Starting phenix.real_space_refine on Wed Aug 5 17:15:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uza_42837/08_2026/8uza_42837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uza_42837/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8uza_42837/08_2026/8uza_42837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uza_42837/08_2026/8uza_42837.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uza_42837/08_2026/8uza_42837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uza_42837/08_2026/8uza_42837.map" } 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-2.2rc3-6140/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: 2.34, per 1000 atoms: 0.21 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: 0.75 Conformation dependent library (CDL) restraints added in 411.3 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: 1.46 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: 2.43 Time building geometry restraints manager: 1.06 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: 15487 1.37 - 2.75: 847 2.75 - 4.12: 138 4.12 - 5.49: 10 5.49 - 6.87: 3 Bond angle restraints: 16485 Sorted by residual: angle pdb=" C3' C B 77 " pdb=" O3' C B 77 " pdb=" P A B 78 " ideal model delta sigma weight residual 119.70 125.37 -5.67 1.20e+00 6.94e-01 2.23e+01 angle pdb=" O5' U B 101 " pdb=" C5' U B 101 " pdb=" C4' U B 101 " ideal model delta sigma weight residual 109.40 112.96 -3.56 8.00e-01 1.56e+00 1.98e+01 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 ... (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: 1211 0.036 - 0.072: 424 0.072 - 0.108: 121 0.108 - 0.144: 127 0.144 - 0.180: 9 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=" 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 2.47 2.31 0.16 2.00e-01 2.50e+01 6.47e-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 ... (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: 1.030 Set stop_for_unknowns flag: 0.010 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.830 ------------------------------------------------------------------------------- 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= 0.359 Angle : 0.683 6.867 16485 Z= 0.537 Chirality : 0.050 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 0.00479 / 0.36 (11646) covalent geometry : angle 0.68316 / 0.54 (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 : 0.241 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.1503 time to fit residues: 12.5690 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 : 0.347 ------------------------------------------------------------------------------- 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: 9.9990 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 = 0.3672 r_free = 0.3672 target = 0.128377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.091755 restraints weight = 17508.023| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.95 r_work: 0.2955 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11646 Z= 0.297 Angle : 0.653 6.508 16485 Z= 0.362 Chirality : 0.048 0.341 1892 Planarity : 0.005 0.042 1505 Dihedral : 22.353 163.391 3447 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.85 % Allowed : 12.30 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.28), residues: 902 helix: 0.99 (0.28), residues: 353 sheet: -1.17 (0.49), residues: 113 loop : -1.04 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 284 TYR 0.026 0.002 TYR A 491 PHE 0.024 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 0.00661 / 0.30 (11646) covalent geometry : angle 0.65314 / 0.36 (16485) hydrogen bonds : bond 0.07527 / 5.11 ( 415) hydrogen bonds : angle 4.22899 / 3.12 ( 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: 0.1393 time to fit residues: 13.8247 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 : 0.317 ------------------------------------------------------------------------------- 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: 9.9990 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.131005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094357 restraints weight = 17424.136| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.97 r_work: 0.2999 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 : 0.003 0.036 11646 Z= 0.155 Angle : 0.518 6.593 16485 Z= 0.301 Chirality : 0.040 0.307 1892 Planarity : 0.004 0.039 1505 Dihedral : 22.305 160.393 3445 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.97 % Allowed : 13.90 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.29), residues: 902 helix: 1.32 (0.29), residues: 353 sheet: -1.01 (0.50), residues: 112 loop : -0.83 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 284 TYR 0.015 0.001 TYR A 491 PHE 0.011 0.001 PHE A 418 TRP 0.007 0.001 TRP A 221 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (11646) covalent geometry : angle 0.51756 / 0.30 (16485) hydrogen bonds : bond 0.06371 / 4.33 ( 415) hydrogen bonds : angle 3.87372 / 2.86 ( 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 80 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7485 (p0) cc_final: 0.7258 (p0) outliers start: 16 outliers final: 8 residues processed: 76 average time/residue: 0.1179 time to fit residues: 12.3055 Evaluate side-chains 70 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.129521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.092873 restraints weight = 17597.907| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.04 r_work: 0.2955 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11646 Z= 0.214 Angle : 0.563 6.520 16485 Z= 0.318 Chirality : 0.043 0.322 1892 Planarity : 0.004 0.039 1505 Dihedral : 22.290 160.253 3445 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.34 % Allowed : 14.76 % Favored : 82.90 % 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: -0.13 (0.28), residues: 902 helix: 1.23 (0.28), residues: 357 sheet: -1.07 (0.50), residues: 112 loop : -0.91 (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 0.012 0.002 PHE A 418 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 0.00468 / 0.21 (11646) covalent geometry : angle 0.56292 / 0.32 (16485) hydrogen bonds : bond 0.06619 / 4.53 ( 415) hydrogen bonds : angle 3.84019 / 2.82 ( 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 83 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7614 (p0) cc_final: 0.7351 (p0) REVERT: A 997 LYS cc_start: 0.8252 (mmmm) cc_final: 0.7748 (mmmm) REVERT: A 1003 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7324 (mp0) outliers start: 19 outliers final: 14 residues processed: 78 average time/residue: 0.1423 time to fit residues: 14.9485 Evaluate side-chains 75 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 394 MET Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 45 optimal weight: 0.0770 chunk 34 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.129008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.092256 restraints weight = 17472.589| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.94 r_work: 0.2966 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11646 Z= 0.237 Angle : 0.582 6.531 16485 Z= 0.326 Chirality : 0.044 0.331 1892 Planarity : 0.004 0.039 1505 Dihedral : 22.316 160.818 3445 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.95 % Allowed : 15.87 % Favored : 81.18 % 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 (0.28), residues: 902 helix: 1.13 (0.28), residues: 357 sheet: -1.06 (0.49), residues: 112 loop : -0.97 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.017 0.002 TYR A 368 PHE 0.012 0.002 PHE A 418 TRP 0.009 0.001 TRP A 16 HIS 0.005 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (11646) covalent geometry : angle 0.58217 / 0.33 (16485) hydrogen bonds : bond 0.06800 / 4.65 ( 415) hydrogen bonds : angle 3.85400 / 2.81 ( 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: 24 poor density : 62 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 997 LYS cc_start: 0.8299 (mmmm) cc_final: 0.7776 (mmmm) REVERT: A 1003 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7425 (mp0) outliers start: 24 outliers final: 15 residues processed: 81 average time/residue: 0.1274 time to fit residues: 13.9561 Evaluate side-chains 75 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 80 optimal weight: 0.6980 chunk 73 optimal weight: 0.0270 chunk 93 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 overall best weight: 1.1840 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.131866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.095306 restraints weight = 17404.309| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.96 r_work: 0.3017 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1002 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= 0.125 Angle : 0.490 6.553 16485 Z= 0.285 Chirality : 0.039 0.314 1892 Planarity : 0.004 0.039 1505 Dihedral : 22.271 160.090 3445 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.97 % Allowed : 17.71 % Favored : 80.32 % 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: 1.42 (0.29), residues: 357 sheet: -0.96 (0.51), residues: 111 loop : -0.67 (0.30), residues: 434 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 0.007 0.001 TRP A 221 HIS 0.003 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (11646) covalent geometry : angle 0.48984 / 0.29 (16485) hydrogen bonds : bond 0.05835 / 3.99 ( 415) hydrogen bonds : angle 3.59864 / 2.65 ( 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 81 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7548 (p0) cc_final: 0.7288 (p0) REVERT: A 997 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7742 (mmmm) REVERT: A 1003 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7365 (mp0) outliers start: 16 outliers final: 10 residues processed: 76 average time/residue: 0.1166 time to fit residues: 11.7936 Evaluate side-chains 75 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 394 MET Chi-restraints excluded: chain A residue 511 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.130598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.093956 restraints weight = 17418.669| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.05 r_work: 0.2974 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11646 Z= 0.169 Angle : 0.520 6.469 16485 Z= 0.296 Chirality : 0.040 0.318 1892 Planarity : 0.004 0.039 1505 Dihedral : 22.262 159.053 3445 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.21 % Allowed : 18.45 % Favored : 79.34 % 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: 0.11 (0.29), residues: 902 helix: 1.40 (0.29), residues: 358 sheet: -0.95 (0.51), residues: 111 loop : -0.75 (0.30), residues: 433 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 0.006 0.001 TRP A 16 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (11646) covalent geometry : angle 0.51965 / 0.30 (16485) hydrogen bonds : bond 0.06064 / 4.17 ( 415) hydrogen bonds : angle 3.62563 / 2.66 ( 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 81 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7561 (p0) cc_final: 0.7283 (p0) REVERT: A 997 LYS cc_start: 0.8229 (mmmm) cc_final: 0.7820 (mmmm) REVERT: A 1003 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7363 (mp0) outliers start: 18 outliers final: 13 residues processed: 77 average time/residue: 0.1177 time to fit residues: 12.4708 Evaluate side-chains 76 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 483 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 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: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.130933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094060 restraints weight = 17446.556| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.97 r_work: 0.3000 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11646 Z= 0.156 Angle : 0.510 6.487 16485 Z= 0.292 Chirality : 0.040 0.316 1892 Planarity : 0.004 0.039 1505 Dihedral : 22.271 159.378 3445 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.21 % Allowed : 18.45 % Favored : 79.34 % 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: 0.11 (0.29), residues: 902 helix: 1.40 (0.29), residues: 359 sheet: -0.91 (0.51), residues: 111 loop : -0.77 (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 0.008 0.001 PHE A 170 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 0.00329 / 0.16 (11646) covalent geometry : angle 0.50962 / 0.29 (16485) hydrogen bonds : bond 0.05968 / 4.10 ( 415) hydrogen bonds : angle 3.59230 / 2.64 ( 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 81 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7521 (p0) cc_final: 0.7243 (p0) REVERT: A 997 LYS cc_start: 0.8207 (mmmm) cc_final: 0.7801 (mmmm) REVERT: A 1003 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7380 (mp0) outliers start: 18 outliers final: 16 residues processed: 77 average time/residue: 0.1207 time to fit residues: 12.6323 Evaluate side-chains 81 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 109 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 394 MET Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 669 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 106 optimal weight: 30.0000 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.129127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092304 restraints weight = 17324.363| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.94 r_work: 0.2969 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11646 Z= 0.230 Angle : 0.579 6.506 16485 Z= 0.323 Chirality : 0.044 0.327 1892 Planarity : 0.004 0.040 1505 Dihedral : 22.309 160.920 3445 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.34 % Allowed : 18.57 % 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: -0.12 (0.28), residues: 902 helix: 1.21 (0.28), residues: 358 sheet: -0.93 (0.51), residues: 107 loop : -0.93 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.017 0.002 TYR A 368 PHE 0.012 0.002 PHE A1032 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 0.00504 / 0.23 (11646) covalent geometry : angle 0.57932 / 0.32 (16485) hydrogen bonds : bond 0.06645 / 4.56 ( 415) hydrogen bonds : angle 3.74575 / 2.73 ( 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 80 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7771 (p0) cc_final: 0.7483 (p0) REVERT: A 997 LYS cc_start: 0.8340 (mmmm) cc_final: 0.7918 (mmmm) REVERT: A 1003 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7471 (mp0) outliers start: 19 outliers final: 15 residues processed: 76 average time/residue: 0.1231 time to fit residues: 12.9698 Evaluate side-chains 76 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 234 GLU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 669 ILE 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: 9.9990 chunk 32 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.131428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094633 restraints weight = 17366.939| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.97 r_work: 0.3010 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11646 Z= 0.137 Angle : 0.499 6.583 16485 Z= 0.287 Chirality : 0.039 0.312 1892 Planarity : 0.004 0.039 1505 Dihedral : 22.287 159.726 3445 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.85 % Allowed : 19.19 % Favored : 78.97 % 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: 1.40 (0.29), residues: 358 sheet: -0.98 (0.50), residues: 111 loop : -0.76 (0.30), residues: 433 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 333 TRP 0.007 0.001 TRP A 221 HIS 0.003 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (11646) covalent geometry : angle 0.49941 / 0.29 (16485) hydrogen bonds : bond 0.05875 / 4.02 ( 415) hydrogen bonds : angle 3.56354 / 2.62 ( 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 78 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7507 (p0) cc_final: 0.7242 (p0) REVERT: A 997 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7797 (mmmm) REVERT: A 1003 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7382 (mp0) outliers start: 15 outliers final: 12 residues processed: 74 average time/residue: 0.1427 time to fit residues: 14.4598 Evaluate side-chains 77 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 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 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 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: 0.0010 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 84 optimal weight: 0.2980 chunk 99 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.134241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097682 restraints weight = 17355.812| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.99 r_work: 0.3057 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11646 Z= 0.104 Angle : 0.460 6.522 16485 Z= 0.268 Chirality : 0.037 0.316 1892 Planarity : 0.003 0.039 1505 Dihedral : 22.244 158.798 3445 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.48 % Allowed : 19.56 % Favored : 78.97 % 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: 0.39 (0.29), residues: 902 helix: 1.65 (0.29), residues: 357 sheet: -0.80 (0.50), residues: 111 loop : -0.61 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 284 TYR 0.011 0.001 TYR A 254 PHE 0.006 0.001 PHE A 333 TRP 0.006 0.001 TRP A 967 HIS 0.003 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.10 (11646) covalent geometry : angle 0.46046 / 0.27 (16485) hydrogen bonds : bond 0.05210 / 3.59 ( 415) hydrogen bonds : angle 3.39942 / 2.53 ( 1057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2420.04 seconds wall clock time: 42 minutes 11.09 seconds (2531.09 seconds total)