Starting phenix.real_space_refine on Tue Jul 29 02:26:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uza_42837/07_2025/8uza_42837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uza_42837/07_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_42837/07_2025/8uza_42837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uza_42837/07_2025/8uza_42837.map" model { file = "/net/cci-nas-00/data/ceres_data/8uza_42837/07_2025/8uza_42837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uza_42837/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.58, per 1000 atoms: 0.68 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: 3.04 Conformation dependent library (CDL) restraints added in 1.2 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: 4.33 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: 5.43 Time building geometry restraints manager: 3.62 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.260 Find NCS groups from input model: 0.100 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.000 ------------------------------------------------------------------------------- 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= 0.190 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 Details of bonding type rmsd hydrogen bonds : bond 0.12957 ( 415) hydrogen bonds : angle 4.89442 ( 1057) covalent geometry : bond 0.00428 (11646) covalent geometry : angle 0.54576 (16485) *********************** 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 : 1.077 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.3233 time to fit residues: 27.0571 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 : 0.918 ------------------------------------------------------------------------------- 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 = 0.128988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.092241 restraints weight = 17259.661| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.97 r_work: 0.2965 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- 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= 0.274 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 Details of bonding type rmsd hydrogen bonds : bond 0.06309 ( 415) hydrogen bonds : angle 4.05829 ( 1057) covalent geometry : bond 0.00619 (11646) covalent geometry : angle 0.59791 (16485) *********************** 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 : 1.036 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 75 average time/residue: 0.3264 time to fit residues: 33.0319 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 : 1.073 ------------------------------------------------------------------------------- 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: 10.0000 chunk 37 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.131478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094639 restraints weight = 17380.313| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.98 r_work: 0.3007 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11646 Z= 0.152 Angle : 0.515 7.006 16485 Z= 0.280 Chirality : 0.036 0.157 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.098 162.048 3445 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.72 % Allowed : 13.90 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.29), residues: 902 helix: 1.46 (0.29), residues: 353 sheet: -1.05 (0.50), residues: 111 loop : -0.73 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 221 HIS 0.002 0.001 HIS A 340 PHE 0.012 0.001 PHE A 418 TYR 0.014 0.001 TYR A 491 ARG 0.006 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.05274 ( 415) hydrogen bonds : angle 3.72620 ( 1057) covalent geometry : bond 0.00335 (11646) covalent geometry : angle 0.51504 (16485) *********************** 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: 14 poor density : 66 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7441 (p0) cc_final: 0.7175 (p0) REVERT: A 997 LYS cc_start: 0.8257 (mmmm) cc_final: 0.8029 (mmmm) outliers start: 14 outliers final: 7 residues processed: 76 average time/residue: 0.3134 time to fit residues: 31.9289 Evaluate side-chains 71 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 0.0270 chunk 77 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 overall best weight: 1.2040 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.132256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095649 restraints weight = 17273.908| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.92 r_work: 0.3022 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0942 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= 0.136 Angle : 0.496 6.890 16485 Z= 0.269 Chirality : 0.036 0.159 1892 Planarity : 0.003 0.037 1505 Dihedral : 22.051 160.831 3445 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.85 % Allowed : 14.39 % Favored : 83.76 % 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: 0.22 (0.29), residues: 902 helix: 1.49 (0.29), residues: 359 sheet: -0.91 (0.51), residues: 111 loop : -0.68 (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 0.008 0.001 PHE A 418 TYR 0.012 0.001 TYR A 368 ARG 0.005 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 415) hydrogen bonds : angle 3.55260 ( 1057) covalent geometry : bond 0.00296 (11646) covalent geometry : angle 0.49573 (16485) *********************** 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 85 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7558 (p0) cc_final: 0.7284 (p0) REVERT: A 997 LYS cc_start: 0.8325 (mmmm) cc_final: 0.7844 (mmmm) REVERT: A 1003 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7432 (mp0) outliers start: 15 outliers final: 9 residues processed: 80 average time/residue: 0.3510 time to fit residues: 38.8300 Evaluate side-chains 72 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL 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 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: 0.8980 chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.130317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.093087 restraints weight = 17326.086| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.02 r_work: 0.2975 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0958 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= 0.209 Angle : 0.543 6.880 16485 Z= 0.293 Chirality : 0.038 0.164 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.091 163.591 3445 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.58 % Allowed : 15.87 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.29), residues: 902 helix: 1.42 (0.29), residues: 358 sheet: -0.91 (0.51), residues: 111 loop : -0.74 (0.30), residues: 433 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 0.010 0.001 PHE A 418 TYR 0.015 0.001 TYR A 368 ARG 0.006 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.05639 ( 415) hydrogen bonds : angle 3.63462 ( 1057) covalent geometry : bond 0.00467 (11646) covalent geometry : angle 0.54262 (16485) *********************** 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: 21 poor density : 64 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7548 (p0) cc_final: 0.7277 (p0) REVERT: A 997 LYS cc_start: 0.8204 (mmmm) cc_final: 0.7796 (mmmm) REVERT: A 1003 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7348 (mp0) outliers start: 21 outliers final: 14 residues processed: 81 average time/residue: 0.2940 time to fit residues: 32.1919 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 : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 679 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 0.1980 chunk 102 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.131139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.094368 restraints weight = 17460.918| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.96 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: 0.8198 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11646 Z= 0.170 Angle : 0.521 6.942 16485 Z= 0.282 Chirality : 0.037 0.161 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.065 162.605 3445 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.58 % Allowed : 17.10 % 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: 0.17 (0.29), residues: 902 helix: 1.45 (0.29), residues: 359 sheet: -0.87 (0.51), residues: 111 loop : -0.74 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 221 HIS 0.003 0.001 HIS A 340 PHE 0.009 0.001 PHE A 170 TYR 0.014 0.001 TYR A 368 ARG 0.006 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.05365 ( 415) hydrogen bonds : angle 3.55510 ( 1057) covalent geometry : bond 0.00380 (11646) covalent geometry : angle 0.52137 (16485) *********************** 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 86 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7578 (p0) cc_final: 0.7266 (p0) REVERT: A 997 LYS cc_start: 0.8198 (mmmm) cc_final: 0.7775 (mmmm) REVERT: A 1003 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7328 (mp0) outliers start: 21 outliers final: 15 residues processed: 80 average time/residue: 0.3168 time to fit residues: 34.2987 Evaluate side-chains 79 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 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 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 32 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 0.0040 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.0270 chunk 72 optimal weight: 0.8980 overall best weight: 0.3850 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.135568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.099318 restraints weight = 17487.250| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.94 r_work: 0.3079 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11646 Z= 0.105 Angle : 0.474 6.907 16485 Z= 0.257 Chirality : 0.034 0.159 1892 Planarity : 0.003 0.037 1505 Dihedral : 21.984 156.967 3445 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.85 % Allowed : 18.33 % 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: 0.45 (0.29), residues: 902 helix: 1.70 (0.29), residues: 359 sheet: -0.68 (0.51), residues: 111 loop : -0.60 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 221 HIS 0.002 0.001 HIS A 380 PHE 0.006 0.001 PHE A 333 TYR 0.009 0.001 TYR A 368 ARG 0.004 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 415) hydrogen bonds : angle 3.30671 ( 1057) covalent geometry : bond 0.00221 (11646) covalent geometry : angle 0.47390 (16485) *********************** 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: 15 poor density : 69 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8221 (t70) cc_final: 0.7915 (t0) REVERT: A 375 ASP cc_start: 0.7406 (p0) cc_final: 0.7107 (p0) REVERT: A 997 LYS cc_start: 0.8192 (mmmm) cc_final: 0.7823 (mmmm) REVERT: A 1003 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7390 (mp0) outliers start: 15 outliers final: 9 residues processed: 79 average time/residue: 0.3163 time to fit residues: 34.2587 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 : 1.093 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 48 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.134295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097877 restraints weight = 17204.866| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.92 r_work: 0.3055 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11646 Z= 0.118 Angle : 0.475 6.870 16485 Z= 0.257 Chirality : 0.034 0.159 1892 Planarity : 0.003 0.037 1505 Dihedral : 21.969 158.443 3445 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.97 % Allowed : 17.96 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.29), residues: 902 helix: 1.74 (0.29), residues: 359 sheet: -0.61 (0.52), residues: 111 loop : -0.60 (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 380 PHE 0.006 0.001 PHE A1032 TYR 0.011 0.001 TYR A 368 ARG 0.004 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 415) hydrogen bonds : angle 3.28251 ( 1057) covalent geometry : bond 0.00257 (11646) covalent geometry : angle 0.47543 (16485) *********************** 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 83 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8270 (t70) cc_final: 0.7971 (t0) REVERT: A 375 ASP cc_start: 0.7528 (p0) cc_final: 0.7233 (p0) REVERT: A 997 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7775 (mmmm) REVERT: A 1003 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7404 (mp0) outliers start: 16 outliers final: 11 residues processed: 77 average time/residue: 0.3120 time to fit residues: 32.6740 Evaluate side-chains 76 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 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: 0.7980 chunk 58 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.130588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.093258 restraints weight = 17532.208| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.98 r_work: 0.2985 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1215 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= 0.219 Angle : 0.548 6.981 16485 Z= 0.294 Chirality : 0.038 0.161 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.002 164.461 3445 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.09 % Allowed : 17.96 % Favored : 79.95 % 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: 0.25 (0.29), residues: 902 helix: 1.54 (0.29), residues: 359 sheet: -0.75 (0.51), residues: 111 loop : -0.73 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 Details of bonding type rmsd hydrogen bonds : bond 0.05662 ( 415) hydrogen bonds : angle 3.52977 ( 1057) covalent geometry : bond 0.00495 (11646) covalent geometry : angle 0.54752 (16485) *********************** 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 81 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7606 (p0) cc_final: 0.7335 (p0) REVERT: A 997 LYS cc_start: 0.8273 (mmmm) cc_final: 0.7809 (mmmm) REVERT: A 1003 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7395 (mp0) outliers start: 17 outliers final: 15 residues processed: 77 average time/residue: 0.2910 time to fit residues: 30.5417 Evaluate side-chains 79 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 GLU 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 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: 0.0270 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 34 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.132833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095644 restraints weight = 17311.100| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.03 r_work: 0.3011 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1337 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= 0.134 Angle : 0.493 6.981 16485 Z= 0.266 Chirality : 0.035 0.158 1892 Planarity : 0.003 0.038 1505 Dihedral : 21.956 160.879 3445 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: 0.39 (0.29), residues: 902 helix: 1.64 (0.29), residues: 359 sheet: -0.68 (0.51), residues: 111 loop : -0.64 (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 340 PHE 0.007 0.001 PHE A 170 TYR 0.012 0.001 TYR A 368 ARG 0.005 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 415) hydrogen bonds : angle 3.37083 ( 1057) covalent geometry : bond 0.00294 (11646) covalent geometry : angle 0.49327 (16485) ********************** 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: 14 poor density : 64 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7560 (p0) cc_final: 0.7262 (p0) REVERT: A 997 LYS cc_start: 0.8233 (mmmm) cc_final: 0.7783 (mmmm) REVERT: A 1003 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7465 (mp0) outliers start: 14 outliers final: 11 residues processed: 75 average time/residue: 0.3061 time to fit residues: 31.2775 Evaluate side-chains 77 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 347 ASP 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: 0.0980 chunk 66 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.129068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.091636 restraints weight = 17527.441| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.09 r_work: 0.2943 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 0.006 0.047 11646 Z= 0.283 Angle : 0.603 7.060 16485 Z= 0.322 Chirality : 0.041 0.181 1892 Planarity : 0.004 0.039 1505 Dihedral : 22.064 166.312 3445 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.09 % Allowed : 18.20 % 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: 1.35 (0.28), residues: 359 sheet: -0.87 (0.50), residues: 111 loop : -0.88 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 16 HIS 0.004 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 Details of bonding type rmsd hydrogen bonds : bond 0.06258 ( 415) hydrogen bonds : angle 3.67800 ( 1057) covalent geometry : bond 0.00640 (11646) covalent geometry : angle 0.60261 (16485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5623.09 seconds wall clock time: 97 minutes 19.18 seconds (5839.18 seconds total)