Starting phenix.real_space_refine
on Wed May 14 20:42:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ony_17002/05_2025/8ony_17002.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ony_17002/05_2025/8ony_17002.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ony_17002/05_2025/8ony_17002.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ony_17002/05_2025/8ony_17002.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ony_17002/05_2025/8ony_17002.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ony_17002/05_2025/8ony_17002.cif"
  }
  resolution = 2.92
  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=  -0.004 sd=   0.150
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: 6
    Type Number    sf(0)   Gaussians
     Co      2      6.85       5
     P     214      5.49       5
     S      38      5.16       5
     C    6966      2.51       5
     N    2321      2.21       5
     O    2852      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12393
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "5"
      Number of atoms: 3348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 3348
          Classifications: {'RNA': 156}
          Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 15, 'rna3p_pur': 73, 'rna3p_pyr': 51}
          Link IDs: {'rna2p': 32, 'rna3p': 123}
          Chain breaks: 6
    Chain: "Lk"
      Number of atoms: 569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 569
          Classifications: {'peptide': 69}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 66}
    Chain: "LY"
      Number of atoms: 1075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 1075
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "Lh"
      Number of atoms: 1015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 1015
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "LX"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 950
          Classifications: {'peptide': 116}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 107}
    Chain: "LR"
      Number of atoms: 1292
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 153, 1281
          Classifications: {'peptide': 153}
          Link IDs: {'PTRANS': 3, 'TRANS': 149}
      Conformer: "B"
        Number of residues, atoms: 153, 1281
          Classifications: {'peptide': 153}
          Link IDs: {'PTRANS': 3, 'TRANS': 149}
          bond proxies already assigned to first conformer: 1285
    Chain: "8"
      Number of atoms: 1237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 1237
          Classifications: {'RNA': 58}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 22, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 13, 'rna3p': 44}
    Chain: "A"
      Number of atoms: 2905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2905
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 350}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CO': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARGLR  16 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARGLR  16 " occ=0.50
  Time building chain proxies: 13.67, per 1000 atoms: 1.10
  Number of scatterers: 12393
  At special positions: 0
  Unit cell: (145.41, 123.21, 196.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Co      2     26.99
     S      38     16.00
     P     214     15.00
     O    2852      8.00
     N    2321      7.00
     C    6966      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.19
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1822

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 13 sheets defined
      44.5% alpha, 16.6% beta
      45 base pairs and 105 stacking pairs defined.
    Time for finding SS restraints: 4.84
  Creating SS restraints...
    Processing helix  chain 'Lk' and resid 7 through 17
      removed outlier: 3.593A  pdb=" N   PHELk  11 " --> pdb=" O   GLULk   7 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEULk  12 " --> pdb=" O   ILELk   8 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ARGLk  17 " --> pdb=" O   LEULk  13 " (cutoff:3.500A)
    Processing helix  chain 'Lk' and resid 49 through 59
      removed outlier: 3.506A  pdb=" N   ALALk  53 " --> pdb=" O   ASPLk  49 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LYSLk  55 " --> pdb=" O   GLULk  51 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLNLk  58 " --> pdb=" O   GLULk  54 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SERLk  59 " --> pdb=" O   LYSLk  55 " (cutoff:3.500A)
    Processing helix  chain 'LY' and resid 10 through 20
    Processing helix  chain 'LY' and resid 22 through 30
      removed outlier: 4.151A  pdb=" N   LYSLY  28 " --> pdb=" O   HISLY  24 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILELY  29 " --> pdb=" O   ILELY  25 " (cutoff:3.500A)
    Processing helix  chain 'LY' and resid 35 through 43
      removed outlier: 3.545A  pdb=" N   LYSLY  41 " --> pdb=" O   GLULY  37 " (cutoff:3.500A)
    Processing helix  chain 'LY' and resid 100 through 102
      No H-bonds generated for 'chain 'LY' and resid 100 through 102'
    Processing helix  chain 'LY' and resid 112 through 129
      removed outlier: 3.519A  pdb=" N   SERLY 125 " --> pdb=" O   ARGLY 121 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARGLY 126 " --> pdb=" O   LYSLY 122 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLYLY 129 " --> pdb=" O   SERLY 125 " (cutoff:3.500A)
    Processing helix  chain 'Lh' and resid 5 through 10
      removed outlier: 3.684A  pdb=" N   LEULh   9 " --> pdb=" O   LYSLh   5 " (cutoff:3.500A)
    Processing helix  chain 'Lh' and resid 13 through 37
      removed outlier: 3.588A  pdb=" N   VALLh  36 " --> pdb=" O   ARGLh  32 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THRLh  37 " --> pdb=" O   VALLh  33 " (cutoff:3.500A)
    Processing helix  chain 'Lh' and resid 40 through 73
      removed outlier: 4.029A  pdb=" N   ILELh  47 " --> pdb=" O   LYSLh  43 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   ARGLh  48 " --> pdb=" O   LEULh  44 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   VALLh  49 " --> pdb=" O   SERLh  45 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LYSLh  66 " --> pdb=" O   ASNLh  62 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLULh  67 " --> pdb=" O   GLNLh  63 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHELh  72 " --> pdb=" O   ASNLh  68 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYRLh  73 " --> pdb=" O   LEULh  69 " (cutoff:3.500A)
    Processing helix  chain 'Lh' and resid 90 through 94
    Processing helix  chain 'Lh' and resid 96 through 101
      removed outlier: 3.756A  pdb=" N   ASNLh 101 " --> pdb=" O   LYSLh  97 " (cutoff:3.500A)
    Processing helix  chain 'Lh' and resid 104 through 114
      removed outlier: 3.518A  pdb=" N   LYSLh 110 " --> pdb=" O   LYSLh 106 " (cutoff:3.500A)
    Processing helix  chain 'LX' and resid 72 through 76
    Processing helix  chain 'LX' and resid 105 through 118
    Processing helix  chain 'LX' and resid 145 through 154
      removed outlier: 3.683A  pdb=" N   VALLX 149 " --> pdb=" O   ASPLX 145 " (cutoff:3.500A)
    Processing helix  chain 'LR' and resid 4 through 15
      removed outlier: 3.618A  pdb=" N   ARGLR   9 " --> pdb=" O   ARGLR   5 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ALALR  11 " --> pdb=" O   GLNLR   7 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   SERLR  12 " --> pdb=" O   LYSLR   8 " (cutoff:3.500A)
    Processing helix  chain 'LR' and resid 28 through 35
      removed outlier: 3.651A  pdb=" N   ASNLR  34 " --> pdb=" O   ASNLR  30 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ALALR  35 " --> pdb=" O   GLULR  31 " (cutoff:3.500A)
    Processing helix  chain 'LR' and resid 37 through 47
    Processing helix  chain 'LR' and resid 60 through 72
      removed outlier: 3.956A  pdb=" N   LYSLR  72 " --> pdb=" O   LEULR  68 " (cutoff:3.500A)
    Processing helix  chain 'LR' and resid 84 through 89
    Processing helix  chain 'LR' and resid 90 through 112
      removed outlier: 3.757A  pdb=" N   LEULR 106 " --> pdb=" O   LEULR 102 " (cutoff:3.500A)
    Processing helix  chain 'LR' and resid 116 through 129
      removed outlier: 3.648A  pdb=" N   SERLR 122 " --> pdb=" O   HISLR 118 " (cutoff:3.500A)
    Processing helix  chain 'LR' and resid 134 through 154
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 153 through 161
      removed outlier: 3.537A  pdb=" N   ALA A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 187
      removed outlier: 3.921A  pdb=" N   ASP A 168 " --> pdb=" O   GLU A 164 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   PHE A 169 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   SER A 185 " --> pdb=" O   LYS A 181 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   TRP A 186 " --> pdb=" O   TYR A 182 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE A 187 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 209
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'A' and resid 273 through 291
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.669A  pdb=" N   VAL A 300 " --> pdb=" O   ARG A 296 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   SER A 310 " --> pdb=" O   GLU A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 410
      removed outlier: 3.511A  pdb=" N   HIS A 401 " --> pdb=" O   PRO A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 424
    Processing helix  chain 'A' and resid 428 through 439
    Processing sheet with id=AA1, first strand: chain 'Lk' and resid 3 through 4
      removed outlier: 4.047A  pdb=" N   SERLk  22 " --> pdb=" O   ARGLk  37 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VALLk  23 " --> pdb=" O   LYSLk  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'LY' and resid 31 through 33
      removed outlier: 3.565A  pdb=" N   METLY  47 " --> pdb=" O   SERLY  32 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'LY' and resid 79 through 82
      removed outlier: 7.081A  pdb=" N   VALLY  79 " --> pdb=" O   VALLY  73 " (cutoff:3.500A)
      removed outlier: 5.195A  pdb=" N   VALLY  73 " --> pdb=" O   VALLY  79 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   TYRLY  81 " --> pdb=" O   VALLY  71 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   GLULY  54 " --> pdb=" O   THRLY 107 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'LY' and resid 86 through 88
    Processing sheet with id=AA5, first strand: chain 'LX' and resid 77 through 80
      removed outlier: 3.502A  pdb=" N   PHELX  79 " --> pdb=" O   ILELX  99 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   LYSLX 134 " --> pdb=" O   VALLX 100 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LYSLX 123 " --> pdb=" O   ARGLX 139 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'LR' and resid 22 through 24
      removed outlier: 3.569A  pdb=" N   ILELR  51 " --> pdb=" O   TRPLR  23 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 133 through 135
    Processing sheet with id=AA8, first strand: chain 'A' and resid 133 through 135
      removed outlier: 4.538A  pdb=" N   VAL A 360 " --> pdb=" O   ILE A 333 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 215 through 216
      removed outlier: 3.575A  pdb=" N   GLY A 216 " --> pdb=" O   HIS A 255 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 215 through 216
      removed outlier: 3.575A  pdb=" N   GLY A 216 " --> pdb=" O   HIS A 255 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE A 252 " --> pdb=" O   CYS A 263 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   CYS A 263 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 228 through 230
      removed outlier: 6.816A  pdb=" N   LEU A 447 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 312 through 315
    Processing sheet with id=AB4, first strand: chain 'A' and resid 415 through 416
      removed outlier: 3.959A  pdb=" N   HIS A 382 " --> pdb=" O   TYR A 444 " (cutoff:3.500A)

    344 hydrogen bonds defined for protein.
    981 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      116 hydrogen bonds
      204 hydrogen bond angles
      0 basepair planarities
      45 basepair parallelities
      105 stacking parallelities
  Total time for adding SS restraints: 4.58

  Time building geometry restraints manager: 3.74 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 2722
        1.33 -     1.45: 3722
        1.45 -     1.57: 6139
        1.57 -     1.69: 420
        1.69 -     1.81: 58
  Bond restraints: 13061
  Sorted by residual:
  bond pdb=" CB  ILE A 394 "
       pdb=" CG2 ILE A 394 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.15e+00
  bond pdb=" CB  THR A 399 "
       pdb=" CG2 THR A 399 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.78e+00
  bond pdb=" C3'   G 53597 "
       pdb=" C2'   G 53597 "
    ideal  model  delta    sigma   weight residual
    1.523  1.543 -0.020 1.50e-02 4.44e+03 1.70e+00
  bond pdb=" C4'   A 52529 "
       pdb=" O4'   A 52529 "
    ideal  model  delta    sigma   weight residual
    1.454  1.435  0.019 1.50e-02 4.44e+03 1.61e+00
  bond pdb=" O4'   G 53597 "
       pdb=" C1'   G 53597 "
    ideal  model  delta    sigma   weight residual
    1.412  1.393  0.019 1.50e-02 4.44e+03 1.60e+00
  ... (remaining 13056 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.96: 18495
        2.96 -     5.92: 106
        5.92 -     8.88: 2
        8.88 -    11.84: 0
       11.84 -    14.79: 1
  Bond angle restraints: 18604
  Sorted by residual:
  angle pdb=" CA  LEU A 396 "
        pdb=" CB  LEU A 396 "
        pdb=" CG  LEU A 396 "
      ideal   model   delta    sigma   weight residual
     116.30  131.09  -14.79 3.50e+00 8.16e-02 1.79e+01
  angle pdb=" C2'   C 52526 "
        pdb=" C1'   C 52526 "
        pdb=" N1    C 52526 "
      ideal   model   delta    sigma   weight residual
     112.00  116.70   -4.70 1.50e+00 4.44e-01 9.82e+00
  angle pdb=" C3'   A 52529 "
        pdb=" C2'   A 52529 "
        pdb=" C1'   A 52529 "
      ideal   model   delta    sigma   weight residual
     101.50  104.33   -2.83 1.00e+00 1.00e+00 8.02e+00
  angle pdb=" N   PRO A 397 "
        pdb=" CA  PRO A 397 "
        pdb=" C   PRO A 397 "
      ideal   model   delta    sigma   weight residual
     113.78  118.13   -4.35 1.62e+00 3.81e-01 7.20e+00
  angle pdb=" O3'   C 52410 "
        pdb=" C3'   C 52410 "
        pdb=" C2'   C 52410 "
      ideal   model   delta    sigma   weight residual
     113.70  109.74    3.96 1.50e+00 4.44e-01 6.96e+00
  ... (remaining 18599 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.74: 7001
       18.74 -    37.48: 737
       37.48 -    56.22: 268
       56.22 -    74.96: 272
       74.96 -    93.69: 14
  Dihedral angle restraints: 8292
    sinusoidal: 5480
      harmonic: 2812
  Sorted by residual:
  dihedral pdb=" C5'   A 52529 "
           pdb=" C4'   A 52529 "
           pdb=" C3'   A 52529 "
           pdb=" O3'   A 52529 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  103.28   43.72     1      8.00e+00 1.56e-02 4.16e+01
  dihedral pdb=" O4'   A 52529 "
           pdb=" C4'   A 52529 "
           pdb=" C3'   A 52529 "
           pdb=" C2'   A 52529 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -18.65   42.65     1      8.00e+00 1.56e-02 3.97e+01
  dihedral pdb=" C4'   A 52529 "
           pdb=" C3'   A 52529 "
           pdb=" C2'   A 52529 "
           pdb=" C1'   A 52529 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00    0.92  -35.92     1      8.00e+00 1.56e-02 2.85e+01
  ... (remaining 8289 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1728
       0.048 -    0.097: 403
       0.097 -    0.145: 94
       0.145 -    0.193: 12
       0.193 -    0.241: 2
  Chirality restraints: 2239
  Sorted by residual:
  chirality pdb=" CB  THR A 399 "
            pdb=" CA  THR A 399 "
            pdb=" OG1 THR A 399 "
            pdb=" CG2 THR A 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" C1'   U 8  69 "
            pdb=" O4'   U 8  69 "
            pdb=" C2'   U 8  69 "
            pdb=" N1    U 8  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.27    0.19 2.00e-01 2.50e+01 9.48e-01
  chirality pdb=" C1'   A 52382 "
            pdb=" O4'   A 52382 "
            pdb=" C2'   A 52382 "
            pdb=" N9    A 52382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.27    0.19 2.00e-01 2.50e+01 9.13e-01
  ... (remaining 2236 not shown)

  Planarity restraints: 1565
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C 52419 "    0.028 2.00e-02 2.50e+03   3.00e-02 2.02e+01
        pdb=" N1    C 52419 "   -0.070 2.00e-02 2.50e+03
        pdb=" C2    C 52419 "    0.045 2.00e-02 2.50e+03
        pdb=" O2    C 52419 "   -0.012 2.00e-02 2.50e+03
        pdb=" N3    C 52419 "   -0.008 2.00e-02 2.50e+03
        pdb=" C4    C 52419 "    0.001 2.00e-02 2.50e+03
        pdb=" N4    C 52419 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    C 52419 "    0.006 2.00e-02 2.50e+03
        pdb=" C6    C 52419 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A 52418 "    0.024 2.00e-02 2.50e+03   2.35e-02 1.51e+01
        pdb=" N9    A 52418 "   -0.062 2.00e-02 2.50e+03
        pdb=" C8    A 52418 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A 52418 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    A 52418 "    0.003 2.00e-02 2.50e+03
        pdb=" C6    A 52418 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6    A 52418 "    0.001 2.00e-02 2.50e+03
        pdb=" N1    A 52418 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A 52418 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3    A 52418 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    A 52418 "    0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C 52526 "   -0.038 2.00e-02 2.50e+03   2.07e-02 9.68e+00
        pdb=" N1    C 52526 "    0.047 2.00e-02 2.50e+03
        pdb=" C2    C 52526 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    C 52526 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    C 52526 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    C 52526 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4    C 52526 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5    C 52526 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    C 52526 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1562 not shown)

  Histogram of nonbonded interaction distances:
        0.91 -     1.71: 1
        1.71 -     2.51: 28
        2.51 -     3.30: 12110
        3.30 -     4.10: 31114
        4.10 -     4.90: 50961
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 94214
  Sorted by model distance:
  nonbonded pdb="CO    CO A 501 "
            pdb="CO    CO A 502 "
     model   vdw
     0.911 1.400
  nonbonded pdb=" OE2 GLU A 364 "
            pdb="CO    CO A 501 "
     model   vdw
     2.114 2.220
  nonbonded pdb=" OD2 ASPLh  82 "
            pdb=" OG  SERLX  64 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OE1 GLNLR  39 "
            pdb=" NH1 ARGLR  42 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OH  TYRLY  74 "
            pdb=" OP2   G 8  75 "
     model   vdw
     2.359 3.040
  ... (remaining 94209 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             36.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     38.730
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.860
  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:             1.060
  Load rotamer database and sin/cos tables:14.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   91.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
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      :  0.003   0.059  13061  Z= 0.153
  Angle     :  0.638  14.794  18604  Z= 0.370
  Chirality :  0.045   0.241   2239
  Planarity :  0.005   0.061   1565
  Dihedral  : 19.924  93.694   6470
  Min Nonbonded Distance : 0.911

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 951
  helix:  1.67 (0.26), residues: 379
  sheet:  1.60 (0.52), residues: 107
  loop : -0.98 (0.24), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 148 
 HIS   0.005   0.001   HISLY  24 
 PHE   0.011   0.001   PHELX  98 
 TYR   0.012   0.001   TYRLX 137 
 ARG   0.004   0.000   ARGLk  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24680 (  445)
  hydrogen bonds       : angle       5.59135 ( 1185)
  covalent geometry    : bond        0.00298 (13061)
  covalent geometry    : angle       0.63798 (18604)

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

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

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.116 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 1.5392
  time to fit residues: 193.5210
Evaluate side-chains
  98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0670
   chunk 88 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 102 optimal weight:    8.9990
   overall best weight:    1.9322

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

Flipped N/Q/H residues before XYZ refinement:
Lk  58 GLN
LY  43 ASN
LX 151 ASN
LR 134 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.102517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.088105 restraints weight = 54517.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.71
r_work: 0.2922 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13061  Z= 0.148
  Angle     :  0.568  10.659  18604  Z= 0.304
  Chirality :  0.039   0.237   2239
  Planarity :  0.005   0.049   1565
  Dihedral  : 20.947  91.687   4363
  Min Nonbonded Distance : 1.309

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  7.97 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.26), residues: 951
  helix:  2.17 (0.26), residues: 399
  sheet:  1.76 (0.50), residues: 105
  loop : -0.90 (0.24), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 186 
 HIS   0.006   0.001   HISLY  24 
 PHE   0.009   0.001   PHELX  79 
 TYR   0.016   0.001   TYRLX 137 
 ARG   0.003   0.000   ARGLR 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06738 (  445)
  hydrogen bonds       : angle       3.85450 ( 1185)
  covalent geometry    : bond        0.00303 (13061)
  covalent geometry    : angle       0.56830 (18604)

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

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

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 1.111 
Fit side-chains
REVERT: Lk   31 ASN cc_start: 0.8470 (p0) cc_final: 0.8153 (p0)
REVERT: Lk   68 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7366 (tm-30)
REVERT: LY  112 ASP cc_start: 0.6234 (m-30) cc_final: 0.5874 (m-30)
REVERT: A  296 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6998 (mtt180)
REVERT: A  457 GLN cc_start: 0.9051 (tt0) cc_final: 0.8768 (tt0)
  outliers start: 11
  outliers final: 4
  residues processed: 111
  average time/residue: 1.4399
  time to fit residues: 172.4714
Evaluate side-chains
  99 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Lk residue   12 LEU
Chi-restraints excluded: chain LX residue  119 ILE
Chi-restraints excluded: chain LR residue    5 ARG
Chi-restraints excluded: chain LR residue  144 LYS
Chi-restraints excluded: chain A residue  296 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 102 optimal weight:   10.0000
   chunk 100 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 89 optimal weight:    9.9990
   chunk 81 optimal weight:    9.9990
   chunk 84 optimal weight:    0.2980
   chunk 30 optimal weight:    9.9990
   chunk 96 optimal weight:    0.9980
   overall best weight:    4.2586

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

Flipped N/Q/H residues before XYZ refinement:
Lk  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.098878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.082768 restraints weight = 42551.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.87
r_work: 0.2858 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2846
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2846 r_free = 0.2846    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2846 r_free = 0.2846    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2846
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13061  Z= 0.256
  Angle     :  0.669  10.459  18604  Z= 0.352
  Chirality :  0.044   0.252   2239
  Planarity :  0.006   0.046   1565
  Dihedral  : 20.917  90.142   4363
  Min Nonbonded Distance : 1.185

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  9.26 %
    Favored  : 88.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.26), residues: 951
  helix:  1.80 (0.26), residues: 396
  sheet:  1.29 (0.49), residues: 115
  loop : -1.17 (0.24), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 186 
 HIS   0.007   0.002   HISLY  24 
 PHE   0.012   0.002   PHE A 366 
 TYR   0.020   0.002   TYRLX 137 
 ARG   0.006   0.001   ARGLR  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08643 (  445)
  hydrogen bonds       : angle       3.77254 ( 1185)
  covalent geometry    : bond        0.00549 (13061)
  covalent geometry    : angle       0.66875 (18604)

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

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

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 1.202 
Fit side-chains
REVERT: Lk   31 ASN cc_start: 0.8568 (p0) cc_final: 0.8325 (p0)
REVERT: Lk   68 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7397 (tm-30)
REVERT: LY  112 ASP cc_start: 0.6275 (OUTLIER) cc_final: 0.5942 (m-30)
REVERT: A  457 GLN cc_start: 0.9073 (tt0) cc_final: 0.8783 (tt0)
  outliers start: 17
  outliers final: 6
  residues processed: 102
  average time/residue: 1.4793
  time to fit residues: 162.5981
Evaluate side-chains
  96 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Lk residue   22 SER
Chi-restraints excluded: chain LY residue  112 ASP
Chi-restraints excluded: chain LX residue  119 ILE
Chi-restraints excluded: chain LR residue    5 ARG
Chi-restraints excluded: chain LR residue   12 SER
Chi-restraints excluded: chain LR residue   91 GLU
Chi-restraints excluded: chain LR residue  112 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 105 optimal weight:    0.8980
   chunk 104 optimal weight:    8.9990
   chunk 48 optimal weight:    5.9990
   chunk 107 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0060
   chunk 89 optimal weight:    9.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    1.9802

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

Flipped N/Q/H residues before XYZ refinement:
Lk  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.100957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.086430 restraints weight = 52193.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.67
r_work: 0.2894 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13061  Z= 0.141
  Angle     :  0.534   8.941  18604  Z= 0.285
  Chirality :  0.038   0.232   2239
  Planarity :  0.005   0.046   1565
  Dihedral  : 20.702  90.537   4363
  Min Nonbonded Distance : 1.209

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.14 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.26), residues: 951
  helix:  2.10 (0.27), residues: 395
  sheet:  1.34 (0.48), residues: 113
  loop : -1.11 (0.25), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 186 
 HIS   0.004   0.001   HISLY  24 
 PHE   0.009   0.001   PHELX  79 
 TYR   0.014   0.001   TYRLX 137 
 ARG   0.003   0.000   ARG A 395 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06151 (  445)
  hydrogen bonds       : angle       3.42619 ( 1185)
  covalent geometry    : bond        0.00290 (13061)
  covalent geometry    : angle       0.53406 (18604)

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

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

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 1.107 
Fit side-chains
REVERT: Lk   19 ASP cc_start: 0.8435 (p0) cc_final: 0.8018 (p0)
REVERT: Lk   68 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7636 (tm-30)
REVERT: LY  112 ASP cc_start: 0.6295 (m-30) cc_final: 0.6028 (m-30)
REVERT: A  457 GLN cc_start: 0.9071 (tt0) cc_final: 0.8845 (tt0)
  outliers start: 15
  outliers final: 8
  residues processed: 101
  average time/residue: 1.4846
  time to fit residues: 161.9077
Evaluate side-chains
  99 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Lk residue   22 SER
Chi-restraints excluded: chain LY residue   84 ARG
Chi-restraints excluded: chain Lh residue   22 ASP
Chi-restraints excluded: chain LX residue  119 ILE
Chi-restraints excluded: chain LR residue    5 ARG
Chi-restraints excluded: chain LR residue   12 SER
Chi-restraints excluded: chain LR residue   91 GLU
Chi-restraints excluded: chain LR residue   96 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 104 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 99 optimal weight:    0.2980
   chunk 53 optimal weight:    0.0060
   chunk 72 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0070
   chunk 57 optimal weight:    3.9990
   chunk 88 optimal weight:   10.0000
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.8618

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

Flipped N/Q/H residues before XYZ refinement:
Lk  58 GLN
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.103518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.082586 restraints weight = 33553.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 1.91
r_work: 0.3031 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  13061  Z= 0.097
  Angle     :  0.474   9.438  18604  Z= 0.253
  Chirality :  0.035   0.201   2239
  Planarity :  0.004   0.044   1565
  Dihedral  : 20.520  95.704   4363
  Min Nonbonded Distance : 1.260

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 12.43 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.27), residues: 951
  helix:  2.33 (0.27), residues: 394
  sheet:  1.39 (0.48), residues: 113
  loop : -0.96 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 186 
 HIS   0.002   0.001   HISLY  24 
 PHE   0.007   0.001   PHELX  79 
 TYR   0.010   0.001   TYRLX 137 
 ARG   0.004   0.000   ARG A 395 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04655 (  445)
  hydrogen bonds       : angle       3.14947 ( 1185)
  covalent geometry    : bond        0.00191 (13061)
  covalent geometry    : angle       0.47364 (18604)

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

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

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 1.160 
Fit side-chains
REVERT: Lk   19 ASP cc_start: 0.8354 (p0) cc_final: 0.7940 (p0)
REVERT: Lk   68 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7555 (tm-30)
REVERT: LY  112 ASP cc_start: 0.6016 (m-30) cc_final: 0.5815 (m-30)
REVERT: LR  151 ARG cc_start: 0.7432 (tpt170) cc_final: 0.7068 (ttp80)
  outliers start: 9
  outliers final: 5
  residues processed: 99
  average time/residue: 1.4833
  time to fit residues: 158.5040
Evaluate side-chains
  94 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain LY residue   84 ARG
Chi-restraints excluded: chain Lh residue   94 ARG
Chi-restraints excluded: chain LX residue  119 ILE
Chi-restraints excluded: chain LR residue    5 ARG
Chi-restraints excluded: chain LR residue   91 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 36 optimal weight:    0.0970
   chunk 68 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0470
   chunk 13 optimal weight:   10.0000
   chunk 2 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
Lk  58 GLN
A 305 GLN
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.106008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.090795 restraints weight = 45318.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 2.76
r_work: 0.3027 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3016
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  13061  Z= 0.086
  Angle     :  0.448  10.116  18604  Z= 0.238
  Chirality :  0.034   0.176   2239
  Planarity :  0.004   0.045   1565
  Dihedral  : 20.396  98.109   4363
  Min Nonbonded Distance : 1.278

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 13.36 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.27), residues: 951
  helix:  2.41 (0.28), residues: 395
  sheet:  1.79 (0.51), residues: 103
  loop : -0.65 (0.26), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 186 
 HIS   0.002   0.001   HISLY  61 
 PHE   0.006   0.001   PHELX  79 
 TYR   0.008   0.001   TYRLR 124 
 ARG   0.004   0.000   ARG A 395 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03876 (  445)
  hydrogen bonds       : angle       2.97817 ( 1185)
  covalent geometry    : bond        0.00171 (13061)
  covalent geometry    : angle       0.44772 (18604)

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

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

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 1.037 
Fit side-chains
REVERT: Lk   19 ASP cc_start: 0.8206 (p0) cc_final: 0.7795 (p0)
REVERT: Lk   68 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7561 (tm-30)
REVERT: LR  151 ARG cc_start: 0.7360 (tpt170) cc_final: 0.7071 (ttp80)
  outliers start: 10
  outliers final: 5
  residues processed: 100
  average time/residue: 1.4113
  time to fit residues: 152.2655
Evaluate side-chains
  89 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain LY residue   84 ARG
Chi-restraints excluded: chain LY residue   93 THR
Chi-restraints excluded: chain LR residue    5 ARG
Chi-restraints excluded: chain LR residue   91 GLU
Chi-restraints excluded: chain LR residue   96 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 104 optimal weight:    9.9990
   chunk 110 optimal weight:    8.9990
   chunk 64 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0060
   chunk 31 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0270
   overall best weight:    1.4058

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

Flipped N/Q/H residues before XYZ refinement:
Lk  58 GLN
LY  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.103698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.081685 restraints weight = 29413.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.67
r_work: 0.3043 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  13061  Z= 0.112
  Angle     :  0.481  10.017  18604  Z= 0.254
  Chirality :  0.035   0.166   2239
  Planarity :  0.004   0.047   1565
  Dihedral  : 20.320  93.273   4363
  Min Nonbonded Distance : 1.220

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.72 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.27), residues: 951
  helix:  2.33 (0.28), residues: 396
  sheet:  1.35 (0.48), residues: 113
  loop : -0.74 (0.26), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 186 
 HIS   0.003   0.001   HISLY  24 
 PHE   0.008   0.001   PHELX  79 
 TYR   0.012   0.001   TYRLX 137 
 ARG   0.002   0.000   ARGLR  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04820 (  445)
  hydrogen bonds       : angle       3.07526 ( 1185)
  covalent geometry    : bond        0.00234 (13061)
  covalent geometry    : angle       0.48092 (18604)

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

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

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 1.032 
Fit side-chains
REVERT: Lk   19 ASP cc_start: 0.8265 (p0) cc_final: 0.7850 (p0)
REVERT: Lk   68 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7573 (tm-30)
REVERT: LR  151 ARG cc_start: 0.7454 (tpt170) cc_final: 0.7174 (ttp80)
  outliers start: 12
  outliers final: 8
  residues processed: 93
  average time/residue: 1.3977
  time to fit residues: 141.0767
Evaluate side-chains
  95 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain LY residue   55 VAL
Chi-restraints excluded: chain LY residue   84 ARG
Chi-restraints excluded: chain LY residue   93 THR
Chi-restraints excluded: chain LX residue  148 ASP
Chi-restraints excluded: chain LR residue    5 ARG
Chi-restraints excluded: chain LR residue   12 SER
Chi-restraints excluded: chain LR residue   91 GLU
Chi-restraints excluded: chain LR residue   96 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 106 optimal weight:    8.9990
   chunk 87 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 81 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
Lk  58 GLN
LY  40 GLN
A 434 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.101334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.085195 restraints weight = 43367.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 3.03
r_work: 0.2906 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2892
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2892
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13061  Z= 0.157
  Angle     :  0.545  10.275  18604  Z= 0.288
  Chirality :  0.038   0.174   2239
  Planarity :  0.005   0.048   1565
  Dihedral  : 20.397  89.440   4363
  Min Nonbonded Distance : 1.201

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 14.65 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.27), residues: 951
  helix:  2.12 (0.28), residues: 396
  sheet:  1.18 (0.47), residues: 113
  loop : -0.88 (0.26), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 186 
 HIS   0.004   0.001   HISLY  24 
 PHE   0.012   0.001   PHE A 366 
 TYR   0.015   0.001   TYRLX 137 
 ARG   0.003   0.000   ARGLR 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06244 (  445)
  hydrogen bonds       : angle       3.26399 ( 1185)
  covalent geometry    : bond        0.00334 (13061)
  covalent geometry    : angle       0.54549 (18604)

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

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

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
REVERT: Lk   58 GLN cc_start: 0.7761 (mt0) cc_final: 0.7503 (mp10)
REVERT: Lk   68 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7459 (tm-30)
REVERT: LR  151 ARG cc_start: 0.7528 (tpt170) cc_final: 0.7278 (ttp80)
  outliers start: 10
  outliers final: 7
  residues processed: 99
  average time/residue: 1.3413
  time to fit residues: 143.6361
Evaluate side-chains
  96 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain LY residue   55 VAL
Chi-restraints excluded: chain LY residue   84 ARG
Chi-restraints excluded: chain LY residue   93 THR
Chi-restraints excluded: chain Lh residue  100 GLU
Chi-restraints excluded: chain LR residue    5 ARG
Chi-restraints excluded: chain LR residue   12 SER
Chi-restraints excluded: chain LR residue   91 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   chunk 51 optimal weight:    0.5980
   chunk 92 optimal weight:    8.9990
   chunk 101 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 102 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
LY  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.101049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.085111 restraints weight = 43121.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.86
r_work: 0.2904 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2891
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2891
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13061  Z= 0.164
  Angle     :  0.551  10.198  18604  Z= 0.291
  Chirality :  0.038   0.178   2239
  Planarity :  0.005   0.046   1565
  Dihedral  : 20.442  89.603   4363
  Min Nonbonded Distance : 1.197

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 15.12 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.27), residues: 951
  helix:  1.98 (0.28), residues: 396
  sheet:  1.04 (0.47), residues: 113
  loop : -0.95 (0.26), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 186 
 HIS   0.004   0.001   HISLY  24 
 PHE   0.011   0.001   PHE A 366 
 TYR   0.015   0.001   TYRLX 137 
 ARG   0.003   0.000   ARGLR 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06221 (  445)
  hydrogen bonds       : angle       3.28039 ( 1185)
  covalent geometry    : bond        0.00350 (13061)
  covalent geometry    : angle       0.55052 (18604)

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

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

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
REVERT: Lk   68 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7642 (tm-30)
REVERT: LX   91 GLU cc_start: 0.8495 (pm20) cc_final: 0.8138 (pp20)
REVERT: LR  151 ARG cc_start: 0.7513 (tpt170) cc_final: 0.7272 (ttp80)
  outliers start: 9
  outliers final: 7
  residues processed: 94
  average time/residue: 1.4064
  time to fit residues: 142.8957
Evaluate side-chains
  94 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Lk residue   22 SER
Chi-restraints excluded: chain LY residue   55 VAL
Chi-restraints excluded: chain LY residue   93 THR
Chi-restraints excluded: chain Lh residue  100 GLU
Chi-restraints excluded: chain LR residue    5 ARG
Chi-restraints excluded: chain LR residue   12 SER
Chi-restraints excluded: chain LR residue   91 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 81 optimal weight:   10.0000
   chunk 84 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 74 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   chunk 49 optimal weight:    8.9990
   chunk 57 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
Lk  58 GLN
LY  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.103895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.088254 restraints weight = 46011.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.80
r_work: 0.2978 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2967
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2967
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  13061  Z= 0.102
  Angle     :  0.498  10.760  18604  Z= 0.263
  Chirality :  0.035   0.171   2239
  Planarity :  0.004   0.045   1565
  Dihedral  : 20.355  95.445   4363
  Min Nonbonded Distance : 1.272

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 15.94 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.27), residues: 951
  helix:  2.15 (0.28), residues: 396
  sheet:  1.10 (0.47), residues: 113
  loop : -0.83 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 186 
 HIS   0.002   0.001   HISLY  24 
 PHE   0.008   0.001   PHE A 366 
 TYR   0.009   0.001   TYRLX 137 
 ARG   0.003   0.000   ARG A 395 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04571 (  445)
  hydrogen bonds       : angle       3.12036 ( 1185)
  covalent geometry    : bond        0.00211 (13061)
  covalent geometry    : angle       0.49807 (18604)

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

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

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1902 Ramachandran restraints generated.
    951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
REVERT: Lk   68 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7641 (tm-30)
REVERT: LX   91 GLU cc_start: 0.8562 (pm20) cc_final: 0.8147 (pp20)
REVERT: LR  151 ARG cc_start: 0.7530 (tpt170) cc_final: 0.7241 (ttp-110)
  outliers start: 6
  outliers final: 5
  residues processed: 94
  average time/residue: 1.3672
  time to fit residues: 139.3516
Evaluate side-chains
  91 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain LY residue   55 VAL
Chi-restraints excluded: chain LY residue   93 THR
Chi-restraints excluded: chain Lh residue  100 GLU
Chi-restraints excluded: chain LR residue    5 ARG
Chi-restraints excluded: chain LR residue   91 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 19 optimal weight:    9.9990
   chunk 50 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 98 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   chunk 73 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0870
   overall best weight:    2.3564

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

Flipped N/Q/H residues before XYZ refinement:
Lk  58 GLN
LY  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.101514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.080464 restraints weight = 25643.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.30
r_work: 0.3026 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13061  Z= 0.155
  Angle     :  0.545  10.522  18604  Z= 0.287
  Chirality :  0.037   0.172   2239
  Planarity :  0.005   0.048   1565
  Dihedral  : 20.388  89.168   4363
  Min Nonbonded Distance : 1.203

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 15.83 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.27), residues: 951
  helix:  2.08 (0.28), residues: 396
  sheet:  1.00 (0.46), residues: 113
  loop : -0.90 (0.26), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 186 
 HIS   0.004   0.001   HISLY  24 
 PHE   0.010   0.001   PHE A 366 
 TYR   0.015   0.001   TYRLX 137 
 ARG   0.003   0.000   ARG A 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05936 (  445)
  hydrogen bonds       : angle       3.24492 ( 1185)
  covalent geometry    : bond        0.00330 (13061)
  covalent geometry    : angle       0.54495 (18604)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10619.90 seconds
wall clock time: 185 minutes 46.99 seconds (11146.99 seconds total)