Starting phenix.real_space_refine on Mon Jun 9 01:51:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k10_22619/06_2025/7k10_22619.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k10_22619/06_2025/7k10_22619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k10_22619/06_2025/7k10_22619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k10_22619/06_2025/7k10_22619.map" model { file = "/net/cci-nas-00/data/ceres_data/7k10_22619/06_2025/7k10_22619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k10_22619/06_2025/7k10_22619.cif" } resolution = 3.3 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 6396 2.51 5 N 1714 2.21 5 O 1870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10037 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 10037 Classifications: {'peptide': 1259} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1205} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 6.26, per 1000 atoms: 0.62 Number of scatterers: 10037 At special positions: 0 Unit cell: (107.88, 96.28, 131.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1870 8.00 N 1714 7.00 C 6396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 3 sheets defined 61.0% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 2801 through 2820 removed outlier: 3.796A pdb=" N SER A2814 " --> pdb=" O SER A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 removed outlier: 3.896A pdb=" N ASN A2830 " --> pdb=" O LEU A2826 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN A2831 " --> pdb=" O SER A2827 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2863 removed outlier: 4.295A pdb=" N CYS A2857 " --> pdb=" O PRO A2853 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A2858 " --> pdb=" O PHE A2854 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN A2859 " --> pdb=" O VAL A2855 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A2860 " --> pdb=" O SER A2856 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A2861 " --> pdb=" O CYS A2857 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A2863 " --> pdb=" O GLN A2859 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2884 removed outlier: 3.935A pdb=" N SER A2877 " --> pdb=" O PRO A2873 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A2878 " --> pdb=" O ALA A2874 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A2882 " --> pdb=" O ALA A2878 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2897 removed outlier: 3.793A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A2891 " --> pdb=" O PRO A2887 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2932 removed outlier: 3.754A pdb=" N ALA A2927 " --> pdb=" O TRP A2923 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2953 through 2962 removed outlier: 3.826A pdb=" N ALA A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A2960 " --> pdb=" O ALA A2956 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2969 through 2977 removed outlier: 3.938A pdb=" N ASP A2973 " --> pdb=" O ALA A2969 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A2975 " --> pdb=" O GLN A2971 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A2977 " --> pdb=" O ASP A2973 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3004 Processing helix chain 'A' and resid 3039 through 3053 removed outlier: 4.481A pdb=" N TYR A3043 " --> pdb=" O THR A3039 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A3044 " --> pdb=" O TYR A3040 " (cutoff:3.500A) Processing helix chain 'A' and resid 3061 through 3069 Processing helix chain 'A' and resid 3083 through 3093 removed outlier: 3.619A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3096 through 3115 removed outlier: 3.646A pdb=" N TYR A3101 " --> pdb=" O ASP A3097 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3147 removed outlier: 3.927A pdb=" N LYS A3147 " --> pdb=" O SER A3143 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3165 removed outlier: 3.642A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A3160 " --> pdb=" O PRO A3156 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A3165 " --> pdb=" O LEU A3161 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3197 removed outlier: 3.644A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A3195 " --> pdb=" O SER A3191 " (cutoff:3.500A) Processing helix chain 'A' and resid 3231 through 3249 removed outlier: 4.064A pdb=" N SER A3237 " --> pdb=" O SER A3233 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A3241 " --> pdb=" O SER A3237 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET A3242 " --> pdb=" O MET A3238 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A3248 " --> pdb=" O ASP A3244 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A3249 " --> pdb=" O SER A3245 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3262 removed outlier: 4.081A pdb=" N LYS A3257 " --> pdb=" O SER A3253 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A3258 " --> pdb=" O LEU A3254 " (cutoff:3.500A) Processing helix chain 'A' and resid 3272 through 3288 Processing helix chain 'A' and resid 3295 through 3303 removed outlier: 3.701A pdb=" N VAL A3300 " --> pdb=" O GLN A3296 " (cutoff:3.500A) Processing helix chain 'A' and resid 3320 through 3341 removed outlier: 4.013A pdb=" N GLN A3326 " --> pdb=" O ALA A3322 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A3327 " --> pdb=" O PHE A3323 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A3332 " --> pdb=" O ILE A3328 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A3334 " --> pdb=" O LEU A3330 " (cutoff:3.500A) Processing helix chain 'A' and resid 3344 through 3349 removed outlier: 4.075A pdb=" N LEU A3348 " --> pdb=" O GLU A3344 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A3349 " --> pdb=" O PRO A3345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3344 through 3349' Processing helix chain 'A' and resid 3354 through 3361 Processing helix chain 'A' and resid 3371 through 3391 removed outlier: 4.563A pdb=" N LEU A3377 " --> pdb=" O VAL A3373 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS A3384 " --> pdb=" O ARG A3380 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A3388 " --> pdb=" O HIS A3384 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL A3389 " --> pdb=" O LEU A3385 " (cutoff:3.500A) Processing helix chain 'A' and resid 3409 through 3429 removed outlier: 3.890A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A3429 " --> pdb=" O ARG A3425 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 4.074A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A3453 " --> pdb=" O LYS A3449 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3464 through 3475 removed outlier: 3.971A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3479 through 3488 removed outlier: 3.982A pdb=" N THR A3484 " --> pdb=" O LEU A3480 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A3486 " --> pdb=" O LEU A3482 " (cutoff:3.500A) Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3514 through 3525 Processing helix chain 'A' and resid 3530 through 3538 removed outlier: 3.632A pdb=" N ILE A3534 " --> pdb=" O VAL A3530 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A3536 " --> pdb=" O PRO A3532 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3562 removed outlier: 3.605A pdb=" N LYS A3550 " --> pdb=" O SER A3546 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A3552 " --> pdb=" O GLY A3548 " (cutoff:3.500A) Processing helix chain 'A' and resid 3568 through 3577 Processing helix chain 'A' and resid 3580 through 3594 removed outlier: 4.323A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3616 removed outlier: 4.173A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3621 through 3627 removed outlier: 3.810A pdb=" N GLY A3626 " --> pdb=" O ALA A3622 " (cutoff:3.500A) Processing helix chain 'A' and resid 3632 through 3637 Processing helix chain 'A' and resid 3644 through 3651 Processing helix chain 'A' and resid 3660 through 3670 removed outlier: 3.636A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3684 removed outlier: 4.048A pdb=" N CYS A3683 " --> pdb=" O LEU A3680 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A3684 " --> pdb=" O LYS A3681 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3680 through 3684' Processing helix chain 'A' and resid 3758 through 3776 removed outlier: 3.758A pdb=" N GLN A3762 " --> pdb=" O LEU A3758 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A3776 " --> pdb=" O ASN A3772 " (cutoff:3.500A) Processing helix chain 'A' and resid 3778 through 3783 removed outlier: 3.532A pdb=" N GLN A3783 " --> pdb=" O SER A3779 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 4.032A pdb=" N MET A3820 " --> pdb=" O LEU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 removed outlier: 3.635A pdb=" N ALA A3826 " --> pdb=" O GLN A3822 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A3827 " --> pdb=" O GLU A3823 " (cutoff:3.500A) Processing helix chain 'A' and resid 3834 through 3848 removed outlier: 3.612A pdb=" N TYR A3839 " --> pdb=" O PRO A3835 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3860 removed outlier: 3.848A pdb=" N TYR A3859 " --> pdb=" O TYR A3855 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 removed outlier: 3.751A pdb=" N THR A3867 " --> pdb=" O ASN A3863 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A3868 " --> pdb=" O ARG A3864 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR A3869 " --> pdb=" O THR A3865 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A3873 " --> pdb=" O THR A3869 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3889 Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 3.971A pdb=" N LEU A3898 " --> pdb=" O PRO A3894 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A3902 " --> pdb=" O LEU A3898 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP A3916 " --> pdb=" O CYS A3912 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A3918 " --> pdb=" O SER A3914 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3970 removed outlier: 3.625A pdb=" N ILE A3968 " --> pdb=" O THR A3964 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3992 removed outlier: 3.832A pdb=" N SER A3982 " --> pdb=" O GLY A3978 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A3983 " --> pdb=" O LEU A3979 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3995 through 4002 removed outlier: 4.252A pdb=" N THR A3999 " --> pdb=" O PRO A3995 " (cutoff:3.500A) Processing helix chain 'A' and resid 4003 through 4008 Processing helix chain 'A' and resid 4010 through 4014 Processing helix chain 'A' and resid 4016 through 4023 Processing helix chain 'A' and resid 4038 through 4052 removed outlier: 3.535A pdb=" N GLN A4042 " --> pdb=" O TRP A4038 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4069 removed outlier: 3.845A pdb=" N THR A4060 " --> pdb=" O PRO A4056 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A4067 " --> pdb=" O GLU A4063 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A4069 " --> pdb=" O LEU A4065 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4081 Processing helix chain 'A' and resid 4088 through 4092 removed outlier: 3.712A pdb=" N ALA A4091 " --> pdb=" O ASN A4088 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4112 removed outlier: 3.594A pdb=" N THR A4112 " --> pdb=" O MET A4108 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4118 Processing sheet with id=AA1, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 3.802A pdb=" N GLY A3721 " --> pdb=" O ARG A3741 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 3.802A pdb=" N GLY A3721 " --> pdb=" O ARG A3741 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3809 through 3811 437 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3195 1.34 - 1.46: 2035 1.46 - 1.58: 4922 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 10246 Sorted by residual: bond pdb=" CB ASP A3563 " pdb=" CG ASP A3563 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 4.95e+00 bond pdb=" C LEU A3041 " pdb=" N PRO A3042 " ideal model delta sigma weight residual 1.335 1.364 -0.028 1.36e-02 5.41e+03 4.29e+00 bond pdb=" C TYR A4039 " pdb=" N PRO A4040 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.01e+00 bond pdb=" C ILE A3701 " pdb=" N PRO A3702 " ideal model delta sigma weight residual 1.326 1.354 -0.028 1.44e-02 4.82e+03 3.74e+00 bond pdb=" CA ASP A3563 " pdb=" CB ASP A3563 " ideal model delta sigma weight residual 1.530 1.562 -0.032 1.69e-02 3.50e+03 3.52e+00 ... (remaining 10241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 13503 2.68 - 5.37: 280 5.37 - 8.05: 42 8.05 - 10.74: 16 10.74 - 13.42: 3 Bond angle restraints: 13844 Sorted by residual: angle pdb=" C LEU A3562 " pdb=" N ASP A3563 " pdb=" CA ASP A3563 " ideal model delta sigma weight residual 121.54 132.05 -10.51 1.91e+00 2.74e-01 3.03e+01 angle pdb=" C SER A3891 " pdb=" N THR A3892 " pdb=" CA THR A3892 " ideal model delta sigma weight residual 121.54 131.02 -9.48 1.91e+00 2.74e-01 2.46e+01 angle pdb=" C HIS A3122 " pdb=" N GLN A3123 " pdb=" CA GLN A3123 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" C GLY A3678 " pdb=" N ASN A3679 " pdb=" CA ASN A3679 " ideal model delta sigma weight residual 121.54 130.06 -8.52 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C GLU A3807 " pdb=" N ASN A3808 " pdb=" CA ASN A3808 " ideal model delta sigma weight residual 122.61 129.38 -6.77 1.56e+00 4.11e-01 1.88e+01 ... (remaining 13839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5487 17.93 - 35.86: 639 35.86 - 53.79: 97 53.79 - 71.72: 16 71.72 - 89.65: 12 Dihedral angle restraints: 6251 sinusoidal: 2552 harmonic: 3699 Sorted by residual: dihedral pdb=" CA GLU A3698 " pdb=" C GLU A3698 " pdb=" N LEU A3699 " pdb=" CA LEU A3699 " ideal model delta harmonic sigma weight residual 180.00 -145.36 -34.64 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" CA LEU A3699 " pdb=" C LEU A3699 " pdb=" N GLU A3700 " pdb=" CA GLU A3700 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA LEU A3918 " pdb=" C LEU A3918 " pdb=" N GLY A3919 " pdb=" CA GLY A3919 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 6248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1164 0.059 - 0.117: 307 0.117 - 0.176: 53 0.176 - 0.235: 6 0.235 - 0.293: 3 Chirality restraints: 1533 Sorted by residual: chirality pdb=" CB ILE A3701 " pdb=" CA ILE A3701 " pdb=" CG1 ILE A3701 " pdb=" CG2 ILE A3701 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASN A3808 " pdb=" N ASN A3808 " pdb=" C ASN A3808 " pdb=" CB ASN A3808 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ASP A3563 " pdb=" N ASP A3563 " pdb=" C ASP A3563 " pdb=" CB ASP A3563 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1530 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A3835 " 0.057 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO A3836 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A3836 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A3836 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A3083 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C SER A3083 " 0.058 2.00e-02 2.50e+03 pdb=" O SER A3083 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN A3084 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A3676 " -0.051 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO A3677 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A3677 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A3677 " -0.043 5.00e-02 4.00e+02 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2996 2.82 - 3.34: 8778 3.34 - 3.86: 15246 3.86 - 4.38: 17624 4.38 - 4.90: 31241 Nonbonded interactions: 75885 Sorted by model distance: nonbonded pdb=" OH TYR A3855 " pdb=" OE1 GLU A4122 " model vdw 2.300 3.040 nonbonded pdb=" O TYR A3043 " pdb=" OG SER A3047 " model vdw 2.304 3.040 nonbonded pdb=" O SER A3657 " pdb=" OG SER A3657 " model vdw 2.315 3.040 nonbonded pdb=" O SER A3228 " pdb=" OG SER A3228 " model vdw 2.316 3.040 nonbonded pdb=" O LEU A3011 " pdb=" OG SER A3015 " model vdw 2.316 3.040 ... (remaining 75880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.920 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.070 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: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 : 0.006 0.085 10246 Z= 0.254 Angle : 0.978 13.419 13844 Z= 0.522 Chirality : 0.055 0.293 1533 Planarity : 0.007 0.085 1774 Dihedral : 15.434 89.646 3843 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.59 % Favored : 89.33 % Rotamer: Outliers : 0.37 % Allowed : 9.69 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.28 (0.17), residues: 1247 helix: -3.20 (0.13), residues: 763 sheet: -1.30 (0.78), residues: 39 loop : -4.03 (0.22), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A4124 HIS 0.004 0.001 HIS A3924 PHE 0.024 0.002 PHE A2809 TYR 0.016 0.002 TYR A3043 ARG 0.006 0.001 ARG A3125 Details of bonding type rmsd hydrogen bonds : bond 0.12149 ( 436) hydrogen bonds : angle 6.02432 ( 1296) covalent geometry : bond 0.00576 (10246) covalent geometry : angle 0.97809 (13844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 1.214 Fit side-chains REVERT: A 3044 MET cc_start: 0.6601 (tmm) cc_final: 0.6317 (ttt) REVERT: A 3154 GLN cc_start: 0.7174 (pp30) cc_final: 0.6925 (pp30) REVERT: A 3194 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6854 (tm-30) REVERT: A 3238 MET cc_start: 0.7481 (mtp) cc_final: 0.7235 (mtm) REVERT: A 3240 MET cc_start: 0.7723 (tpp) cc_final: 0.7410 (tpp) REVERT: A 3526 PRO cc_start: 0.8490 (Cg_endo) cc_final: 0.8245 (Cg_exo) REVERT: A 3544 ASP cc_start: 0.7241 (t0) cc_final: 0.6979 (t0) REVERT: A 3604 LYS cc_start: 0.7084 (tptt) cc_final: 0.6677 (ttpp) REVERT: A 3665 MET cc_start: 0.5941 (ppp) cc_final: 0.5561 (ppp) REVERT: A 3718 ARG cc_start: 0.8095 (mmt-90) cc_final: 0.7796 (mpt180) REVERT: A 3918 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8474 (pp) outliers start: 4 outliers final: 1 residues processed: 153 average time/residue: 0.2760 time to fit residues: 58.1825 Evaluate side-chains 122 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 3918 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 63 optimal weight: 0.0970 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2971 GLN A3113 ASN A3459 ASN A3590 ASN A3605 ASN A3743 HIS A3760 GLN A3787 GLN A3924 HIS A3969 ASN A4088 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.170196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140405 restraints weight = 12313.130| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.58 r_work: 0.3588 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10246 Z= 0.136 Angle : 0.646 7.451 13844 Z= 0.332 Chirality : 0.041 0.157 1533 Planarity : 0.005 0.064 1774 Dihedral : 5.729 45.947 1356 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.58 % Favored : 91.34 % Rotamer: Outliers : 1.65 % Allowed : 12.89 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -3.81 (0.20), residues: 1247 helix: -1.90 (0.17), residues: 767 sheet: -1.21 (0.81), residues: 39 loop : -3.66 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A4124 HIS 0.003 0.001 HIS A3924 PHE 0.015 0.001 PHE A3110 TYR 0.014 0.001 TYR A3043 ARG 0.004 0.000 ARG A3357 Details of bonding type rmsd hydrogen bonds : bond 0.04352 ( 436) hydrogen bonds : angle 4.72661 ( 1296) covalent geometry : bond 0.00310 (10246) covalent geometry : angle 0.64615 (13844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3044 MET cc_start: 0.7470 (tmm) cc_final: 0.6626 (tmm) REVERT: A 3154 GLN cc_start: 0.7812 (pp30) cc_final: 0.7410 (pp30) REVERT: A 3194 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A 3238 MET cc_start: 0.7828 (mtp) cc_final: 0.7571 (mtm) REVERT: A 3240 MET cc_start: 0.8472 (tpp) cc_final: 0.8243 (tpp) REVERT: A 3526 PRO cc_start: 0.8597 (Cg_endo) cc_final: 0.8344 (Cg_exo) REVERT: A 3544 ASP cc_start: 0.7898 (t0) cc_final: 0.7569 (t0) REVERT: A 3631 LYS cc_start: 0.6131 (pttt) cc_final: 0.5783 (ttpt) REVERT: A 3718 ARG cc_start: 0.8282 (mmt-90) cc_final: 0.7735 (mpt180) outliers start: 18 outliers final: 8 residues processed: 144 average time/residue: 0.2297 time to fit residues: 47.3109 Evaluate side-chains 127 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3117 ILE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3524 ASN Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 3918 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 123 optimal weight: 0.2980 chunk 102 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3113 ASN A3516 HIS A3969 ASN A4042 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.171295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141005 restraints weight = 12654.273| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.66 r_work: 0.3599 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10246 Z= 0.122 Angle : 0.609 7.266 13844 Z= 0.310 Chirality : 0.040 0.153 1533 Planarity : 0.004 0.055 1774 Dihedral : 5.337 47.059 1356 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.22 % Favored : 90.70 % Rotamer: Outliers : 2.19 % Allowed : 15.17 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -3.00 (0.22), residues: 1247 helix: -1.20 (0.18), residues: 770 sheet: -1.25 (0.81), residues: 41 loop : -3.42 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A4124 HIS 0.004 0.001 HIS A3924 PHE 0.015 0.001 PHE A3110 TYR 0.013 0.001 TYR A3043 ARG 0.005 0.000 ARG A3357 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 436) hydrogen bonds : angle 4.41405 ( 1296) covalent geometry : bond 0.00279 (10246) covalent geometry : angle 0.60900 (13844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 2.234 Fit side-chains REVERT: A 3044 MET cc_start: 0.7481 (tmm) cc_final: 0.6625 (tmm) REVERT: A 3154 GLN cc_start: 0.7930 (pp30) cc_final: 0.7605 (pp30) REVERT: A 3194 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 3240 MET cc_start: 0.8574 (tpp) cc_final: 0.8348 (tpp) REVERT: A 3526 PRO cc_start: 0.8581 (Cg_endo) cc_final: 0.8301 (Cg_exo) REVERT: A 3544 ASP cc_start: 0.7742 (t0) cc_final: 0.7538 (t0) REVERT: A 3778 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6806 (t0) REVERT: A 3959 MET cc_start: 0.8609 (pmm) cc_final: 0.8311 (pmm) REVERT: A 4002 MET cc_start: 0.6943 (mtt) cc_final: 0.6521 (mtm) outliers start: 24 outliers final: 15 residues processed: 146 average time/residue: 0.3533 time to fit residues: 76.0767 Evaluate side-chains 135 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2945 SER Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3330 LEU Chi-restraints excluded: chain A residue 3336 ILE Chi-restraints excluded: chain A residue 3524 ASN Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3778 ASP Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3969 ASN Chi-restraints excluded: chain A residue 4033 VAL Chi-restraints excluded: chain A residue 4112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 26 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 112 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3104 GLN A3327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.170261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.139839 restraints weight = 12555.372| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.64 r_work: 0.3594 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10246 Z= 0.142 Angle : 0.621 7.154 13844 Z= 0.316 Chirality : 0.042 0.171 1533 Planarity : 0.004 0.057 1774 Dihedral : 5.310 43.805 1356 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.30 % Favored : 90.62 % Rotamer: Outliers : 2.56 % Allowed : 16.09 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -2.75 (0.23), residues: 1247 helix: -0.99 (0.19), residues: 766 sheet: -1.16 (0.82), residues: 41 loop : -3.35 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A4124 HIS 0.005 0.001 HIS A3924 PHE 0.014 0.001 PHE A3110 TYR 0.014 0.001 TYR A3043 ARG 0.006 0.000 ARG A3357 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 436) hydrogen bonds : angle 4.44649 ( 1296) covalent geometry : bond 0.00334 (10246) covalent geometry : angle 0.62148 (13844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 3044 MET cc_start: 0.7407 (tmm) cc_final: 0.6471 (tmm) REVERT: A 3154 GLN cc_start: 0.7954 (pp30) cc_final: 0.7624 (pp30) REVERT: A 3194 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 3240 MET cc_start: 0.8595 (tpp) cc_final: 0.8384 (tpp) REVERT: A 3260 LYS cc_start: 0.8452 (mmtp) cc_final: 0.8064 (tmtt) REVERT: A 3289 ARG cc_start: 0.8615 (mtp180) cc_final: 0.8166 (ttt-90) REVERT: A 3526 PRO cc_start: 0.8603 (Cg_endo) cc_final: 0.8324 (Cg_exo) REVERT: A 3718 ARG cc_start: 0.8375 (mmt-90) cc_final: 0.7899 (mpt180) REVERT: A 3895 GLU cc_start: 0.7250 (tt0) cc_final: 0.7006 (tt0) REVERT: A 3959 MET cc_start: 0.8691 (pmm) cc_final: 0.8443 (pmm) outliers start: 28 outliers final: 20 residues processed: 137 average time/residue: 0.3080 time to fit residues: 61.2608 Evaluate side-chains 136 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2830 ASN Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2945 SER Chi-restraints excluded: chain A residue 3026 ASP Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3104 GLN Chi-restraints excluded: chain A residue 3259 LEU Chi-restraints excluded: chain A residue 3299 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3330 LEU Chi-restraints excluded: chain A residue 3336 ILE Chi-restraints excluded: chain A residue 3472 ILE Chi-restraints excluded: chain A residue 3524 ASN Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 4033 VAL Chi-restraints excluded: chain A residue 4112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 80 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 123 optimal weight: 0.0870 chunk 3 optimal weight: 0.8980 chunk 101 optimal weight: 0.0570 chunk 70 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2841 ASN A2885 GLN A3104 GLN A3969 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.170445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139989 restraints weight = 12582.104| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.66 r_work: 0.3598 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10246 Z= 0.131 Angle : 0.606 7.121 13844 Z= 0.308 Chirality : 0.041 0.163 1533 Planarity : 0.004 0.055 1774 Dihedral : 5.044 44.125 1354 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.54 % Favored : 90.38 % Rotamer: Outliers : 2.74 % Allowed : 16.64 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -2.57 (0.23), residues: 1247 helix: -0.84 (0.19), residues: 766 sheet: -1.13 (0.82), residues: 41 loop : -3.28 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A4124 HIS 0.005 0.001 HIS A3924 PHE 0.014 0.001 PHE A3110 TYR 0.014 0.001 TYR A3043 ARG 0.006 0.000 ARG A3357 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 436) hydrogen bonds : angle 4.35759 ( 1296) covalent geometry : bond 0.00307 (10246) covalent geometry : angle 0.60618 (13844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.315 Fit side-chains REVERT: A 3044 MET cc_start: 0.7404 (tmm) cc_final: 0.6468 (tmm) REVERT: A 3154 GLN cc_start: 0.7954 (pp30) cc_final: 0.7654 (pp30) REVERT: A 3194 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 3238 MET cc_start: 0.7808 (mtm) cc_final: 0.7420 (mtm) REVERT: A 3260 LYS cc_start: 0.8422 (mmtp) cc_final: 0.8093 (tmtt) REVERT: A 3289 ARG cc_start: 0.8612 (mtp180) cc_final: 0.8167 (ttt-90) REVERT: A 3526 PRO cc_start: 0.8590 (Cg_endo) cc_final: 0.8310 (Cg_exo) REVERT: A 3718 ARG cc_start: 0.8383 (mmt-90) cc_final: 0.7882 (mpt180) REVERT: A 3858 MET cc_start: 0.7800 (tmm) cc_final: 0.7317 (ttp) REVERT: A 3959 MET cc_start: 0.8668 (pmm) cc_final: 0.8427 (pmm) outliers start: 30 outliers final: 23 residues processed: 140 average time/residue: 0.2838 time to fit residues: 58.7971 Evaluate side-chains 136 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2830 ASN Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2945 SER Chi-restraints excluded: chain A residue 3026 ASP Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3259 LEU Chi-restraints excluded: chain A residue 3299 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3330 LEU Chi-restraints excluded: chain A residue 3336 ILE Chi-restraints excluded: chain A residue 3472 ILE Chi-restraints excluded: chain A residue 3524 ASN Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3778 ASP Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 3969 ASN Chi-restraints excluded: chain A residue 4033 VAL Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 33 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 82 optimal weight: 0.0030 chunk 98 optimal weight: 0.0030 chunk 37 optimal weight: 0.2980 overall best weight: 0.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.173140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.143392 restraints weight = 12314.515| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.60 r_work: 0.3653 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10246 Z= 0.104 Angle : 0.584 10.927 13844 Z= 0.293 Chirality : 0.039 0.163 1533 Planarity : 0.004 0.049 1774 Dihedral : 4.755 43.237 1354 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.10 % Allowed : 17.82 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -2.25 (0.23), residues: 1247 helix: -0.56 (0.19), residues: 779 sheet: -0.97 (0.82), residues: 41 loop : -3.29 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A3498 HIS 0.003 0.001 HIS A3501 PHE 0.011 0.001 PHE A3110 TYR 0.011 0.001 TYR A3043 ARG 0.008 0.000 ARG A3357 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 436) hydrogen bonds : angle 4.13531 ( 1296) covalent geometry : bond 0.00232 (10246) covalent geometry : angle 0.58430 (13844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.070 Fit side-chains REVERT: A 3044 MET cc_start: 0.7325 (tmm) cc_final: 0.6420 (tmm) REVERT: A 3154 GLN cc_start: 0.7851 (pp30) cc_final: 0.7566 (pp30) REVERT: A 3194 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7460 (tm-30) REVERT: A 3238 MET cc_start: 0.7781 (mtm) cc_final: 0.7358 (mtm) REVERT: A 3289 ARG cc_start: 0.8573 (mtp180) cc_final: 0.8128 (ttt-90) REVERT: A 3544 ASP cc_start: 0.7493 (t0) cc_final: 0.7285 (t0) REVERT: A 3858 MET cc_start: 0.7805 (tmm) cc_final: 0.7345 (ttp) outliers start: 23 outliers final: 18 residues processed: 147 average time/residue: 0.2281 time to fit residues: 47.5603 Evaluate side-chains 138 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2945 SER Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3112 GLN Chi-restraints excluded: chain A residue 3259 LEU Chi-restraints excluded: chain A residue 3299 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3472 ILE Chi-restraints excluded: chain A residue 3524 ASN Chi-restraints excluded: chain A residue 3689 ASP Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3778 ASP Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 4033 VAL Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4112 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 21 optimal weight: 0.9980 chunk 123 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3748 HIS A3772 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.170586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140488 restraints weight = 12767.709| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.69 r_work: 0.3610 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10246 Z= 0.139 Angle : 0.633 9.463 13844 Z= 0.316 Chirality : 0.041 0.153 1533 Planarity : 0.004 0.054 1774 Dihedral : 4.896 44.052 1354 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.70 % Favored : 90.22 % Rotamer: Outliers : 2.47 % Allowed : 18.74 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -2.19 (0.24), residues: 1247 helix: -0.61 (0.19), residues: 787 sheet: -0.48 (0.86), residues: 39 loop : -3.12 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A4124 HIS 0.005 0.001 HIS A3924 PHE 0.015 0.001 PHE A3554 TYR 0.015 0.001 TYR A3043 ARG 0.007 0.000 ARG A3357 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 436) hydrogen bonds : angle 4.26016 ( 1296) covalent geometry : bond 0.00329 (10246) covalent geometry : angle 0.63269 (13844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.119 Fit side-chains REVERT: A 3044 MET cc_start: 0.7464 (tmm) cc_final: 0.6522 (tmm) REVERT: A 3154 GLN cc_start: 0.7918 (pp30) cc_final: 0.7616 (pp30) REVERT: A 3194 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7507 (tm-30) REVERT: A 3238 MET cc_start: 0.7809 (mtm) cc_final: 0.7380 (mtm) REVERT: A 3260 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7587 (mptt) REVERT: A 3289 ARG cc_start: 0.8626 (mtp180) cc_final: 0.8181 (ttt-90) REVERT: A 3526 PRO cc_start: 0.8534 (Cg_endo) cc_final: 0.8263 (Cg_exo) REVERT: A 3544 ASP cc_start: 0.7706 (t0) cc_final: 0.7447 (t0) REVERT: A 3718 ARG cc_start: 0.8342 (mmt-90) cc_final: 0.7874 (mpt180) REVERT: A 3858 MET cc_start: 0.7815 (tmm) cc_final: 0.7342 (ttp) outliers start: 27 outliers final: 20 residues processed: 138 average time/residue: 0.2683 time to fit residues: 51.7678 Evaluate side-chains 129 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2830 ASN Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2945 SER Chi-restraints excluded: chain A residue 3026 ASP Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3299 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3330 LEU Chi-restraints excluded: chain A residue 3472 ILE Chi-restraints excluded: chain A residue 3524 ASN Chi-restraints excluded: chain A residue 3689 ASP Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3778 ASP Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 4033 VAL Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4112 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 76 optimal weight: 0.0170 chunk 57 optimal weight: 0.3980 chunk 122 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.171380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141773 restraints weight = 12502.644| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.76 r_work: 0.3673 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10246 Z= 0.114 Angle : 0.606 8.528 13844 Z= 0.304 Chirality : 0.040 0.144 1533 Planarity : 0.004 0.048 1774 Dihedral : 4.736 43.600 1354 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 2.29 % Allowed : 19.38 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -1.98 (0.24), residues: 1247 helix: -0.42 (0.19), residues: 787 sheet: -0.26 (0.87), residues: 39 loop : -3.12 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3498 HIS 0.003 0.001 HIS A3924 PHE 0.011 0.001 PHE A3110 TYR 0.011 0.001 TYR A3043 ARG 0.007 0.000 ARG A3864 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 436) hydrogen bonds : angle 4.14376 ( 1296) covalent geometry : bond 0.00260 (10246) covalent geometry : angle 0.60617 (13844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.055 Fit side-chains REVERT: A 3044 MET cc_start: 0.7286 (tmm) cc_final: 0.6319 (tmm) REVERT: A 3154 GLN cc_start: 0.7810 (pp30) cc_final: 0.7507 (pp30) REVERT: A 3194 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 3260 LYS cc_start: 0.7969 (tmtt) cc_final: 0.7454 (mptt) REVERT: A 3289 ARG cc_start: 0.8523 (mtp180) cc_final: 0.8080 (ttt-90) REVERT: A 3526 PRO cc_start: 0.8591 (Cg_endo) cc_final: 0.8327 (Cg_exo) REVERT: A 3544 ASP cc_start: 0.7539 (t0) cc_final: 0.7251 (t0) REVERT: A 3718 ARG cc_start: 0.8276 (mmt-90) cc_final: 0.7758 (mpt180) REVERT: A 3858 MET cc_start: 0.7811 (tmm) cc_final: 0.7338 (ttp) outliers start: 25 outliers final: 20 residues processed: 141 average time/residue: 0.2271 time to fit residues: 45.0452 Evaluate side-chains 136 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2830 ASN Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2945 SER Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3299 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3472 ILE Chi-restraints excluded: chain A residue 3524 ASN Chi-restraints excluded: chain A residue 3689 ASP Chi-restraints excluded: chain A residue 3695 LEU Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3778 ASP Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 4033 VAL Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4112 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 38 optimal weight: 0.0060 chunk 47 optimal weight: 0.0030 chunk 89 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3772 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.171957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.142331 restraints weight = 12414.736| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.61 r_work: 0.3627 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10246 Z= 0.119 Angle : 0.614 8.529 13844 Z= 0.307 Chirality : 0.040 0.144 1533 Planarity : 0.004 0.048 1774 Dihedral : 4.715 43.785 1354 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.29 % Allowed : 19.74 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -1.93 (0.24), residues: 1247 helix: -0.39 (0.19), residues: 787 sheet: -0.08 (0.90), residues: 39 loop : -3.09 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A3588 HIS 0.004 0.001 HIS A3501 PHE 0.017 0.001 PHE A3554 TYR 0.012 0.001 TYR A3043 ARG 0.008 0.000 ARG A2940 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 436) hydrogen bonds : angle 4.14552 ( 1296) covalent geometry : bond 0.00276 (10246) covalent geometry : angle 0.61353 (13844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.075 Fit side-chains REVERT: A 3044 MET cc_start: 0.7387 (tmm) cc_final: 0.6460 (tmm) REVERT: A 3154 GLN cc_start: 0.7912 (pp30) cc_final: 0.7616 (pp30) REVERT: A 3194 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7510 (tm-30) REVERT: A 3260 LYS cc_start: 0.8011 (tmtt) cc_final: 0.7497 (mptt) REVERT: A 3289 ARG cc_start: 0.8643 (mtp180) cc_final: 0.8201 (ttt-90) REVERT: A 3526 PRO cc_start: 0.8481 (Cg_endo) cc_final: 0.8218 (Cg_exo) REVERT: A 3718 ARG cc_start: 0.8423 (mmt-90) cc_final: 0.7875 (mpt180) REVERT: A 3858 MET cc_start: 0.7843 (tmm) cc_final: 0.7369 (ttp) outliers start: 25 outliers final: 19 residues processed: 140 average time/residue: 0.2389 time to fit residues: 46.7361 Evaluate side-chains 136 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 3026 ASP Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3299 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3472 ILE Chi-restraints excluded: chain A residue 3524 ASN Chi-restraints excluded: chain A residue 3689 ASP Chi-restraints excluded: chain A residue 3695 LEU Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3778 ASP Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 4033 VAL Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 116 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 33 optimal weight: 0.0670 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.172660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.142469 restraints weight = 12642.728| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.64 r_work: 0.3613 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10246 Z= 0.121 Angle : 0.617 8.767 13844 Z= 0.309 Chirality : 0.041 0.143 1533 Planarity : 0.004 0.047 1774 Dihedral : 4.714 43.803 1354 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.29 % Allowed : 19.74 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -1.90 (0.24), residues: 1247 helix: -0.38 (0.19), residues: 789 sheet: 0.01 (0.91), residues: 39 loop : -3.05 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A3588 HIS 0.005 0.001 HIS A3501 PHE 0.019 0.001 PHE A2823 TYR 0.014 0.001 TYR A3791 ARG 0.008 0.000 ARG A2940 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 436) hydrogen bonds : angle 4.13991 ( 1296) covalent geometry : bond 0.00282 (10246) covalent geometry : angle 0.61745 (13844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.242 Fit side-chains REVERT: A 3044 MET cc_start: 0.7410 (tmm) cc_final: 0.6496 (tmm) REVERT: A 3154 GLN cc_start: 0.7860 (pp30) cc_final: 0.7588 (pp30) REVERT: A 3194 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 3260 LYS cc_start: 0.8028 (tmtt) cc_final: 0.7505 (mptt) REVERT: A 3289 ARG cc_start: 0.8650 (mtp180) cc_final: 0.8216 (ttt-90) REVERT: A 3526 PRO cc_start: 0.8522 (Cg_endo) cc_final: 0.8267 (Cg_exo) REVERT: A 3718 ARG cc_start: 0.8424 (mmt-90) cc_final: 0.7907 (mpt180) REVERT: A 3858 MET cc_start: 0.7875 (tmm) cc_final: 0.7402 (ttp) outliers start: 25 outliers final: 22 residues processed: 138 average time/residue: 0.2401 time to fit residues: 46.4204 Evaluate side-chains 138 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2830 ASN Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2945 SER Chi-restraints excluded: chain A residue 3026 ASP Chi-restraints excluded: chain A residue 3027 LEU Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3259 LEU Chi-restraints excluded: chain A residue 3299 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3472 ILE Chi-restraints excluded: chain A residue 3524 ASN Chi-restraints excluded: chain A residue 3689 ASP Chi-restraints excluded: chain A residue 3695 LEU Chi-restraints excluded: chain A residue 3728 VAL Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3778 ASP Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 4033 VAL Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 57 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 38 optimal weight: 0.0070 chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.173846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.143941 restraints weight = 12414.130| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.59 r_work: 0.3632 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10246 Z= 0.113 Angle : 0.611 9.019 13844 Z= 0.306 Chirality : 0.040 0.144 1533 Planarity : 0.004 0.045 1774 Dihedral : 4.624 43.535 1354 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.29 % Allowed : 19.93 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -1.79 (0.24), residues: 1247 helix: -0.29 (0.19), residues: 791 sheet: 0.08 (0.91), residues: 39 loop : -3.06 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A3588 HIS 0.004 0.001 HIS A3501 PHE 0.018 0.001 PHE A3554 TYR 0.013 0.001 TYR A3791 ARG 0.008 0.000 ARG A2940 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 436) hydrogen bonds : angle 4.08414 ( 1296) covalent geometry : bond 0.00259 (10246) covalent geometry : angle 0.61141 (13844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6038.16 seconds wall clock time: 106 minutes 54.57 seconds (6414.57 seconds total)