Starting phenix.real_space_refine
on Wed Feb 12 04:34:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t4f_25675/02_2025/7t4f_25675.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t4f_25675/02_2025/7t4f_25675.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t4f_25675/02_2025/7t4f_25675.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t4f_25675/02_2025/7t4f_25675.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t4f_25675/02_2025/7t4f_25675.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t4f_25675/02_2025/7t4f_25675.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    4516      2.51       5
     N    1216      2.21       5
     O    1472      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7224
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1806
          Classifications: {'peptide': 245}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232}
    Chain: "B"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1806
          Classifications: {'peptide': 245}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232}
    Chain: "C"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1806
          Classifications: {'peptide': 245}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232}
    Chain: "D"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1806
          Classifications: {'peptide': 245}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232}
  Time building chain proxies: 4.94, per 1000 atoms: 0.68
  Number of scatterers: 7224
  At special positions: 0
  Unit cell: (108.9, 108.9, 127.6, 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      20     16.00
     O    1472      8.00
     N    1216      7.00
     C    4516      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: 1.73
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1776

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 16 sheets defined
      8.2% alpha, 44.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 103
    Processing helix  chain 'A' and resid 151 through 156
    Processing helix  chain 'B' and resid 90 through 103
    Processing helix  chain 'B' and resid 151 through 156
      removed outlier: 3.556A  pdb=" N   SER B 156 " --> pdb=" O   GLU B 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 103
    Processing helix  chain 'C' and resid 151 through 156
      removed outlier: 3.504A  pdb=" N   SER C 156 " --> pdb=" O   GLU C 153 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 103
    Processing helix  chain 'D' and resid 151 through 156
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39
      removed outlier: 4.601A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   ALA A 107 " --> pdb=" O   TYR A  20 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   LYS A 142 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE A 127 " --> pdb=" O   THR A 140 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   THR A 140 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   LYS A 129 " --> pdb=" O   THR A 138 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   THR A 138 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   VAL A 131 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 8.402A  pdb=" N   VAL A 136 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   SER A  81 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   LEU A  45 " --> pdb=" O   SER A  81 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   THR A  83 " --> pdb=" O   LYS A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39
      removed outlier: 4.601A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   ALA A 107 " --> pdb=" O   TYR A  20 " (cutoff:3.500A)
      removed outlier: 17.808A  pdb=" N   ARG A 121 " --> pdb=" O   ASP C  56 " (cutoff:3.500A)
      removed outlier: 14.231A  pdb=" N   ASP C  56 " --> pdb=" O   ARG A 121 " (cutoff:3.500A)
      removed outlier: 12.286A  pdb=" N   TRP A 123 " --> pdb=" O   SER C  54 " (cutoff:3.500A)
      removed outlier: 9.384A  pdb=" N   SER C  54 " --> pdb=" O   TRP A 123 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   SER A 125 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   THR C  51 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   LYS C  75 " --> pdb=" O   THR C  51 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   GLU C  53 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 56
      removed outlier: 6.744A  pdb=" N   THR A  51 " --> pdb=" O   LYS A  75 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   LYS A  75 " --> pdb=" O   THR A  51 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   GLU A  53 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 167
    Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 174
      removed outlier: 6.687A  pdb=" N   THR A 171 " --> pdb=" O   THR A 242 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   THR A 244 " --> pdb=" O   THR A 171 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   VAL A 173 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 38
      removed outlier: 5.449A  pdb=" N   ALA B 107 " --> pdb=" O   TYR B  20 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   LYS B 142 " --> pdb=" O   SER B 125 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ILE B 127 " --> pdb=" O   THR B 140 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   THR B 140 " --> pdb=" O   ILE B 127 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   LYS B 129 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   THR B 138 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASP B  44 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ALA B  85 " --> pdb=" O   VAL B  42 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   VAL B  42 " --> pdb=" O   ALA B  85 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 38
      removed outlier: 5.449A  pdb=" N   ALA B 107 " --> pdb=" O   TYR B  20 " (cutoff:3.500A)
      removed outlier: 17.775A  pdb=" N   ARG B 121 " --> pdb=" O   ASP D  56 " (cutoff:3.500A)
      removed outlier: 14.331A  pdb=" N   ASP D  56 " --> pdb=" O   ARG B 121 " (cutoff:3.500A)
      removed outlier: 12.231A  pdb=" N   TRP B 123 " --> pdb=" O   SER D  54 " (cutoff:3.500A)
      removed outlier: 9.286A  pdb=" N   SER D  54 " --> pdb=" O   TRP B 123 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   SER B 125 " --> pdb=" O   ALA D  52 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   THR D  51 " --> pdb=" O   LYS D  75 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   LYS D  75 " --> pdb=" O   THR D  51 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   GLU D  53 " --> pdb=" O   GLY D  73 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 56
      removed outlier: 6.715A  pdb=" N   THR B  51 " --> pdb=" O   LYS B  75 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   LYS B  75 " --> pdb=" O   THR B  51 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   GLU B  53 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 167
    Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 174
      removed outlier: 6.688A  pdb=" N   THR B 171 " --> pdb=" O   THR B 242 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   THR B 244 " --> pdb=" O   THR B 171 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   VAL B 173 " --> pdb=" O   THR B 244 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 36 through 38
      removed outlier: 5.478A  pdb=" N   ALA C 107 " --> pdb=" O   TYR C  20 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   LYS C 142 " --> pdb=" O   SER C 125 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   ILE C 127 " --> pdb=" O   THR C 140 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   THR C 140 " --> pdb=" O   ILE C 127 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   LYS C 129 " --> pdb=" O   THR C 138 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   THR C 138 " --> pdb=" O   LYS C 129 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   VAL C 131 " --> pdb=" O   VAL C 136 " (cutoff:3.500A)
      removed outlier: 8.448A  pdb=" N   VAL C 136 " --> pdb=" O   VAL C 131 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   SER C  81 " --> pdb=" O   LEU C  45 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   LEU C  45 " --> pdb=" O   SER C  81 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   THR C  83 " --> pdb=" O   LYS C  43 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 163 through 167
    Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 174
      removed outlier: 6.688A  pdb=" N   THR C 171 " --> pdb=" O   THR C 242 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   THR C 244 " --> pdb=" O   THR C 171 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   VAL C 173 " --> pdb=" O   THR C 244 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 36 through 38
      removed outlier: 5.322A  pdb=" N   ALA D 107 " --> pdb=" O   TYR D  20 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LYS D 142 " --> pdb=" O   SER D 125 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   ILE D 127 " --> pdb=" O   THR D 140 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   THR D 140 " --> pdb=" O   ILE D 127 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   LYS D 129 " --> pdb=" O   THR D 138 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   THR D 138 " --> pdb=" O   LYS D 129 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASP D  44 " --> pdb=" O   THR D  83 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   ALA D  85 " --> pdb=" O   VAL D  42 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   VAL D  42 " --> pdb=" O   ALA D  85 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 163 through 167
    Processing sheet with id=AB7, first strand: chain 'D' and resid 170 through 174
      removed outlier: 6.688A  pdb=" N   THR D 171 " --> pdb=" O   THR D 242 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   THR D 244 " --> pdb=" O   THR D 171 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   VAL D 173 " --> pdb=" O   THR D 244 " (cutoff:3.500A)

    296 hydrogen bonds defined for protein.
    768 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: 2.29

  Time building geometry restraints manager: 2.06 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1249
        1.31 -     1.44: 1883
        1.44 -     1.56: 4196
        1.56 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 7368
  Sorted by residual:
  bond pdb=" C   PRO B   9 "
       pdb=" O   PRO B   9 "
    ideal  model  delta    sigma   weight residual
    1.233  1.187  0.046 1.16e-02 7.43e+03 1.55e+01
  bond pdb=" C   PRO D   9 "
       pdb=" O   PRO D   9 "
    ideal  model  delta    sigma   weight residual
    1.233  1.189  0.044 1.19e-02 7.06e+03 1.37e+01
  bond pdb=" N   VAL D  10 "
       pdb=" CA  VAL D  10 "
    ideal  model  delta    sigma   weight residual
    1.456  1.498 -0.042 1.14e-02 7.69e+03 1.35e+01
  bond pdb=" N   VAL C  10 "
       pdb=" CA  VAL C  10 "
    ideal  model  delta    sigma   weight residual
    1.459  1.502 -0.043 1.19e-02 7.06e+03 1.31e+01
  bond pdb=" CA  ALA A  13 "
       pdb=" CB  ALA A  13 "
    ideal  model  delta    sigma   weight residual
    1.527  1.477  0.050 1.44e-02 4.82e+03 1.20e+01
  ... (remaining 7363 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 9700
        1.78 -     3.55: 305
        3.55 -     5.33: 49
        5.33 -     7.11: 8
        7.11 -     8.88: 2
  Bond angle restraints: 10064
  Sorted by residual:
  angle pdb=" N   GLY B  12 "
        pdb=" CA  GLY B  12 "
        pdb=" C   GLY B  12 "
      ideal   model   delta    sigma   weight residual
     114.67  121.24   -6.57 1.10e+00 8.26e-01 3.57e+01
  angle pdb=" N   PRO D   9 "
        pdb=" CA  PRO D   9 "
        pdb=" CB  PRO D   9 "
      ideal   model   delta    sigma   weight residual
     103.35   98.89    4.46 8.70e-01 1.32e+00 2.62e+01
  angle pdb=" C   THR C  15 "
        pdb=" CA  THR C  15 "
        pdb=" CB  THR C  15 "
      ideal   model   delta    sigma   weight residual
     109.53  117.59   -8.06 1.69e+00 3.50e-01 2.27e+01
  angle pdb=" C   LYS C  11 "
        pdb=" CA  LYS C  11 "
        pdb=" CB  LYS C  11 "
      ideal   model   delta    sigma   weight residual
     109.68  118.56   -8.88 2.05e+00 2.38e-01 1.88e+01
  angle pdb=" C   GLY B 147 "
        pdb=" N   ARG B 148 "
        pdb=" CA  ARG B 148 "
      ideal   model   delta    sigma   weight residual
     121.83  128.46   -6.63 1.56e+00 4.11e-01 1.81e+01
  ... (remaining 10059 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 3958
       17.68 -    35.35: 298
       35.35 -    53.02: 71
       53.02 -    70.70: 24
       70.70 -    88.37: 9
  Dihedral angle restraints: 4360
    sinusoidal: 1588
      harmonic: 2772
  Sorted by residual:
  dihedral pdb=" CA  ASP C  64 "
           pdb=" CB  ASP C  64 "
           pdb=" CG  ASP C  64 "
           pdb=" OD1 ASP C  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.53   57.53     1      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CB  GLU C 135 "
           pdb=" CG  GLU C 135 "
           pdb=" CD  GLU C 135 "
           pdb=" OE1 GLU C 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.37   88.37     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CG  ARG B 139 "
           pdb=" CD  ARG B 139 "
           pdb=" NE  ARG B 139 "
           pdb=" CZ  ARG B 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.84   43.84     2      1.50e+01 4.44e-03 1.02e+01
  ... (remaining 4357 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 883
       0.046 -    0.092: 177
       0.092 -    0.138: 110
       0.138 -    0.184: 14
       0.184 -    0.230: 8
  Chirality restraints: 1192
  Sorted by residual:
  chirality pdb=" CA  VAL C 228 "
            pdb=" N   VAL C 228 "
            pdb=" C   VAL C 228 "
            pdb=" CB  VAL C 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  VAL A  10 "
            pdb=" N   VAL A  10 "
            pdb=" C   VAL A  10 "
            pdb=" CB  VAL A  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  VAL B  10 "
            pdb=" N   VAL B  10 "
            pdb=" C   VAL B  10 "
            pdb=" CB  VAL B  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1189 not shown)

  Planarity restraints: 1292
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  13 "   -0.013 2.00e-02 2.50e+03   2.74e-02 7.50e+00
        pdb=" C   ALA B  13 "    0.047 2.00e-02 2.50e+03
        pdb=" O   ALA B  13 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLY B  14 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B  14 "    0.011 2.00e-02 2.50e+03   2.34e-02 5.45e+00
        pdb=" C   GLY B  14 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   GLY B  14 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR B  15 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D  13 "   -0.010 2.00e-02 2.50e+03   2.00e-02 3.99e+00
        pdb=" C   ALA D  13 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ALA D  13 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLY D  14 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1289 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 901
        2.76 -     3.30: 6247
        3.30 -     3.83: 11438
        3.83 -     4.37: 12925
        4.37 -     4.90: 23496
  Nonbonded interactions: 55007
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 108 "
            pdb=" OD1 ASN B 145 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" ND2 ASN A  29 "
            pdb=" OD1 ASP A 192 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" OG  SER A 126 "
            pdb=" OE2 GLU C  49 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OH  TYR A 108 "
            pdb=" OD1 ASN A 145 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OG  SER B  32 "
            pdb=" OG  SER B 194 "
     model   vdw
     2.337 3.040
  ... (remaining 55002 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     21.160
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6873
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7368  Z= 0.302
  Angle     :  0.701   8.884  10064  Z= 0.474
  Chirality :  0.052   0.230   1192
  Planarity :  0.004   0.043   1292
  Dihedral  : 14.605  88.374   2584
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.18 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.54 (0.25), residues: 972
  helix:  2.35 (0.64), residues: 54
  sheet:  1.09 (0.23), residues: 494
  loop : -0.82 (0.25), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 123 
 PHE   0.010   0.001   PHE B  82 
 TYR   0.007   0.001   TYR A 108 
 ARG   0.004   0.000   ARG D 148 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.736 
Fit side-chains
REVERT: A    8 MET cc_start: 0.8167 (mtm) cc_final: 0.7897 (mtm)
REVERT: A   11 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.7037 (mmmt)
REVERT: B   11 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.6947 (mmpt)
REVERT: C   31 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8864 (mm)
REVERT: C  148 ARG cc_start: 0.8413 (ttt180) cc_final: 0.6756 (mmp80)
REVERT: D   43 LYS cc_start: 0.8722 (mtpp) cc_final: 0.7805 (mmtm)
REVERT: D  151 MET cc_start: 0.9054 (mmm) cc_final: 0.8804 (mmm)
  outliers start: 19
  outliers final: 7
  residues processed: 108
  average time/residue: 1.2419
  time to fit residues: 141.6565
Evaluate side-chains
  98 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 LYS
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   11 LYS
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   83 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 40 optimal weight:   40.0000
   chunk 24 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:   40.0000
   chunk 56 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
D 177 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.195094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.108377 restraints weight = 7753.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.35
r_work: 0.3131 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7368  Z= 0.237
  Angle     :  0.517   4.795  10064  Z= 0.277
  Chirality :  0.047   0.154   1192
  Planarity :  0.004   0.031   1292
  Dihedral  :  5.444  56.705   1048
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.44 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.46 (0.25), residues: 972
  helix:  1.93 (0.70), residues: 56
  sheet:  1.04 (0.23), residues: 494
  loop : -0.83 (0.25), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  18 
 PHE   0.017   0.002   PHE A 120 
 TYR   0.010   0.001   TYR B 108 
 ARG   0.002   0.000   ARG C 155 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8141 (ttt90)
REVERT: B   11 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.7325 (mmpt)
REVERT: B   63 GLU cc_start: 0.7090 (pm20) cc_final: 0.6844 (pt0)
REVERT: B   91 GLN cc_start: 0.8736 (mm110) cc_final: 0.8426 (mm110)
REVERT: C   43 LYS cc_start: 0.8835 (mtpp) cc_final: 0.7414 (mmtt)
REVERT: C  134 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8334 (mtpm)
REVERT: C  148 ARG cc_start: 0.8623 (ttt180) cc_final: 0.6376 (tpp-160)
REVERT: D    5 ASN cc_start: 0.7563 (t0) cc_final: 0.7294 (t0)
REVERT: D   43 LYS cc_start: 0.8775 (mtpp) cc_final: 0.7669 (mmtm)
  outliers start: 18
  outliers final: 7
  residues processed: 89
  average time/residue: 1.4972
  time to fit residues: 139.7042
Evaluate side-chains
  94 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain B residue   11 LYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:   30.0000
   chunk 43 optimal weight:   20.0000
   chunk 47 optimal weight:   40.0000
   chunk 26 optimal weight:    6.9990
   chunk 64 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 86 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   overall best weight:    5.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.191226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.104856 restraints weight = 7839.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 2.37
r_work: 0.3086 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.058   7368  Z= 0.586
  Angle     :  0.689   8.200  10064  Z= 0.369
  Chirality :  0.054   0.173   1192
  Planarity :  0.006   0.045   1292
  Dihedral  :  5.380  57.863   1034
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 12.31 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.02 (0.25), residues: 972
  helix:  1.21 (0.72), residues: 56
  sheet:  0.67 (0.22), residues: 506
  loop : -0.98 (0.26), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP D  67 
 PHE   0.030   0.003   PHE A 120 
 TYR   0.013   0.002   TYR B 108 
 ARG   0.006   0.001   ARG A 139 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8066 (ttt90)
REVERT: B   11 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.7331 (mmpt)
REVERT: B   41 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8770 (mttp)
REVERT: B   91 GLN cc_start: 0.8749 (mm110) cc_final: 0.8408 (mm110)
REVERT: C   31 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8670 (mm)
REVERT: C   43 LYS cc_start: 0.8876 (mtpp) cc_final: 0.7592 (mmtt)
REVERT: C  134 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8326 (mtpm)
REVERT: C  148 ARG cc_start: 0.8510 (ttt180) cc_final: 0.6266 (tpp-160)
REVERT: C  151 MET cc_start: 0.8877 (mmp) cc_final: 0.8652 (mmp)
REVERT: D   43 LYS cc_start: 0.8751 (mtpp) cc_final: 0.7612 (mmtm)
REVERT: D  135 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8157 (mt-10)
  outliers start: 26
  outliers final: 11
  residues processed: 90
  average time/residue: 1.5847
  time to fit residues: 149.0924
Evaluate side-chains
  88 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   11 LYS
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 44 optimal weight:   50.0000
   chunk 87 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 90 optimal weight:   20.0000
   chunk 35 optimal weight:    0.9980
   chunk 71 optimal weight:   40.0000
   chunk 3 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 68 optimal weight:   40.0000
   chunk 59 optimal weight:    0.0670
   overall best weight:    0.9722

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

Flipped N/Q/H residues before XYZ refinement:
D   5 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.195484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.109559 restraints weight = 7831.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.39
r_work: 0.3150 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7368  Z= 0.138
  Angle     :  0.444   5.631  10064  Z= 0.238
  Chirality :  0.045   0.148   1192
  Planarity :  0.004   0.039   1292
  Dihedral  :  4.535  59.553   1034
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.97 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 972
  helix:  1.83 (0.71), residues: 56
  sheet:  0.68 (0.22), residues: 514
  loop : -0.86 (0.27), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  18 
 PHE   0.013   0.001   PHE D  82 
 TYR   0.007   0.001   TYR B 108 
 ARG   0.002   0.000   ARG D 121 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A  135 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8392 (mt-10)
REVERT: B   11 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.7451 (mmpt)
REVERT: B   41 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8692 (mttp)
REVERT: B   91 GLN cc_start: 0.8667 (mm110) cc_final: 0.8319 (mm110)
REVERT: C   31 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8681 (mm)
REVERT: C   43 LYS cc_start: 0.8783 (mtpp) cc_final: 0.7413 (mmtt)
REVERT: C  148 ARG cc_start: 0.8547 (ttt180) cc_final: 0.6338 (tpp-160)
REVERT: D   29 ASN cc_start: 0.8704 (t0) cc_final: 0.8450 (t0)
REVERT: D   43 LYS cc_start: 0.8720 (mtpp) cc_final: 0.7620 (mmtm)
  outliers start: 18
  outliers final: 5
  residues processed: 87
  average time/residue: 1.5006
  time to fit residues: 136.7749
Evaluate side-chains
  83 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain B residue   11 LYS
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 43 optimal weight:   40.0000
   chunk 22 optimal weight:    9.9990
   chunk 80 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0370
   chunk 73 optimal weight:    0.0770
   chunk 66 optimal weight:    9.9990
   overall best weight:    2.6222

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

Flipped N/Q/H residues before XYZ refinement:
D   5 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.193620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.107195 restraints weight = 7778.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.38
r_work: 0.3113 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7368  Z= 0.289
  Angle     :  0.531   7.307  10064  Z= 0.281
  Chirality :  0.047   0.160   1192
  Planarity :  0.005   0.040   1292
  Dihedral  :  4.782  59.695   1034
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.13 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.16 (0.26), residues: 972
  helix:  1.58 (0.70), residues: 56
  sheet:  0.69 (0.23), residues: 512
  loop : -0.84 (0.27), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  18 
 PHE   0.019   0.002   PHE A 120 
 TYR   0.010   0.001   TYR B 108 
 ARG   0.002   0.000   ARG D 106 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.731 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8024 (ttt90)
REVERT: B   11 LYS cc_start: 0.8888 (mmmm) cc_final: 0.7443 (mmpt)
REVERT: B   41 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8644 (mttp)
REVERT: B   91 GLN cc_start: 0.8652 (mm110) cc_final: 0.8265 (mm110)
REVERT: C   31 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8673 (mm)
REVERT: C   43 LYS cc_start: 0.8857 (mtpp) cc_final: 0.7573 (mmtt)
REVERT: C  134 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8295 (mtpm)
REVERT: C  148 ARG cc_start: 0.8540 (ttt180) cc_final: 0.6325 (tpp-160)
REVERT: D   29 ASN cc_start: 0.8771 (t0) cc_final: 0.8544 (t0)
REVERT: D   43 LYS cc_start: 0.8702 (mtpp) cc_final: 0.7604 (mmtm)
REVERT: D  135 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8136 (mt-10)
  outliers start: 20
  outliers final: 12
  residues processed: 88
  average time/residue: 1.5310
  time to fit residues: 141.0360
Evaluate side-chains
  90 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 73 optimal weight:    0.3980
   chunk 94 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 20 optimal weight:   50.0000
   chunk 9 optimal weight:    3.9990
   chunk 65 optimal weight:   40.0000
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
D   5 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.194570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.108748 restraints weight = 7801.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.36
r_work: 0.3155 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7368  Z= 0.130
  Angle     :  0.439   6.295  10064  Z= 0.233
  Chirality :  0.045   0.147   1192
  Planarity :  0.004   0.042   1292
  Dihedral  :  4.082  58.465   1030
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.51 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.36 (0.26), residues: 972
  helix:  1.92 (0.68), residues: 56
  sheet:  0.82 (0.23), residues: 508
  loop : -0.73 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  18 
 PHE   0.012   0.001   PHE B  82 
 TYR   0.007   0.001   TYR B 108 
 ARG   0.001   0.000   ARG D 121 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A  135 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8463 (mt-10)
REVERT: B   11 LYS cc_start: 0.8884 (mmmm) cc_final: 0.7459 (mmpt)
REVERT: B   41 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8657 (mttp)
REVERT: B   91 GLN cc_start: 0.8648 (mm110) cc_final: 0.8256 (mm110)
REVERT: C   31 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8673 (mm)
REVERT: C   43 LYS cc_start: 0.8780 (mtpp) cc_final: 0.7430 (mmtt)
REVERT: C  134 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8326 (mtpm)
REVERT: C  148 ARG cc_start: 0.8556 (ttt180) cc_final: 0.6422 (tpp-160)
REVERT: D   29 ASN cc_start: 0.8737 (t0) cc_final: 0.8424 (t0)
REVERT: D   43 LYS cc_start: 0.8686 (mtpp) cc_final: 0.7598 (mmtm)
  outliers start: 17
  outliers final: 6
  residues processed: 97
  average time/residue: 1.3926
  time to fit residues: 141.9521
Evaluate side-chains
  90 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 88 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9990
   chunk 40 optimal weight:   40.0000
   chunk 75 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 31 optimal weight:    7.9990
   chunk 71 optimal weight:   20.0000
   chunk 85 optimal weight:    1.9990
   chunk 68 optimal weight:   30.0000
   chunk 56 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
D   5 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.191657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.105664 restraints weight = 7773.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.37
r_work: 0.3107 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   7368  Z= 0.366
  Angle     :  0.565   7.316  10064  Z= 0.299
  Chirality :  0.049   0.163   1192
  Planarity :  0.005   0.058   1292
  Dihedral  :  4.627  59.808   1030
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.77 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.26), residues: 972
  helix:  1.46 (0.69), residues: 56
  sheet:  0.72 (0.23), residues: 496
  loop : -0.79 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  18 
 PHE   0.022   0.002   PHE A 120 
 TYR   0.011   0.001   TYR B 108 
 ARG   0.003   0.001   ARG A 139 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.779 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.8019 (mm)
REVERT: A   38 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8027 (ttt90)
REVERT: B   11 LYS cc_start: 0.8883 (mmmm) cc_final: 0.7389 (mmpt)
REVERT: B   41 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8641 (mttp)
REVERT: B   91 GLN cc_start: 0.8756 (mm110) cc_final: 0.8374 (mm110)
REVERT: C   31 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8677 (mm)
REVERT: C   43 LYS cc_start: 0.8821 (mtpp) cc_final: 0.7563 (mmtt)
REVERT: C  134 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8308 (mtpm)
REVERT: C  148 ARG cc_start: 0.8541 (ttt180) cc_final: 0.6332 (tpp-160)
REVERT: D   43 LYS cc_start: 0.8714 (mtpp) cc_final: 0.7553 (mmtm)
REVERT: D   53 GLU cc_start: 0.8461 (pt0) cc_final: 0.8239 (pt0)
REVERT: D  135 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8140 (mt-10)
  outliers start: 22
  outliers final: 12
  residues processed: 91
  average time/residue: 1.5640
  time to fit residues: 148.6072
Evaluate side-chains
  92 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
D   5 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.193054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.107242 restraints weight = 7915.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.35
r_work: 0.3131 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7368  Z= 0.190
  Angle     :  0.471   6.508  10064  Z= 0.251
  Chirality :  0.046   0.151   1192
  Planarity :  0.005   0.052   1292
  Dihedral  :  4.282  58.585   1030
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.28 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.26 (0.26), residues: 972
  helix:  1.75 (0.68), residues: 56
  sheet:  0.76 (0.23), residues: 496
  loop : -0.74 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  18 
 PHE   0.014   0.002   PHE A 120 
 TYR   0.007   0.001   TYR B 108 
 ARG   0.002   0.000   ARG A 139 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.761 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8163 (ttt90)
REVERT: B   11 LYS cc_start: 0.8882 (mmmm) cc_final: 0.7421 (mmpt)
REVERT: B   41 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8683 (mttp)
REVERT: B   91 GLN cc_start: 0.8731 (mm110) cc_final: 0.8357 (mm110)
REVERT: C   31 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8691 (mm)
REVERT: C   43 LYS cc_start: 0.8826 (mtpp) cc_final: 0.7449 (mmtt)
REVERT: C  134 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8306 (mtpm)
REVERT: C  148 ARG cc_start: 0.8566 (ttt180) cc_final: 0.6385 (tpp-160)
REVERT: D   29 ASN cc_start: 0.8783 (t0) cc_final: 0.8482 (t0)
REVERT: D   43 LYS cc_start: 0.8691 (mtpp) cc_final: 0.7597 (mmtm)
  outliers start: 17
  outliers final: 8
  residues processed: 88
  average time/residue: 1.6096
  time to fit residues: 147.9689
Evaluate side-chains
  88 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   44 ASP
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 70 optimal weight:   20.0000
   chunk 94 optimal weight:   50.0000
   chunk 95 optimal weight:   30.0000
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:   30.0000
   chunk 1 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
D   5 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.191183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.105330 restraints weight = 7844.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.37
r_work: 0.3101 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   7368  Z= 0.404
  Angle     :  0.590   7.326  10064  Z= 0.312
  Chirality :  0.050   0.164   1192
  Planarity :  0.005   0.050   1292
  Dihedral  :  4.736  59.639   1030
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.15 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.07 (0.26), residues: 972
  helix:  1.34 (0.69), residues: 56
  sheet:  0.69 (0.24), residues: 496
  loop : -0.91 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  18 
 PHE   0.024   0.002   PHE A 120 
 TYR   0.010   0.002   TYR B 108 
 ARG   0.003   0.001   ARG A 139 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8043 (ttt90)
REVERT: B   11 LYS cc_start: 0.8885 (mmmm) cc_final: 0.7411 (mmpt)
REVERT: B   41 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8683 (mttp)
REVERT: B   91 GLN cc_start: 0.8801 (mm110) cc_final: 0.8421 (mm110)
REVERT: C   31 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8686 (mm)
REVERT: C   43 LYS cc_start: 0.8837 (mtpp) cc_final: 0.7583 (mmtt)
REVERT: C  134 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8326 (mtpm)
REVERT: C  148 ARG cc_start: 0.8545 (ttt180) cc_final: 0.6346 (tpp-160)
REVERT: D   43 LYS cc_start: 0.8712 (mtpp) cc_final: 0.7631 (mmtm)
REVERT: D   53 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8301 (pt0)
  outliers start: 18
  outliers final: 10
  residues processed: 86
  average time/residue: 1.5516
  time to fit residues: 139.4808
Evaluate side-chains
  89 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   53 GLU
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 90 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 54 optimal weight:    5.9990
   chunk 46 optimal weight:   40.0000
   chunk 41 optimal weight:   40.0000
   chunk 51 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   overall best weight:    4.7388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.190437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.104795 restraints weight = 7973.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.35
r_work: 0.3089 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051   7368  Z= 0.498
  Angle     :  0.637   7.385  10064  Z= 0.340
  Chirality :  0.052   0.166   1192
  Planarity :  0.006   0.050   1292
  Dihedral  :  4.925  59.553   1030
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.41 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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: -0.07 (0.26), residues: 972
  helix:  1.17 (0.71), residues: 56
  sheet:  0.67 (0.24), residues: 490
  loop : -1.06 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP D  18 
 PHE   0.026   0.003   PHE A 120 
 TYR   0.010   0.002   TYR A  20 
 ARG   0.004   0.001   ARG A 139 

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

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

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1944 Ramachandran restraints generated.
    972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8025 (ttt90)
REVERT: B   11 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.7419 (mmpt)
REVERT: B   41 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8724 (mttp)
REVERT: B   91 GLN cc_start: 0.8804 (mm110) cc_final: 0.8445 (mm110)
REVERT: C   31 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8697 (mm)
REVERT: C   43 LYS cc_start: 0.8851 (mtpp) cc_final: 0.7586 (mmtt)
REVERT: C  134 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8324 (mtpm)
REVERT: C  148 ARG cc_start: 0.8567 (ttt180) cc_final: 0.6366 (tpp-160)
REVERT: D   43 LYS cc_start: 0.8719 (mtpp) cc_final: 0.7624 (mmtm)
REVERT: D   53 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8286 (pt0)
  outliers start: 19
  outliers final: 12
  residues processed: 85
  average time/residue: 1.6167
  time to fit residues: 143.5474
Evaluate side-chains
  89 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   11 LYS
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain D residue   46 THR
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   53 GLU
Chi-restraints excluded: chain D residue   83 THR
Chi-restraints excluded: chain D residue   97 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 71 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 65 optimal weight:   50.0000
   chunk 26 optimal weight:    0.4980
   chunk 77 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.8584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.193810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.108735 restraints weight = 7808.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.37
r_work: 0.3147 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7368  Z= 0.131
  Angle     :  0.446   5.842  10064  Z= 0.238
  Chirality :  0.045   0.149   1192
  Planarity :  0.005   0.049   1292
  Dihedral  :  4.186  58.827   1030
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.44 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.26), residues: 972
  helix:  1.74 (0.69), residues: 56
  sheet:  0.79 (0.24), residues: 492
  loop : -0.84 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  18 
 PHE   0.012   0.001   PHE B  82 
 TYR   0.005   0.001   TYR B 108 
 ARG   0.001   0.000   ARG C 196 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7278.24 seconds
wall clock time: 128 minutes 38.75 seconds (7718.75 seconds total)