Starting phenix.real_space_refine on Fri Aug 22 16:39:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcs_44436/08_2025/9bcs_44436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcs_44436/08_2025/9bcs_44436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bcs_44436/08_2025/9bcs_44436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcs_44436/08_2025/9bcs_44436.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bcs_44436/08_2025/9bcs_44436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcs_44436/08_2025/9bcs_44436.map" } resolution = 4.4 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= 0.002 sd= 0.026 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 7 5.16 5 C 3655 2.51 5 N 1135 2.21 5 O 1113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s 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: 5916 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 2871 Classifications: {'peptide': 515} Incomplete info: {'truncation_to_alanine': 372} Link IDs: {'PTRANS': 21, 'TRANS': 493} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1279 Unresolved non-hydrogen angles: 1622 Unresolved non-hydrogen dihedrals: 1005 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'GLU:plan': 46, 'ARG:plan': 36, 'ASP:plan': 22, 'TYR:plan': 5, 'ASN:plan1': 16, 'PHE:plan': 8, 'HIS:plan': 8, 'GLN:plan1': 17, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 696 Chain: "B" Number of atoms: 2983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 2983 Classifications: {'peptide': 523} Incomplete info: {'truncation_to_alanine': 362} Link IDs: {'PTRANS': 21, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 1225 Unresolved non-hydrogen angles: 1551 Unresolved non-hydrogen dihedrals: 950 Unresolved non-hydrogen chiralities: 140 Planarities with less than four sites: {'GLU:plan': 47, 'TRP:plan': 1, 'ARG:plan': 35, 'ASP:plan': 24, 'TYR:plan': 6, 'ASN:plan1': 14, 'PHE:plan': 7, 'HIS:plan': 6, 'GLN:plan1': 17} Unresolved non-hydrogen planarities: 668 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.67, per 1000 atoms: 0.28 Number of scatterers: 5916 At special positions: 0 Unit cell: (82.11, 110.67, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 7 16.00 P 6 15.00 O 1113 8.00 N 1135 7.00 C 3655 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 395.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 42.9% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 545 through 557 Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 600 through 620 Processing helix chain 'A' and resid 660 through 669 Processing helix chain 'A' and resid 685 through 703 Processing helix chain 'A' and resid 715 through 726 Processing helix chain 'A' and resid 742 through 752 Processing helix chain 'A' and resid 761 through 774 Processing helix chain 'A' and resid 781 through 818 removed outlier: 3.886A pdb=" N TYR A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 831 removed outlier: 3.712A pdb=" N ARG A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 857 removed outlier: 3.840A pdb=" N LEU A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 868 through 877 removed outlier: 3.702A pdb=" N TYR A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 874 " --> pdb=" O ASN A 870 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 922 removed outlier: 3.956A pdb=" N VAL A 913 " --> pdb=" O HIS A 909 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 917 " --> pdb=" O VAL A 913 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 976 removed outlier: 4.455A pdb=" N ASN A 968 " --> pdb=" O GLY A 964 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 969 " --> pdb=" O ASP A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 996 removed outlier: 3.599A pdb=" N VAL A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 558 Processing helix chain 'B' and resid 587 through 594 removed outlier: 3.842A pdb=" N ASN B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 621 removed outlier: 3.562A pdb=" N GLY B 621 " --> pdb=" O PHE B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.723A pdb=" N CYS B 634 " --> pdb=" O SER B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 667 Processing helix chain 'B' and resid 671 through 677 Processing helix chain 'B' and resid 685 through 702 Processing helix chain 'B' and resid 715 through 726 Processing helix chain 'B' and resid 741 through 752 removed outlier: 3.533A pdb=" N ARG B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 773 Processing helix chain 'B' and resid 781 through 818 removed outlier: 3.827A pdb=" N LEU B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR B 818 " --> pdb=" O GLU B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 832 removed outlier: 3.816A pdb=" N GLY B 832 " --> pdb=" O GLN B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 857 Processing helix chain 'B' and resid 861 through 877 removed outlier: 3.933A pdb=" N LEU B 868 " --> pdb=" O GLN B 864 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 869 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN B 870 " --> pdb=" O VAL B 866 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP B 871 " --> pdb=" O THR B 867 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 912 removed outlier: 4.037A pdb=" N HIS B 909 " --> pdb=" O GLY B 906 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA B 910 " --> pdb=" O ARG B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 920 removed outlier: 3.544A pdb=" N ALA B 919 " --> pdb=" O ARG B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 975 removed outlier: 4.227A pdb=" N ASN B 968 " --> pdb=" O GLY B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 996 removed outlier: 3.579A pdb=" N VAL B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 533 through 536 Processing sheet with id=AA2, first strand: chain 'A' and resid 634 through 635 Processing sheet with id=AA3, first strand: chain 'A' and resid 886 through 887 removed outlier: 3.718A pdb=" N THR A 844 " --> pdb=" O SER A 899 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER A 842 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY A 946 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR A 844 " --> pdb=" O HIS A 944 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS A 944 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR A 846 " --> pdb=" O GLY A 942 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY A 942 " --> pdb=" O TYR A 846 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 848 " --> pdb=" O ARG A 940 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG A 940 " --> pdb=" O SER A 848 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 951 " --> pdb=" O CYS A 961 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS A 961 " --> pdb=" O GLY A 951 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 953 " --> pdb=" O ARG A 959 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 886 through 887 removed outlier: 3.718A pdb=" N THR A 844 " --> pdb=" O SER A 899 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER A 842 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY A 946 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR A 844 " --> pdb=" O HIS A 944 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS A 944 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR A 846 " --> pdb=" O GLY A 942 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY A 942 " --> pdb=" O TYR A 846 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 848 " --> pdb=" O ARG A 940 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG A 940 " --> pdb=" O SER A 848 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N HIS A 983 " --> pdb=" O LEU A 939 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 941 " --> pdb=" O HIS A 983 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N SER A 985 " --> pdb=" O ILE A 941 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE A 943 " --> pdb=" O SER A 985 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE A 982 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU A1019 " --> pdb=" O GLU A1001 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU A1001 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A1021 " --> pdb=" O GLU A 999 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.917A pdb=" N LEU B 579 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 838 through 839 removed outlier: 3.695A pdb=" N GLU B 838 " --> pdb=" O ALA B 950 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 886 through 891 removed outlier: 4.046A pdb=" N VAL B 888 " --> pdb=" O MET B 896 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N MET B 896 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N THR B 890 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA B 894 " --> pdb=" O THR B 890 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 844 " --> pdb=" O SER B 899 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS B 981 " --> pdb=" O LEU B 939 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE B 941 " --> pdb=" O LYS B 981 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 983 " --> pdb=" O ILE B 941 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE B 982 " --> pdb=" O LEU B1019 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR B1017 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR B1016 " --> pdb=" O ARG B1003 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU B 999 " --> pdb=" O LEU B1020 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 981 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: 0.88 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2169 1.34 - 1.46: 1205 1.46 - 1.58: 2634 1.58 - 1.69: 10 1.69 - 1.81: 12 Bond restraints: 6030 Sorted by residual: bond pdb=" C PRO B 573 " pdb=" N PRO B 574 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.04e+00 bond pdb=" N TYR B 895 " pdb=" CA TYR B 895 " ideal model delta sigma weight residual 1.454 1.470 -0.016 1.23e-02 6.61e+03 1.72e+00 bond pdb=" C GLU B 484 " pdb=" N PRO B 485 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.05e+00 bond pdb=" C PRO A 573 " pdb=" N PRO A 574 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.63e-01 bond pdb=" C LEU A 817 " pdb=" N TYR A 818 " ideal model delta sigma weight residual 1.330 1.341 -0.011 1.36e-02 5.41e+03 6.56e-01 ... (remaining 6025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 8069 1.27 - 2.54: 223 2.54 - 3.81: 61 3.81 - 5.08: 16 5.08 - 6.36: 7 Bond angle restraints: 8376 Sorted by residual: angle pdb=" N ASP A 646 " pdb=" CA ASP A 646 " pdb=" C ASP A 646 " ideal model delta sigma weight residual 110.80 116.71 -5.91 2.13e+00 2.20e-01 7.69e+00 angle pdb=" N LEU A 817 " pdb=" CA LEU A 817 " pdb=" C LEU A 817 " ideal model delta sigma weight residual 112.38 115.68 -3.30 1.22e+00 6.72e-01 7.31e+00 angle pdb=" N PRO B 584 " pdb=" CA PRO B 584 " pdb=" C PRO B 584 " ideal model delta sigma weight residual 110.40 114.55 -4.15 1.61e+00 3.86e-01 6.65e+00 angle pdb=" C ARG B 787 " pdb=" CA ARG B 787 " pdb=" CB ARG B 787 " ideal model delta sigma weight residual 110.85 115.17 -4.32 1.70e+00 3.46e-01 6.47e+00 angle pdb=" C ALA B 894 " pdb=" N TYR B 895 " pdb=" CA TYR B 895 " ideal model delta sigma weight residual 122.81 118.86 3.95 1.57e+00 4.06e-01 6.33e+00 ... (remaining 8371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3339 17.93 - 35.86: 113 35.86 - 53.79: 33 53.79 - 71.73: 3 71.73 - 89.66: 5 Dihedral angle restraints: 3493 sinusoidal: 496 harmonic: 2997 Sorted by residual: dihedral pdb=" CA THR A 645 " pdb=" C THR A 645 " pdb=" N ASP A 646 " pdb=" CA ASP A 646 " ideal model delta harmonic sigma weight residual 180.00 151.74 28.26 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA TYR B 527 " pdb=" C TYR B 527 " pdb=" N LYS B 528 " pdb=" CA LYS B 528 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA PHE B 707 " pdb=" C PHE B 707 " pdb=" N HIS B 708 " pdb=" CA HIS B 708 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 755 0.044 - 0.089: 174 0.089 - 0.133: 69 0.133 - 0.177: 1 0.177 - 0.221: 1 Chirality restraints: 1000 Sorted by residual: chirality pdb=" CB ILE A 542 " pdb=" CA ILE A 542 " pdb=" CG1 ILE A 542 " pdb=" CG2 ILE A 542 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA TYR B 895 " pdb=" N TYR B 895 " pdb=" C TYR B 895 " pdb=" CB TYR B 895 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ILE A 578 " pdb=" N ILE A 578 " pdb=" C ILE A 578 " pdb=" CB ILE A 578 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 997 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 752 " 0.022 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP B 752 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP B 752 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 752 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 752 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 752 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 752 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 752 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 752 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 752 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 656 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO B 657 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 657 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 657 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 572 " 0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A 573 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 573 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 573 " 0.021 5.00e-02 4.00e+02 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 857 2.76 - 3.29: 5517 3.29 - 3.83: 9092 3.83 - 4.36: 7918 4.36 - 4.90: 14630 Nonbonded interactions: 38014 Sorted by model distance: nonbonded pdb=" O ILE B 820 " pdb=" OH TYR B 886 " model vdw 2.221 3.040 nonbonded pdb=" N GLN A 686 " pdb=" OE1 GLN A 686 " model vdw 2.302 3.120 nonbonded pdb=" OD1 ASN A 633 " pdb=" O1G ATP A1100 " model vdw 2.315 2.432 nonbonded pdb=" O ILE A 820 " pdb=" OH TYR A 886 " model vdw 2.377 3.040 nonbonded pdb=" O PRO B 761 " pdb=" N GLN B 764 " model vdw 2.385 3.120 ... (remaining 38009 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 'A' and ((resid 473 through 479 and (name N or name CA or name C or name \ O or name CB )) or resid 480 through 485 or (resid 525 through 567 and (name N o \ r name CA or name C or name O or name CB )) or resid 568 through 587 or (resid 5 \ 88 through 602 and (name N or name CA or name C or name O or name CB )) or resid \ 603 or (resid 604 through 613 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 614 through 626 and (name N or name CA or name C or name O or \ name CB )) or resid 627 through 646 or (resid 647 and (name N or name CA or name \ C or name O or name CB )) or (resid 648 through 656 and (name N or name CA or n \ ame C or name O or name CB )) or resid 657 through 665 or (resid 666 through 671 \ and (name N or name CA or name C or name O or name CB )) or resid 672 through 6 \ 85 or (resid 686 through 687 and (name N or name CA or name C or name O or name \ CB )) or resid 688 through 707 or (resid 708 through 710 and (name N or name CA \ or name C or name O or name CB )) or resid 711 through 754 or (resid 755 and (na \ me N or name CA or name C or name O or name CB )) or resid 756 through 783 or (r \ esid 784 through 790 and (name N or name CA or name C or name O or name CB )) or \ resid 791 through 811 or (resid 812 through 817 and (name N or name CA or name \ C or name O or name CB )) or resid 818 through 869 or (resid 870 through 872 and \ (name N or name CA or name C or name O or name CB )) or resid 873 through 874 o \ r (resid 875 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 76 through 881 or (resid 882 and (name N or name CA or name C or name O or name \ CB )) or resid 883 or (resid 884 through 885 and (name N or name CA or name C or \ name O or name CB )) or resid 886 through 898 or (resid 899 and (name N or name \ CA or name C or name O or name CB )) or resid 900 through 917 or (resid 918 thr \ ough 926 and (name N or name CA or name C or name O or name CB )) or resid 927 t \ hrough 1016 or (resid 1017 and (name N or name CA or name C or name O or name CB \ )) or resid 1018 through 1100)) selection = (chain 'B' and (resid 473 through 485 or resid 495 or (resid 526 through 567 and \ (name N or name CA or name C or name O or name CB )) or resid 568 through 581 o \ r (resid 582 through 583 and (name N or name CA or name C or name O or name CB ) \ ) or resid 584 or (resid 585 and (name N or name CA or name C or name O or name \ CB )) or resid 586 or (resid 587 through 602 and (name N or name CA or name C or \ name O or name CB )) or resid 603 through 606 or (resid 607 through 613 and (na \ me N or name CA or name C or name O or name CB )) or (resid 614 through 620 and \ (name N or name CA or name C or name O or name CB )) or (resid 621 through 632 a \ nd (name N or name CA or name C or name O or name CB )) or resid 633 through 641 \ or (resid 642 through 647 and (name N or name CA or name C or name O or name CB \ )) or resid 648 through 667 or (resid 668 through 671 and (name N or name CA or \ name C or name O or name CB )) or resid 672 through 690 or (resid 691 through 6 \ 93 and (name N or name CA or name C or name O or name CB )) or resid 694 through \ 733 or (resid 734 through 739 and (name N or name CA or name C or name O or nam \ e CB )) or resid 740 through 743 or (resid 744 and (name N or name CA or name C \ or name O or name CB )) or (resid 745 through 755 and (name N or name CA or name \ C or name O or name CB )) or resid 756 through 760 or (resid 761 through 790 an \ d (name N or name CA or name C or name O or name CB )) or resid 791 through 792 \ or (resid 793 and (name N or name CA or name C or name O or name CB )) or resid \ 794 through 818 or (resid 819 through 821 and (name N or name CA or name C or na \ me O or name CB )) or resid 822 through 835 or (resid 836 through 839 and (name \ N or name CA or name C or name O or name CB )) or resid 840 through 862 or (resi \ d 863 through 872 and (name N or name CA or name C or name O or name CB )) or re \ sid 873 through 886 or (resid 887 through 891 and (name N or name CA or name C o \ r name O or name CB )) or resid 892 through 915 or (resid 916 through 926 and (n \ ame N or name CA or name C or name O or name CB )) or resid 927 through 930 or ( \ resid 931 and (name N or name CA or name C or name O or name CB )) or resid 932 \ through 939 or (resid 940 through 941 and (name N or name CA or name C or name O \ or name CB )) or resid 942 through 958 or (resid 959 and (name N or name CA or \ name C or name O or name CB )) or resid 960 through 962 or (resid 963 and (name \ N or name CA or name C or name O or name CB )) or (resid 964 through 994 and (na \ me N or name CA or name C or name O or name CB )) or resid 995 through 997 or (r \ esid 998 through 1003 and (name N or name CA or name C or name O or name CB )) o \ r resid 1004 through 1100)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.200 Find NCS groups from input model: 0.130 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.002 0.038 6033 Z= 0.121 Angle : 0.570 6.356 8376 Z= 0.313 Chirality : 0.043 0.221 1000 Planarity : 0.004 0.049 1171 Dihedral : 12.172 89.657 1551 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.57 % Allowed : 0.57 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.28), residues: 1030 helix: 1.36 (0.27), residues: 441 sheet: -1.15 (0.46), residues: 116 loop : -1.89 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.024 0.002 TYR A 647 PHE 0.010 0.001 PHE A 566 TRP 0.068 0.003 TRP B 752 HIS 0.002 0.000 HIS B 491 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6030) covalent geometry : angle 0.56984 ( 8376) hydrogen bonds : bond 0.15421 ( 336) hydrogen bonds : angle 5.47217 ( 981) Misc. bond : bond 0.00073 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: B 895 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8465 (m-10) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.0456 time to fit residues: 4.1164 Evaluate side-chains 50 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 30.0000 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 708 HIS B 794 ASN B 983 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.111588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093165 restraints weight = 27121.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092541 restraints weight = 47031.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.092964 restraints weight = 41909.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.092863 restraints weight = 28446.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093159 restraints weight = 25936.041| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6033 Z= 0.234 Angle : 0.635 6.404 8376 Z= 0.364 Chirality : 0.044 0.178 1000 Planarity : 0.006 0.054 1171 Dihedral : 8.347 83.863 1136 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.27), residues: 1030 helix: 0.90 (0.26), residues: 451 sheet: -0.60 (0.48), residues: 116 loop : -2.39 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 802 TYR 0.019 0.003 TYR B 895 PHE 0.016 0.002 PHE B 603 TRP 0.022 0.002 TRP B 752 HIS 0.007 0.002 HIS A 708 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 6030) covalent geometry : angle 0.63531 ( 8376) hydrogen bonds : bond 0.04649 ( 336) hydrogen bonds : angle 5.22834 ( 981) Misc. bond : bond 0.00078 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.176 Fit side-chains REVERT: A 896 MET cc_start: 0.8299 (tpp) cc_final: 0.8095 (tpp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0393 time to fit residues: 3.1932 Evaluate side-chains 43 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 76 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 31 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 0.0070 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 708 HIS B 794 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.112598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.094245 restraints weight = 27158.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092260 restraints weight = 43274.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.093008 restraints weight = 40827.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093261 restraints weight = 25372.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093470 restraints weight = 24664.025| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6033 Z= 0.177 Angle : 0.573 6.843 8376 Z= 0.319 Chirality : 0.043 0.167 1000 Planarity : 0.005 0.058 1171 Dihedral : 7.787 80.224 1136 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.27), residues: 1030 helix: 1.19 (0.26), residues: 455 sheet: -0.09 (0.56), residues: 81 loop : -2.36 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 930 TYR 0.019 0.002 TYR A 886 PHE 0.014 0.002 PHE A 566 TRP 0.014 0.001 TRP B1018 HIS 0.004 0.001 HIS B 931 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6030) covalent geometry : angle 0.57342 ( 8376) hydrogen bonds : bond 0.03859 ( 336) hydrogen bonds : angle 4.54282 ( 981) Misc. bond : bond 0.00059 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.261 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0550 time to fit residues: 4.1860 Evaluate side-chains 44 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 88 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 794 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.112473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.094579 restraints weight = 27012.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.093781 restraints weight = 30612.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094121 restraints weight = 29887.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094063 restraints weight = 22260.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094234 restraints weight = 22348.593| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6033 Z= 0.144 Angle : 0.544 6.646 8376 Z= 0.299 Chirality : 0.043 0.138 1000 Planarity : 0.005 0.053 1171 Dihedral : 7.120 82.560 1136 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.28), residues: 1030 helix: 1.55 (0.26), residues: 455 sheet: -0.02 (0.58), residues: 78 loop : -2.28 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 802 TYR 0.019 0.002 TYR A 605 PHE 0.016 0.001 PHE A 847 TRP 0.014 0.002 TRP B1018 HIS 0.004 0.001 HIS B 931 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6030) covalent geometry : angle 0.54370 ( 8376) hydrogen bonds : bond 0.03310 ( 336) hydrogen bonds : angle 4.22794 ( 981) Misc. bond : bond 0.00095 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.233 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0548 time to fit residues: 3.9867 Evaluate side-chains 42 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 42 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 794 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.111515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093196 restraints weight = 27515.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091782 restraints weight = 43607.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092227 restraints weight = 40576.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092397 restraints weight = 25585.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092592 restraints weight = 24452.453| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6033 Z= 0.162 Angle : 0.558 7.253 8376 Z= 0.308 Chirality : 0.043 0.146 1000 Planarity : 0.005 0.052 1171 Dihedral : 7.122 87.354 1136 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.28), residues: 1030 helix: 1.66 (0.26), residues: 454 sheet: -0.19 (0.53), residues: 90 loop : -2.35 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 932 TYR 0.018 0.002 TYR A 605 PHE 0.013 0.002 PHE A 566 TRP 0.010 0.001 TRP A1018 HIS 0.005 0.001 HIS B 931 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6030) covalent geometry : angle 0.55788 ( 8376) hydrogen bonds : bond 0.03519 ( 336) hydrogen bonds : angle 4.33953 ( 981) Misc. bond : bond 0.00065 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0564 time to fit residues: 4.0717 Evaluate side-chains 41 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 83 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 37 optimal weight: 0.0060 chunk 86 optimal weight: 0.0040 chunk 75 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 overall best weight: 3.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 794 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.109262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.090241 restraints weight = 26641.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088644 restraints weight = 42122.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089380 restraints weight = 37079.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089295 restraints weight = 23457.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089513 restraints weight = 23925.328| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6033 Z= 0.219 Angle : 0.606 6.489 8376 Z= 0.343 Chirality : 0.044 0.158 1000 Planarity : 0.005 0.054 1171 Dihedral : 7.399 84.393 1136 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.27), residues: 1030 helix: 1.38 (0.26), residues: 453 sheet: -0.20 (0.50), residues: 101 loop : -2.56 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 930 TYR 0.028 0.003 TYR B 895 PHE 0.017 0.002 PHE A 847 TRP 0.013 0.002 TRP A1018 HIS 0.006 0.002 HIS A 708 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 6030) covalent geometry : angle 0.60551 ( 8376) hydrogen bonds : bond 0.04125 ( 336) hydrogen bonds : angle 4.88211 ( 981) Misc. bond : bond 0.00072 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.148 Fit side-chains REVERT: B 846 TYR cc_start: 0.8679 (t80) cc_final: 0.8403 (t80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0424 time to fit residues: 3.2656 Evaluate side-chains 41 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 794 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.109905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.091293 restraints weight = 26732.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089607 restraints weight = 39866.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.090113 restraints weight = 39367.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090091 restraints weight = 25133.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.090302 restraints weight = 24537.433| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6033 Z= 0.184 Angle : 0.581 6.313 8376 Z= 0.325 Chirality : 0.044 0.236 1000 Planarity : 0.005 0.054 1171 Dihedral : 7.255 86.200 1136 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.28), residues: 1030 helix: 1.65 (0.26), residues: 448 sheet: -0.26 (0.49), residues: 101 loop : -2.61 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 585 TYR 0.030 0.003 TYR A 605 PHE 0.013 0.002 PHE A 566 TRP 0.011 0.002 TRP A1018 HIS 0.006 0.001 HIS B 931 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6030) covalent geometry : angle 0.58090 ( 8376) hydrogen bonds : bond 0.03669 ( 336) hydrogen bonds : angle 4.58484 ( 981) Misc. bond : bond 0.00068 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0471 time to fit residues: 3.5600 Evaluate side-chains 41 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 68 optimal weight: 0.0370 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 8 optimal weight: 20.0000 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 794 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.112978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.094268 restraints weight = 26457.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.092327 restraints weight = 37810.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.092867 restraints weight = 34529.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.093499 restraints weight = 24369.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093548 restraints weight = 21362.500| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6033 Z= 0.106 Angle : 0.516 6.161 8376 Z= 0.279 Chirality : 0.043 0.224 1000 Planarity : 0.004 0.049 1171 Dihedral : 6.757 88.977 1136 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.28), residues: 1030 helix: 2.29 (0.27), residues: 446 sheet: -0.18 (0.49), residues: 108 loop : -2.40 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 585 TYR 0.020 0.001 TYR B 960 PHE 0.012 0.001 PHE A 566 TRP 0.014 0.001 TRP A 480 HIS 0.002 0.001 HIS B 931 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 6030) covalent geometry : angle 0.51585 ( 8376) hydrogen bonds : bond 0.02735 ( 336) hydrogen bonds : angle 3.72883 ( 981) Misc. bond : bond 0.00059 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.215 Fit side-chains REVERT: B 607 LEU cc_start: 0.9537 (tt) cc_final: 0.9327 (pp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0646 time to fit residues: 4.5942 Evaluate side-chains 42 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 794 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.113624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095490 restraints weight = 26707.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.094438 restraints weight = 35802.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094767 restraints weight = 37178.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.094733 restraints weight = 24295.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094976 restraints weight = 22301.034| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6033 Z= 0.098 Angle : 0.501 6.059 8376 Z= 0.267 Chirality : 0.042 0.223 1000 Planarity : 0.004 0.046 1171 Dihedral : 6.449 89.494 1136 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.29), residues: 1030 helix: 2.66 (0.26), residues: 445 sheet: 0.11 (0.51), residues: 108 loop : -2.28 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 585 TYR 0.017 0.001 TYR B 960 PHE 0.012 0.001 PHE A 847 TRP 0.014 0.001 TRP A 480 HIS 0.002 0.001 HIS B 931 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 6030) covalent geometry : angle 0.50114 ( 8376) hydrogen bonds : bond 0.02388 ( 336) hydrogen bonds : angle 3.40087 ( 981) Misc. bond : bond 0.00054 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.248 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0623 time to fit residues: 4.7284 Evaluate side-chains 44 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 8 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 794 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.106426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087417 restraints weight = 26856.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086072 restraints weight = 34420.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.086486 restraints weight = 35437.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086478 restraints weight = 24081.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.086665 restraints weight = 24810.146| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 6033 Z= 0.310 Angle : 0.692 6.265 8376 Z= 0.401 Chirality : 0.047 0.229 1000 Planarity : 0.006 0.054 1171 Dihedral : 7.578 82.967 1136 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.27), residues: 1030 helix: 1.23 (0.25), residues: 446 sheet: -0.07 (0.52), residues: 99 loop : -2.72 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 930 TYR 0.019 0.003 TYR B 873 PHE 0.019 0.002 PHE A 847 TRP 0.025 0.003 TRP B 480 HIS 0.007 0.002 HIS B 931 Details of bonding type rmsd covalent geometry : bond 0.00587 ( 6030) covalent geometry : angle 0.69239 ( 8376) hydrogen bonds : bond 0.04767 ( 336) hydrogen bonds : angle 5.39192 ( 981) Misc. bond : bond 0.00062 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.233 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0675 time to fit residues: 4.1436 Evaluate side-chains 38 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 794 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.110852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.091515 restraints weight = 26629.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.090257 restraints weight = 34928.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.090785 restraints weight = 29984.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090733 restraints weight = 20349.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090781 restraints weight = 22292.461| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6033 Z= 0.134 Angle : 0.564 7.338 8376 Z= 0.308 Chirality : 0.044 0.220 1000 Planarity : 0.004 0.049 1171 Dihedral : 7.003 87.188 1136 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.28), residues: 1030 helix: 2.05 (0.26), residues: 448 sheet: 0.08 (0.55), residues: 86 loop : -2.56 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 585 TYR 0.016 0.002 TYR B 960 PHE 0.013 0.001 PHE A 847 TRP 0.018 0.002 TRP B 480 HIS 0.004 0.001 HIS B 931 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6030) covalent geometry : angle 0.56355 ( 8376) hydrogen bonds : bond 0.03223 ( 336) hydrogen bonds : angle 4.14427 ( 981) Misc. bond : bond 0.00071 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 906.56 seconds wall clock time: 16 minutes 16.57 seconds (976.57 seconds total)