Starting phenix.real_space_refine on Fri Jan 17 14:14:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uza_42837/01_2025/8uza_42837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uza_42837/01_2025/8uza_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_42837/01_2025/8uza_42837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uza_42837/01_2025/8uza_42837.map" model { file = "/net/cci-nas-00/data/ceres_data/8uza_42837/01_2025/8uza_42837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uza_42837/01_2025/8uza_42837.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 6.64, per 1000 atoms: 0.60 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: 2.69 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 3.94 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: 5.45 Time building geometry restraints manager: 3.14 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' DG C 16 " pdb=" O3' DG C 16 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CB PRO A 760 " pdb=" CG PRO A 760 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.05e+00 bond pdb=" CG PRO A 760 " pdb=" CD PRO A 760 " ideal model delta sigma weight residual 1.503 1.548 -0.045 3.40e-02 8.65e+02 1.77e+00 bond pdb=" C3' C B 77 " pdb=" O3' C B 77 " ideal model delta sigma weight residual 1.427 1.445 -0.018 1.50e-02 4.44e+03 1.47e+00 bond pdb=" O4' DC C 23 " pdb=" C1' DC C 23 " ideal model delta sigma weight residual 1.414 1.393 0.021 2.00e-02 2.50e+03 1.14e+00 ... (remaining 11641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 15987 1.37 - 2.75: 411 2.75 - 4.12: 74 4.12 - 5.49: 11 5.49 - 6.87: 2 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 120.20 125.37 -5.17 1.50e+00 4.44e-01 1.19e+01 angle pdb=" C THR A 416 " pdb=" N LYS A 417 " pdb=" CA LYS A 417 " ideal model delta sigma weight residual 122.41 127.82 -5.41 2.09e+00 2.29e-01 6.70e+00 angle pdb=" CB LYS A 997 " pdb=" CG LYS A 997 " pdb=" CD LYS A 997 " ideal model delta sigma weight residual 111.30 117.07 -5.77 2.30e+00 1.89e-01 6.30e+00 angle pdb=" CA PRO A 760 " pdb=" N PRO A 760 " pdb=" CD PRO A 760 " ideal model delta sigma weight residual 112.00 108.56 3.44 1.40e+00 5.10e-01 6.04e+00 angle pdb=" C4' C B 77 " pdb=" C3' C B 77 " pdb=" O3' C B 77 " ideal model delta sigma weight residual 109.40 113.02 -3.62 1.50e+00 4.44e-01 5.81e+00 ... (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 - 0.031: 1286 0.031 - 0.063: 441 0.063 - 0.094: 108 0.094 - 0.125: 48 0.125 - 0.157: 9 Chirality restraints: 1892 Sorted by residual: 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 chirality pdb=" P A B 78 " pdb=" OP1 A B 78 " pdb=" OP2 A B 78 " pdb=" O5' A B 78 " both_signs ideal model delta sigma weight residual True 2.41 -2.55 -0.14 2.00e-01 2.50e+01 5.22e-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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 30.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.004 0.072 11646 Z= 0.269 Angle : 0.546 6.867 16485 Z= 0.297 Chirality : 0.037 0.157 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (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 TRP 0.007 0.001 TRP A 16 HIS 0.004 0.001 HIS A 340 PHE 0.027 0.001 PHE A 418 TYR 0.016 0.001 TYR A 368 ARG 0.003 0.000 ARG A 284 *********************** 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 : 1.002 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.3376 time to fit residues: 28.4587 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 : 0.989 ------------------------------------------------------------------------------- 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 90 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.128987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.092240 restraints weight = 17259.814| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.97 r_work: 0.2965 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11646 Z= 0.389 Angle : 0.598 6.796 16485 Z= 0.323 Chirality : 0.040 0.181 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.233 165.037 3447 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.85 % Allowed : 12.18 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.28), residues: 902 helix: 1.18 (0.28), residues: 353 sheet: -1.06 (0.49), residues: 112 loop : -0.93 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 16 HIS 0.005 0.001 HIS A 340 PHE 0.022 0.002 PHE A 418 TYR 0.023 0.002 TYR A 491 ARG 0.008 0.000 ARG A 284 *********************** 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 79 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 1.068 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 75 average time/residue: 0.3318 time to fit residues: 33.5166 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 : 0.937 ------------------------------------------------------------------------------- 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 32 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 72 optimal weight: 0.0070 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3729 r_free = 0.3729 target = 0.132867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096289 restraints weight = 17346.497| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.96 r_work: 0.3033 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11646 Z= 0.163 Angle : 0.496 6.995 16485 Z= 0.270 Chirality : 0.035 0.159 1892 Planarity : 0.003 0.037 1505 Dihedral : 22.058 160.425 3445 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.48 % Allowed : 13.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.29), residues: 902 helix: 1.55 (0.29), residues: 354 sheet: -0.99 (0.50), residues: 111 loop : -0.66 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 221 HIS 0.002 0.001 HIS A 680 PHE 0.010 0.001 PHE A 418 TYR 0.012 0.001 TYR A 491 ARG 0.005 0.000 ARG A 284 *********************** 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: 12 poor density : 68 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7371 (p0) cc_final: 0.7112 (p0) outliers start: 12 outliers final: 7 residues processed: 76 average time/residue: 0.3379 time to fit residues: 34.7481 Evaluate side-chains 75 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET 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 511 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 1009 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 60 optimal weight: 30.0000 chunk 38 optimal weight: 0.3980 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3674 r_free = 0.3674 target = 0.128625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.091796 restraints weight = 17398.993| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.96 r_work: 0.2957 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 11646 Z= 0.409 Angle : 0.606 6.876 16485 Z= 0.325 Chirality : 0.041 0.181 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.169 165.700 3445 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.71 % Allowed : 14.76 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.28), residues: 902 helix: 1.17 (0.28), residues: 358 sheet: -1.03 (0.50), residues: 112 loop : -0.92 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 16 HIS 0.006 0.001 HIS A 340 PHE 0.014 0.002 PHE A 418 TYR 0.019 0.002 TYR A 368 ARG 0.006 0.000 ARG A 284 *********************** 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: 22 poor density : 61 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 997 LYS cc_start: 0.8336 (mmmm) cc_final: 0.7978 (mmmm) REVERT: A 1003 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7441 (mp0) outliers start: 22 outliers final: 13 residues processed: 77 average time/residue: 0.3556 time to fit residues: 37.0026 Evaluate side-chains 75 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 331 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3730 r_free = 0.3730 target = 0.132919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.096405 restraints weight = 17284.493| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.95 r_work: 0.3034 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11646 Z= 0.156 Angle : 0.492 6.978 16485 Z= 0.267 Chirality : 0.035 0.158 1892 Planarity : 0.003 0.037 1505 Dihedral : 22.028 160.171 3445 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.72 % Allowed : 16.48 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.29), residues: 902 helix: 1.53 (0.29), residues: 359 sheet: -0.92 (0.51), residues: 111 loop : -0.69 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 221 HIS 0.002 0.001 HIS A 380 PHE 0.007 0.001 PHE A 170 TYR 0.011 0.001 TYR A 254 ARG 0.005 0.000 ARG A 284 *********************** 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 85 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7430 (p0) cc_final: 0.7121 (p0) REVERT: A 997 LYS cc_start: 0.8207 (mmmm) cc_final: 0.7882 (mmmm) REVERT: A 1003 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7377 (mp0) outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 0.3227 time to fit residues: 35.0656 Evaluate side-chains 74 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 679 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.131769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095138 restraints weight = 17430.708| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.94 r_work: 0.3013 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11646 Z= 0.209 Angle : 0.504 6.879 16485 Z= 0.273 Chirality : 0.036 0.158 1892 Planarity : 0.004 0.037 1505 Dihedral : 22.035 161.326 3445 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.46 % Allowed : 17.34 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.29), residues: 902 helix: 1.55 (0.29), residues: 359 sheet: -0.83 (0.51), residues: 111 loop : -0.69 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.002 0.001 HIS A 340 PHE 0.008 0.001 PHE A 170 TYR 0.013 0.001 TYR A 368 ARG 0.005 0.000 ARG A 284 *********************** 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 84 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7544 (p0) cc_final: 0.7247 (p0) REVERT: A 997 LYS cc_start: 0.8139 (mmmm) cc_final: 0.7808 (mmmm) REVERT: A 1003 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7417 (mp0) outliers start: 20 outliers final: 14 residues processed: 79 average time/residue: 0.3406 time to fit residues: 36.5296 Evaluate side-chains 80 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 347 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 679 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3698 r_free = 0.3698 target = 0.130455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.093616 restraints weight = 17556.958| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.96 r_work: 0.2986 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1078 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= 0.282 Angle : 0.542 7.000 16485 Z= 0.292 Chirality : 0.038 0.163 1892 Planarity : 0.004 0.037 1505 Dihedral : 22.067 163.448 3445 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.46 % Allowed : 17.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.29), residues: 902 helix: 1.43 (0.29), residues: 359 sheet: -0.90 (0.51), residues: 111 loop : -0.75 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 16 HIS 0.004 0.001 HIS A 340 PHE 0.009 0.001 PHE A1032 TYR 0.015 0.001 TYR A 368 ARG 0.006 0.000 ARG A 284 *********************** 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 84 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7527 (p0) cc_final: 0.7257 (p0) REVERT: A 997 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7953 (mmmm) REVERT: A 1003 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7475 (mm-30) outliers start: 20 outliers final: 13 residues processed: 80 average time/residue: 0.2984 time to fit residues: 32.9524 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 : 1.048 ------------------------------------------------------------------------------- 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 347 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 679 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 48 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3739 r_free = 0.3739 target = 0.133665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.097124 restraints weight = 17217.762| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.95 r_work: 0.3044 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11646 Z= 0.149 Angle : 0.485 6.954 16485 Z= 0.262 Chirality : 0.035 0.158 1892 Planarity : 0.003 0.036 1505 Dihedral : 21.994 159.290 3445 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.72 % Allowed : 18.45 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.29), residues: 902 helix: 1.63 (0.29), residues: 359 sheet: -0.79 (0.51), residues: 111 loop : -0.62 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 221 HIS 0.002 0.001 HIS A 380 PHE 0.006 0.001 PHE A 170 TYR 0.010 0.001 TYR A 368 ARG 0.005 0.000 ARG A 284 *********************** 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 82 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8280 (t70) cc_final: 0.8050 (t0) REVERT: A 375 ASP cc_start: 0.7478 (p0) cc_final: 0.7172 (p0) REVERT: A 997 LYS cc_start: 0.8236 (mmmm) cc_final: 0.8016 (mmmm) REVERT: A 1003 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7488 (mm-30) outliers start: 14 outliers final: 12 residues processed: 79 average time/residue: 0.3012 time to fit residues: 32.3818 Evaluate side-chains 79 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 347 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 679 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3679 r_free = 0.3679 target = 0.129057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.091697 restraints weight = 17620.665| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.07 r_work: 0.2955 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11646 Z= 0.398 Angle : 0.600 7.033 16485 Z= 0.320 Chirality : 0.041 0.180 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.100 165.951 3445 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.46 % Allowed : 17.84 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 902 helix: 1.32 (0.28), residues: 359 sheet: -0.89 (0.50), residues: 112 loop : -0.88 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 16 HIS 0.005 0.001 HIS A 340 PHE 0.013 0.002 PHE A1032 TYR 0.019 0.002 TYR A 368 ARG 0.006 0.001 ARG A 284 *********************** 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 84 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7688 (p0) cc_final: 0.7408 (p0) REVERT: A 997 LYS cc_start: 0.8252 (mmmm) cc_final: 0.7947 (mmmm) REVERT: A 1003 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7512 (mm-30) outliers start: 20 outliers final: 16 residues processed: 79 average time/residue: 0.2993 time to fit residues: 32.2757 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 : 1.090 ------------------------------------------------------------------------------- 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 331 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 679 GLU 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 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.131892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095170 restraints weight = 17362.135| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.94 r_work: 0.3014 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11646 Z= 0.201 Angle : 0.513 7.042 16485 Z= 0.277 Chirality : 0.036 0.159 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.018 162.124 3445 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.97 % Allowed : 18.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.29), residues: 902 helix: 1.48 (0.29), residues: 359 sheet: -0.88 (0.51), residues: 111 loop : -0.71 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 16 HIS 0.003 0.001 HIS A 340 PHE 0.008 0.001 PHE A 170 TYR 0.013 0.001 TYR A 368 ARG 0.006 0.000 ARG A 284 ********************** 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 81 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7528 (p0) cc_final: 0.7228 (p0) REVERT: A 997 LYS cc_start: 0.8222 (mmmm) cc_final: 0.7961 (mmmm) REVERT: A 1003 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7497 (mm-30) outliers start: 16 outliers final: 15 residues processed: 76 average time/residue: 0.3082 time to fit residues: 32.0669 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 : 0.978 ------------------------------------------------------------------------------- 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 347 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 679 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 8 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.130012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.092543 restraints weight = 17515.774| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.05 r_work: 0.2960 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1224 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= 0.321 Angle : 0.565 7.068 16485 Z= 0.303 Chirality : 0.039 0.170 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.064 164.333 3445 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.46 % Allowed : 18.82 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.29), residues: 902 helix: 1.35 (0.28), residues: 359 sheet: -0.91 (0.51), residues: 106 loop : -0.87 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 16 HIS 0.004 0.001 HIS A 340 PHE 0.011 0.001 PHE A1032 TYR 0.016 0.001 TYR A 368 ARG 0.006 0.000 ARG A 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5035.22 seconds wall clock time: 90 minutes 17.56 seconds (5417.56 seconds total)