Starting phenix.real_space_refine on Thu Jul 2 23:31:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uza_42837/07_2026/8uza_42837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uza_42837/07_2026/8uza_42837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uza_42837/07_2026/8uza_42837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uza_42837/07_2026/8uza_42837.map" model { file = "/net/cci-nas-00/data/ceres_data/8uza_42837/07_2026/8uza_42837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uza_42837/07_2026/8uza_42837.cif" } resolution = 3.17 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= -0.001 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 171 5.49 5 S 19 5.16 5 C 6378 2.51 5 N 2004 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11072 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 7488 Classifications: {'peptide': 910} Link IDs: {'PTRANS': 40, 'TRANS': 869} Chain breaks: 3 Chain: "B" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 2267 Classifications: {'RNA': 107} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 53} Link IDs: {'rna2p': 9, 'rna3p': 97} Chain breaks: 2 Chain: "C" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 912 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "D" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 405 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 2.85, per 1000 atoms: 0.26 Number of scatterers: 11072 At special positions: 0 Unit cell: (96.72, 133.92, 148.8, 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 19 16.00 P 171 15.00 O 2500 8.00 N 2004 7.00 C 6378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 389.1 milliseconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1732 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 42.4% alpha, 13.0% beta 51 base pairs and 98 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 46 through 77 removed outlier: 4.492A pdb=" N ARG A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 88 through 91 removed outlier: 4.088A pdb=" N GLU A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.909A pdb=" N ARG A 124 " --> pdb=" O HIS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 removed outlier: 3.856A pdb=" N SER A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 187 through 205 Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 253 through 268 removed outlier: 3.513A pdb=" N LEU A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 337 through 351 Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.834A pdb=" N PHE A 358 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 373 removed outlier: 3.514A pdb=" N PHE A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 422 through 433 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 470 through 492 Processing helix chain 'A' and resid 508 through 523 Processing helix chain 'A' and resid 667 through 679 removed outlier: 3.732A pdb=" N ARG A 671 " --> pdb=" O ARG A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 Processing helix chain 'A' and resid 718 through 727 removed outlier: 3.540A pdb=" N VAL A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 725 " --> pdb=" O ALA A 721 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 744 removed outlier: 3.545A pdb=" N ILE A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA A 736 " --> pdb=" O PRO A 732 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 775 removed outlier: 3.587A pdb=" N LEU A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 removed outlier: 3.660A pdb=" N SER A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 removed outlier: 3.816A pdb=" N GLU A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 860 through 873 removed outlier: 3.570A pdb=" N GLU A 865 " --> pdb=" O PRO A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 882 removed outlier: 3.748A pdb=" N PHE A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 951 Processing helix chain 'A' and resid 963 through 967 Processing sheet with id=AA1, first strand: chain 'A' and resid 692 through 694 Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 297 through 298 removed outlier: 6.835A pdb=" N ILE A 297 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 822 through 826 removed outlier: 6.932A pdb=" N GLN A 834 " --> pdb=" O VAL A 824 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 886 through 889 removed outlier: 4.487A pdb=" N LEU A 886 " --> pdb=" O ILE A 899 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 912 through 913 Processing sheet with id=AA7, first strand: chain 'A' and resid 937 through 944 removed outlier: 6.465A pdb=" N LYS A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU A 933 " --> pdb=" O LYS A 937 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 939 " --> pdb=" O VAL A 931 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A 931 " --> pdb=" O TYR A 939 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL A 941 " --> pdb=" O VAL A 929 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A 929 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A 943 " --> pdb=" O VAL A 927 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 931 " --> pdb=" O ARG A 977 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 956 through 957 removed outlier: 3.881A pdb=" N LYS A 968 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 5.507A pdb=" N LEU A1023 " --> pdb=" O GLY A1036 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU A1024 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A1006 " --> pdb=" O LYS A 994 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 994 " --> pdb=" O VAL A1006 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP A1008 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 11.547A pdb=" N ARG A 992 " --> pdb=" O ASP A1008 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N PHE A1010 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 11.176A pdb=" N LEU A 990 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N TYR A1012 " --> pdb=" O ILE A 988 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N ILE A 988 " --> pdb=" O TYR A1012 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N LYS A1014 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 11.612A pdb=" N ILE A 986 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 985 " --> pdb=" O TYR A1048 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A1044 " --> pdb=" O GLU A 989 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 98 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2482 1.33 - 1.45: 3190 1.45 - 1.57: 5604 1.57 - 1.69: 337 1.69 - 1.81: 33 Bond restraints: 11646 Sorted by residual: bond pdb=" C3' DA C 43 " pdb=" C2' DA C 43 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.77e+00 bond pdb=" C3' DC D 40 " pdb=" C2' DC D 40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.10e+00 bond pdb=" C3' DA C 22 " pdb=" C2' DA C 22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.03e+00 bond pdb=" C5' DA D 46 " pdb=" C4' DA D 46 " ideal model delta sigma weight residual 1.512 1.531 -0.019 7.00e-03 2.04e+04 7.75e+00 bond pdb=" C3' DT C 13 " pdb=" C2' DT C 13 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.68e+00 ... (remaining 11641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 15792 1.37 - 2.75: 602 2.75 - 4.12: 78 4.12 - 5.49: 11 5.49 - 6.87: 2 Bond angle restraints: 16485 Sorted by residual: angle pdb=" N3 DT C 15 " pdb=" C4 DT C 15 " pdb=" O4 DT C 15 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT C 5 " pdb=" C4 DT C 5 " pdb=" O4 DT C 5 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT C 35 " pdb=" C4 DT C 35 " pdb=" O4 DT C 35 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 40 " pdb=" C4 DT C 40 " pdb=" O4 DT C 40 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" C1' C B 105 " pdb=" N1 C B 105 " pdb=" C2 C B 105 " ideal model delta sigma weight residual 118.80 123.35 -4.55 1.10e+00 8.26e-01 1.71e+01 ... (remaining 16480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.67: 6433 32.67 - 65.34: 659 65.34 - 98.01: 40 98.01 - 130.68: 0 130.68 - 163.35: 3 Dihedral angle restraints: 7135 sinusoidal: 4459 harmonic: 2676 Sorted by residual: dihedral pdb=" O4' C B 105 " pdb=" C1' C B 105 " pdb=" N1 C B 105 " pdb=" C2 C B 105 " ideal model delta sinusoidal sigma weight residual 200.00 36.65 163.35 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" CA THR A 416 " pdb=" C THR A 416 " pdb=" N LYS A 417 " pdb=" CA LYS A 417 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DG C 16 " pdb=" C3' DG C 16 " pdb=" O3' DG C 16 " pdb=" P DG C 17 " ideal model delta sinusoidal sigma weight residual 220.00 59.84 160.16 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 7132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1321 0.036 - 0.072: 423 0.072 - 0.108: 110 0.108 - 0.144: 34 0.144 - 0.180: 4 Chirality restraints: 1892 Sorted by residual: chirality pdb=" C3' DG C 16 " pdb=" C4' DG C 16 " pdb=" O3' DG C 16 " pdb=" C2' DG C 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" C3' C B 77 " pdb=" C4' C B 77 " pdb=" O3' C B 77 " pdb=" C2' C B 77 " both_signs ideal model delta sigma weight residual False -2.74 -2.59 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" C1' G B 93 " pdb=" O4' G B 93 " pdb=" C2' G B 93 " pdb=" N9 G B 93 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1889 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT C 13 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.46e+00 pdb=" N1 DT C 13 " -0.030 2.00e-02 2.50e+03 pdb=" C2 DT C 13 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT C 13 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT C 13 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT C 13 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT C 13 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT C 13 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT C 13 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT C 13 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 93 " -0.024 2.00e-02 2.50e+03 1.03e-02 3.19e+00 pdb=" N9 G B 93 " 0.025 2.00e-02 2.50e+03 pdb=" C8 G B 93 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B 93 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 93 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 93 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B 93 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B 93 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G B 93 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G B 93 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 93 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 93 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 418 " 0.011 2.00e-02 2.50e+03 1.19e-02 2.50e+00 pdb=" CG PHE A 418 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 418 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 418 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 418 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 418 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 418 " -0.000 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 367 2.68 - 3.23: 9698 3.23 - 3.79: 18199 3.79 - 4.34: 24612 4.34 - 4.90: 36978 Nonbonded interactions: 89854 Sorted by model distance: nonbonded pdb=" OG SER A 381 " pdb=" O GLU A 386 " model vdw 2.122 3.040 nonbonded pdb=" OH TYR A 350 " pdb=" OD2 ASP A 403 " model vdw 2.160 3.040 nonbonded pdb=" O GLY A 178 " pdb=" O2' U B 21 " model vdw 2.167 3.040 nonbonded pdb=" O6 G B 38 " pdb=" N1 A B 41 " model vdw 2.209 2.496 nonbonded pdb=" OD2 ASP A 688 " pdb=" OH TYR A 693 " model vdw 2.229 3.040 ... (remaining 89849 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.050 Find NCS groups from input model: 0.040 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.005 0.072 11646 Z= 0.351 Angle : 0.594 6.867 16485 Z= 0.471 Chirality : 0.040 0.180 1892 Planarity : 0.004 0.035 1505 Dihedral : 21.343 163.347 5403 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.25 % Allowed : 12.05 % Favored : 87.70 % 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 are not related in a simple way. whole: -0.15 (0.28), residues: 902 helix: 1.26 (0.29), residues: 349 sheet: -1.16 (0.48), residues: 115 loop : -0.90 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 284 TYR 0.016 0.001 TYR A 368 PHE 0.027 0.001 PHE A 418 TRP 0.007 0.001 TRP A 16 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.35 (11646) covalent geometry : angle 0.59350 / 0.47 (16485) hydrogen bonds : bond 0.12957 / 8.21 ( 415) hydrogen bonds : angle 4.89442 / 3.65 ( 1057) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.354 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.1503 time to fit residues: 12.4162 Evaluate side-chains 60 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 765 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS 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 = 0.128215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091482 restraints weight = 17520.509| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.03 r_work: 0.2952 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 11646 Z= 0.307 Angle : 0.630 6.435 16485 Z= 0.358 Chirality : 0.045 0.329 1892 Planarity : 0.005 0.042 1505 Dihedral : 22.355 163.490 3447 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.85 % Allowed : 12.42 % Favored : 85.73 % 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 are not related in a simple way. whole: -0.42 (0.28), residues: 902 helix: 0.97 (0.28), residues: 353 sheet: -1.18 (0.49), residues: 113 loop : -1.05 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 284 TYR 0.027 0.002 TYR A 491 PHE 0.025 0.002 PHE A 418 TRP 0.010 0.002 TRP A 16 HIS 0.006 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.31 (11646) covalent geometry : angle 0.63003 / 0.36 (16485) hydrogen bonds : bond 0.07410 / 5.03 ( 415) hydrogen bonds : angle 4.21111 / 3.10 ( 1057) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.345 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 74 average time/residue: 0.1454 time to fit residues: 14.4659 Evaluate side-chains 66 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 1009 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.131576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094933 restraints weight = 17368.581| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.94 r_work: 0.3010 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11646 Z= 0.125 Angle : 0.493 6.897 16485 Z= 0.290 Chirality : 0.038 0.270 1892 Planarity : 0.004 0.039 1505 Dihedral : 22.329 161.071 3445 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.72 % Allowed : 13.65 % Favored : 84.62 % 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 are not related in a simple way. whole: 0.10 (0.29), residues: 902 helix: 1.41 (0.29), residues: 352 sheet: -0.97 (0.51), residues: 111 loop : -0.72 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.014 0.001 TYR A 368 PHE 0.007 0.001 PHE A 170 TRP 0.007 0.001 TRP A 221 HIS 0.003 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (11646) covalent geometry : angle 0.49273 / 0.29 (16485) hydrogen bonds : bond 0.06024 / 4.10 ( 415) hydrogen bonds : angle 3.83217 / 2.84 ( 1057) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7424 (p0) cc_final: 0.7200 (p0) REVERT: A 860 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8140 (t70) outliers start: 14 outliers final: 8 residues processed: 75 average time/residue: 0.1240 time to fit residues: 12.7099 Evaluate side-chains 71 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 47 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 0.0000 chunk 13 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.129933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.092918 restraints weight = 17582.049| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.98 r_work: 0.2978 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11646 Z= 0.200 Angle : 0.527 6.835 16485 Z= 0.306 Chirality : 0.040 0.298 1892 Planarity : 0.004 0.039 1505 Dihedral : 22.288 160.698 3445 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.34 % Allowed : 14.39 % Favored : 83.27 % 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 are not related in a simple way. whole: 0.02 (0.29), residues: 902 helix: 1.38 (0.29), residues: 353 sheet: -1.02 (0.51), residues: 111 loop : -0.81 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.015 0.001 TYR A 368 PHE 0.012 0.001 PHE A 418 TRP 0.007 0.001 TRP A 16 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (11646) covalent geometry : angle 0.52735 / 0.31 (16485) hydrogen bonds : bond 0.06293 / 4.31 ( 415) hydrogen bonds : angle 3.79867 / 2.79 ( 1057) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7590 (p0) cc_final: 0.7325 (p0) REVERT: A 997 LYS cc_start: 0.8230 (mmmm) cc_final: 0.7752 (mmmm) REVERT: A 1003 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7331 (mp0) outliers start: 19 outliers final: 13 residues processed: 78 average time/residue: 0.1300 time to fit residues: 13.7287 Evaluate side-chains 77 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 45 optimal weight: 0.0050 chunk 34 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 2.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.092892 restraints weight = 17446.804| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.05 r_work: 0.2956 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11646 Z= 0.212 Angle : 0.540 6.857 16485 Z= 0.311 Chirality : 0.041 0.301 1892 Planarity : 0.004 0.039 1505 Dihedral : 22.300 161.129 3445 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.71 % Allowed : 15.38 % Favored : 81.92 % 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 are not related in a simple way. whole: -0.10 (0.28), residues: 902 helix: 1.25 (0.28), residues: 357 sheet: -1.04 (0.50), residues: 112 loop : -0.89 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.016 0.001 TYR A 368 PHE 0.011 0.001 PHE A 418 TRP 0.008 0.001 TRP A 16 HIS 0.005 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (11646) covalent geometry : angle 0.54016 / 0.31 (16485) hydrogen bonds : bond 0.06395 / 4.39 ( 415) hydrogen bonds : angle 3.76663 / 2.76 ( 1057) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7652 (p0) cc_final: 0.7371 (p0) REVERT: A 997 LYS cc_start: 0.8228 (mmmm) cc_final: 0.7723 (mmmm) REVERT: A 1003 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7330 (mp0) outliers start: 22 outliers final: 13 residues processed: 81 average time/residue: 0.1227 time to fit residues: 13.5534 Evaluate side-chains 74 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 8 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 0.0470 chunk 93 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 90 optimal weight: 0.0270 chunk 20 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.9538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095549 restraints weight = 17360.091| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.96 r_work: 0.3022 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11646 Z= 0.118 Angle : 0.474 6.913 16485 Z= 0.278 Chirality : 0.038 0.258 1892 Planarity : 0.003 0.039 1505 Dihedral : 22.267 160.760 3445 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.72 % Allowed : 17.71 % Favored : 80.57 % 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 are not related in a simple way. whole: 0.21 (0.29), residues: 902 helix: 1.49 (0.29), residues: 358 sheet: -0.92 (0.50), residues: 111 loop : -0.68 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.012 0.001 TYR A 368 PHE 0.007 0.001 PHE A 170 TRP 0.006 0.001 TRP A 221 HIS 0.002 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (11646) covalent geometry : angle 0.47417 / 0.28 (16485) hydrogen bonds : bond 0.05526 / 3.78 ( 415) hydrogen bonds : angle 3.53812 / 2.62 ( 1057) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7590 (p0) cc_final: 0.7281 (p0) REVERT: A 997 LYS cc_start: 0.8190 (mmmm) cc_final: 0.7800 (mmmm) REVERT: A 1003 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7364 (mp0) outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 0.1330 time to fit residues: 13.6199 Evaluate side-chains 73 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 106 optimal weight: 30.0000 chunk 47 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.131715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.094921 restraints weight = 17398.423| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.97 r_work: 0.3011 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11646 Z= 0.140 Angle : 0.481 6.822 16485 Z= 0.280 Chirality : 0.038 0.270 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.247 159.881 3445 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.21 % Allowed : 17.71 % Favored : 80.07 % 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 are not related in a simple way. whole: 0.23 (0.29), residues: 902 helix: 1.50 (0.29), residues: 359 sheet: -0.84 (0.51), residues: 111 loop : -0.70 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.013 0.001 TYR A 368 PHE 0.007 0.001 PHE A1010 TRP 0.005 0.001 TRP A 16 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (11646) covalent geometry : angle 0.48059 / 0.28 (16485) hydrogen bonds : bond 0.05585 / 3.85 ( 415) hydrogen bonds : angle 3.51557 / 2.60 ( 1057) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7570 (p0) cc_final: 0.7253 (p0) REVERT: A 997 LYS cc_start: 0.8188 (mmmm) cc_final: 0.7790 (mmmm) REVERT: A 1003 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7350 (mp0) outliers start: 18 outliers final: 15 residues processed: 78 average time/residue: 0.1344 time to fit residues: 14.3765 Evaluate side-chains 78 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.129954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.092974 restraints weight = 17489.077| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.96 r_work: 0.2978 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11646 Z= 0.202 Angle : 0.530 6.789 16485 Z= 0.305 Chirality : 0.041 0.296 1892 Planarity : 0.004 0.037 1505 Dihedral : 22.275 160.807 3445 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.46 % Allowed : 18.33 % Favored : 79.21 % 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 are not related in a simple way. whole: 0.05 (0.29), residues: 902 helix: 1.36 (0.28), residues: 359 sheet: -0.94 (0.51), residues: 111 loop : -0.80 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.015 0.001 TYR A 368 PHE 0.011 0.002 PHE A1032 TRP 0.007 0.001 TRP A 16 HIS 0.005 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (11646) covalent geometry : angle 0.52988 / 0.30 (16485) hydrogen bonds : bond 0.06185 / 4.27 ( 415) hydrogen bonds : angle 3.63300 / 2.66 ( 1057) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7577 (p0) cc_final: 0.7299 (p0) REVERT: A 829 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7918 (mtp180) REVERT: A 997 LYS cc_start: 0.8195 (mmmm) cc_final: 0.7776 (mmmm) REVERT: A 1003 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7375 (mp0) outliers start: 20 outliers final: 15 residues processed: 81 average time/residue: 0.1474 time to fit residues: 16.4349 Evaluate side-chains 80 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.0370 chunk 94 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 106 optimal weight: 30.0000 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 overall best weight: 2.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN 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 = 0.130461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.093681 restraints weight = 17273.805| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.94 r_work: 0.2991 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11646 Z= 0.175 Angle : 0.511 6.857 16485 Z= 0.295 Chirality : 0.040 0.287 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.282 160.272 3445 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.46 % Allowed : 18.45 % Favored : 79.09 % 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 are not related in a simple way. whole: 0.07 (0.29), residues: 902 helix: 1.37 (0.28), residues: 359 sheet: -0.95 (0.51), residues: 111 loop : -0.79 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.014 0.001 TYR A 368 PHE 0.009 0.001 PHE A1032 TRP 0.007 0.001 TRP A 16 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (11646) covalent geometry : angle 0.51096 / 0.30 (16485) hydrogen bonds : bond 0.06013 / 4.14 ( 415) hydrogen bonds : angle 3.60340 / 2.64 ( 1057) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7531 (p0) cc_final: 0.7252 (p0) REVERT: A 997 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7786 (mmmm) REVERT: A 1003 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7373 (mp0) outliers start: 20 outliers final: 15 residues processed: 80 average time/residue: 0.1380 time to fit residues: 14.9827 Evaluate side-chains 80 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN 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 = 0.131245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094390 restraints weight = 17356.972| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.97 r_work: 0.3005 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11646 Z= 0.146 Angle : 0.492 6.893 16485 Z= 0.285 Chirality : 0.039 0.275 1892 Planarity : 0.004 0.037 1505 Dihedral : 22.279 160.240 3445 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.97 % Allowed : 19.19 % Favored : 78.84 % 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 are not related in a simple way. whole: 0.16 (0.29), residues: 902 helix: 1.45 (0.29), residues: 359 sheet: -0.89 (0.51), residues: 111 loop : -0.74 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.013 0.001 TYR A 368 PHE 0.007 0.001 PHE A1010 TRP 0.006 0.001 TRP A 16 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (11646) covalent geometry : angle 0.49193 / 0.29 (16485) hydrogen bonds : bond 0.05744 / 3.96 ( 415) hydrogen bonds : angle 3.53970 / 2.61 ( 1057) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7582 (p0) cc_final: 0.7277 (p0) REVERT: A 997 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7799 (mmmm) REVERT: A 1003 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7377 (mp0) outliers start: 16 outliers final: 14 residues processed: 76 average time/residue: 0.1371 time to fit residues: 14.0974 Evaluate side-chains 79 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 104 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.130353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.093562 restraints weight = 17402.928| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.94 r_work: 0.2990 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11646 Z= 0.184 Angle : 0.516 6.922 16485 Z= 0.297 Chirality : 0.040 0.287 1892 Planarity : 0.004 0.037 1505 Dihedral : 22.280 160.052 3445 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.21 % Allowed : 18.70 % Favored : 79.09 % 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 are not related in a simple way. whole: 0.07 (0.29), residues: 902 helix: 1.38 (0.28), residues: 359 sheet: -0.93 (0.51), residues: 111 loop : -0.80 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.015 0.001 TYR A 368 PHE 0.009 0.001 PHE A1032 TRP 0.007 0.001 TRP A 16 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (11646) covalent geometry : angle 0.51620 / 0.30 (16485) hydrogen bonds : bond 0.06035 / 4.16 ( 415) hydrogen bonds : angle 3.59693 / 2.64 ( 1057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2466.82 seconds wall clock time: 43 minutes 6.98 seconds (2586.98 seconds total)