Starting phenix.real_space_refine on Sat Aug 23 01:36:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xci_38244/08_2025/8xci_38244.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xci_38244/08_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_38244/08_2025/8xci_38244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xci_38244/08_2025/8xci_38244.map" model { file = "/net/cci-nas-00/data/ceres_data/8xci_38244/08_2025/8xci_38244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xci_38244/08_2025/8xci_38244.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.39, per 1000 atoms: 0.27 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: 0.77 Conformation dependent library (CDL) restraints added in 358.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.36 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: 1.53 Time building geometry restraints manager: 1.00 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: 2.040 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 9.760 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- 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= 1.273 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 : 43.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.011 0.001 ARG J 806 TYR 0.091 0.010 TYR J 876 PHE 0.065 0.011 PHE J 904 TRP 0.035 0.007 TRP F 772 HIS 0.014 0.004 HIS Z 734 Details of bonding type rmsd covalent geometry : bond 0.01716 ( 9034) covalent geometry : angle 2.34357 (12293) hydrogen bonds : bond 0.21239 ( 301) hydrogen bonds : angle 9.81114 ( 810) *********************** 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 : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 679 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8558 (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: 0.8341 (ttm110) 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: 0.8064 (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 844 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7569 (ttp80) 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: 0.8798 (mt) outliers start: 135 outliers final: 75 residues processed: 202 average time/residue: 0.0998 time to fit residues: 27.4321 Evaluate side-chains 153 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 63 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 844 ARG 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 108 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.133340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.110330 restraints weight = 21108.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.111538 restraints weight = 13021.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.112880 restraints weight = 8986.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.113049 restraints weight = 7015.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.113171 restraints weight = 6954.275| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2051 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= 0.182 Angle : 0.814 10.493 12293 Z= 0.421 Chirality : 0.048 0.168 1395 Planarity : 0.006 0.104 1594 Dihedral : 11.880 86.822 1405 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.44 % Favored : 91.12 % Rotamer: Outliers : 7.46 % Allowed : 29.00 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.23), residues: 1137 helix: -1.32 (0.58), residues: 65 sheet: -0.87 (0.25), residues: 413 loop : -2.61 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 901 TYR 0.016 0.002 TYR F 726 PHE 0.038 0.002 PHE Z 916 TRP 0.018 0.002 TRP Z 698 HIS 0.004 0.001 HIS J 875 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9034) covalent geometry : angle 0.81410 (12293) hydrogen bonds : bond 0.04237 ( 301) hydrogen bonds : angle 7.29961 ( 810) *********************** 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: 70 poor density : 82 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 900 ASN cc_start: 0.6903 (OUTLIER) cc_final: 0.6146 (t0) REVERT: F 992 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7575 (mmtt) REVERT: J 666 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7438 (tmt170) REVERT: J 764 ARG cc_start: 0.7285 (tpp80) cc_final: 0.6466 (ttt-90) REVERT: J 772 TRP cc_start: 0.4359 (OUTLIER) cc_final: 0.2099 (m100) REVERT: J 814 TYR cc_start: 0.6058 (m-80) cc_final: 0.5207 (m-80) REVERT: J 837 LEU cc_start: 0.8316 (mt) cc_final: 0.7953 (mt) REVERT: J 925 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7622 (mtm) REVERT: Z 672 ARG cc_start: 0.5501 (OUTLIER) cc_final: 0.2592 (ptt-90) REVERT: Z 698 TRP cc_start: 0.7308 (m-90) cc_final: 0.7026 (m-90) REVERT: Z 771 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7595 (p90) outliers start: 70 outliers final: 34 residues processed: 139 average time/residue: 0.1015 time to fit residues: 19.2504 Evaluate side-chains 106 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 801 VAL 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 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 917 VAL Chi-restraints excluded: chain F residue 992 LYS Chi-restraints excluded: chain J residue 666 ARG Chi-restraints excluded: chain J residue 772 TRP Chi-restraints excluded: chain J residue 787 PHE Chi-restraints excluded: chain J residue 921 ASN Chi-restraints excluded: chain J residue 925 MET 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 994 VAL Chi-restraints excluded: chain Z residue 621 VAL Chi-restraints excluded: chain Z residue 635 TYR 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 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 65 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 12 optimal weight: 0.0270 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 981 ASN Z 919 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.136656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.113912 restraints weight = 20864.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.115823 restraints weight = 11867.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.116794 restraints weight = 8235.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.117190 restraints weight = 6456.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.117256 restraints weight = 6287.935| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9034 Z= 0.129 Angle : 0.692 12.270 12293 Z= 0.353 Chirality : 0.046 0.158 1395 Planarity : 0.005 0.088 1594 Dihedral : 8.282 59.219 1276 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.74 % Favored : 91.91 % Rotamer: Outliers : 6.40 % Allowed : 29.42 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.24), residues: 1137 helix: -0.38 (0.67), residues: 65 sheet: -0.67 (0.24), residues: 456 loop : -2.40 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 901 TYR 0.026 0.002 TYR Z 785 PHE 0.016 0.001 PHE Z 916 TRP 0.014 0.001 TRP F 772 HIS 0.003 0.001 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9034) covalent geometry : angle 0.69230 (12293) hydrogen bonds : bond 0.03618 ( 301) hydrogen bonds : angle 6.70399 ( 810) *********************** 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 142 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 82 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.7965 (pp) cc_final: 0.7563 (mt) REVERT: F 900 ASN cc_start: 0.6743 (OUTLIER) cc_final: 0.5989 (t0) REVERT: F 992 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7496 (mptt) REVERT: J 634 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6158 (tp30) REVERT: J 764 ARG cc_start: 0.7166 (tpp80) cc_final: 0.6327 (ttt-90) REVERT: J 772 TRP cc_start: 0.4121 (OUTLIER) cc_final: 0.1882 (m100) REVERT: J 814 TYR cc_start: 0.5736 (m-80) cc_final: 0.5202 (m-80) REVERT: Z 672 ARG cc_start: 0.5607 (OUTLIER) cc_final: 0.2767 (ptt-90) REVERT: Z 698 TRP cc_start: 0.7291 (m-90) cc_final: 0.7007 (m-90) REVERT: Z 710 ARG cc_start: 0.7557 (ttm110) cc_final: 0.7104 (ttm-80) REVERT: Z 743 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6448 (tm-30) REVERT: Z 771 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7661 (p90) REVERT: Z 931 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7858 (tptm) outliers start: 60 outliers final: 24 residues processed: 134 average time/residue: 0.0962 time to fit residues: 18.1103 Evaluate side-chains 101 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 815 LEU Chi-restraints excluded: chain F residue 836 GLU Chi-restraints excluded: chain F residue 837 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 992 LYS Chi-restraints excluded: chain J residue 634 GLU Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain J residue 656 LEU 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 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 771 TYR Chi-restraints excluded: chain Z residue 790 ARG 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 919 GLN Chi-restraints excluded: chain Z residue 931 LYS 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 69 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 922 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 = 0.4153 r_free = 0.4153 target = 0.131012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.109482 restraints weight = 21698.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.109754 restraints weight = 12850.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.111348 restraints weight = 9858.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.111501 restraints weight = 7437.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.112077 restraints weight = 7461.586| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.130 9034 Z= 0.306 Angle : 0.799 12.882 12293 Z= 0.410 Chirality : 0.048 0.177 1395 Planarity : 0.006 0.082 1594 Dihedral : 7.994 53.963 1254 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.05 % Favored : 87.60 % Rotamer: Outliers : 7.46 % Allowed : 29.42 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.24), residues: 1137 helix: -0.63 (0.67), residues: 65 sheet: -0.81 (0.25), residues: 439 loop : -2.47 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 790 TYR 0.024 0.002 TYR F 814 PHE 0.046 0.003 PHE Z 916 TRP 0.016 0.002 TRP F 772 HIS 0.005 0.001 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00726 ( 9034) covalent geometry : angle 0.79899 (12293) hydrogen bonds : bond 0.04417 ( 301) hydrogen bonds : angle 6.89763 ( 810) *********************** 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 135 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 65 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 845 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7794 (tt) REVERT: F 900 ASN cc_start: 0.6902 (OUTLIER) cc_final: 0.6030 (t0) REVERT: F 992 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7593 (mptt) REVERT: J 635 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: J 772 TRP cc_start: 0.4491 (OUTLIER) cc_final: 0.2192 (m100) REVERT: J 814 TYR cc_start: 0.6183 (m-80) cc_final: 0.5385 (m-80) REVERT: Z 653 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8763 (tt) REVERT: Z 672 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.3790 (ptt180) REVERT: Z 698 TRP cc_start: 0.7232 (m-90) cc_final: 0.6896 (m-90) REVERT: Z 711 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6625 (pp) REVERT: Z 991 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7207 (mp0) outliers start: 70 outliers final: 44 residues processed: 121 average time/residue: 0.0995 time to fit residues: 16.6519 Evaluate side-chains 111 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 58 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 865 VAL 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 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 772 TRP Chi-restraints excluded: chain J residue 887 THR Chi-restraints excluded: chain J residue 921 ASN Chi-restraints excluded: chain J residue 950 THR Chi-restraints excluded: chain J residue 962 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 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 711 ILE Chi-restraints excluded: chain Z residue 723 THR Chi-restraints excluded: chain Z residue 768 THR Chi-restraints excluded: chain Z residue 771 TYR 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 921 ASN Chi-restraints excluded: chain Z residue 931 LYS Chi-restraints excluded: chain Z residue 939 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4172 r_free = 0.4172 target = 0.132317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.111141 restraints weight = 21333.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.111635 restraints weight = 12344.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.112688 restraints weight = 9390.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.113119 restraints weight = 7745.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.113356 restraints weight = 7277.835| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 9034 Z= 0.221 Angle : 0.725 10.919 12293 Z= 0.373 Chirality : 0.046 0.163 1395 Planarity : 0.005 0.078 1594 Dihedral : 7.720 54.079 1254 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.94 % Favored : 89.71 % Rotamer: Outliers : 7.04 % Allowed : 29.74 % Favored : 63.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.24), residues: 1137 helix: -0.34 (0.68), residues: 65 sheet: -0.71 (0.25), residues: 421 loop : -2.47 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 901 TYR 0.013 0.002 TYR F 814 PHE 0.031 0.002 PHE Z 916 TRP 0.017 0.002 TRP J 852 HIS 0.004 0.001 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 9034) covalent geometry : angle 0.72517 (12293) hydrogen bonds : bond 0.03887 ( 301) hydrogen bonds : angle 6.73904 ( 810) *********************** 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 128 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 62 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.8205 (pp) cc_final: 0.7852 (mt) REVERT: F 845 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7788 (tt) REVERT: F 900 ASN cc_start: 0.6929 (OUTLIER) cc_final: 0.6319 (t0) REVERT: F 984 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7538 (mp) REVERT: F 992 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7571 (mptt) REVERT: J 635 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6682 (m-80) REVERT: J 772 TRP cc_start: 0.4377 (OUTLIER) cc_final: 0.2098 (m100) REVERT: J 814 TYR cc_start: 0.6077 (m-80) cc_final: 0.5407 (m-80) REVERT: Z 653 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8617 (tt) REVERT: Z 672 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.3369 (ptt-90) REVERT: Z 698 TRP cc_start: 0.7222 (m-90) cc_final: 0.6885 (m-90) REVERT: Z 743 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6370 (tm-30) REVERT: Z 991 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7220 (mp0) outliers start: 66 outliers final: 40 residues processed: 115 average time/residue: 0.0931 time to fit residues: 15.1014 Evaluate side-chains 110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 60 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 865 VAL Chi-restraints excluded: chain F residue 900 ASN 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 635 TYR Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain J residue 666 ARG 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 950 THR Chi-restraints excluded: chain J residue 962 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 629 THR 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 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 823 THR 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 931 LYS Chi-restraints excluded: chain Z residue 961 ASP 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 48 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 95 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.134956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.112713 restraints weight = 21158.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.115076 restraints weight = 11912.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.115957 restraints weight = 7876.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.116172 restraints weight = 6249.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.116337 restraints weight = 6159.674| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9034 Z= 0.140 Angle : 0.666 9.318 12293 Z= 0.341 Chirality : 0.045 0.177 1395 Planarity : 0.005 0.074 1594 Dihedral : 7.350 58.969 1254 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.36 % Favored : 91.20 % Rotamer: Outliers : 5.01 % Allowed : 32.73 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.24), residues: 1137 helix: -0.06 (0.70), residues: 65 sheet: -0.58 (0.25), residues: 444 loop : -2.37 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 710 TYR 0.008 0.001 TYR F 814 PHE 0.022 0.002 PHE Z 916 TRP 0.015 0.001 TRP F 772 HIS 0.003 0.001 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9034) covalent geometry : angle 0.66596 (12293) hydrogen bonds : bond 0.03363 ( 301) hydrogen bonds : angle 6.49197 ( 810) *********************** 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 122 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 75 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.8073 (pp) cc_final: 0.7707 (mt) REVERT: F 815 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7777 (mp) REVERT: F 900 ASN cc_start: 0.6708 (OUTLIER) cc_final: 0.6183 (t0) REVERT: F 984 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7467 (mp) REVERT: F 992 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7440 (mptt) REVERT: J 635 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6297 (m-80) REVERT: J 662 ASP cc_start: 0.7535 (p0) cc_final: 0.6094 (m-30) REVERT: J 666 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7461 (tmt170) REVERT: J 747 TRP cc_start: 0.7563 (m100) cc_final: 0.6238 (m100) REVERT: J 772 TRP cc_start: 0.4122 (OUTLIER) cc_final: 0.1810 (m100) REVERT: J 814 TYR cc_start: 0.5926 (m-80) cc_final: 0.5349 (m-80) REVERT: Z 672 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.3130 (ptt-90) REVERT: Z 743 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6364 (tm-30) REVERT: Z 991 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7198 (mp0) outliers start: 47 outliers final: 31 residues processed: 113 average time/residue: 0.1116 time to fit residues: 17.1921 Evaluate side-chains 104 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 63 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 815 LEU Chi-restraints excluded: chain F residue 836 GLU Chi-restraints excluded: chain F residue 837 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 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 778 ASN 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 771 TYR Chi-restraints excluded: chain Z residue 773 ILE Chi-restraints excluded: chain Z residue 790 ARG Chi-restraints excluded: chain Z residue 791 SER Chi-restraints excluded: chain Z residue 795 VAL Chi-restraints excluded: chain Z residue 804 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4150 r_free = 0.4150 target = 0.131028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.109824 restraints weight = 21617.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.110441 restraints weight = 13022.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.111589 restraints weight = 9492.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.111719 restraints weight = 7683.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.111802 restraints weight = 6995.776| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 9034 Z= 0.279 Angle : 0.763 11.845 12293 Z= 0.391 Chirality : 0.047 0.162 1395 Planarity : 0.006 0.075 1594 Dihedral : 7.594 54.211 1250 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.75 % Favored : 86.90 % Rotamer: Outliers : 7.36 % Allowed : 31.02 % Favored : 61.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.24), residues: 1137 helix: -0.20 (0.69), residues: 65 sheet: -0.69 (0.25), residues: 429 loop : -2.50 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Z 710 TYR 0.016 0.002 TYR Z 876 PHE 0.036 0.002 PHE Z 916 TRP 0.028 0.002 TRP Z 698 HIS 0.005 0.001 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 9034) covalent geometry : angle 0.76267 (12293) hydrogen bonds : bond 0.04151 ( 301) hydrogen bonds : angle 6.69021 ( 810) *********************** 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 133 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 64 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.8232 (pp) cc_final: 0.7879 (mt) REVERT: F 815 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7880 (mp) REVERT: F 845 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7836 (tt) REVERT: F 900 ASN cc_start: 0.6919 (OUTLIER) cc_final: 0.6300 (t0) REVERT: F 984 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7607 (mp) REVERT: F 992 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7576 (mptt) REVERT: J 634 GLU cc_start: 0.6411 (tp30) cc_final: 0.6138 (tp30) REVERT: J 635 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6365 (m-80) REVERT: J 747 TRP cc_start: 0.7742 (m100) cc_final: 0.6358 (m100) REVERT: J 772 TRP cc_start: 0.4412 (OUTLIER) cc_final: 0.2097 (m100) REVERT: J 814 TYR cc_start: 0.6160 (m-80) cc_final: 0.5885 (m-80) REVERT: Z 653 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8581 (tt) REVERT: Z 672 ARG cc_start: 0.6397 (OUTLIER) cc_final: 0.4103 (ptt180) REVERT: Z 698 TRP cc_start: 0.7437 (m-90) cc_final: 0.7025 (m-90) REVERT: Z 991 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7210 (mp0) outliers start: 69 outliers final: 43 residues processed: 121 average time/residue: 0.0979 time to fit residues: 16.7148 Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 60 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 865 VAL 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 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 921 ASN 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 768 THR Chi-restraints excluded: chain Z residue 771 TYR Chi-restraints excluded: chain Z residue 773 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 882 LEU Chi-restraints excluded: chain Z residue 904 PHE Chi-restraints excluded: chain Z residue 921 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 82 optimal weight: 0.2980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 922 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 = 0.4174 r_free = 0.4174 target = 0.132566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.110701 restraints weight = 21260.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.112304 restraints weight = 12087.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.113143 restraints weight = 8063.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.113433 restraints weight = 6862.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.113749 restraints weight = 6452.765| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9034 Z= 0.193 Angle : 0.705 9.033 12293 Z= 0.364 Chirality : 0.046 0.164 1395 Planarity : 0.006 0.072 1594 Dihedral : 7.451 57.334 1250 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.76 % Favored : 89.80 % 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 : 4.17 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.24), residues: 1137 helix: -0.09 (0.69), residues: 65 sheet: -0.61 (0.25), residues: 427 loop : -2.47 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Z 710 TYR 0.012 0.001 TYR F 814 PHE 0.026 0.002 PHE Z 916 TRP 0.021 0.002 TRP Z 698 HIS 0.004 0.001 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 9034) covalent geometry : angle 0.70536 (12293) hydrogen bonds : bond 0.03623 ( 301) hydrogen bonds : angle 6.57694 ( 810) *********************** 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 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 63 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.8189 (pp) cc_final: 0.7842 (mt) REVERT: F 815 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7840 (mp) REVERT: F 845 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7827 (tt) REVERT: F 900 ASN cc_start: 0.6734 (OUTLIER) cc_final: 0.6118 (t0) REVERT: F 984 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7564 (mp) REVERT: F 992 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7461 (mptt) REVERT: J 635 TYR cc_start: 0.6798 (OUTLIER) cc_final: 0.6273 (m-80) REVERT: J 747 TRP cc_start: 0.7605 (m100) cc_final: 0.6193 (m100) REVERT: J 772 TRP cc_start: 0.4214 (OUTLIER) cc_final: 0.1877 (m100) REVERT: J 814 TYR cc_start: 0.6034 (m-80) cc_final: 0.5787 (m-80) REVERT: Z 653 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8532 (tt) REVERT: Z 672 ARG cc_start: 0.6363 (OUTLIER) cc_final: 0.3416 (ptt-90) REVERT: Z 698 TRP cc_start: 0.7286 (m-90) cc_final: 0.6821 (m-90) REVERT: Z 991 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7198 (mp0) outliers start: 56 outliers final: 40 residues processed: 109 average time/residue: 0.1041 time to fit residues: 15.8143 Evaluate side-chains 109 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 59 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 865 VAL 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 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 777 ILE 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 629 THR 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 768 THR Chi-restraints excluded: chain Z residue 771 TYR Chi-restraints excluded: chain Z residue 773 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 0.0270 chunk 9 optimal weight: 7.9990 chunk 107 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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 826 HIS Z 919 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.137065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.115287 restraints weight = 21087.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.116840 restraints weight = 11786.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.118586 restraints weight = 7908.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.118374 restraints weight = 6323.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.118549 restraints weight = 6128.944| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9034 Z= 0.122 Angle : 0.661 7.362 12293 Z= 0.341 Chirality : 0.045 0.304 1395 Planarity : 0.005 0.068 1594 Dihedral : 6.936 55.566 1250 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.30 % Favored : 92.26 % Rotamer: Outliers : 5.01 % Allowed : 32.73 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.25), residues: 1137 helix: -0.02 (0.70), residues: 65 sheet: -0.45 (0.25), residues: 439 loop : -2.29 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Z 710 TYR 0.008 0.001 TYR F 814 PHE 0.023 0.001 PHE Z 744 TRP 0.015 0.001 TRP F 772 HIS 0.003 0.001 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9034) covalent geometry : angle 0.66130 (12293) hydrogen bonds : bond 0.03110 ( 301) hydrogen bonds : angle 6.28125 ( 810) *********************** 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 131 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 84 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.8029 (pp) cc_final: 0.7660 (mt) REVERT: F 815 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7693 (mp) REVERT: F 845 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7864 (tt) REVERT: F 900 ASN cc_start: 0.6336 (OUTLIER) cc_final: 0.6074 (t0) REVERT: F 984 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7622 (mp) REVERT: F 992 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7424 (mptt) REVERT: J 662 ASP cc_start: 0.7530 (p0) cc_final: 0.5949 (m-30) REVERT: J 666 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7312 (tmt170) REVERT: J 688 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.6586 (m-80) REVERT: J 747 TRP cc_start: 0.7542 (m100) cc_final: 0.6026 (m100) REVERT: J 772 TRP cc_start: 0.3816 (OUTLIER) cc_final: 0.1183 (m100) REVERT: J 814 TYR cc_start: 0.5865 (m-80) cc_final: 0.5379 (m-80) REVERT: Z 672 ARG cc_start: 0.6185 (OUTLIER) cc_final: 0.3210 (ptt-90) REVERT: Z 698 TRP cc_start: 0.7190 (m-90) cc_final: 0.6745 (m-90) REVERT: Z 743 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6326 (tm-30) REVERT: Z 771 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7875 (p90) outliers start: 47 outliers final: 32 residues processed: 123 average time/residue: 0.0975 time to fit residues: 16.7738 Evaluate side-chains 116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 73 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 815 LEU 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 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 654 LEU Chi-restraints excluded: chain J residue 666 ARG Chi-restraints excluded: chain J residue 688 TYR 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 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 823 THR 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 909 ASN Chi-restraints excluded: chain Z residue 919 GLN Chi-restraints excluded: chain Z residue 975 ASN Chi-restraints excluded: chain Z residue 976 VAL 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 4 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- 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 700 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.135921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.114075 restraints weight = 21238.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.115688 restraints weight = 11852.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.117246 restraints weight = 7938.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.117125 restraints weight = 6532.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.117298 restraints weight = 6254.446| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9034 Z= 0.144 Angle : 0.676 7.095 12293 Z= 0.348 Chirality : 0.045 0.242 1395 Planarity : 0.005 0.068 1594 Dihedral : 6.872 53.569 1250 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.27 % Favored : 91.29 % Rotamer: Outliers : 4.69 % Allowed : 33.80 % Favored : 61.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.25), residues: 1137 helix: 0.05 (0.70), residues: 65 sheet: -0.51 (0.25), residues: 450 loop : -2.28 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Z 710 TYR 0.008 0.001 TYR F 814 PHE 0.023 0.002 PHE J 817 TRP 0.014 0.001 TRP F 772 HIS 0.003 0.001 HIS F 734 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9034) covalent geometry : angle 0.67621 (12293) hydrogen bonds : bond 0.03295 ( 301) hydrogen bonds : angle 6.24757 ( 810) ********************** 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 116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 72 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 773 ILE cc_start: 0.8077 (pp) cc_final: 0.7701 (mt) REVERT: F 815 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7773 (mp) REVERT: F 845 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7895 (tt) REVERT: F 900 ASN cc_start: 0.6333 (OUTLIER) cc_final: 0.6094 (t0) REVERT: F 984 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7685 (mp) REVERT: F 992 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7511 (mptt) REVERT: J 662 ASP cc_start: 0.7543 (p0) cc_final: 0.5941 (m-30) REVERT: J 666 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7463 (tmt170) REVERT: J 747 TRP cc_start: 0.7597 (m100) cc_final: 0.6081 (m100) REVERT: J 772 TRP cc_start: 0.4039 (OUTLIER) cc_final: 0.1342 (m100) REVERT: J 814 TYR cc_start: 0.5948 (m-80) cc_final: 0.5394 (m-80) REVERT: Z 672 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.3440 (ptt-90) REVERT: Z 743 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6326 (tm-30) REVERT: Z 771 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7876 (p90) REVERT: Z 884 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6818 (ppp) outliers start: 44 outliers final: 31 residues processed: 107 average time/residue: 0.0996 time to fit residues: 15.1175 Evaluate side-chains 114 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 72 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 815 LEU 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 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 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 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 823 THR Chi-restraints excluded: chain Z residue 882 LEU Chi-restraints excluded: chain Z residue 884 MET 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 994 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4173 r_free = 0.4173 target = 0.132630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.111755 restraints weight = 21287.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.112410 restraints weight = 13116.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.113663 restraints weight = 9349.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.113785 restraints weight = 7382.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.114029 restraints weight = 6852.742| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3503 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= 0.228 Angle : 0.741 10.405 12293 Z= 0.380 Chirality : 0.046 0.227 1395 Planarity : 0.006 0.070 1594 Dihedral : 7.245 53.684 1248 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.26 % Favored : 88.30 % Rotamer: Outliers : 5.12 % Allowed : 33.58 % Favored : 61.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.24), residues: 1137 helix: -0.02 (0.70), residues: 65 sheet: -0.55 (0.25), residues: 432 loop : -2.38 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Z 710 TYR 0.013 0.002 TYR F 814 PHE 0.029 0.002 PHE Z 916 TRP 0.022 0.002 TRP Z 698 HIS 0.004 0.001 HIS Z 826 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 9034) covalent geometry : angle 0.74053 (12293) hydrogen bonds : bond 0.03837 ( 301) hydrogen bonds : angle 6.45034 ( 810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1622.14 seconds wall clock time: 29 minutes 0.60 seconds (1740.60 seconds total)