Starting phenix.real_space_refine on Tue Mar 11 14:28:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcs_44436/03_2025/9bcs_44436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcs_44436/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bcs_44436/03_2025/9bcs_44436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcs_44436/03_2025/9bcs_44436.map" model { file = "/net/cci-nas-00/data/ceres_data/9bcs_44436/03_2025/9bcs_44436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcs_44436/03_2025/9bcs_44436.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 17, 'HIS:plan': 8, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 3, 'ASP:plan': 22, 'PHE:plan': 8, 'GLU:plan': 46, 'ARG:plan': 36} 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: {'GLN:plan1': 17, 'HIS:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 24, 'PHE:plan': 7, 'GLU:plan': 47, 'ARG:plan': 35} 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: 4.53, per 1000 atoms: 0.77 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: 3.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.62 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: 1.37 Time building geometry restraints manager: 1.86 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 1023 or resid 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 1023 or resid 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: 0.880 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.590 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.850 ------------------------------------------------------------------------------- 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 6030 Z= 0.160 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.068 0.003 TRP B 752 HIS 0.002 0.000 HIS B 491 PHE 0.010 0.001 PHE A 566 TYR 0.024 0.002 TYR A 647 ARG 0.003 0.000 ARG B 585 *********************** 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 : 0.672 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: 0.1140 time to fit residues: 10.1730 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 : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 60 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 794 ASN B 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.113472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.095129 restraints weight = 26819.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.093944 restraints weight = 37998.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094309 restraints weight = 37180.569| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6030 Z= 0.235 Angle : 0.582 6.392 8376 Z= 0.328 Chirality : 0.043 0.168 1000 Planarity : 0.005 0.052 1171 Dihedral : 8.250 84.588 1136 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 1030 helix: 1.11 (0.26), residues: 456 sheet: -0.23 (0.51), residues: 107 loop : -2.26 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1018 HIS 0.007 0.002 HIS A 708 PHE 0.015 0.002 PHE B 876 TYR 0.019 0.002 TYR A 605 ARG 0.005 0.001 ARG B 802 *********************** 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 52 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.617 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0948 time to fit residues: 8.1477 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 : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 42 optimal weight: 9.9990 chunk 64 optimal weight: 30.0000 chunk 35 optimal weight: 0.0070 chunk 99 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 overall best weight: 3.9604 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.109542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090851 restraints weight = 27079.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088937 restraints weight = 46750.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.089555 restraints weight = 42376.884| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6030 Z= 0.334 Angle : 0.662 6.803 8376 Z= 0.381 Chirality : 0.045 0.180 1000 Planarity : 0.006 0.060 1171 Dihedral : 8.296 77.792 1136 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.27), residues: 1030 helix: 0.69 (0.26), residues: 451 sheet: -0.17 (0.57), residues: 82 loop : -2.47 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 752 HIS 0.008 0.002 HIS B 931 PHE 0.019 0.002 PHE B 603 TYR 0.025 0.003 TYR A 886 ARG 0.004 0.001 ARG B 930 *********************** 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 45 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.604 Fit side-chains REVERT: B 752 TRP cc_start: 0.8392 (m-90) cc_final: 0.8036 (m100) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1028 time to fit residues: 7.6558 Evaluate side-chains 39 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 93 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 1 optimal weight: 0.0770 chunk 57 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 overall best weight: 2.9142 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.110580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091987 restraints weight = 26913.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.090064 restraints weight = 38792.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.090730 restraints weight = 35424.611| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6030 Z= 0.251 Angle : 0.590 6.595 8376 Z= 0.330 Chirality : 0.044 0.143 1000 Planarity : 0.005 0.059 1171 Dihedral : 7.563 81.085 1136 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.27), residues: 1030 helix: 1.10 (0.26), residues: 453 sheet: -0.24 (0.54), residues: 84 loop : -2.44 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 752 HIS 0.005 0.001 HIS B 931 PHE 0.025 0.002 PHE A 847 TYR 0.021 0.002 TYR B 895 ARG 0.003 0.000 ARG B 802 *********************** 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 : 0.660 Fit side-chains REVERT: B 752 TRP cc_start: 0.8288 (m-90) cc_final: 0.7911 (m100) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1356 time to fit residues: 9.5197 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 : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 77 optimal weight: 5.9990 chunk 93 optimal weight: 0.0670 chunk 88 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.112092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.093990 restraints weight = 27028.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092124 restraints weight = 44908.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092802 restraints weight = 40355.261| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6030 Z= 0.192 Angle : 0.533 6.393 8376 Z= 0.294 Chirality : 0.043 0.138 1000 Planarity : 0.005 0.055 1171 Dihedral : 7.130 88.443 1136 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.28), residues: 1030 helix: 1.64 (0.26), residues: 455 sheet: -0.56 (0.53), residues: 90 loop : -2.33 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 752 HIS 0.004 0.001 HIS B 931 PHE 0.014 0.001 PHE A 566 TYR 0.018 0.002 TYR A 605 ARG 0.002 0.000 ARG B 802 *********************** 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 51 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.580 Fit side-chains REVERT: B 752 TRP cc_start: 0.8129 (m-90) cc_final: 0.7815 (m100) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1153 time to fit residues: 9.1923 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 : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 44 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 37 optimal weight: 0.0670 chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 1.9522 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.112000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.093577 restraints weight = 26203.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091674 restraints weight = 36908.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.092440 restraints weight = 34401.775| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6030 Z= 0.191 Angle : 0.530 6.262 8376 Z= 0.292 Chirality : 0.043 0.245 1000 Planarity : 0.004 0.051 1171 Dihedral : 6.894 86.552 1136 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.28), residues: 1030 helix: 1.91 (0.26), residues: 448 sheet: -0.50 (0.49), residues: 107 loop : -2.38 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 480 HIS 0.004 0.001 HIS B 931 PHE 0.013 0.001 PHE A 566 TYR 0.025 0.002 TYR B 791 ARG 0.002 0.000 ARG B 585 *********************** 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 50 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.651 Fit side-chains REVERT: B 607 LEU cc_start: 0.9466 (tt) cc_final: 0.9252 (pp) REVERT: B 752 TRP cc_start: 0.8230 (m-90) cc_final: 0.7846 (m100) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1247 time to fit residues: 9.8950 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 : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 14 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 17 optimal weight: 0.0170 chunk 35 optimal weight: 0.0270 chunk 97 optimal weight: 0.0570 chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.112680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089010 restraints weight = 25454.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088228 restraints weight = 17919.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.088488 restraints weight = 13723.527| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6030 Z= 0.130 Angle : 0.491 6.123 8376 Z= 0.261 Chirality : 0.042 0.194 1000 Planarity : 0.004 0.044 1171 Dihedral : 6.448 88.244 1136 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.28), residues: 1030 helix: 2.51 (0.26), residues: 447 sheet: -0.45 (0.52), residues: 99 loop : -2.23 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 752 HIS 0.001 0.000 HIS A 823 PHE 0.011 0.001 PHE A 566 TYR 0.013 0.001 TYR B 791 ARG 0.002 0.000 ARG B 585 *********************** 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 56 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.605 Fit side-chains REVERT: B 607 LEU cc_start: 0.9517 (tt) cc_final: 0.9310 (pp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1143 time to fit residues: 9.8332 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 : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 74 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 39 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.109303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.087085 restraints weight = 25684.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.084128 restraints weight = 30642.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084626 restraints weight = 26981.889| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6030 Z= 0.141 Angle : 0.488 6.052 8376 Z= 0.260 Chirality : 0.042 0.198 1000 Planarity : 0.004 0.044 1171 Dihedral : 6.340 89.298 1136 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.29), residues: 1030 helix: 2.66 (0.26), residues: 447 sheet: -0.32 (0.51), residues: 111 loop : -2.12 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.002 0.001 HIS B 931 PHE 0.014 0.001 PHE A 883 TYR 0.026 0.002 TYR A 605 ARG 0.002 0.000 ARG B 585 *********************** 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 : 0.653 Fit side-chains REVERT: A 647 TYR cc_start: 0.8363 (m-80) cc_final: 0.8059 (m-80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1312 time to fit residues: 9.9231 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 : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 36 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 87 optimal weight: 0.0570 chunk 49 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.110468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.091940 restraints weight = 26674.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090400 restraints weight = 39763.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090788 restraints weight = 37846.660| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6030 Z= 0.238 Angle : 0.572 7.390 8376 Z= 0.320 Chirality : 0.044 0.196 1000 Planarity : 0.004 0.045 1171 Dihedral : 6.857 86.336 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 : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.28), residues: 1030 helix: 2.19 (0.26), residues: 449 sheet: -0.14 (0.50), residues: 107 loop : -2.29 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1018 HIS 0.006 0.001 HIS B 931 PHE 0.014 0.002 PHE A 847 TYR 0.033 0.002 TYR A 605 ARG 0.002 0.000 ARG B 930 *********************** 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 45 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.611 Fit side-chains REVERT: A 896 MET cc_start: 0.8133 (tpp) cc_final: 0.7903 (tpp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1169 time to fit residues: 8.3087 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 : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 83 optimal weight: 0.0050 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.114178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.095620 restraints weight = 26521.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094612 restraints weight = 35457.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.095146 restraints weight = 34424.301| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6030 Z= 0.144 Angle : 0.513 6.945 8376 Z= 0.274 Chirality : 0.043 0.191 1000 Planarity : 0.004 0.043 1171 Dihedral : 6.473 89.638 1136 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 1030 helix: 2.67 (0.26), residues: 448 sheet: 0.02 (0.49), residues: 110 loop : -2.15 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 480 HIS 0.002 0.000 HIS B 931 PHE 0.012 0.001 PHE A 883 TYR 0.035 0.002 TYR A 605 ARG 0.001 0.000 ARG A 802 ********************** 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 49 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.609 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1462 time to fit residues: 10.3572 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 : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 50 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.105826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082265 restraints weight = 25803.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.080920 restraints weight = 24759.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.081380 restraints weight = 20623.838| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6030 Z= 0.201 Angle : 0.544 6.877 8376 Z= 0.299 Chirality : 0.043 0.192 1000 Planarity : 0.004 0.047 1171 Dihedral : 6.667 87.033 1136 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.28), residues: 1030 helix: 2.50 (0.26), residues: 449 sheet: 0.25 (0.50), residues: 99 loop : -2.23 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 480 HIS 0.005 0.001 HIS B 931 PHE 0.012 0.001 PHE A 566 TYR 0.017 0.002 TYR B 791 ARG 0.004 0.000 ARG B 585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1679.85 seconds wall clock time: 30 minutes 1.58 seconds (1801.58 seconds total)