Starting phenix.real_space_refine on Sat Aug 23 08:36:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uza_42837/08_2025/8uza_42837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uza_42837/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8uza_42837/08_2025/8uza_42837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uza_42837/08_2025/8uza_42837.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uza_42837/08_2025/8uza_42837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uza_42837/08_2025/8uza_42837.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 171 5.49 5 S 19 5.16 5 C 6378 2.51 5 N 2004 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11072 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 7488 Classifications: {'peptide': 910} Link IDs: {'PTRANS': 40, 'TRANS': 869} Chain breaks: 3 Chain: "B" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 2267 Classifications: {'RNA': 107} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 53} Link IDs: {'rna2p': 9, 'rna3p': 97} Chain breaks: 2 Chain: "C" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 912 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "D" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 405 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 2.55, per 1000 atoms: 0.23 Number of scatterers: 11072 At special positions: 0 Unit cell: (96.72, 133.92, 148.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 171 15.00 O 2500 8.00 N 2004 7.00 C 6378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 408.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1732 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 42.4% alpha, 13.0% beta 51 base pairs and 98 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 46 through 77 removed outlier: 4.492A pdb=" N ARG A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 88 through 91 removed outlier: 4.088A pdb=" N GLU A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.909A pdb=" N ARG A 124 " --> pdb=" O HIS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 removed outlier: 3.856A pdb=" N SER A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 187 through 205 Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 253 through 268 removed outlier: 3.513A pdb=" N LEU A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 337 through 351 Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.834A pdb=" N PHE A 358 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 373 removed outlier: 3.514A pdb=" N PHE A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 422 through 433 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 470 through 492 Processing helix chain 'A' and resid 508 through 523 Processing helix chain 'A' and resid 667 through 679 removed outlier: 3.732A pdb=" N ARG A 671 " --> pdb=" O ARG A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 Processing helix chain 'A' and resid 718 through 727 removed outlier: 3.540A pdb=" N VAL A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 725 " --> pdb=" O ALA A 721 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 744 removed outlier: 3.545A pdb=" N ILE A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA A 736 " --> pdb=" O PRO A 732 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 775 removed outlier: 3.587A pdb=" N LEU A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 removed outlier: 3.660A pdb=" N SER A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 removed outlier: 3.816A pdb=" N GLU A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 860 through 873 removed outlier: 3.570A pdb=" N GLU A 865 " --> pdb=" O PRO A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 882 removed outlier: 3.748A pdb=" N PHE A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 951 Processing helix chain 'A' and resid 963 through 967 Processing sheet with id=AA1, first strand: chain 'A' and resid 692 through 694 Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 297 through 298 removed outlier: 6.835A pdb=" N ILE A 297 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 822 through 826 removed outlier: 6.932A pdb=" N GLN A 834 " --> pdb=" O VAL A 824 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 886 through 889 removed outlier: 4.487A pdb=" N LEU A 886 " --> pdb=" O ILE A 899 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 912 through 913 Processing sheet with id=AA7, first strand: chain 'A' and resid 937 through 944 removed outlier: 6.465A pdb=" N LYS A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU A 933 " --> pdb=" O LYS A 937 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 939 " --> pdb=" O VAL A 931 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A 931 " --> pdb=" O TYR A 939 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL A 941 " --> pdb=" O VAL A 929 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A 929 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A 943 " --> pdb=" O VAL A 927 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 931 " --> pdb=" O ARG A 977 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 956 through 957 removed outlier: 3.881A pdb=" N LYS A 968 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 5.507A pdb=" N LEU A1023 " --> pdb=" O GLY A1036 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU A1024 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A1006 " --> pdb=" O LYS A 994 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 994 " --> pdb=" O VAL A1006 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP A1008 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 11.547A pdb=" N ARG A 992 " --> pdb=" O ASP A1008 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N PHE A1010 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 11.176A pdb=" N LEU A 990 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N TYR A1012 " --> pdb=" O ILE A 988 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N ILE A 988 " --> pdb=" O TYR A1012 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N LYS A1014 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 11.612A pdb=" N ILE A 986 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 985 " --> pdb=" O TYR A1048 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A1044 " --> pdb=" O GLU A 989 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 98 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.03 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.170 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.28), residues: 902 helix: 1.26 (0.29), residues: 349 sheet: -1.16 (0.48), residues: 115 loop : -0.90 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 284 TYR 0.016 0.001 TYR A 368 PHE 0.027 0.001 PHE A 418 TRP 0.007 0.001 TRP A 16 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00428 (11646) covalent geometry : angle 0.54576 (16485) hydrogen bonds : bond 0.12957 ( 415) hydrogen bonds : angle 4.89442 ( 1057) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.360 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.1216 time to fit residues: 10.2885 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 : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 765 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.127910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091044 restraints weight = 17617.101| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.08 r_work: 0.2942 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 11646 Z= 0.345 Angle : 0.654 6.871 16485 Z= 0.351 Chirality : 0.043 0.197 1892 Planarity : 0.005 0.037 1505 Dihedral : 22.287 166.482 3447 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.85 % Allowed : 12.67 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.28), residues: 902 helix: 0.96 (0.28), residues: 353 sheet: -1.14 (0.49), residues: 112 loop : -1.06 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 284 TYR 0.022 0.002 TYR A 491 PHE 0.026 0.002 PHE A 418 TRP 0.010 0.002 TRP A 16 HIS 0.006 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00779 (11646) covalent geometry : angle 0.65370 (16485) hydrogen bonds : bond 0.06859 ( 415) hydrogen bonds : angle 4.17075 ( 1057) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.349 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 73 average time/residue: 0.1360 time to fit residues: 13.0978 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 : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 1009 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.132385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095769 restraints weight = 17422.050| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.96 r_work: 0.3024 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0849 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= 0.126 Angle : 0.508 7.007 16485 Z= 0.276 Chirality : 0.036 0.159 1892 Planarity : 0.004 0.037 1505 Dihedral : 22.072 161.194 3445 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.72 % Allowed : 13.78 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.29), residues: 902 helix: 1.48 (0.29), residues: 352 sheet: -1.04 (0.50), residues: 111 loop : -0.69 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.012 0.001 TYR A 491 PHE 0.009 0.001 PHE A 418 TRP 0.006 0.001 TRP A 221 HIS 0.002 0.001 HIS A 851 Details of bonding type rmsd covalent geometry : bond 0.00274 (11646) covalent geometry : angle 0.50781 (16485) hydrogen bonds : bond 0.05069 ( 415) hydrogen bonds : angle 3.71857 ( 1057) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7443 (p0) cc_final: 0.7192 (p0) REVERT: A 997 LYS cc_start: 0.8222 (mmmm) cc_final: 0.8001 (mmmm) outliers start: 14 outliers final: 8 residues processed: 77 average time/residue: 0.1388 time to fit residues: 14.3466 Evaluate side-chains 72 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 47 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 0.0570 chunk 13 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.8902 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.130938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093990 restraints weight = 17570.926| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.98 r_work: 0.2997 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0890 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= 0.177 Angle : 0.523 6.883 16485 Z= 0.284 Chirality : 0.037 0.160 1892 Planarity : 0.004 0.037 1505 Dihedral : 22.079 162.376 3445 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.34 % Allowed : 14.88 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.29), residues: 902 helix: 1.43 (0.29), residues: 358 sheet: -0.98 (0.50), residues: 111 loop : -0.72 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.014 0.001 TYR A 368 PHE 0.009 0.001 PHE A 418 TRP 0.006 0.001 TRP A 16 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00396 (11646) covalent geometry : angle 0.52302 (16485) hydrogen bonds : bond 0.05367 ( 415) hydrogen bonds : angle 3.64986 ( 1057) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7513 (p0) cc_final: 0.7241 (p0) REVERT: A 997 LYS cc_start: 0.8188 (mmmm) cc_final: 0.7725 (mmmm) REVERT: A 1003 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7313 (mp0) outliers start: 19 outliers final: 10 residues processed: 80 average time/residue: 0.1375 time to fit residues: 14.7191 Evaluate side-chains 74 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 765 HIS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 72 optimal weight: 0.0170 chunk 45 optimal weight: 0.0370 chunk 34 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.132481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095707 restraints weight = 17394.094| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.97 r_work: 0.3024 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1032 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= 0.133 Angle : 0.495 6.903 16485 Z= 0.268 Chirality : 0.035 0.158 1892 Planarity : 0.003 0.037 1505 Dihedral : 22.040 160.450 3445 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.09 % Allowed : 16.48 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.29), residues: 902 helix: 1.53 (0.29), residues: 359 sheet: -0.84 (0.51), residues: 111 loop : -0.68 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 284 TYR 0.012 0.001 TYR A 368 PHE 0.008 0.001 PHE A 418 TRP 0.006 0.001 TRP A 221 HIS 0.002 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00292 (11646) covalent geometry : angle 0.49453 (16485) hydrogen bonds : bond 0.04944 ( 415) hydrogen bonds : angle 3.48175 ( 1057) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7518 (p0) cc_final: 0.7228 (p0) REVERT: A 997 LYS cc_start: 0.8188 (mmmm) cc_final: 0.7792 (mmmm) REVERT: A 1003 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7357 (mp0) outliers start: 17 outliers final: 13 residues processed: 80 average time/residue: 0.1520 time to fit residues: 16.2646 Evaluate side-chains 77 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 483 VAL 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 1003 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 8 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 0.0270 chunk 93 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 overall best weight: 3.0044 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.129280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.092045 restraints weight = 17491.796| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.03 r_work: 0.2959 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11646 Z= 0.252 Angle : 0.580 6.923 16485 Z= 0.311 Chirality : 0.040 0.176 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.118 164.983 3445 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.83 % Allowed : 16.85 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.29), residues: 902 helix: 1.31 (0.28), residues: 358 sheet: -0.95 (0.51), residues: 111 loop : -0.79 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.018 0.002 TYR A 368 PHE 0.011 0.002 PHE A1032 TRP 0.009 0.001 TRP A 16 HIS 0.005 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00567 (11646) covalent geometry : angle 0.57977 (16485) hydrogen bonds : bond 0.06039 ( 415) hydrogen bonds : angle 3.69712 ( 1057) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7620 (p0) cc_final: 0.7342 (p0) REVERT: A 997 LYS cc_start: 0.8222 (mmmm) cc_final: 0.7828 (mmmm) REVERT: A 1003 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7348 (mp0) outliers start: 23 outliers final: 17 residues processed: 81 average time/residue: 0.1076 time to fit residues: 12.1372 Evaluate side-chains 80 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 292 PHE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.130121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093425 restraints weight = 17460.027| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.04 r_work: 0.2965 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1074 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= 0.202 Angle : 0.546 7.069 16485 Z= 0.294 Chirality : 0.038 0.169 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.097 163.581 3445 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.58 % Allowed : 16.97 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.29), residues: 902 helix: 1.34 (0.28), residues: 358 sheet: -0.96 (0.51), residues: 112 loop : -0.80 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.015 0.001 TYR A 368 PHE 0.009 0.001 PHE A 170 TRP 0.007 0.001 TRP A 16 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00451 (11646) covalent geometry : angle 0.54575 (16485) hydrogen bonds : bond 0.05654 ( 415) hydrogen bonds : angle 3.61888 ( 1057) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7560 (p0) cc_final: 0.7282 (p0) REVERT: A 997 LYS cc_start: 0.8269 (mmmm) cc_final: 0.7816 (mmmm) REVERT: A 1003 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7338 (mp0) outliers start: 21 outliers final: 18 residues processed: 80 average time/residue: 0.1273 time to fit residues: 13.9444 Evaluate side-chains 81 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.128731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.091439 restraints weight = 17554.502| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.05 r_work: 0.2950 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11646 Z= 0.268 Angle : 0.593 7.088 16485 Z= 0.318 Chirality : 0.040 0.180 1892 Planarity : 0.004 0.039 1505 Dihedral : 22.149 165.123 3445 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.71 % Allowed : 17.22 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.28), residues: 902 helix: 1.14 (0.28), residues: 359 sheet: -1.00 (0.50), residues: 112 loop : -0.94 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 284 TYR 0.017 0.002 TYR A 368 PHE 0.012 0.002 PHE A1032 TRP 0.009 0.002 TRP A 16 HIS 0.005 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00604 (11646) covalent geometry : angle 0.59291 (16485) hydrogen bonds : bond 0.06214 ( 415) hydrogen bonds : angle 3.73745 ( 1057) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7649 (p0) cc_final: 0.7373 (p0) REVERT: A 997 LYS cc_start: 0.8280 (mmmm) cc_final: 0.7809 (mmmm) REVERT: A 1003 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7314 (mp0) outliers start: 22 outliers final: 18 residues processed: 80 average time/residue: 0.1196 time to fit residues: 12.9989 Evaluate side-chains 82 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.128092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090827 restraints weight = 17424.064| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.06 r_work: 0.2936 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1207 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= 0.288 Angle : 0.614 7.206 16485 Z= 0.329 Chirality : 0.041 0.187 1892 Planarity : 0.005 0.042 1505 Dihedral : 22.196 165.699 3445 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.34 % Allowed : 18.08 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.28), residues: 902 helix: 1.01 (0.28), residues: 358 sheet: -1.10 (0.48), residues: 112 loop : -1.03 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 284 TYR 0.018 0.002 TYR A 368 PHE 0.013 0.002 PHE A1032 TRP 0.010 0.002 TRP A 16 HIS 0.006 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00648 (11646) covalent geometry : angle 0.61413 (16485) hydrogen bonds : bond 0.06430 ( 415) hydrogen bonds : angle 3.82425 ( 1057) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7726 (p0) cc_final: 0.7447 (p0) REVERT: A 997 LYS cc_start: 0.8317 (mmmm) cc_final: 0.7821 (mmmm) REVERT: A 1003 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7303 (mp0) outliers start: 19 outliers final: 17 residues processed: 77 average time/residue: 0.1552 time to fit residues: 15.9273 Evaluate side-chains 80 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 331 ILE 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 694 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1059 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.133070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096501 restraints weight = 17400.411| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.96 r_work: 0.3038 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1321 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= 0.119 Angle : 0.504 7.056 16485 Z= 0.272 Chirality : 0.035 0.168 1892 Planarity : 0.004 0.038 1505 Dihedral : 22.042 159.661 3445 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.85 % Allowed : 18.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.29), residues: 902 helix: 1.47 (0.29), residues: 357 sheet: -0.94 (0.51), residues: 111 loop : -0.71 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.012 0.001 TYR A 368 PHE 0.007 0.001 PHE A 333 TRP 0.006 0.001 TRP A 221 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00254 (11646) covalent geometry : angle 0.50367 (16485) hydrogen bonds : bond 0.04837 ( 415) hydrogen bonds : angle 3.44677 ( 1057) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 375 ASP cc_start: 0.7456 (p0) cc_final: 0.7125 (p0) REVERT: A 997 LYS cc_start: 0.8204 (mmmm) cc_final: 0.7742 (mmmm) REVERT: A 1003 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7356 (mp0) outliers start: 15 outliers final: 12 residues processed: 79 average time/residue: 0.1388 time to fit residues: 14.6412 Evaluate side-chains 80 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.133560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.096951 restraints weight = 17428.863| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.95 r_work: 0.3042 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1454 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= 0.121 Angle : 0.490 6.912 16485 Z= 0.264 Chirality : 0.035 0.158 1892 Planarity : 0.003 0.037 1505 Dihedral : 22.014 158.752 3445 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.97 % Allowed : 18.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.29), residues: 902 helix: 1.61 (0.29), residues: 359 sheet: -0.75 (0.52), residues: 111 loop : -0.68 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 284 TYR 0.012 0.001 TYR A 368 PHE 0.006 0.001 PHE A 333 TRP 0.005 0.001 TRP A 221 HIS 0.002 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00263 (11646) covalent geometry : angle 0.48964 (16485) hydrogen bonds : bond 0.04705 ( 415) hydrogen bonds : angle 3.34388 ( 1057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2368.31 seconds wall clock time: 41 minutes 18.25 seconds (2478.25 seconds total)