Starting phenix.real_space_refine on Wed Jun 26 18:51:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xck_38246/06_2024/8xck_38246.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xck_38246/06_2024/8xck_38246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xck_38246/06_2024/8xck_38246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xck_38246/06_2024/8xck_38246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xck_38246/06_2024/8xck_38246.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xck_38246/06_2024/8xck_38246.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6717 2.51 5 N 1851 2.21 5 O 2061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J GLU 868": "OE1" <-> "OE2" Residue "J PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 961": "OD1" <-> "OD2" Residue "J GLU 1075": "OE1" <-> "OE2" Residue "j PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 86": "OE1" <-> "OE2" Residue "j ASP 102": "OD1" <-> "OD2" Residue "j ASP 133": "OD1" <-> "OD2" Residue "j ASP 143": "OD1" <-> "OD2" Residue "j ASP 157": "OD1" <-> "OD2" Residue "j ASP 169": "OD1" <-> "OD2" Residue "z GLU 41": "OE1" <-> "OE2" Residue "z ASP 58": "OD1" <-> "OD2" Residue "z PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 133": "OD1" <-> "OD2" Residue "z ASP 138": "OD1" <-> "OD2" Residue "Z TYR 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 1075": "OE1" <-> "OE2" Residue "f ASP 58": "OD1" <-> "OD2" Residue "f PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 86": "OE1" <-> "OE2" Residue "f ASP 160": "OD1" <-> "OD2" Residue "F ASP 927": "OD1" <-> "OD2" Residue "F ASP 961": "OD1" <-> "OD2" Residue "F TYR 1054": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1085": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 10671 Number of models: 1 Model: "" Number of chains: 6 Chain: "J" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2323 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain: "j" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1234 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "z" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1234 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "Z" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2323 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain: "f" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1234 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2323 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Time building chain proxies: 7.91, per 1000 atoms: 0.74 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 1.8 seconds 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 34 sheets defined 13.8% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 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: 4.28 Time building geometry restraints manager: 4.36 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: 96.13 - 103.71: 134 103.71 - 111.30: 3790 111.30 - 118.88: 5602 118.88 - 126.47: 5120 126.47 - 134.05: 102 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 2.520 nonbonded pdb=" OD2 ASP Z1085 " pdb=" NZ LYS Z1124 " model vdw 2.273 2.520 nonbonded pdb=" OE1 GLN J 919 " pdb=" NH2 ARG F 932 " model vdw 2.285 2.520 nonbonded pdb=" OG SER F1011 " pdb=" N SER F1012 " model vdw 2.286 2.520 nonbonded pdb=" O ASP j 119 " pdb=" OG SER j 122 " model vdw 2.287 2.440 ... (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 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: 5.060 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: 22.760 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.910 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.162 10872 Z= 1.026 Angle : 1.664 9.002 14748 Z= 1.163 Chirality : 0.099 0.384 1692 Planarity : 0.009 0.098 1932 Dihedral : 18.704 89.671 3975 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.51 % Allowed : 11.35 % Favored : 88.14 % Rotamer: Outliers : 5.40 % Allowed : 25.96 % Favored : 68.64 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.21), residues: 1383 helix: 0.55 (0.40), residues: 150 sheet: 0.02 (0.27), residues: 351 loop : -2.01 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.006 TRP Z 859 HIS 0.010 0.003 HIS Z1028 PHE 0.043 0.012 PHE F1113 TYR 0.050 0.011 TYR j 146 ARG 0.015 0.002 ARG z 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 153 time to evaluate : 1.133 Fit side-chains REVERT: J 846 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6817 (pp20) REVERT: J 853 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.6972 (tptt) REVERT: J 862 MET cc_start: 0.8832 (tpp) cc_final: 0.8545 (tpp) REVERT: j 46 LYS cc_start: 0.8192 (mttp) cc_final: 0.7777 (tmmm) REVERT: j 156 MET cc_start: 0.7621 (tpt) cc_final: 0.7049 (tpt) REVERT: j 160 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: j 187 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6540 (ttmm) REVERT: z 58 ASP cc_start: 0.7863 (m-30) cc_final: 0.7574 (m-30) REVERT: z 98 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7877 (mptm) REVERT: z 187 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6520 (ttmp) REVERT: f 46 LYS cc_start: 0.8352 (mtmt) cc_final: 0.7689 (tttp) REVERT: f 160 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: f 187 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6771 (ttmm) REVERT: F 991 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8197 (pm20) outliers start: 63 outliers final: 30 residues processed: 200 average time/residue: 1.1732 time to fit residues: 252.6982 Evaluate side-chains 179 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 853 LYS Chi-restraints excluded: chain J residue 856 SER Chi-restraints excluded: chain J residue 925 MET Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 974 SER Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1098 THR Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain J residue 1130 SER Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain j residue 187 LYS Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain z residue 98 LYS Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 856 SER Chi-restraints excluded: chain Z residue 925 MET Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 974 SER Chi-restraints excluded: chain Z residue 989 ARG Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 187 LYS Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain F residue 856 SER Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 974 SER Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 989 ARG Chi-restraints excluded: chain F residue 991 GLU Chi-restraints excluded: chain F residue 1100 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 0.0060 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 HIS ** f 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 89 GLN ** f 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10872 Z= 0.264 Angle : 0.701 15.708 14748 Z= 0.363 Chirality : 0.050 0.202 1692 Planarity : 0.005 0.092 1932 Dihedral : 9.481 88.570 1547 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.91 % Favored : 89.88 % Rotamer: Outliers : 5.74 % Allowed : 26.99 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.22), residues: 1383 helix: 1.08 (0.43), residues: 150 sheet: -0.32 (0.26), residues: 381 loop : -1.87 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 852 HIS 0.007 0.001 HIS f 139 PHE 0.014 0.002 PHE f 128 TYR 0.019 0.002 TYR z 146 ARG 0.004 0.000 ARG J1090 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 152 time to evaluate : 1.182 Fit side-chains REVERT: J 981 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8058 (p0) REVERT: J 999 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8266 (mtpp) REVERT: j 32 LEU cc_start: 0.6706 (mm) cc_final: 0.6452 (mm) REVERT: j 46 LYS cc_start: 0.8046 (mttp) cc_final: 0.7691 (tttp) REVERT: j 156 MET cc_start: 0.7609 (tpt) cc_final: 0.7016 (tpt) REVERT: j 160 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: z 160 ASP cc_start: 0.8314 (m-30) cc_final: 0.7933 (m-30) REVERT: z 187 LYS cc_start: 0.6421 (OUTLIER) cc_final: 0.5780 (ptpp) REVERT: f 157 ASP cc_start: 0.7750 (m-30) cc_final: 0.7038 (p0) REVERT: f 169 ASP cc_start: 0.5234 (t70) cc_final: 0.4826 (t0) REVERT: f 187 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.6775 (ttmm) REVERT: F 981 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8207 (p0) REVERT: F 991 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7852 (pm20) outliers start: 67 outliers final: 28 residues processed: 200 average time/residue: 1.0785 time to fit residues: 234.1810 Evaluate side-chains 175 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 981 ASN Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 999 LYS 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 42 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 109 ARG Chi-restraints excluded: chain z residue 124 THR 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 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 187 LYS Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 991 GLU 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 69 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 chunk 124 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 67 ASN j 126 GLN z 30 HIS z 139 HIS z 174 GLN Z 922 GLN ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 141 GLN F 975 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10872 Z= 0.330 Angle : 0.718 16.217 14748 Z= 0.368 Chirality : 0.051 0.197 1692 Planarity : 0.006 0.095 1932 Dihedral : 8.721 87.268 1506 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.92 % Favored : 89.01 % Rotamer: Outliers : 6.77 % Allowed : 26.82 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.22), residues: 1383 helix: 0.98 (0.43), residues: 150 sheet: -0.25 (0.26), residues: 381 loop : -1.94 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 859 HIS 0.006 0.001 HIS f 139 PHE 0.016 0.002 PHE f 136 TYR 0.020 0.002 TYR z 146 ARG 0.003 0.000 ARG J1090 *********************** 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 228 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 149 time to evaluate : 1.199 Fit side-chains REVERT: J 850 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7657 (mmpt) REVERT: J 981 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8093 (p0) REVERT: j 32 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6654 (mm) REVERT: j 46 LYS cc_start: 0.8070 (mttp) cc_final: 0.7703 (tttp) REVERT: j 156 MET cc_start: 0.7618 (tpt) cc_final: 0.7156 (tpt) REVERT: j 160 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: z 187 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.6025 (ttmp) REVERT: f 157 ASP cc_start: 0.7767 (m-30) cc_final: 0.7024 (p0) REVERT: f 160 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: f 161 LYS cc_start: 0.6672 (tmtt) cc_final: 0.6292 (tmtt) REVERT: f 169 ASP cc_start: 0.5081 (t70) cc_final: 0.4637 (t0) REVERT: F 981 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8140 (p0) outliers start: 79 outliers final: 40 residues processed: 205 average time/residue: 1.0424 time to fit residues: 232.2621 Evaluate side-chains 190 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 143 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 850 LYS 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 981 ASN Chi-restraints excluded: chain J residue 988 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1098 THR Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain J residue 1130 SER Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 85 THR Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain j residue 124 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 53 VAL Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 124 THR 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 1013 VAL Chi-restraints excluded: chain Z residue 1053 THR Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 102 ASP 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 923 ILE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 981 ASN 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 1098 THR Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1130 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 0.0010 chunk 59 optimal weight: 0.0670 chunk 84 optimal weight: 0.0980 chunk 125 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.2524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN ** J 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1008 GLN j 30 HIS j 67 ASN j 126 GLN z 30 HIS z 139 HIS z 174 GLN Z 975 ASN F 975 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10872 Z= 0.167 Angle : 0.632 15.558 14748 Z= 0.321 Chirality : 0.047 0.183 1692 Planarity : 0.005 0.087 1932 Dihedral : 7.736 75.747 1498 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 5.40 % Allowed : 29.22 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.22), residues: 1383 helix: 1.26 (0.43), residues: 150 sheet: -0.06 (0.27), residues: 375 loop : -1.91 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Z 859 HIS 0.008 0.001 HIS z 139 PHE 0.013 0.001 PHE F 916 TYR 0.014 0.001 TYR z 146 ARG 0.010 0.000 ARG Z1042 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 150 time to evaluate : 1.210 Fit side-chains REVERT: J 981 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8051 (p0) REVERT: J 988 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7694 (tp) REVERT: j 32 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6662 (mm) REVERT: j 46 LYS cc_start: 0.8057 (mttp) cc_final: 0.7686 (tttp) REVERT: j 156 MET cc_start: 0.7530 (tpt) cc_final: 0.7037 (tpt) REVERT: j 160 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7379 (m-30) REVERT: z 187 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5918 (ttmp) REVERT: f 46 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7632 (tttp) REVERT: F 981 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8201 (p0) REVERT: F 1099 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8587 (tp) outliers start: 63 outliers final: 23 residues processed: 195 average time/residue: 1.0839 time to fit residues: 229.8529 Evaluate side-chains 173 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 981 ASN 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 85 THR Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 109 ARG Chi-restraints excluded: chain z residue 143 ASP Chi-restraints excluded: chain z residue 187 LYS Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 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 97 ILE Chi-restraints excluded: chain f residue 102 ASP Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain F residue 850 LYS Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 922 GLN ** J 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1008 GLN j 67 ASN j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 975 ASN ** f 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10872 Z= 0.329 Angle : 0.716 15.863 14748 Z= 0.363 Chirality : 0.051 0.259 1692 Planarity : 0.006 0.092 1932 Dihedral : 7.848 79.975 1492 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.56 % Favored : 89.37 % Rotamer: Outliers : 6.51 % Allowed : 28.11 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.22), residues: 1383 helix: 1.08 (0.43), residues: 150 sheet: -0.20 (0.27), residues: 381 loop : -1.94 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 859 HIS 0.007 0.001 HIS z 139 PHE 0.016 0.002 PHE f 136 TYR 0.021 0.002 TYR z 146 ARG 0.007 0.000 ARG Z1042 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 153 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: J 981 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8111 (p0) REVERT: j 32 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6662 (mm) REVERT: j 46 LYS cc_start: 0.8113 (mttp) cc_final: 0.7710 (tttp) REVERT: j 67 ASN cc_start: 0.8414 (t0) cc_final: 0.8191 (t0) REVERT: j 87 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.6514 (tt0) REVERT: j 156 MET cc_start: 0.7579 (tpt) cc_final: 0.7011 (tpt) REVERT: j 160 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: z 160 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7802 (m-30) REVERT: z 187 LYS cc_start: 0.6336 (OUTLIER) cc_final: 0.5888 (ttmp) REVERT: Z 1082 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8505 (tpp-160) REVERT: f 46 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7610 (tttp) REVERT: f 78 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7659 (pp-130) REVERT: f 157 ASP cc_start: 0.7735 (m-30) cc_final: 0.7013 (p0) REVERT: f 169 ASP cc_start: 0.4928 (t70) cc_final: 0.4469 (t0) REVERT: F 929 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: F 981 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8236 (p0) REVERT: F 1060 LYS cc_start: 0.8797 (tttt) cc_final: 0.8551 (ttmt) outliers start: 76 outliers final: 41 residues processed: 207 average time/residue: 1.0410 time to fit residues: 234.4179 Evaluate side-chains 199 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 147 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 929 PHE Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 981 ASN 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 102 ASP Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 139 HIS Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 124 THR 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 886 ASP Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 988 LEU Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1082 ARG Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 102 ASP Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain F residue 850 LYS Chi-restraints excluded: chain F residue 871 LYS Chi-restraints excluded: chain F residue 886 ASP Chi-restraints excluded: chain F residue 923 ILE Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 1062 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1130 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 128 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1008 GLN j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN Z 975 ASN f 67 ASN ** f 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10872 Z= 0.217 Angle : 0.662 15.824 14748 Z= 0.334 Chirality : 0.048 0.225 1692 Planarity : 0.006 0.089 1932 Dihedral : 7.628 77.150 1492 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 6.08 % Allowed : 28.53 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.22), residues: 1383 helix: 1.21 (0.43), residues: 150 sheet: -0.18 (0.27), residues: 381 loop : -1.91 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Z 859 HIS 0.009 0.001 HIS z 139 PHE 0.012 0.002 PHE f 128 TYR 0.017 0.001 TYR z 146 ARG 0.006 0.000 ARG Z1042 *********************** REFINEMENT MACRO_CYCLE 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 224 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 153 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 981 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8051 (p0) REVERT: j 32 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6731 (mm) REVERT: j 46 LYS cc_start: 0.8081 (mttp) cc_final: 0.7680 (tttp) REVERT: j 156 MET cc_start: 0.7569 (tpt) cc_final: 0.6983 (tpt) REVERT: j 160 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7447 (m-30) REVERT: z 160 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: z 187 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.5853 (ttmp) REVERT: Z 859 TRP cc_start: 0.7411 (m-10) cc_final: 0.6920 (m100) REVERT: f 46 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7611 (tttp) REVERT: f 78 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.7391 (pp-130) REVERT: f 161 LYS cc_start: 0.6723 (tmtt) cc_final: 0.6327 (tmtt) REVERT: F 929 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: F 981 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8212 (p0) REVERT: F 1060 LYS cc_start: 0.8780 (tttt) cc_final: 0.8538 (ttmt) REVERT: F 1099 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8581 (tp) outliers start: 71 outliers final: 40 residues processed: 205 average time/residue: 1.0381 time to fit residues: 231.8191 Evaluate side-chains 195 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 146 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 973 LEU Chi-restraints excluded: chain J residue 981 ASN 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 85 THR Chi-restraints excluded: chain j residue 102 ASP Chi-restraints excluded: chain j residue 139 HIS 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 832 LEU Chi-restraints excluded: chain Z residue 886 ASP Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 988 LEU Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1098 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 102 ASP Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain F residue 850 LYS Chi-restraints excluded: chain F residue 871 LYS Chi-restraints excluded: chain F residue 886 ASP Chi-restraints excluded: chain F residue 925 MET Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 983 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.0470 chunk 74 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 83 optimal weight: 0.0070 chunk 81 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1008 GLN j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN Z 975 ASN f 139 HIS f 141 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1624 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= 0.240 Angle : 0.675 15.787 14748 Z= 0.340 Chirality : 0.049 0.278 1692 Planarity : 0.006 0.090 1932 Dihedral : 7.541 77.310 1490 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 6.08 % Allowed : 28.62 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.22), residues: 1383 helix: 1.27 (0.43), residues: 150 sheet: -0.17 (0.27), residues: 381 loop : -1.92 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 859 HIS 0.009 0.001 HIS z 139 PHE 0.013 0.002 PHE f 128 TYR 0.018 0.001 TYR z 146 ARG 0.005 0.000 ARG Z1042 *********************** 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 224 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 153 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: J 981 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8094 (p0) REVERT: j 32 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6749 (mm) REVERT: j 46 LYS cc_start: 0.8056 (mttp) cc_final: 0.7665 (tttp) REVERT: j 87 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6545 (tt0) REVERT: j 156 MET cc_start: 0.7630 (tpt) cc_final: 0.7006 (tpt) REVERT: j 160 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: z 160 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7784 (m-30) REVERT: z 187 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.5854 (ttmp) REVERT: Z 859 TRP cc_start: 0.7484 (m-10) cc_final: 0.6933 (m100) REVERT: Z 1082 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8499 (tpp-160) REVERT: f 78 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.7429 (pp-130) REVERT: F 929 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7251 (m-80) REVERT: F 981 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8240 (p0) REVERT: F 1060 LYS cc_start: 0.8786 (tttt) cc_final: 0.8547 (ttmt) REVERT: F 1099 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8627 (tp) outliers start: 71 outliers final: 46 residues processed: 209 average time/residue: 1.0404 time to fit residues: 236.4725 Evaluate side-chains 210 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 152 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 929 PHE Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 981 ASN 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 102 ASP Chi-restraints excluded: chain j residue 160 ASP Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 32 LEU Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 57 VAL Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 157 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 886 ASP Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 950 THR Chi-restraints excluded: chain Z residue 988 LEU Chi-restraints excluded: chain Z residue 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 1127 LEU Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 102 ASP Chi-restraints excluded: chain f residue 125 SER Chi-restraints excluded: chain F residue 850 LYS Chi-restraints excluded: chain F residue 886 ASP Chi-restraints excluded: chain F residue 923 ILE Chi-restraints excluded: chain F residue 925 MET Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1062 LEU Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1098 THR Chi-restraints excluded: chain F residue 1099 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 26 optimal weight: 0.0270 chunk 25 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 104 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1008 GLN j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN Z 975 ASN f 67 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10872 Z= 0.208 Angle : 0.657 15.806 14748 Z= 0.331 Chirality : 0.048 0.251 1692 Planarity : 0.005 0.089 1932 Dihedral : 7.442 75.664 1490 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 5.74 % Allowed : 29.48 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1383 helix: 1.37 (0.43), residues: 150 sheet: 0.03 (0.27), residues: 369 loop : -1.94 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 859 HIS 0.008 0.001 HIS z 139 PHE 0.012 0.002 PHE f 128 TYR 0.017 0.001 TYR z 146 ARG 0.006 0.000 ARG Z1042 *********************** REFINEMENT MACRO_CYCLE 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 223 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 156 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: J 981 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8071 (p0) REVERT: J 989 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6811 (mmm160) REVERT: j 32 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6726 (mm) REVERT: j 46 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7744 (tttp) REVERT: j 87 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6524 (tt0) REVERT: j 156 MET cc_start: 0.7593 (tpt) cc_final: 0.6977 (tpt) REVERT: j 160 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7266 (m-30) REVERT: z 160 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: z 187 LYS cc_start: 0.6203 (OUTLIER) cc_final: 0.5812 (ttmp) REVERT: Z 859 TRP cc_start: 0.7476 (m-10) cc_final: 0.6930 (m100) REVERT: Z 1082 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8495 (tpp-160) REVERT: f 46 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7609 (tttp) REVERT: f 78 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.7395 (pp-130) REVERT: f 160 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: F 929 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: F 981 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8170 (p0) REVERT: F 1060 LYS cc_start: 0.8777 (tttt) cc_final: 0.8540 (ttmt) REVERT: F 1099 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8582 (tp) outliers start: 67 outliers final: 42 residues processed: 204 average time/residue: 1.1087 time to fit residues: 246.0457 Evaluate side-chains 208 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 152 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 981 ASN Chi-restraints excluded: chain J residue 988 LEU Chi-restraints excluded: chain J residue 989 ARG Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1100 THR Chi-restraints excluded: chain J residue 1115 SER Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 46 LYS 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 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 157 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 886 ASP Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 988 LEU 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 f residue 42 LEU Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 102 ASP 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 886 ASP Chi-restraints excluded: chain F residue 923 ILE Chi-restraints excluded: chain F residue 925 MET Chi-restraints excluded: chain F residue 929 PHE Chi-restraints excluded: chain F residue 950 THR Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1062 LEU Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1098 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1127 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 1.9990 chunk 116 optimal weight: 0.1980 chunk 123 optimal weight: 2.9990 chunk 74 optimal weight: 0.0000 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 0.4980 chunk 117 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1008 GLN j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN Z 975 ASN f 30 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10872 Z= 0.219 Angle : 0.667 15.584 14748 Z= 0.335 Chirality : 0.048 0.258 1692 Planarity : 0.005 0.088 1932 Dihedral : 7.347 75.803 1488 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 5.83 % Allowed : 29.22 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.22), residues: 1383 helix: 1.38 (0.43), residues: 150 sheet: -0.06 (0.27), residues: 375 loop : -1.91 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 859 HIS 0.009 0.001 HIS z 139 PHE 0.012 0.002 PHE f 128 TYR 0.017 0.001 TYR z 146 ARG 0.005 0.000 ARG Z1042 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 154 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: J 932 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8138 (mtm-85) REVERT: J 981 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.7991 (p0) REVERT: J 989 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6831 (mmm160) REVERT: j 32 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6725 (mm) REVERT: j 46 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7743 (tttp) REVERT: j 87 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6549 (tt0) REVERT: j 156 MET cc_start: 0.7585 (tpt) cc_final: 0.6965 (tpt) REVERT: j 160 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7254 (m-30) REVERT: z 160 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: z 187 LYS cc_start: 0.6191 (OUTLIER) cc_final: 0.5810 (ttmp) REVERT: Z 859 TRP cc_start: 0.7466 (m-10) cc_final: 0.6923 (m100) REVERT: f 46 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7609 (tttp) REVERT: f 78 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7375 (pp-130) REVERT: f 160 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: F 929 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: F 981 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8184 (p0) REVERT: F 1060 LYS cc_start: 0.8777 (tttt) cc_final: 0.8542 (ttmt) REVERT: F 1099 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8615 (tp) outliers start: 68 outliers final: 41 residues processed: 205 average time/residue: 1.0255 time to fit residues: 229.0806 Evaluate side-chains 210 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 154 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 932 ARG 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 981 ASN 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 1115 SER Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 46 LYS 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 124 THR 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 157 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 886 ASP Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1098 THR Chi-restraints excluded: chain f residue 42 LEU Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 102 ASP 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 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 981 ASN Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1062 LEU Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1098 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 137 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 11 optimal weight: 0.0970 chunk 84 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN Z 975 ASN f 30 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10872 Z= 0.296 Angle : 0.715 15.912 14748 Z= 0.361 Chirality : 0.050 0.270 1692 Planarity : 0.006 0.090 1932 Dihedral : 7.569 78.265 1487 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.70 % Favored : 89.23 % Rotamer: Outliers : 5.66 % Allowed : 29.48 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.22), residues: 1383 helix: 1.21 (0.44), residues: 150 sheet: -0.18 (0.27), residues: 381 loop : -1.91 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 859 HIS 0.010 0.001 HIS z 139 PHE 0.014 0.002 PHE Z 904 TYR 0.019 0.002 TYR z 146 ARG 0.005 0.000 ARG J1090 ********************** 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 217 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 151 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: J 929 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: J 932 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8142 (mtm-85) REVERT: J 981 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8116 (p0) REVERT: J 989 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6865 (mmm160) REVERT: j 32 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6761 (mm) REVERT: j 46 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7668 (tttp) REVERT: j 87 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.6561 (tt0) REVERT: j 156 MET cc_start: 0.7602 (tpt) cc_final: 0.6998 (tpt) REVERT: j 160 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: z 160 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: z 187 LYS cc_start: 0.6267 (OUTLIER) cc_final: 0.5838 (ttmp) REVERT: Z 859 TRP cc_start: 0.7546 (m-10) cc_final: 0.6943 (m100) REVERT: Z 1082 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8512 (tpp-160) REVERT: f 46 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7618 (tttp) REVERT: f 120 LYS cc_start: 0.8085 (mptt) cc_final: 0.7733 (mttp) REVERT: f 160 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: F 929 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: F 981 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8127 (p0) REVERT: F 1060 LYS cc_start: 0.8786 (tttt) cc_final: 0.8551 (ttmt) REVERT: F 1099 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8619 (tp) outliers start: 66 outliers final: 42 residues processed: 199 average time/residue: 1.0512 time to fit residues: 227.5264 Evaluate side-chains 206 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 149 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain J residue 838 THR Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 929 PHE Chi-restraints excluded: chain J residue 932 ARG 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 981 ASN 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 1115 SER Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 46 LYS 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 124 THR 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 124 THR Chi-restraints excluded: chain z residue 157 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 886 ASP Chi-restraints excluded: chain Z residue 923 ILE 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 f residue 57 VAL Chi-restraints excluded: chain f residue 97 ILE Chi-restraints excluded: chain f residue 102 ASP 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 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 981 ASN Chi-restraints excluded: chain F residue 983 THR Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1062 LEU Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1098 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1127 LEU Chi-restraints excluded: chain F residue 1130 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 20 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 126 GLN z 30 HIS ** z 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 174 GLN Z 975 ASN f 30 HIS f 141 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127068 restraints weight = 12035.119| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.04 r_work: 0.3243 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10872 Z= 0.249 Angle : 0.696 15.835 14748 Z= 0.351 Chirality : 0.049 0.270 1692 Planarity : 0.006 0.089 1932 Dihedral : 7.530 77.519 1487 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.63 % Favored : 89.30 % Rotamer: Outliers : 5.57 % Allowed : 29.56 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.22), residues: 1383 helix: 1.21 (0.43), residues: 150 sheet: -0.12 (0.27), residues: 375 loop : -1.91 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 859 HIS 0.009 0.001 HIS z 139 PHE 0.013 0.002 PHE f 128 TYR 0.018 0.002 TYR z 146 ARG 0.005 0.000 ARG Z1042 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.28 seconds wall clock time: 83 minutes 52.71 seconds (5032.71 seconds total)