Starting phenix.real_space_refine (version: 1.20rc4)
on Wed Dec  1 23:42:48 2021 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/12_2021/7k11_22620.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/12_2021/7k11_22620.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/12_2021/7k11_22620.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/12_2021/7k11_22620.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/12_2021/7k11_22620.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/12_2021/7k11_22620.pdb"
  }
  resolution = 3.21
  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
-------------------------------------------------------------------------------
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
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "A PHE 3904": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib"
  Total number of atoms: 10011
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 10011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1254, 10011
          Classifications: {'peptide': 1254}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 51, 'TRANS': 1201, 'PCIS': 1}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 63
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 53
  Time building chain proxies: 5.99, per 1000 atoms: 0.60
  Number of scatterers: 10011
  At special positions: 0
  Unit cell: (113.68, 100.92, 122.96, 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    1860      8.00
     N    1716      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  - 3.50
        Amimo acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.99
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2398

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 2 sheets defined
      64.5% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2801 through 2820
      removed outlier: 3.728A  pdb=" N   ALA A2805 " --> pdb=" O   ASP A2801 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   SER A2814 " --> pdb=" O   SER A2810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2825 through 2847
      removed outlier: 3.797A  pdb=" N   ASN A2830 " --> pdb=" O   LEU A2826 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ASN A2831 " --> pdb=" O   SER A2827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2851 through 2863
      removed outlier: 4.192A  pdb=" N   CYS A2857 " --> pdb=" O   PRO A2853 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   CYS A2863 " --> pdb=" O   GLN A2859 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2872 through 2884
      removed outlier: 3.794A  pdb=" N   SER A2877 " --> pdb=" O   PRO A2873 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA A2878 " --> pdb=" O   ALA A2874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2885 through 2898
      removed outlier: 3.962A  pdb=" N   GLY A2889 " --> pdb=" O   GLN A2885 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ARG A2891 " --> pdb=" O   PRO A2887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2918 through 2932
      removed outlier: 3.609A  pdb=" N   ARG A2922 " --> pdb=" O   PRO A2918 " (cutoff:3.500A)
      removed outlier: 5.060A  pdb=" N   TRP A2923 " --> pdb=" O   ASP A2919 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   SER A2932 " --> pdb=" O   LYS A2928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2935 through 2940
      removed outlier: 3.684A  pdb=" N   ARG A2940 " --> pdb=" O   TYR A2936 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2941 through 2946
      removed outlier: 3.960A  pdb=" N   SER A2945 " --> pdb=" O   GLY A2941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2952 through 2962
      removed outlier: 4.192A  pdb=" N   ARG A2962 " --> pdb=" O   LEU A2958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2966 through 2977
      removed outlier: 4.081A  pdb=" N   TYR A2972 " --> pdb=" O   ALA A2968 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASP A2973 " --> pdb=" O   ALA A2969 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   ALA A2975 " --> pdb=" O   GLN A2971 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ASN A2977 " --> pdb=" O   ASP A2973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2991 through 3005
      removed outlier: 3.974A  pdb=" N   GLU A2995 " --> pdb=" O   LYS A2991 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU A3005 " --> pdb=" O   CYS A3001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3011 through 3017
    Processing helix  chain 'A' and resid 3034 through 3039
      removed outlier: 3.661A  pdb=" N   THR A3039 " --> pdb=" O   PHE A3035 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3039 through 3053
      removed outlier: 4.610A  pdb=" N   TYR A3043 " --> pdb=" O   THR A3039 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   MET A3044 " --> pdb=" O   TYR A3040 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A3051 " --> pdb=" O   SER A3047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3060 through 3069
      removed outlier: 3.562A  pdb=" N   PHE A3064 " --> pdb=" O   SER A3060 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3075 through 3081
    Processing helix  chain 'A' and resid 3083 through 3093
    Processing helix  chain 'A' and resid 3096 through 3115
    Processing helix  chain 'A' and resid 3123 through 3130
    Processing helix  chain 'A' and resid 3131 through 3147
      removed outlier: 3.905A  pdb=" N   LYS A3147 " --> pdb=" O   SER A3143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3154 through 3165
    Processing helix  chain 'A' and resid 3175 through 3197
      removed outlier: 3.594A  pdb=" N   TRP A3179 " --> pdb=" O   PRO A3175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3227 through 3249
      removed outlier: 3.818A  pdb=" N   ILE A3231 " --> pdb=" O   ILE A3227 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG A3232 " --> pdb=" O   SER A3228 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   CYS A3234 " --> pdb=" O   LEU A3230 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LYS A3248 " --> pdb=" O   ASP A3244 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLN A3249 " --> pdb=" O   SER A3245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3251 through 3262
      removed outlier: 3.800A  pdb=" N   LYS A3257 " --> pdb=" O   SER A3253 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A3258 " --> pdb=" O   LEU A3254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3269 through 3288
    Processing helix  chain 'A' and resid 3292 through 3297
      removed outlier: 4.076A  pdb=" N   VAL A3297 " --> pdb=" O   CYS A3293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3304 through 3308
    Processing helix  chain 'A' and resid 3320 through 3344
      removed outlier: 3.905A  pdb=" N   ASN A3327 " --> pdb=" O   PHE A3323 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER A3342 " --> pdb=" O   ALA A3338 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER A3343 " --> pdb=" O   ASN A3339 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLU A3344 " --> pdb=" O   ALA A3340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3346 through 3351
    Processing helix  chain 'A' and resid 3354 through 3361
    Processing helix  chain 'A' and resid 3373 through 3391
      removed outlier: 3.633A  pdb=" N   GLN A3379 " --> pdb=" O   ALA A3375 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   HIS A3384 " --> pdb=" O   ARG A3380 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA A3388 " --> pdb=" O   HIS A3384 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   VAL A3389 " --> pdb=" O   LEU A3385 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   GLN A3390 " --> pdb=" O   SER A3386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3409 through 3428
      removed outlier: 3.970A  pdb=" N   LEU A3416 " --> pdb=" O   ALA A3412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3441 through 3455
      removed outlier: 3.892A  pdb=" N   LEU A3445 " --> pdb=" O   ALA A3441 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL A3447 " --> pdb=" O   PRO A3443 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLU A3448 " --> pdb=" O   ALA A3444 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LYS A3449 " --> pdb=" O   LEU A3445 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ALA A3453 " --> pdb=" O   LYS A3449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3464 through 3475
      removed outlier: 3.855A  pdb=" N   LEU A3468 " --> pdb=" O   LYS A3464 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLU A3473 " --> pdb=" O   LEU A3469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3480 through 3488
    Processing helix  chain 'A' and resid 3498 through 3503
    Processing helix  chain 'A' and resid 3515 through 3525
    Processing helix  chain 'A' and resid 3529 through 3537
      removed outlier: 3.909A  pdb=" N   ILE A3535 " --> pdb=" O   TYR A3531 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   SER A3536 " --> pdb=" O   PRO A3532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3545 through 3548
    Processing helix  chain 'A' and resid 3549 through 3562
      removed outlier: 3.949A  pdb=" N   GLU A3553 " --> pdb=" O   HIS A3549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3567 through 3577
    Processing helix  chain 'A' and resid 3581 through 3594
      removed outlier: 3.877A  pdb=" N   LYS A3586 " --> pdb=" O   GLU A3582 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ASP A3587 " --> pdb=" O   LEU A3583 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ALA A3594 " --> pdb=" O   ASN A3590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3604 through 3617
      removed outlier: 4.325A  pdb=" N   GLU A3611 " --> pdb=" O   GLU A3607 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   ARG A3612 " --> pdb=" O   LYS A3608 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   MET A3613 " --> pdb=" O   MET A3609 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ALA A3616 " --> pdb=" O   ARG A3612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3620 through 3627
      removed outlier: 3.898A  pdb=" N   GLY A3624 " --> pdb=" O   PRO A3620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3632 through 3637
    Processing helix  chain 'A' and resid 3644 through 3650
    Processing helix  chain 'A' and resid 3651 through 3654
      removed outlier: 3.636A  pdb=" N   MET A3654 " --> pdb=" O   LEU A3651 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3651 through 3654'
    Processing helix  chain 'A' and resid 3660 through 3670
      removed outlier: 3.730A  pdb=" N   LEU A3666 " --> pdb=" O   ILE A3662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3684 through 3689
      removed outlier: 3.895A  pdb=" N   SER A3688 " --> pdb=" O   SER A3684 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ASP A3689 " --> pdb=" O   PRO A3685 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3684 through 3689'
    Processing helix  chain 'A' and resid 3758 through 3775
      removed outlier: 3.621A  pdb=" N   GLN A3762 " --> pdb=" O   LEU A3758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3778 through 3783
    Processing helix  chain 'A' and resid 3812 through 3820
      removed outlier: 4.008A  pdb=" N   MET A3820 " --> pdb=" O   LEU A3816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3823 through 3830
    Processing helix  chain 'A' and resid 3834 through 3847
      removed outlier: 3.715A  pdb=" N   TYR A3839 " --> pdb=" O   PRO A3835 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LYS A3840 " --> pdb=" O   PRO A3836 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3853 through 3859
      removed outlier: 3.650A  pdb=" N   LEU A3857 " --> pdb=" O   GLY A3853 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TYR A3859 " --> pdb=" O   TYR A3855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3863 through 3876
      removed outlier: 3.952A  pdb=" N   THR A3867 " --> pdb=" O   ASN A3863 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3883 through 3890
      removed outlier: 3.831A  pdb=" N   MET A3890 " --> pdb=" O   ALA A3886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3893 through 3918
      removed outlier: 3.895A  pdb=" N   LEU A3898 " --> pdb=" O   PRO A3894 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   ALA A3899 " --> pdb=" O   GLU A3895 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   HIS A3903 " --> pdb=" O   ALA A3899 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   PHE A3904 " --> pdb=" O   LEU A3900 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   TRP A3916 " --> pdb=" O   CYS A3912 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ILE A3917 " --> pdb=" O   ILE A3913 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   LEU A3918 " --> pdb=" O   SER A3914 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3964 through 3970
    Processing helix  chain 'A' and resid 3978 through 3992
    Processing helix  chain 'A' and resid 3996 through 4007
    Processing helix  chain 'A' and resid 4013 through 4022
    Processing helix  chain 'A' and resid 4033 through 4037
    Processing helix  chain 'A' and resid 4039 through 4052
      removed outlier: 3.970A  pdb=" N   LYS A4043 " --> pdb=" O   TYR A4039 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   ILE A4044 " --> pdb=" O   PRO A4040 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4055 through 4068
      removed outlier: 3.508A  pdb=" N   ILE A4059 " --> pdb=" O   ASN A4055 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   THR A4060 " --> pdb=" O   PRO A4056 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   CYS A4061 " --> pdb=" O   ALA A4057 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4074 through 4081
    Processing helix  chain 'A' and resid 4088 through 4092
      removed outlier: 3.527A  pdb=" N   ALA A4091 " --> pdb=" O   ASN A4088 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4099 through 4112
    Processing helix  chain 'A' and resid 4113 through 4118
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3727 through 3728
      removed outlier: 3.559A  pdb=" N   THR A3727 " --> pdb=" O   ARG A3737 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LYS A3753 " --> pdb=" O   GLY A3801 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   LEU A3800 " --> pdb=" O   MET A3796 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 3809 through 3811

    465 hydrogen bonds defined for protein.
    1374 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: 3.22

  Time building geometry restraints manager: 4.37 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: 3245
        1.34 -     1.46: 2180
        1.46 -     1.58: 4699
        1.58 -     1.70: 0
        1.70 -     1.82: 94
  Bond restraints: 10218
  Sorted by residual:
  bond pdb=" CB  ASN A3311 "
       pdb=" CG  ASN A3311 "
    ideal  model  delta    sigma   weight residual
    1.516  1.573 -0.057 2.50e-02 1.60e+03 5.23e+00
  bond pdb=" C   LEU A3041 "
       pdb=" N   PRO A3042 "
    ideal  model  delta    sigma   weight residual
    1.335  1.364 -0.029 1.36e-02 5.41e+03 4.53e+00
  bond pdb=" C   PRO A2852 "
       pdb=" N   PRO A2853 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 4.10e+00
  bond pdb=" C   PRO A3676 "
       pdb=" N   PRO A3677 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.046 2.34e-02 1.83e+03 3.79e+00
  bond pdb=" CB  PRO A2853 "
       pdb=" CG  PRO A2853 "
    ideal  model  delta    sigma   weight residual
    1.492  1.405  0.087 5.00e-02 4.00e+02 3.05e+00
  ... (remaining 10213 not shown)

  Histogram of bond angle deviations from ideal:
       99.48 -   106.74: 294
      106.74 -   114.00: 5731
      114.00 -   121.26: 5249
      121.26 -   128.52: 2434
      128.52 -   135.78: 93
  Bond angle restraints: 13801
  Sorted by residual:
  angle pdb=" C   ASN A3310 "
        pdb=" N   ASN A3311 "
        pdb=" CA  ASN A3311 "
      ideal   model   delta    sigma   weight residual
     125.66  134.84   -9.18 1.85e+00 2.92e-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  131.01   -9.47 1.91e+00 2.74e-01 2.46e+01
  angle pdb=" C   ASP A4012 "
        pdb=" N   TRP A4013 "
        pdb=" CA  TRP A4013 "
      ideal   model   delta    sigma   weight residual
     121.54  130.92   -9.38 1.91e+00 2.74e-01 2.41e+01
  angle pdb=" C   ASP A3058 "
        pdb=" N   GLN A3059 "
        pdb=" CA  GLN A3059 "
      ideal   model   delta    sigma   weight residual
     121.54  130.91   -9.37 1.91e+00 2.74e-01 2.40e+01
  angle pdb=" C   ASP A3369 "
        pdb=" N   SER A3370 "
        pdb=" CA  SER A3370 "
      ideal   model   delta    sigma   weight residual
     121.54  129.95   -8.41 1.91e+00 2.74e-01 1.94e+01
  ... (remaining 13796 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.05: 5340
       16.05 -    32.10: 699
       32.10 -    48.15: 163
       48.15 -    64.20: 26
       64.20 -    80.25: 10
  Dihedral angle restraints: 6238
    sinusoidal: 2555
      harmonic: 3683
  Sorted by residual:
  dihedral pdb=" CA  GLY A3707 "
           pdb=" C   GLY A3707 "
           pdb=" N   ARG A3708 "
           pdb=" CA  ARG A3708 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.35   25.65     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  SER A3314 "
           pdb=" C   SER A3314 "
           pdb=" N   TYR A3315 "
           pdb=" CA  TYR A3315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.49   24.51     0      5.00e+00 4.00e-02 2.40e+01
  dihedral pdb=" CA  GLU A3344 "
           pdb=" C   GLU A3344 "
           pdb=" N   PRO A3345 "
           pdb=" CA  PRO A3345 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.12  -23.88     0      5.00e+00 4.00e-02 2.28e+01
  ... (remaining 6235 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1094
       0.053 -    0.105: 351
       0.105 -    0.158: 62
       0.158 -    0.210: 19
       0.210 -    0.263: 2
  Chirality restraints: 1528
  Sorted by residual:
  chirality pdb=" CB  ILE A3739 "
            pdb=" CA  ILE A3739 "
            pdb=" CG1 ILE A3739 "
            pdb=" CG2 ILE A3739 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.91   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  ILE A4031 "
            pdb=" CA  ILE A4031 "
            pdb=" CG1 ILE A4031 "
            pdb=" CG2 ILE A4031 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CB  VAL A3514 "
            pdb=" CA  VAL A3514 "
            pdb=" CG1 VAL A3514 "
            pdb=" CG2 VAL A3514 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.93e-01
  ... (remaining 1525 not shown)

  Planarity restraints: 1767
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A3531 "   -0.054 5.00e-02 4.00e+02   8.12e-02 1.05e+01
        pdb=" N   PRO A3532 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A3532 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A3532 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A3123 "    0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   GLN A3123 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   GLN A3123 "    0.020 2.00e-02 2.50e+03
        pdb=" N   SER A3124 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A3676 "   -0.050 5.00e-02 4.00e+02   7.60e-02 9.24e+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 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 1764 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2567
        2.80 -     3.32: 8733
        3.32 -     3.85: 15323
        3.85 -     4.37: 17838
        4.37 -     4.90: 31736
  Nonbonded interactions: 76197
  Sorted by model distance:
  nonbonded pdb=" O   TYR A3043 "
            pdb=" OG  SER A3047 "
     model   vdw
     2.271 2.440
  nonbonded pdb=" O   PHE A3887 "
            pdb=" OG  SER A3891 "
     model   vdw
     2.302 2.440
  nonbonded pdb=" O   SER A3489 "
            pdb=" OG  SER A3489 "
     model   vdw
     2.311 2.440
  nonbonded pdb=" O   ASP A3180 "
            pdb=" OG1 THR A3184 "
     model   vdw
     2.317 2.440
  nonbonded pdb=" O   MET A4108 "
            pdb=" OG1 THR A4112 "
     model   vdw
     2.333 2.440
  ... (remaining 76192 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
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    6378      2.51       5
     N    1716      2.21       5
     O    1860      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
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
Write .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:             1.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          9.260
  Check model and map are aligned:         0.140
  Convert atoms to be neutral:             0.080
  Process input model:                     29.890
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:2.240
  Set ADP refinement strategy:             0.000
  Write .geo file:                         0.000
  Internal consistency checks:             0.000
  Total:   43.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.087  10218  Z= 0.348
  Angle     :  0.924  10.777  13801  Z= 0.501
  Chirality :  0.053   0.263   1528
  Planarity :  0.008   0.081   1767
  Dihedral  : 15.327  80.254   3840
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.58 %
    Favored  : 90.34 %
  Rotamer Outliers :  0.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -5.00 (0.17), residues: 1242
  helix: -2.91 (0.13), residues: 793
  sheet: -3.07 (0.73), residues: 32
  loop : -3.84 (0.23), residues: 417

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 161
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 166
  average time/residue: 0.2463
  time to fit residues: 56.1562
Evaluate side-chains
  117 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 115
  time to evaluate  : 1.223 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0895
  time to fit residues: 2.0508
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    0.7980
   chunk 94 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0000
   chunk 97 optimal weight:    2.9990
   chunk 37 optimal weight:    0.4980
   chunk 59 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   chunk 113 optimal weight:    0.6980
   overall best weight:    0.5384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A2859 GLN
A2885 GLN
A3104 GLN
A3150 ASN
A3327 ASN
A3423 GLN
A3459 ASN
A3510 GLN
A3590 ASN
A3602 ASN
A3679 ASN
A4088 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.077  10218  Z= 0.208
  Angle     :  0.596   7.913  13801  Z= 0.316
  Chirality :  0.040   0.153   1528
  Planarity :  0.006   0.084   1767
  Dihedral  :  5.256  21.321   1349
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.50 %
    Favored  : 90.42 %
  Rotamer Outliers :  1.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -3.25 (0.21), residues: 1242
  helix: -1.40 (0.17), residues: 805
  sheet: -2.39 (0.89), residues: 26
  loop : -3.55 (0.25), residues: 411

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 1.253 
Fit side-chains
  outliers start: 19
  outliers final: 10
  residues processed: 150
  average time/residue: 0.2293
  time to fit residues: 48.6059
Evaluate side-chains
  131 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 1.293 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0936
  time to fit residues: 3.5959
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 113 optimal weight:    0.6980
   chunk 122 optimal weight:    0.0870
   chunk 101 optimal weight:    0.0980
   chunk 112 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.3958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A3643 HIS
A3679 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.088  10218  Z= 0.187
  Angle     :  0.567   7.788  13801  Z= 0.297
  Chirality :  0.040   0.161   1528
  Planarity :  0.005   0.049   1767
  Dihedral  :  4.882  19.787   1349
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.66 %
    Favored  : 90.26 %
  Rotamer Outliers :  1.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -2.37 (0.23), residues: 1242
  helix: -0.65 (0.18), residues: 798
  sheet: -2.00 (0.92), residues: 26
  loop : -3.31 (0.26), residues: 418

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 7
  residues processed: 161
  average time/residue: 0.2479
  time to fit residues: 55.3465
Evaluate side-chains
  139 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 1.315 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1013
  time to fit residues: 3.1227
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 112 optimal weight:    0.5980
   chunk 85 optimal weight:    0.0010
   chunk 59 optimal weight:    0.9980
   chunk 12 optimal weight:    0.4980
   chunk 54 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 114 optimal weight:    1.9990
   chunk 120 optimal weight:    0.5980
   chunk 108 optimal weight:    0.0980
   chunk 32 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A3679 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.093  10218  Z= 0.173
  Angle     :  0.552   7.579  13801  Z= 0.289
  Chirality :  0.039   0.154   1528
  Planarity :  0.004   0.045   1767
  Dihedral  :  4.683  18.841   1349
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer Outliers :  1.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -1.95 (0.23), residues: 1242
  helix: -0.32 (0.19), residues: 799
  sheet: -1.78 (0.94), residues: 26
  loop : -3.18 (0.26), residues: 417

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 1.287 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 12
  residues processed: 154
  average time/residue: 0.2144
  time to fit residues: 47.2850
Evaluate side-chains
  142 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 1.247 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0935
  time to fit residues: 3.8569
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 89 optimal weight:    0.0870
   chunk 49 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0050
   chunk 0 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 108 optimal weight:    0.7980
   chunk 30 optimal weight:    0.3980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.4172

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A3590 ASN
A3679 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.106  10218  Z= 0.183
  Angle     :  0.564   7.396  13801  Z= 0.294
  Chirality :  0.040   0.148   1528
  Planarity :  0.004   0.050   1767
  Dihedral  :  4.641  19.132   1349
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer Outliers :  1.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -1.67 (0.24), residues: 1242
  helix: -0.08 (0.19), residues: 792
  sheet: -1.61 (0.95), residues: 26
  loop : -3.07 (0.26), residues: 424

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 4
  residues processed: 151
  average time/residue: 0.2213
  time to fit residues: 47.8522
Evaluate side-chains
  136 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 132
  time to evaluate  : 1.186 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1076
  time to fit residues: 2.4157
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 120 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A3590 ASN
A3679 ASN
** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4068 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10218  Z= 0.245
  Angle     :  0.612   9.097  13801  Z= 0.316
  Chirality :  0.042   0.163   1528
  Planarity :  0.005   0.046   1767
  Dihedral  :  4.862  19.752   1349
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 10.23 %
    Favored  : 89.69 %
  Rotamer Outliers :  1.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -1.76 (0.24), residues: 1242
  helix: -0.17 (0.19), residues: 796
  sheet: -1.82 (0.92), residues: 26
  loop : -3.06 (0.27), residues: 420

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 1.328 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 10
  residues processed: 150
  average time/residue: 0.2219
  time to fit residues: 48.2472
Evaluate side-chains
  142 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 1.316 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0977
  time to fit residues: 3.5291
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 13 optimal weight:    0.0770
   chunk 68 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0040
   chunk 120 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0770
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.3108

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.137  10218  Z= 0.171
  Angle     :  0.571   8.439  13801  Z= 0.297
  Chirality :  0.039   0.148   1528
  Planarity :  0.004   0.057   1767
  Dihedral  :  4.583  18.665   1349
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer Outliers :  0.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -1.38 (0.24), residues: 1242
  helix:  0.12 (0.19), residues: 796
  sheet: -1.55 (0.92), residues: 26
  loop : -2.90 (0.27), residues: 420

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 139
  time to evaluate  : 1.280 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 144
  average time/residue: 0.2275
  time to fit residues: 47.5209
Evaluate side-chains
  134 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 130
  time to evaluate  : 1.127 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1138
  time to fit residues: 2.6730
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0470
   chunk 94 optimal weight:    0.9990
   chunk 109 optimal weight:    0.7980
   chunk 115 optimal weight:    0.7980
   chunk 105 optimal weight:    0.0870
   overall best weight:    0.4856

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A3590 ASN
A3679 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.083  10218  Z= 0.194
  Angle     :  0.597   9.092  13801  Z= 0.305
  Chirality :  0.041   0.161   1528
  Planarity :  0.004   0.045   1767
  Dihedral  :  4.599  18.845   1349
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer Outliers :  0.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -1.34 (0.24), residues: 1242
  helix:  0.14 (0.19), residues: 796
  sheet: -1.40 (0.93), residues: 26
  loop : -2.88 (0.28), residues: 420

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 134
  average time/residue: 0.2170
  time to fit residues: 42.2785
Evaluate side-chains
  127 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 124
  time to evaluate  : 1.143 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1003
  time to fit residues: 2.2638
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 112 optimal weight:    0.9990
   chunk 115 optimal weight:    0.0980
   chunk 67 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 101 optimal weight:    0.0000
   chunk 106 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 118 optimal weight:    0.9980
   overall best weight:    0.4384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3679 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.071  10218  Z= 0.183
  Angle     :  0.588   8.643  13801  Z= 0.301
  Chirality :  0.040   0.149   1528
  Planarity :  0.004   0.046   1767
  Dihedral  :  4.539  18.782   1349
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.42 %
    Favored  : 90.58 %
  Rotamer Outliers :  0.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -1.25 (0.24), residues: 1242
  helix:  0.20 (0.19), residues: 796
  sheet: -1.31 (0.95), residues: 26
  loop : -2.83 (0.28), residues: 420

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 133
  average time/residue: 0.2213
  time to fit residues: 42.7033
Evaluate side-chains
  128 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 1.232 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1014
  time to fit residues: 2.4537
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0670
   chunk 124 optimal weight:    0.9990
   chunk 114 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0010
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.5728

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3679 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.343  10218  Z= 0.266
  Angle     :  0.661  18.041  13801  Z= 0.352
  Chirality :  0.042   0.174   1528
  Planarity :  0.005   0.116   1767
  Dihedral  :  4.640  19.306   1349
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.98 %
    Favored  : 89.94 %
  Rotamer Outliers :  0.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -1.30 (0.24), residues: 1242
  helix:  0.15 (0.19), residues: 796
  sheet: -1.29 (0.96), residues: 26
  loop : -2.82 (0.28), residues: 420

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 1.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 128
  average time/residue: 0.2306
  time to fit residues: 42.3805
Evaluate side-chains
  124 residues out of total 1110 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 1.257 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0908
  time to fit residues: 1.9494
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 91 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0980
   chunk 101 optimal weight:    0.6980
   chunk 12 optimal weight:    0.2980
   chunk 18 optimal weight:    0.0010
   chunk 87 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A3510 GLN ** 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 = 0.4077 r_free = 0.4077 target = 0.174551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.146915 restraints weight = 13272.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 1.79
r_work: 0.3754 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3739 rms_B_bonded: 1.61 restraints_weight: 0.2500
r_work: 0.3723 rms_B_bonded: 1.75 restraints_weight: 0.1250
r_work: 0.3703 rms_B_bonded: 1.99 restraints_weight: 0.0625
r_work: 0.3678 rms_B_bonded: 2.37 restraints_weight: 0.0312
r_work: 0.3645 rms_B_bonded: 2.95 restraints_weight: 0.0156
r_work: 0.3599 rms_B_bonded: 3.85 restraints_weight: 0.0078
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.131  10218  Z= 0.167
  Angle     :  0.597  13.882  13801  Z= 0.308
  Chirality :  0.039   0.147   1528
  Planarity :  0.005   0.081   1767
  Dihedral  :  4.365  18.680   1349
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer Outliers :  0.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -1.01 (0.25), residues: 1242
  helix:  0.37 (0.19), residues: 796
  sheet: -1.28 (0.87), residues: 31
  loop : -2.69 (0.29), residues: 415

===============================================================================
Job complete
usr+sys time: 2069.62 seconds
wall clock time: 38 minutes 48.22 seconds (2328.22 seconds total)