix: 1.62 (0.43), residues: 150 sheet: 0.23 (0.26), residues: 369 loop : -1.92 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z1042 TYR 0.016 0.001 TYR z 146 PHE 0.010 0.001 PHE f 128 TRP 0.009 0.001 TRP Z 859 HIS 0.010 0.001 HIS f 139 Details of bonding type rmsd covalent geometry : bond 0.00263 (10872) covalent geometry : angle 0.65989 (14748) hydrogen bonds : bond 0.03492 ( 373) hydrogen bonds : angle 5.09580 ( 1056) *********************** 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 202 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 989 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6484 (mmm160) REVERT: J 1098 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8751 (m) REVERT: j 32 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6377 (mm) REVERT: j 46 LYS cc_start: 0.7838 (mttp) cc_final: 0.7538 (tttp) REVERT: j 87 GLN cc_start: 0.6284 (OUTLIER) cc_final: 0.5819 (tt0) REVERT: j 160 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7071 (m-30) REVERT: z 160 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: z 187 LYS cc_start: 0.6163 (OUTLIER) cc_final: 0.5891 (ttmp) REVERT: Z 859 TRP cc_start: 0.7240 (m-10) cc_final: 0.6769 (m100) REVERT: Z 989 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6940 (mmm160) REVERT: Z 1082 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8534 (tpp-160) REVERT: f 78 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7055 (pp-130) REVERT: f 160 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.6865 (m-30) REVERT: F 929 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: F 1060 LYS cc_start: 0.8862 (tttt) cc_final: 0.8550 (ttmt) REVERT: F 1103 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7646 (mtp85) outliers start: 51 outliers final: 26 residues processed: 192 average time/residue: 0.5917 time to fit residues: 122.1828 Evaluate side-chains 187 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 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 87 GLN Chi-restraints excluded: chain j residue 138 ASP Chi-restraints excluded: chain j residue 141 GLN Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain z residue 68 THR Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 160 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 831 LEU Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1082 ARG Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain f residue 160 ASP 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 1062 LEU 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 11 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 chunk 120 optimal weight: 0.0980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.165959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131665 restraints weight = 12665.669| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.17 r_work: 0.3317 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10872 Z= 0.130 Angle : 0.672 15.367 14748 Z= 0.339 Chirality : 0.049 0.269 1692 Planarity : 0.005 0.084 1932 Dihedral : 7.324 73.269 1493 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 3.94 % Allowed : 30.68 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.22), residues: 1383 helix: 1.56 (0.43), residues: 150 sheet: 0.25 (0.26), residues: 369 loop : -1.92 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z1042 TYR 0.017 0.001 TYR z 146 PHE 0.011 0.001 PHE f 128 TRP 0.008 0.001 TRP Z 859 HIS 0.010 0.001 HIS f 139 Details of bonding type rmsd covalent geometry : bond 0.00288 (10872) covalent geometry : angle 0.67196 (14748) hydrogen bonds : bond 0.03577 ( 373) hydrogen bonds : angle 5.08265 ( 1056) ********************** 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 192 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 989 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6485 (mmm160) REVERT: J 1098 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8749 (m) REVERT: j 32 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6330 (mm) REVERT: j 46 LYS cc_start: 0.7830 (mttp) cc_final: 0.7547 (tttp) REVERT: j 87 GLN cc_start: 0.6273 (OUTLIER) cc_final: 0.5819 (tt0) REVERT: j 143 ASP cc_start: 0.3390 (OUTLIER) cc_final: 0.3178 (t70) REVERT: j 160 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7088 (m-30) REVERT: z 160 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: z 187 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5869 (ttmp) REVERT: Z 859 TRP cc_start: 0.7248 (m-10) cc_final: 0.6767 (m100) REVERT: Z 989 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6863 (mmm160) REVERT: Z 1082 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8540 (tpp-160) REVERT: f 46 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7510 (tttp) REVERT: f 78 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7084 (pp-130) REVERT: f 160 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.6872 (m-30) REVERT: F 929 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: F 1060 LYS cc_start: 0.8842 (tttt) cc_final: 0.8542 (ttmt) outliers start: 46 outliers final: 26 residues processed: 183 average time/residue: 0.6235 time to fit residues: 122.4829 Evaluate side-chains 182 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 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 87 GLN Chi-restraints excluded: chain j residue 138 ASP Chi-restraints excluded: chain j residue 141 GLN Chi-restraints excluded: chain j residue 143 ASP Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain z residue 68 THR Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 160 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 831 LEU Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1082 ARG Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain F residue 850 LYS 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 1062 LEU 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 18 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 119 optimal weight: 0.0980 chunk 109 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 45 optimal weight: 0.0070 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 overall best weight: 0.3198 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.166109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131915 restraints weight = 12843.266| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.28 r_work: 0.3315 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10872 Z= 0.130 Angle : 0.685 15.349 14748 Z= 0.344 Chirality : 0.049 0.267 1692 Planarity : 0.005 0.083 1932 Dihedral : 7.291 73.326 1493 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 4.11 % Allowed : 30.42 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.22), residues: 1383 helix: 1.51 (0.43), residues: 150 sheet: 0.23 (0.26), residues: 369 loop : -1.91 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 142 TYR 0.017 0.001 TYR z 146 PHE 0.011 0.001 PHE f 128 TRP 0.008 0.001 TRP Z 859 HIS 0.006 0.001 HIS f 139 Details of bonding type rmsd covalent geometry : bond 0.00289 (10872) covalent geometry : angle 0.68533 (14748) hydrogen bonds : bond 0.03568 ( 373) hydrogen bonds : angle 5.06797 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4977.89 seconds wall clock time: 85 minutes 30.39 seconds (5130.39 seconds total)