Starting phenix.real_space_refine on Thu Jan 16 02:40:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xci_38244/01_2025/8xci_38244.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xci_38244/01_2025/8xci_38244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xci_38244/01_2025/8xci_38244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xci_38244/01_2025/8xci_38244.map" model { file = "/net/cci-nas-00/data/ceres_data/8xci_38244/01_2025/8xci_38244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xci_38244/01_2025/8xci_38244.cif" } resolution = 3.57 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= 0.004 sd= 0.047 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 15 5.16 5 C 5603 2.51 5 N 1501 2.21 5 O 1723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2941 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 16, 'TRANS': 363} Chain: "J" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2941 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 16, 'TRANS': 363} Chain: "Z" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2960 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Time building chain proxies: 5.79, per 1000 atoms: 0.65 Number of scatterers: 8842 At special positions: 0 Unit cell: (128.904, 135.349, 107.42, 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 15 16.00 O 1723 8.00 N 1501 7.00 C 5603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 25 sheets defined 7.6% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'F' and resid 755 through 759 removed outlier: 3.827A pdb=" N GLN F 758 " --> pdb=" O ASP F 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 824 Processing helix chain 'F' and resid 825 through 831 Processing helix chain 'F' and resid 907 through 911 Processing helix chain 'J' and resid 758 through 763 Processing helix chain 'J' and resid 810 through 824 removed outlier: 3.901A pdb=" N TYR J 814 " --> pdb=" O ASP J 810 " (cutoff:3.500A) Processing helix chain 'J' and resid 825 through 832 Processing helix chain 'Z' and resid 758 through 763 removed outlier: 3.622A pdb=" N THR Z 763 " --> pdb=" O VAL Z 759 " (cutoff:3.500A) Processing helix chain 'Z' and resid 811 through 824 removed outlier: 3.877A pdb=" N ASP Z 816 " --> pdb=" O GLU Z 812 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE Z 817 " --> pdb=" O GLY Z 813 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU Z 824 " --> pdb=" O GLY Z 820 " (cutoff:3.500A) Processing helix chain 'Z' and resid 827 through 832 removed outlier: 3.633A pdb=" N LEU Z 832 " --> pdb=" O GLY Z 828 " (cutoff:3.500A) Processing helix chain 'Z' and resid 907 through 911 Processing sheet with id=AA1, first strand: chain 'F' and resid 636 through 640 Processing sheet with id=AA2, first strand: chain 'F' and resid 665 through 673 removed outlier: 5.646A pdb=" N LEU F 667 " --> pdb=" O VAL F 658 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL F 658 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN F 687 " --> pdb=" O THR F 659 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 717 through 725 Processing sheet with id=AA4, first strand: chain 'F' and resid 764 through 769 removed outlier: 5.357A pdb=" N TYR F 765 " --> pdb=" O PHE F 748 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE F 748 " --> pdb=" O TYR F 765 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 842 through 848 removed outlier: 6.226A pdb=" N PHE F 895 " --> pdb=" O ALA Z 903 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ILE Z 905 " --> pdb=" O PHE F 895 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL F 897 " --> pdb=" O ILE Z 905 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE Z 904 " --> pdb=" O PHE Z 916 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE Z 916 " --> pdb=" O PHE Z 904 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 852 through 853 Processing sheet with id=AA7, first strand: chain 'F' and resid 885 through 886 removed outlier: 3.636A pdb=" N LEU F 892 " --> pdb=" O GLU F 885 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 843 through 854 removed outlier: 3.735A pdb=" N LYS J 858 " --> pdb=" O ASP J 854 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 843 through 854 removed outlier: 3.735A pdb=" N LYS J 858 " --> pdb=" O ASP J 854 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU J 882 " --> pdb=" O TRP J 863 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG F 901 " --> pdb=" O PHE J 895 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL J 897 " --> pdb=" O ARG F 901 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ALA F 903 " --> pdb=" O VAL J 897 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE F 916 " --> pdb=" O PHE F 904 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N MET F 915 " --> pdb=" O ASN F 926 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE F 924 " --> pdb=" O PHE Z 929 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LYS Z 931 " --> pdb=" O PHE F 924 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASN F 926 " --> pdb=" O LYS Z 931 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR J 934 " --> pdb=" O LEU Z 930 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG Z 932 " --> pdb=" O THR J 934 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 932 through 934 removed outlier: 6.071A pdb=" N ARG F 932 " --> pdb=" O VAL J 928 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 955 through 957 Processing sheet with id=AB3, first strand: chain 'F' and resid 961 through 965 removed outlier: 3.952A pdb=" N ALA J 957 " --> pdb=" O ASP F 961 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN J 959 " --> pdb=" O SER F 963 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER F 965 " --> pdb=" O ASN J 959 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER J 948 " --> pdb=" O THR J 956 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 970 through 971 removed outlier: 6.539A pdb=" N ASN F 975 " --> pdb=" O GLY J 971 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ARG J 989 " --> pdb=" O ILE Z 984 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY Z 986 " --> pdb=" O ARG J 989 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU J 991 " --> pdb=" O GLY Z 986 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU Z 988 " --> pdb=" O GLU J 991 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE J 993 " --> pdb=" O LEU Z 988 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 983 through 984 removed outlier: 6.138A pdb=" N THR F 983 " --> pdb=" O ILE J 978 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 987 through 988 Processing sheet with id=AB7, first strand: chain 'J' and resid 622 through 629 removed outlier: 5.403A pdb=" N HIS J 623 " --> pdb=" O ASP J 642 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP J 642 " --> pdb=" O HIS J 623 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 665 through 673 removed outlier: 5.646A pdb=" N LEU J 667 " --> pdb=" O VAL J 658 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL J 658 " --> pdb=" O LEU J 667 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR J 688 " --> pdb=" O SER J 708 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER J 708 " --> pdb=" O TYR J 688 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU J 690 " --> pdb=" O SER J 706 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER J 706 " --> pdb=" O LEU J 690 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL J 692 " --> pdb=" O PRO J 704 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALA J 694 " --> pdb=" O GLY J 702 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 719 through 722 Processing sheet with id=AC1, first strand: chain 'J' and resid 764 through 769 removed outlier: 5.744A pdb=" N TYR J 765 " --> pdb=" O PHE J 748 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE J 748 " --> pdb=" O TYR J 765 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 924 through 925 removed outlier: 3.751A pdb=" N PHE J 916 " --> pdb=" O PHE J 904 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG J 901 " --> pdb=" O PHE Z 895 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL Z 897 " --> pdb=" O ARG J 901 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA J 903 " --> pdb=" O VAL Z 897 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP Z 886 " --> pdb=" O TRP Z 859 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N TRP Z 859 " --> pdb=" O ASP Z 886 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Z' and resid 622 through 629 removed outlier: 6.054A pdb=" N HIS Z 623 " --> pdb=" O ASP Z 642 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP Z 642 " --> pdb=" O HIS Z 623 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Z' and resid 665 through 673 removed outlier: 5.731A pdb=" N LEU Z 667 " --> pdb=" O VAL Z 658 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL Z 658 " --> pdb=" O LEU Z 667 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN Z 687 " --> pdb=" O THR Z 659 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Z' and resid 719 through 721 Processing sheet with id=AC6, first strand: chain 'Z' and resid 764 through 769 removed outlier: 5.664A pdb=" N TYR Z 765 " --> pdb=" O PHE Z 748 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE Z 748 " --> pdb=" O TYR Z 765 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER Z 791 " --> pdb=" O ALA Z 799 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA Z 799 " --> pdb=" O SER Z 791 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 938 through 939 312 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1745 1.32 - 1.47: 2371 1.47 - 1.62: 4891 1.62 - 1.77: 0 1.77 - 1.91: 27 Bond restraints: 9034 Sorted by residual: bond pdb=" C VAL F 621 " pdb=" O VAL F 621 " ideal model delta sigma weight residual 1.236 1.309 -0.073 1.03e-02 9.43e+03 5.03e+01 bond pdb=" C PHE F 924 " pdb=" O PHE F 924 " ideal model delta sigma weight residual 1.235 1.322 -0.087 1.23e-02 6.61e+03 5.01e+01 bond pdb=" C ILE F 938 " pdb=" O ILE F 938 " ideal model delta sigma weight residual 1.233 1.304 -0.071 1.08e-02 8.57e+03 4.33e+01 bond pdb=" C LEU Z 667 " pdb=" O LEU Z 667 " ideal model delta sigma weight residual 1.234 1.312 -0.077 1.20e-02 6.94e+03 4.14e+01 bond pdb=" C ILE F 923 " pdb=" O ILE F 923 " ideal model delta sigma weight residual 1.235 1.302 -0.066 1.05e-02 9.07e+03 4.01e+01 ... (remaining 9029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 9990 2.94 - 5.88: 2066 5.88 - 8.82: 203 8.82 - 11.76: 24 11.76 - 14.70: 10 Bond angle restraints: 12293 Sorted by residual: angle pdb=" C SER J 970 " pdb=" N GLY J 971 " pdb=" CA GLY J 971 " ideal model delta sigma weight residual 121.61 129.44 -7.83 7.70e-01 1.69e+00 1.03e+02 angle pdb=" C PHE J 895 " pdb=" N LEU J 896 " pdb=" CA LEU J 896 " ideal model delta sigma weight residual 123.07 108.53 14.54 1.46e+00 4.69e-01 9.92e+01 angle pdb=" C PHE Z 895 " pdb=" CA PHE Z 895 " pdb=" CB PHE Z 895 " ideal model delta sigma weight residual 111.82 98.36 13.46 1.38e+00 5.25e-01 9.51e+01 angle pdb=" CA TYR J 771 " pdb=" C TYR J 771 " pdb=" O TYR J 771 " ideal model delta sigma weight residual 121.11 109.99 11.12 1.17e+00 7.31e-01 9.03e+01 angle pdb=" CA ASN J 900 " pdb=" CB ASN J 900 " pdb=" CG ASN J 900 " ideal model delta sigma weight residual 112.60 103.77 8.83 1.00e+00 1.00e+00 7.80e+01 ... (remaining 12288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 4353 17.59 - 35.19: 767 35.19 - 52.78: 175 52.78 - 70.38: 43 70.38 - 87.97: 15 Dihedral angle restraints: 5353 sinusoidal: 2055 harmonic: 3298 Sorted by residual: dihedral pdb=" CA ALA F 713 " pdb=" C ALA F 713 " pdb=" N PRO F 714 " pdb=" CA PRO F 714 " ideal model delta harmonic sigma weight residual -180.00 -116.58 -63.42 0 5.00e+00 4.00e-02 1.61e+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 180.00 120.30 59.70 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA ALA Z 878 " pdb=" C ALA Z 878 " pdb=" N GLY Z 879 " pdb=" CA GLY Z 879 " ideal model delta harmonic sigma weight residual 180.00 -137.99 -42.01 0 5.00e+00 4.00e-02 7.06e+01 ... (remaining 5350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 564 0.064 - 0.127: 488 0.127 - 0.190: 238 0.190 - 0.254: 89 0.254 - 0.317: 16 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CA GLN Z 922 " pdb=" N GLN Z 922 " pdb=" C GLN Z 922 " pdb=" CB GLN Z 922 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA ILE J 905 " pdb=" N ILE J 905 " pdb=" C ILE J 905 " pdb=" CB ILE J 905 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA PHE Z 904 " pdb=" N PHE Z 904 " pdb=" C PHE Z 904 " pdb=" CB PHE Z 904 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1392 not shown) Planarity restraints: 1594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 876 " 0.091 2.00e-02 2.50e+03 4.66e-02 4.34e+01 pdb=" CG TYR J 876 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR J 876 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR J 876 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR J 876 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR J 876 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR J 876 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR J 876 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 814 " -0.028 2.00e-02 2.50e+03 4.01e-02 3.22e+01 pdb=" CG TYR J 814 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR J 814 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR J 814 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR J 814 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR J 814 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR J 814 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR J 814 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 929 " -0.057 2.00e-02 2.50e+03 4.00e-02 2.80e+01 pdb=" CG PHE F 929 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE F 929 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE F 929 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 PHE F 929 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 929 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE F 929 " -0.056 2.00e-02 2.50e+03 ... (remaining 1591 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 17 2.20 - 2.88: 2940 2.88 - 3.55: 12999 3.55 - 4.23: 20810 4.23 - 4.90: 33700 Nonbonded interactions: 70466 Sorted by model distance: nonbonded pdb=" N ASN J 900 " pdb=" OG SER Z 893 " model vdw 1.529 3.120 nonbonded pdb=" OG SER Z 776 " pdb=" OD1 ASN Z 778 " model vdw 1.973 3.040 nonbonded pdb=" O TRP J 859 " pdb=" NZ LYS J 891 " model vdw 1.988 3.120 nonbonded pdb=" O ALA Z 684 " pdb=" OH TYR Z 688 " model vdw 2.006 3.040 nonbonded pdb=" OE1 GLU Z 721 " pdb=" OG1 THR Z 732 " model vdw 2.030 3.040 ... (remaining 70461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'J' selection = (chain 'Z' and resid 616 through 995) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.690 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.017 0.111 9034 Z= 1.137 Angle : 2.344 14.704 12293 Z= 1.597 Chirality : 0.108 0.317 1395 Planarity : 0.010 0.064 1594 Dihedral : 19.303 87.972 3231 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 43.22 Ramachandran Plot: Outliers : 3.34 % Allowed : 14.07 % Favored : 82.59 % Rotamer: Outliers : 14.39 % Allowed : 25.05 % Favored : 60.55 % Cbeta Deviations : 1.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.22), residues: 1137 helix: -3.24 (0.45), residues: 60 sheet: -1.60 (0.28), residues: 332 loop : -3.03 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.007 TRP F 772 HIS 0.014 0.004 HIS Z 734 PHE 0.065 0.011 PHE J 904 TYR 0.091 0.010 TYR J 876 ARG 0.011 0.001 ARG J 806 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 78 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 679 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8557 (tmm-80) REVERT: F 797 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7489 (mmtt) REVERT: F 837 LEU cc_start: 0.4958 (OUTLIER) cc_final: 0.4594 (tm) REVERT: F 839 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: F 844 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8861 (ttt180) REVERT: F 847 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: F 932 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8340 (ttp80) REVERT: F 943 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7780 (t0) REVERT: F 976 VAL cc_start: 0.8040 (t) cc_final: 0.7734 (p) REVERT: J 764 ARG cc_start: 0.7536 (tpp80) cc_final: 0.6855 (ttt-90) REVERT: J 772 TRP cc_start: 0.6886 (OUTLIER) cc_final: 0.3674 (m100) REVERT: J 837 LEU cc_start: 0.8642 (mt) cc_final: 0.8141 (mt) REVERT: J 917 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.9049 (t) REVERT: J 923 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8577 (mp) REVERT: J 932 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8064 (mtm-85) REVERT: Z 771 TYR cc_start: 0.9275 (OUTLIER) cc_final: 0.8856 (p90) REVERT: Z 812 GLU cc_start: 0.9447 (OUTLIER) cc_final: 0.9219 (tm-30) REVERT: Z 832 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6357 (mt) REVERT: Z 884 MET cc_start: 0.8328 (ptm) cc_final: 0.8125 (ptm) REVERT: Z 902 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8799 (mt) outliers start: 135 outliers final: 75 residues processed: 202 average time/residue: 0.2265 time to fit residues: 62.1089 Evaluate side-chains 153 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 64 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain F residue 679 ARG Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain F residue 797 LYS Chi-restraints excluded: chain F residue 815 LEU Chi-restraints excluded: chain F residue 821 LYS Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain F residue 839 GLU Chi-restraints excluded: chain F residue 844 ARG Chi-restraints excluded: chain F residue 847 GLU Chi-restraints excluded: chain F residue 849 SER Chi-restraints excluded: chain F residue 865 VAL Chi-restraints excluded: chain F residue 892 LEU Chi-restraints excluded: chain F residue 893 SER Chi-restraints excluded: chain F residue 900 ASN Chi-restraints excluded: chain F residue 902 ILE Chi-restraints excluded: chain F residue 913 THR Chi-restraints excluded: chain F residue 915 MET Chi-restraints excluded: chain F residue 917 VAL Chi-restraints excluded: chain F residue 921 ASN Chi-restraints excluded: chain F residue 943 ASN Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 985 ASN Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain J residue 677 THR Chi-restraints excluded: chain J residue 685 LEU Chi-restraints excluded: chain J residue 687 ASN Chi-restraints excluded: chain J residue 720 ILE Chi-restraints excluded: chain J residue 721 GLU Chi-restraints excluded: chain J residue 762 SER Chi-restraints excluded: chain J residue 772 TRP Chi-restraints excluded: chain J residue 773 ILE Chi-restraints excluded: chain J residue 780 LYS Chi-restraints excluded: chain J residue 822 ILE Chi-restraints excluded: chain J residue 845 LEU Chi-restraints excluded: chain J residue 880 ILE Chi-restraints excluded: chain J residue 905 ILE Chi-restraints excluded: chain J residue 917 VAL Chi-restraints excluded: chain J residue 921 ASN Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 928 VAL Chi-restraints excluded: chain J residue 940 SER Chi-restraints excluded: chain J residue 949 LEU Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 961 ASP Chi-restraints excluded: chain J residue 962 ILE Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 983 THR Chi-restraints excluded: chain J residue 994 VAL Chi-restraints excluded: chain Z residue 621 VAL Chi-restraints excluded: chain Z residue 632 SER Chi-restraints excluded: chain Z residue 635 TYR Chi-restraints excluded: chain Z residue 646 VAL Chi-restraints excluded: chain Z residue 656 LEU Chi-restraints excluded: chain Z residue 661 ASP Chi-restraints excluded: chain Z residue 682 GLN Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 771 TYR Chi-restraints excluded: chain Z residue 777 ILE Chi-restraints excluded: chain Z residue 780 LYS Chi-restraints excluded: chain Z residue 791 SER Chi-restraints excluded: chain Z residue 792 VAL Chi-restraints excluded: chain Z residue 812 GLU Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 867 ILE Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 880 ILE Chi-restraints excluded: chain Z residue 897 VAL Chi-restraints excluded: chain Z residue 902 ILE Chi-restraints excluded: chain Z residue 904 PHE Chi-restraints excluded: chain Z residue 916 PHE Chi-restraints excluded: chain Z residue 921 ASN Chi-restraints excluded: chain Z residue 929 PHE Chi-restraints excluded: chain Z residue 931 LYS Chi-restraints excluded: chain Z residue 933 LEU Chi-restraints excluded: chain Z residue 945 PRO Chi-restraints excluded: chain Z residue 958 LYS Chi-restraints excluded: chain Z residue 961 ASP Chi-restraints excluded: chain Z residue 976 VAL Chi-restraints excluded: chain Z residue 982 CYS Chi-restraints excluded: chain Z residue 994 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 30.0000 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 728 GLN J 981 ASN Z 826 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.134241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.111355 restraints weight = 20820.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.112999 restraints weight = 12207.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.113933 restraints weight = 8689.737| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9034 Z= 0.241 Angle : 0.801 9.347 12293 Z= 0.414 Chirality : 0.049 0.166 1395 Planarity : 0.006 0.103 1594 Dihedral : 11.784 87.622 1401 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.09 % Favored : 91.47 % Rotamer: Outliers : 6.93 % Allowed : 29.21 % Favored : 63.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.23), residues: 1137 helix: -1.31 (0.58), residues: 65 sheet: -0.85 (0.25), residues: 413 loop : -2.55 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Z 698 HIS 0.004 0.001 HIS J 875 PHE 0.040 0.002 PHE Z 916 TYR 0.015 0.002 TYR F 814 ARG 0.008 0.001 ARG F 901 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 87 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 900 ASN cc_start: 0.6910 (OUTLIER) cc_final: 0.6125 (t0) REVERT: F 992 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7559 (mptt) REVERT: J 634 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6659 (tp30) REVERT: J 666 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7439 (tmt170) REVERT: J 764 ARG cc_start: 0.7249 (tpp80) cc_final: 0.6453 (ttt-90) REVERT: J 772 TRP cc_start: 0.4306 (OUTLIER) cc_final: 0.2070 (m100) REVERT: J 814 TYR cc_start: 0.5970 (m-80) cc_final: 0.5121 (m-80) REVERT: J 837 LEU cc_start: 0.8300 (mt) cc_final: 0.7964 (mt) REVERT: Z 672 ARG cc_start: 0.5472 (OUTLIER) cc_final: 0.2550 (ptt-90) REVERT: Z 698 TRP cc_start: 0.7298 (m-90) cc_final: 0.7022 (m-90) REVERT: Z 771 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7599 (p90) outliers start: 65 outliers final: 33 residues processed: 139 average time/residue: 0.2342 time to fit residues: 44.1284 Evaluate side-chains 107 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 67 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 734 HIS Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 815 LEU Chi-restraints excluded: chain F residue 836 GLU Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain F residue 900 ASN Chi-restraints excluded: chain F residue 913 THR Chi-restraints excluded: chain F residue 915 MET Chi-restraints excluded: chain F residue 917 VAL Chi-restraints excluded: chain F residue 992 LYS Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 666 ARG Chi-restraints excluded: chain J residue 720 ILE Chi-restraints excluded: chain J residue 772 TRP Chi-restraints excluded: chain J residue 787 PHE Chi-restraints excluded: chain J residue 880 ILE Chi-restraints excluded: chain J residue 921 ASN Chi-restraints excluded: chain J residue 949 LEU Chi-restraints excluded: chain J residue 962 ILE Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 980 GLU Chi-restraints excluded: chain J residue 994 VAL Chi-restraints excluded: chain Z residue 621 VAL Chi-restraints excluded: chain Z residue 661 ASP Chi-restraints excluded: chain Z residue 672 ARG Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 771 TYR Chi-restraints excluded: chain Z residue 790 ARG Chi-restraints excluded: chain Z residue 795 VAL Chi-restraints excluded: chain Z residue 827 LEU Chi-restraints excluded: chain Z residue 867 ILE Chi-restraints excluded: chain Z residue 904 PHE Chi-restraints excluded: chain Z residue 916 PHE Chi-restraints excluded: chain Z residue 931 LYS Chi-restraints excluded: chain Z residue 961 ASP Chi-restraints excluded: chain Z residue 976 VAL Chi-restraints excluded: chain Z residue 994 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 16 optimal weight: 0.0170 chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 overall best weight: 3.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 981 ASN Z 826 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.130626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.108707 restraints weight = 21564.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.109275 restraints weight = 12737.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.110091 restraints weight = 9321.674| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 9034 Z= 0.417 Angle : 0.817 12.585 12293 Z= 0.414 Chirality : 0.048 0.185 1395 Planarity : 0.006 0.091 1594 Dihedral : 9.503 87.655 1279 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.40 % Favored : 87.25 % Rotamer: Outliers : 8.00 % Allowed : 30.28 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.24), residues: 1137 helix: -0.78 (0.67), residues: 65 sheet: -0.84 (0.25), residues: 430 loop : -2.60 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 772 HIS 0.005 0.001 HIS Z 734 PHE 0.038 0.002 PHE Z 916 TYR 0.022 0.002 TYR Z 785 ARG 0.006 0.001 ARG F 901 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 69 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 900 ASN cc_start: 0.7018 (OUTLIER) cc_final: 0.6189 (t0) REVERT: F 992 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7604 (mptt) REVERT: J 634 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6567 (tp30) REVERT: J 764 ARG cc_start: 0.7274 (tpp80) cc_final: 0.6397 (ttp80) REVERT: J 772 TRP cc_start: 0.4584 (OUTLIER) cc_final: 0.2298 (m100) REVERT: J 814 TYR cc_start: 0.6161 (m-80) cc_final: 0.5370 (m-80) REVERT: Z 653 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8779 (tt) REVERT: Z 672 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.3084 (ptt-90) REVERT: Z 698 TRP cc_start: 0.7303 (m-90) cc_final: 0.6983 (m-90) outliers start: 75 outliers final: 44 residues processed: 131 average time/residue: 0.2306 time to fit residues: 41.3035 Evaluate side-chains 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 65 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 734 HIS Chi-restraints excluded: chain F residue 742 VAL Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain F residue 786 TYR Chi-restraints excluded: chain F residue 801 VAL Chi-restraints excluded: chain F residue 815 LEU Chi-restraints excluded: chain F residue 822 ILE Chi-restraints excluded: chain F residue 836 GLU Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain F residue 865 VAL Chi-restraints excluded: chain F residue 893 SER Chi-restraints excluded: chain F residue 900 ASN Chi-restraints excluded: chain F residue 913 THR Chi-restraints excluded: chain F residue 915 MET Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 992 LYS Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain J residue 666 ARG Chi-restraints excluded: chain J residue 772 TRP Chi-restraints excluded: chain J residue 887 THR Chi-restraints excluded: chain J residue 949 LEU Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 962 ILE Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 994 VAL Chi-restraints excluded: chain Z residue 621 VAL Chi-restraints excluded: chain Z residue 628 VAL Chi-restraints excluded: chain Z residue 646 VAL Chi-restraints excluded: chain Z residue 653 LEU Chi-restraints excluded: chain Z residue 661 ASP Chi-restraints excluded: chain Z residue 672 ARG Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 771 TYR Chi-restraints excluded: chain Z residue 790 ARG Chi-restraints excluded: chain Z residue 792 VAL Chi-restraints excluded: chain Z residue 795 VAL Chi-restraints excluded: chain Z residue 827 LEU Chi-restraints excluded: chain Z residue 867 ILE Chi-restraints excluded: chain Z residue 904 PHE Chi-restraints excluded: chain Z residue 921 ASN Chi-restraints excluded: chain Z residue 931 LYS Chi-restraints excluded: chain Z residue 939 THR Chi-restraints excluded: chain Z residue 961 ASP Chi-restraints excluded: chain Z residue 976 VAL Chi-restraints excluded: chain Z residue 994 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 17 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.133785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.111123 restraints weight = 20894.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.112838 restraints weight = 12108.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.113823 restraints weight = 8061.630| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9034 Z= 0.254 Angle : 0.704 9.604 12293 Z= 0.360 Chirality : 0.046 0.161 1395 Planarity : 0.005 0.082 1594 Dihedral : 8.718 90.499 1270 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.56 % Favored : 92.08 % Rotamer: Outliers : 7.36 % Allowed : 29.64 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.24), residues: 1137 helix: -0.29 (0.68), residues: 65 sheet: -0.75 (0.25), residues: 442 loop : -2.49 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 772 HIS 0.003 0.001 HIS F 734 PHE 0.038 0.002 PHE Z 916 TYR 0.010 0.001 TYR J 876 ARG 0.003 0.000 ARG F 901 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 69 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 845 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7892 (tt) REVERT: F 900 ASN cc_start: 0.6907 (OUTLIER) cc_final: 0.6160 (t0) REVERT: F 984 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7382 (mp) REVERT: F 992 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7566 (mptt) REVERT: J 634 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6482 (tp30) REVERT: J 764 ARG cc_start: 0.7216 (tpp80) cc_final: 0.6972 (tpp80) REVERT: J 772 TRP cc_start: 0.4308 (OUTLIER) cc_final: 0.2039 (m100) REVERT: J 814 TYR cc_start: 0.6031 (m-80) cc_final: 0.5418 (m-80) REVERT: Z 672 ARG cc_start: 0.6113 (OUTLIER) cc_final: 0.3040 (ptt-90) REVERT: Z 698 TRP cc_start: 0.7285 (m-90) cc_final: 0.6980 (m-90) REVERT: Z 743 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6385 (tm-30) REVERT: Z 991 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7165 (mp0) outliers start: 69 outliers final: 41 residues processed: 127 average time/residue: 0.2325 time to fit residues: 40.4594 Evaluate side-chains 112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 62 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 734 HIS Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain F residue 801 VAL Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 815 LEU Chi-restraints excluded: chain F residue 822 ILE Chi-restraints excluded: chain F residue 836 GLU Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 845 LEU Chi-restraints excluded: chain F residue 900 ASN Chi-restraints excluded: chain F residue 913 THR Chi-restraints excluded: chain F residue 915 MET Chi-restraints excluded: chain F residue 939 THR Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 984 ILE Chi-restraints excluded: chain F residue 992 LYS Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain J residue 666 ARG Chi-restraints excluded: chain J residue 691 THR Chi-restraints excluded: chain J residue 761 THR Chi-restraints excluded: chain J residue 766 LEU Chi-restraints excluded: chain J residue 772 TRP Chi-restraints excluded: chain J residue 887 THR Chi-restraints excluded: chain J residue 962 ILE Chi-restraints excluded: chain J residue 973 LEU Chi-restraints excluded: chain J residue 980 GLU Chi-restraints excluded: chain J residue 994 VAL Chi-restraints excluded: chain Z residue 621 VAL Chi-restraints excluded: chain Z residue 628 VAL Chi-restraints excluded: chain Z residue 661 ASP Chi-restraints excluded: chain Z residue 672 ARG Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 723 THR Chi-restraints excluded: chain Z residue 743 GLN Chi-restraints excluded: chain Z residue 768 THR Chi-restraints excluded: chain Z residue 771 TYR Chi-restraints excluded: chain Z residue 777 ILE Chi-restraints excluded: chain Z residue 790 ARG Chi-restraints excluded: chain Z residue 791 SER Chi-restraints excluded: chain Z residue 792 VAL Chi-restraints excluded: chain Z residue 795 VAL Chi-restraints excluded: chain Z residue 867 ILE Chi-restraints excluded: chain Z residue 904 PHE Chi-restraints excluded: chain Z residue 909 ASN Chi-restraints excluded: chain Z residue 976 VAL Chi-restraints excluded: chain Z residue 991 GLU Chi-restraints excluded: chain Z residue 994 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 0.0570 chunk 39 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.135395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.113022 restraints weight = 21049.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.114756 restraints weight = 11887.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.115690 restraints weight = 7943.625| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9034 Z= 0.207 Angle : 0.663 8.412 12293 Z= 0.339 Chirality : 0.045 0.159 1395 Planarity : 0.005 0.077 1594 Dihedral : 7.951 91.697 1261 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.09 % Favored : 91.56 % Rotamer: Outliers : 5.65 % Allowed : 31.88 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.24), residues: 1137 helix: -0.09 (0.70), residues: 65 sheet: -0.64 (0.24), residues: 450 loop : -2.37 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 852 HIS 0.003 0.001 HIS F 734 PHE 0.024 0.001 PHE Z 916 TYR 0.008 0.001 TYR J 876 ARG 0.003 0.000 ARG Z 710 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 79 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.8069 (pp) cc_final: 0.7667 (mt) REVERT: F 845 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7896 (tt) REVERT: F 900 ASN cc_start: 0.6876 (OUTLIER) cc_final: 0.6096 (t0) REVERT: F 984 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7320 (mp) REVERT: F 992 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7400 (mptt) REVERT: J 634 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6504 (tp30) REVERT: J 662 ASP cc_start: 0.7702 (p0) cc_final: 0.6240 (m-30) REVERT: J 666 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7343 (tmt170) REVERT: J 764 ARG cc_start: 0.7156 (tpp80) cc_final: 0.6902 (tpp80) REVERT: J 772 TRP cc_start: 0.4136 (OUTLIER) cc_final: 0.1818 (m100) REVERT: J 814 TYR cc_start: 0.5994 (m-80) cc_final: 0.5394 (m-80) REVERT: Z 672 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.3132 (ptt-90) REVERT: Z 698 TRP cc_start: 0.7232 (m-90) cc_final: 0.6919 (m-90) REVERT: Z 743 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6350 (tm-30) REVERT: Z 771 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7875 (p90) REVERT: Z 991 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7153 (mp0) outliers start: 53 outliers final: 29 residues processed: 124 average time/residue: 0.2224 time to fit residues: 38.1554 Evaluate side-chains 106 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 66 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 734 HIS Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain F residue 801 VAL Chi-restraints excluded: chain F residue 822 ILE Chi-restraints excluded: chain F residue 836 GLU Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 845 LEU Chi-restraints excluded: chain F residue 865 VAL Chi-restraints excluded: chain F residue 900 ASN Chi-restraints excluded: chain F residue 915 MET Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 984 ILE Chi-restraints excluded: chain F residue 992 LYS Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain J residue 666 ARG Chi-restraints excluded: chain J residue 691 THR Chi-restraints excluded: chain J residue 766 LEU Chi-restraints excluded: chain J residue 772 TRP Chi-restraints excluded: chain J residue 980 GLU Chi-restraints excluded: chain J residue 994 VAL Chi-restraints excluded: chain Z residue 621 VAL Chi-restraints excluded: chain Z residue 628 VAL Chi-restraints excluded: chain Z residue 661 ASP Chi-restraints excluded: chain Z residue 672 ARG Chi-restraints excluded: chain Z residue 743 GLN Chi-restraints excluded: chain Z residue 768 THR Chi-restraints excluded: chain Z residue 771 TYR Chi-restraints excluded: chain Z residue 791 SER Chi-restraints excluded: chain Z residue 792 VAL Chi-restraints excluded: chain Z residue 795 VAL Chi-restraints excluded: chain Z residue 867 ILE Chi-restraints excluded: chain Z residue 882 LEU Chi-restraints excluded: chain Z residue 904 PHE Chi-restraints excluded: chain Z residue 975 ASN Chi-restraints excluded: chain Z residue 976 VAL Chi-restraints excluded: chain Z residue 991 GLU Chi-restraints excluded: chain Z residue 994 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 102 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 687 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.136634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.114390 restraints weight = 20850.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.116591 restraints weight = 11674.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.117484 restraints weight = 7996.636| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9034 Z= 0.197 Angle : 0.652 8.677 12293 Z= 0.334 Chirality : 0.045 0.169 1395 Planarity : 0.005 0.074 1594 Dihedral : 7.470 92.007 1253 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.04 % Favored : 92.52 % Rotamer: Outliers : 5.33 % Allowed : 32.52 % Favored : 62.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.24), residues: 1137 helix: 0.03 (0.70), residues: 65 sheet: -0.48 (0.25), residues: 451 loop : -2.25 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 772 HIS 0.003 0.001 HIS Z 734 PHE 0.029 0.002 PHE Z 709 TYR 0.015 0.001 TYR F 814 ARG 0.004 0.000 ARG Z 710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 78 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.8060 (pp) cc_final: 0.7733 (mt) REVERT: F 845 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7893 (tt) REVERT: F 900 ASN cc_start: 0.6800 (OUTLIER) cc_final: 0.6014 (t0) REVERT: F 984 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7322 (mp) REVERT: F 992 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7472 (mptt) REVERT: J 662 ASP cc_start: 0.7585 (p0) cc_final: 0.6242 (m-30) REVERT: J 666 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7307 (tmt170) REVERT: J 772 TRP cc_start: 0.3798 (OUTLIER) cc_final: 0.1395 (m100) REVERT: J 814 TYR cc_start: 0.5936 (m-80) cc_final: 0.5406 (m-80) REVERT: Z 653 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8525 (tt) REVERT: Z 672 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.3103 (ptt-90) REVERT: Z 698 TRP cc_start: 0.7137 (m-90) cc_final: 0.6792 (m-90) REVERT: Z 743 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6386 (tm-30) REVERT: Z 771 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.7866 (p90) REVERT: Z 991 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7153 (mp0) outliers start: 50 outliers final: 28 residues processed: 120 average time/residue: 0.2091 time to fit residues: 35.1637 Evaluate side-chains 110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 71 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain F residue 734 HIS Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 822 ILE Chi-restraints excluded: chain F residue 836 GLU Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 845 LEU Chi-restraints excluded: chain F residue 865 VAL Chi-restraints excluded: chain F residue 893 SER Chi-restraints excluded: chain F residue 900 ASN Chi-restraints excluded: chain F residue 915 MET Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 984 ILE Chi-restraints excluded: chain F residue 992 LYS Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain J residue 666 ARG Chi-restraints excluded: chain J residue 691 THR Chi-restraints excluded: chain J residue 761 THR Chi-restraints excluded: chain J residue 766 LEU Chi-restraints excluded: chain J residue 772 TRP Chi-restraints excluded: chain J residue 980 GLU Chi-restraints excluded: chain J residue 994 VAL Chi-restraints excluded: chain Z residue 621 VAL Chi-restraints excluded: chain Z residue 628 VAL Chi-restraints excluded: chain Z residue 653 LEU Chi-restraints excluded: chain Z residue 672 ARG Chi-restraints excluded: chain Z residue 743 GLN Chi-restraints excluded: chain Z residue 768 THR Chi-restraints excluded: chain Z residue 771 TYR Chi-restraints excluded: chain Z residue 792 VAL Chi-restraints excluded: chain Z residue 795 VAL Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 904 PHE Chi-restraints excluded: chain Z residue 909 ASN Chi-restraints excluded: chain Z residue 975 ASN Chi-restraints excluded: chain Z residue 976 VAL Chi-restraints excluded: chain Z residue 991 GLU Chi-restraints excluded: chain Z residue 994 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 778 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.135311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.113145 restraints weight = 21093.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.115123 restraints weight = 11805.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.116038 restraints weight = 8135.408| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9034 Z= 0.241 Angle : 0.669 7.977 12293 Z= 0.341 Chirality : 0.045 0.169 1395 Planarity : 0.005 0.073 1594 Dihedral : 6.766 52.462 1246 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.71 % Favored : 90.85 % Rotamer: Outliers : 5.97 % Allowed : 31.56 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.25), residues: 1137 helix: 0.09 (0.71), residues: 65 sheet: -0.42 (0.25), residues: 443 loop : -2.26 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 772 HIS 0.004 0.001 HIS F 734 PHE 0.027 0.002 PHE Z 916 TYR 0.012 0.001 TYR F 814 ARG 0.004 0.000 ARG Z 710 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 71 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.7991 (pp) cc_final: 0.7688 (mt) REVERT: F 845 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7828 (tt) REVERT: F 900 ASN cc_start: 0.6807 (OUTLIER) cc_final: 0.5942 (t0) REVERT: F 925 MET cc_start: 0.7948 (ttm) cc_final: 0.7743 (ttp) REVERT: F 984 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7393 (mp) REVERT: F 992 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7466 (mptt) REVERT: J 634 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6295 (tp30) REVERT: J 772 TRP cc_start: 0.4041 (OUTLIER) cc_final: 0.1591 (m100) REVERT: J 814 TYR cc_start: 0.6013 (m-80) cc_final: 0.5422 (m-80) REVERT: Z 653 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8534 (tt) REVERT: Z 672 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.3244 (ptt-90) REVERT: Z 743 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: Z 771 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7806 (p90) REVERT: Z 991 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7172 (mp0) outliers start: 56 outliers final: 36 residues processed: 118 average time/residue: 0.1952 time to fit residues: 33.0253 Evaluate side-chains 112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 65 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 734 HIS Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 822 ILE Chi-restraints excluded: chain F residue 836 GLU Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 845 LEU Chi-restraints excluded: chain F residue 865 VAL Chi-restraints excluded: chain F residue 893 SER Chi-restraints excluded: chain F residue 900 ASN Chi-restraints excluded: chain F residue 913 THR Chi-restraints excluded: chain F residue 915 MET Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 965 SER Chi-restraints excluded: chain F residue 984 ILE Chi-restraints excluded: chain F residue 992 LYS Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain J residue 666 ARG Chi-restraints excluded: chain J residue 691 THR Chi-restraints excluded: chain J residue 766 LEU Chi-restraints excluded: chain J residue 772 TRP Chi-restraints excluded: chain J residue 980 GLU Chi-restraints excluded: chain J residue 994 VAL Chi-restraints excluded: chain Z residue 621 VAL Chi-restraints excluded: chain Z residue 628 VAL Chi-restraints excluded: chain Z residue 653 LEU Chi-restraints excluded: chain Z residue 672 ARG Chi-restraints excluded: chain Z residue 723 THR Chi-restraints excluded: chain Z residue 743 GLN Chi-restraints excluded: chain Z residue 768 THR Chi-restraints excluded: chain Z residue 771 TYR Chi-restraints excluded: chain Z residue 773 ILE Chi-restraints excluded: chain Z residue 791 SER Chi-restraints excluded: chain Z residue 792 VAL Chi-restraints excluded: chain Z residue 795 VAL Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 823 THR Chi-restraints excluded: chain Z residue 904 PHE Chi-restraints excluded: chain Z residue 909 ASN Chi-restraints excluded: chain Z residue 928 VAL Chi-restraints excluded: chain Z residue 975 ASN Chi-restraints excluded: chain Z residue 976 VAL Chi-restraints excluded: chain Z residue 991 GLU Chi-restraints excluded: chain Z residue 994 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 0.0370 chunk 44 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.133511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.112375 restraints weight = 21503.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.113143 restraints weight = 12441.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.114396 restraints weight = 9039.446| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 9034 Z= 0.309 Angle : 0.711 9.589 12293 Z= 0.362 Chirality : 0.046 0.182 1395 Planarity : 0.006 0.073 1594 Dihedral : 6.928 53.019 1246 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.03 % Favored : 89.53 % Rotamer: Outliers : 6.29 % Allowed : 31.88 % Favored : 61.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.24), residues: 1137 helix: 0.03 (0.71), residues: 65 sheet: -0.46 (0.25), residues: 433 loop : -2.28 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Z 698 HIS 0.004 0.001 HIS F 734 PHE 0.032 0.002 PHE Z 916 TYR 0.011 0.001 TYR F 814 ARG 0.012 0.000 ARG Z 710 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 66 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.8043 (pp) cc_final: 0.7701 (mt) REVERT: F 845 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7895 (tt) REVERT: F 900 ASN cc_start: 0.6820 (OUTLIER) cc_final: 0.6031 (t0) REVERT: F 925 MET cc_start: 0.7999 (ttm) cc_final: 0.7771 (ttp) REVERT: F 984 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7484 (mp) REVERT: F 992 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7549 (mptt) REVERT: J 772 TRP cc_start: 0.4202 (OUTLIER) cc_final: 0.1855 (m100) REVERT: J 814 TYR cc_start: 0.6088 (m-80) cc_final: 0.5429 (m-80) REVERT: Z 653 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8551 (tt) REVERT: Z 672 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.3371 (ptt-90) REVERT: Z 698 TRP cc_start: 0.7363 (m-90) cc_final: 0.6974 (m-90) REVERT: Z 743 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: Z 991 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7203 (mp0) outliers start: 59 outliers final: 41 residues processed: 116 average time/residue: 0.2061 time to fit residues: 33.6990 Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 63 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 734 HIS Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain F residue 801 VAL Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 822 ILE Chi-restraints excluded: chain F residue 836 GLU Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain F residue 845 LEU Chi-restraints excluded: chain F residue 865 VAL Chi-restraints excluded: chain F residue 893 SER Chi-restraints excluded: chain F residue 900 ASN Chi-restraints excluded: chain F residue 913 THR Chi-restraints excluded: chain F residue 915 MET Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 965 SER Chi-restraints excluded: chain F residue 984 ILE Chi-restraints excluded: chain F residue 992 LYS Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain J residue 666 ARG Chi-restraints excluded: chain J residue 691 THR Chi-restraints excluded: chain J residue 766 LEU Chi-restraints excluded: chain J residue 772 TRP Chi-restraints excluded: chain J residue 852 TRP Chi-restraints excluded: chain J residue 880 ILE Chi-restraints excluded: chain J residue 980 GLU Chi-restraints excluded: chain J residue 994 VAL Chi-restraints excluded: chain Z residue 621 VAL Chi-restraints excluded: chain Z residue 628 VAL Chi-restraints excluded: chain Z residue 653 LEU Chi-restraints excluded: chain Z residue 672 ARG Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 723 THR Chi-restraints excluded: chain Z residue 743 GLN Chi-restraints excluded: chain Z residue 768 THR Chi-restraints excluded: chain Z residue 771 TYR Chi-restraints excluded: chain Z residue 773 ILE Chi-restraints excluded: chain Z residue 791 SER Chi-restraints excluded: chain Z residue 792 VAL Chi-restraints excluded: chain Z residue 795 VAL Chi-restraints excluded: chain Z residue 823 THR Chi-restraints excluded: chain Z residue 882 LEU Chi-restraints excluded: chain Z residue 904 PHE Chi-restraints excluded: chain Z residue 909 ASN Chi-restraints excluded: chain Z residue 975 ASN Chi-restraints excluded: chain Z residue 976 VAL Chi-restraints excluded: chain Z residue 991 GLU Chi-restraints excluded: chain Z residue 994 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 112 optimal weight: 0.0470 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.134154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.111828 restraints weight = 21377.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.113373 restraints weight = 12163.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.115179 restraints weight = 8227.735| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9034 Z= 0.277 Angle : 0.702 9.055 12293 Z= 0.359 Chirality : 0.045 0.190 1395 Planarity : 0.005 0.072 1594 Dihedral : 6.916 52.729 1246 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.67 % Favored : 89.89 % Rotamer: Outliers : 5.97 % Allowed : 32.20 % Favored : 61.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.25), residues: 1137 helix: -0.04 (0.71), residues: 65 sheet: -0.47 (0.25), residues: 443 loop : -2.29 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Z 698 HIS 0.004 0.001 HIS Z 826 PHE 0.028 0.002 PHE Z 916 TYR 0.011 0.001 TYR F 814 ARG 0.014 0.000 ARG Z 710 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 68 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.8048 (pp) cc_final: 0.7718 (mt) REVERT: F 845 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7857 (tt) REVERT: F 900 ASN cc_start: 0.6828 (OUTLIER) cc_final: 0.6094 (t0) REVERT: F 984 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7429 (mp) REVERT: F 992 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7539 (mptt) REVERT: J 772 TRP cc_start: 0.4125 (OUTLIER) cc_final: 0.1784 (m100) REVERT: J 814 TYR cc_start: 0.6062 (m-80) cc_final: 0.5417 (m-80) REVERT: J 987 THR cc_start: 0.7408 (m) cc_final: 0.7044 (p) REVERT: Z 653 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8533 (tt) REVERT: Z 672 ARG cc_start: 0.6347 (OUTLIER) cc_final: 0.3374 (ptt-90) REVERT: Z 698 TRP cc_start: 0.7247 (m-90) cc_final: 0.6813 (m-90) REVERT: Z 743 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6379 (tm-30) REVERT: Z 991 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7157 (mp0) outliers start: 56 outliers final: 45 residues processed: 115 average time/residue: 0.2008 time to fit residues: 32.8247 Evaluate side-chains 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 65 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 656 LEU Chi-restraints excluded: chain F residue 734 HIS Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain F residue 801 VAL Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 822 ILE Chi-restraints excluded: chain F residue 836 GLU Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain F residue 845 LEU Chi-restraints excluded: chain F residue 865 VAL Chi-restraints excluded: chain F residue 893 SER Chi-restraints excluded: chain F residue 900 ASN Chi-restraints excluded: chain F residue 913 THR Chi-restraints excluded: chain F residue 915 MET Chi-restraints excluded: chain F residue 939 THR Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 965 SER Chi-restraints excluded: chain F residue 984 ILE Chi-restraints excluded: chain F residue 992 LYS Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain J residue 666 ARG Chi-restraints excluded: chain J residue 691 THR Chi-restraints excluded: chain J residue 766 LEU Chi-restraints excluded: chain J residue 772 TRP Chi-restraints excluded: chain J residue 852 TRP Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 980 GLU Chi-restraints excluded: chain J residue 994 VAL Chi-restraints excluded: chain Z residue 621 VAL Chi-restraints excluded: chain Z residue 628 VAL Chi-restraints excluded: chain Z residue 653 LEU Chi-restraints excluded: chain Z residue 661 ASP Chi-restraints excluded: chain Z residue 672 ARG Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 723 THR Chi-restraints excluded: chain Z residue 743 GLN Chi-restraints excluded: chain Z residue 768 THR Chi-restraints excluded: chain Z residue 771 TYR Chi-restraints excluded: chain Z residue 773 ILE Chi-restraints excluded: chain Z residue 777 ILE Chi-restraints excluded: chain Z residue 791 SER Chi-restraints excluded: chain Z residue 792 VAL Chi-restraints excluded: chain Z residue 795 VAL Chi-restraints excluded: chain Z residue 823 THR Chi-restraints excluded: chain Z residue 882 LEU Chi-restraints excluded: chain Z residue 904 PHE Chi-restraints excluded: chain Z residue 909 ASN Chi-restraints excluded: chain Z residue 975 ASN Chi-restraints excluded: chain Z residue 976 VAL Chi-restraints excluded: chain Z residue 991 GLU Chi-restraints excluded: chain Z residue 994 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 67 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.137303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.115260 restraints weight = 21142.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.117657 restraints weight = 11859.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.118560 restraints weight = 7997.409| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9034 Z= 0.191 Angle : 0.668 8.397 12293 Z= 0.341 Chirality : 0.045 0.194 1395 Planarity : 0.005 0.068 1594 Dihedral : 6.702 53.587 1246 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.48 % Favored : 92.08 % Rotamer: Outliers : 4.90 % Allowed : 33.16 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.09 % 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: -1.90 (0.25), residues: 1137 helix: 0.02 (0.70), residues: 65 sheet: -0.39 (0.25), residues: 447 loop : -2.14 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 698 HIS 0.003 0.001 HIS F 734 PHE 0.023 0.002 PHE Z 929 TYR 0.008 0.001 TYR F 814 ARG 0.018 0.000 ARG Z 710 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 77 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.7988 (pp) cc_final: 0.7666 (mt) REVERT: F 845 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7985 (tt) REVERT: F 900 ASN cc_start: 0.6559 (OUTLIER) cc_final: 0.5997 (t0) REVERT: F 984 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7430 (mp) REVERT: F 992 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7472 (mptt) REVERT: J 635 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6671 (t80) REVERT: J 662 ASP cc_start: 0.7518 (p0) cc_final: 0.5931 (m-30) REVERT: J 666 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7340 (tmt170) REVERT: J 772 TRP cc_start: 0.3917 (OUTLIER) cc_final: 0.1396 (m100) REVERT: J 814 TYR cc_start: 0.5961 (m-80) cc_final: 0.5418 (m-80) REVERT: J 824 GLU cc_start: 0.7928 (pp20) cc_final: 0.7625 (pp20) REVERT: Z 672 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.3376 (ptt-90) REVERT: Z 743 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6237 (tm-30) REVERT: Z 771 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7859 (p90) REVERT: Z 991 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: Z 994 VAL cc_start: 0.4665 (OUTLIER) cc_final: 0.4401 (p) outliers start: 46 outliers final: 30 residues processed: 114 average time/residue: 0.2017 time to fit residues: 32.7776 Evaluate side-chains 112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 70 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 624 LEU Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 656 LEU Chi-restraints excluded: chain F residue 734 HIS Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 822 ILE Chi-restraints excluded: chain F residue 836 GLU Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain F residue 845 LEU Chi-restraints excluded: chain F residue 865 VAL Chi-restraints excluded: chain F residue 893 SER Chi-restraints excluded: chain F residue 900 ASN Chi-restraints excluded: chain F residue 915 MET Chi-restraints excluded: chain F residue 984 ILE Chi-restraints excluded: chain F residue 992 LYS Chi-restraints excluded: chain J residue 635 TYR Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain J residue 666 ARG Chi-restraints excluded: chain J residue 691 THR Chi-restraints excluded: chain J residue 766 LEU Chi-restraints excluded: chain J residue 772 TRP Chi-restraints excluded: chain J residue 852 TRP Chi-restraints excluded: chain J residue 980 GLU Chi-restraints excluded: chain J residue 994 VAL Chi-restraints excluded: chain Z residue 621 VAL Chi-restraints excluded: chain Z residue 628 VAL Chi-restraints excluded: chain Z residue 672 ARG Chi-restraints excluded: chain Z residue 743 GLN Chi-restraints excluded: chain Z residue 768 THR Chi-restraints excluded: chain Z residue 771 TYR Chi-restraints excluded: chain Z residue 773 ILE Chi-restraints excluded: chain Z residue 791 SER Chi-restraints excluded: chain Z residue 792 VAL Chi-restraints excluded: chain Z residue 795 VAL Chi-restraints excluded: chain Z residue 882 LEU Chi-restraints excluded: chain Z residue 904 PHE Chi-restraints excluded: chain Z residue 909 ASN Chi-restraints excluded: chain Z residue 976 VAL Chi-restraints excluded: chain Z residue 991 GLU Chi-restraints excluded: chain Z residue 994 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 46 optimal weight: 40.0000 chunk 79 optimal weight: 0.0470 chunk 53 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.4880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 826 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.139737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.117895 restraints weight = 21101.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.120181 restraints weight = 11595.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.121131 restraints weight = 7831.882| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9034 Z= 0.174 Angle : 0.644 8.207 12293 Z= 0.328 Chirality : 0.044 0.204 1395 Planarity : 0.005 0.064 1594 Dihedral : 6.433 58.573 1246 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.30 % Favored : 92.26 % Rotamer: Outliers : 4.48 % Allowed : 33.80 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.09 % 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: -1.78 (0.25), residues: 1137 helix: 0.07 (0.70), residues: 65 sheet: -0.38 (0.25), residues: 451 loop : -2.00 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Z 698 HIS 0.003 0.001 HIS F 734 PHE 0.023 0.002 PHE J 817 TYR 0.007 0.001 TYR F 814 ARG 0.014 0.000 ARG Z 710 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.29 seconds wall clock time: 52 minutes 4.86 seconds (3124.86 seconds total)