Starting phenix.real_space_refine
on Tue Sep 24 06:48:09 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4f_25675/09_2024/7t4f_25675.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4f_25675/09_2024/7t4f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4f_25675/09_2024/7t4f_25675.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4f_25675/09_2024/7t4f_25675.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4f_25675/09_2024/7t4f_25675.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4f_25675/09_2024/7t4f_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-5461/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: 4.84, per 1000 atoms: 0.67
  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 1.0 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: 2.27

  Time building geometry restraints manager: 2.02 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: 0.00
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:             1.190
  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:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.120
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.410
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.687 
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: 1.1765
  time to fit residues: 134.0987
Evaluate side-chains
  98 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
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 fitting.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A    8 MET cc_start: 0.8078 (mtm) cc_final: 0.7854 (mtm)
REVERT: A   38 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8169 (ttt90)
REVERT: B   11 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.7013 (mmpt)
REVERT: C   43 LYS cc_start: 0.8877 (mtpp) cc_final: 0.7565 (mmtt)
REVERT: C  134 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8410 (mtpm)
REVERT: C  148 ARG cc_start: 0.8396 (ttt180) cc_final: 0.6722 (tpp-160)
REVERT: D    5 ASN cc_start: 0.7571 (t0) cc_final: 0.7318 (t0)
REVERT: D   43 LYS cc_start: 0.8756 (mtpp) cc_final: 0.7777 (mmtm)
  outliers start: 18
  outliers final: 7
  residues processed: 89
  average time/residue: 1.4280
  time to fit residues: 133.4233
Evaluate side-chains
  94 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
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 48 optimal weight:    0.0000
   chunk 27 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0870
   chunk 59 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 87 optimal weight:    5.9990
   chunk 94 optimal weight:   30.0000
   chunk 77 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 29 optimal weight:    8.9990
   chunk 70 optimal weight:    9.9990
   overall best weight:    2.4168

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.1622

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= 0.269
  Angle     :  0.528   8.165  10064  Z= 0.280
  Chirality :  0.047   0.158   1192
  Planarity :  0.005   0.037   1292
  Dihedral  :  4.752  54.505   1034
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 12.44 %
    Favored  : 84.62 %
  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:  0.31 (0.25), residues: 972
  helix:  1.75 (0.70), residues: 56
  sheet:  0.88 (0.23), residues: 492
  loop : -0.81 (0.25), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D  67 
 PHE   0.018   0.002   PHE A 120 
 TYR   0.010   0.001   TYR B 108 
 ARG   0.002   0.000   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
  99 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8058 (ttt90)
REVERT: A  212 MET cc_start: 0.5951 (OUTLIER) cc_final: 0.5261 (tpt)
REVERT: B   11 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7084 (mmpt)
REVERT: B   41 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8606 (mttp)
REVERT: C   31 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8857 (mm)
REVERT: C   43 LYS cc_start: 0.8886 (mtpp) cc_final: 0.7726 (mmtt)
REVERT: C  134 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8406 (mtpm)
REVERT: C  148 ARG cc_start: 0.8393 (ttt180) cc_final: 0.6694 (tpp-160)
REVERT: D    5 ASN cc_start: 0.7617 (t0) cc_final: 0.7276 (t0)
REVERT: D   43 LYS cc_start: 0.8709 (mtpp) cc_final: 0.7700 (mmtm)
REVERT: D   53 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7699 (pt0)
REVERT: D  135 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7956 (mt-10)
  outliers start: 23
  outliers final: 9
  residues processed: 88
  average time/residue: 1.4115
  time to fit residues: 130.2350
Evaluate side-chains
  89 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
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  212 MET
Chi-restraints excluded: chain B residue   11 LYS
Chi-restraints excluded: chain B residue   41 LYS
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   53 GLU
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 86 optimal weight:    4.9990
   chunk 65 optimal weight:   30.0000
   chunk 45 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 41 optimal weight:   20.0000
   chunk 58 optimal weight:    0.9990
   chunk 87 optimal weight:    8.9990
   chunk 92 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    1.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7368  Z= 0.184
  Angle     :  0.466   5.995  10064  Z= 0.248
  Chirality :  0.046   0.150   1192
  Planarity :  0.004   0.040   1292
  Dihedral  :  4.484  56.046   1034
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 13.21 %
    Favored  : 83.97 %
  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:  0.32 (0.25), residues: 972
  helix:  1.82 (0.69), residues: 56
  sheet:  0.87 (0.23), residues: 492
  loop : -0.78 (0.26), residues: 424

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   0.008   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
  109 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.786 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8152 (mm)
REVERT: A   38 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8139 (ttt90)
REVERT: A  212 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.5291 (tpt)
REVERT: B   11 LYS cc_start: 0.8743 (mmmm) cc_final: 0.7164 (mmpt)
REVERT: B   41 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8604 (mttp)
REVERT: C   31 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8859 (mm)
REVERT: C   43 LYS cc_start: 0.8860 (mtpp) cc_final: 0.7576 (mmtt)
REVERT: C  134 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8396 (mtpm)
REVERT: C  148 ARG cc_start: 0.8346 (ttt180) cc_final: 0.6690 (tpp-160)
REVERT: D    5 ASN cc_start: 0.7679 (t0) cc_final: 0.7354 (t0)
REVERT: D   29 ASN cc_start: 0.8804 (t0) cc_final: 0.8570 (t0)
REVERT: D   43 LYS cc_start: 0.8708 (mtpp) cc_final: 0.7698 (mmtm)
REVERT: D   53 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7672 (pt0)
REVERT: D  135 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7949 (mt-10)
  outliers start: 22
  outliers final: 9
  residues processed: 99
  average time/residue: 1.3528
  time to fit residues: 140.7538
Evaluate side-chains
  93 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
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  136 VAL
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain B residue   41 LYS
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   50 LEU
Chi-restraints excluded: chain D residue   53 GLU
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 69 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 79 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:   50.0000
   chunk 83 optimal weight:    4.9990
   chunk 23 optimal weight:   30.0000
   chunk 31 optimal weight:    0.6980
   overall best weight:    4.1388

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

Flipped N/Q/H residues before XYZ refinement:
B  91 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   7368  Z= 0.441
  Angle     :  0.610   7.561  10064  Z= 0.324
  Chirality :  0.050   0.169   1192
  Planarity :  0.005   0.040   1292
  Dihedral  :  4.781  58.132   1030
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.36 %
    Favored  : 82.56 %
  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:  0.13 (0.26), residues: 972
  helix:  1.27 (0.71), residues: 56
  sheet:  0.71 (0.23), residues: 508
  loop : -0.86 (0.26), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP D  67 
 PHE   0.025   0.002   PHE A 120 
 TYR   0.012   0.002   TYR B 108 
 ARG   0.004   0.001   ARG A 139 

*********************** 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
  99 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A   31 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8226 (mm)
REVERT: A   38 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8031 (ttt90)
REVERT: B   11 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.7134 (mmpt)
REVERT: B   41 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8647 (mttp)
REVERT: C   31 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8835 (mm)
REVERT: C   43 LYS cc_start: 0.8897 (mtpp) cc_final: 0.7748 (mmtt)
REVERT: C  134 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8415 (mtpm)
REVERT: C  148 ARG cc_start: 0.8341 (ttt180) cc_final: 0.6635 (tpp-160)
REVERT: D    5 ASN cc_start: 0.7747 (t0) cc_final: 0.7372 (t0)
REVERT: D   43 LYS cc_start: 0.8723 (mtpp) cc_final: 0.7714 (mmtm)
REVERT: D   53 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7989 (pt0)
REVERT: D  135 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7991 (mt-10)
  outliers start: 24
  outliers final: 12
  residues processed: 91
  average time/residue: 1.5281
  time to fit residues: 145.4129
Evaluate side-chains
  94 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
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  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   87 MET
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain C residue   17 LEU
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
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 83 optimal weight:    0.6980
   chunk 18 optimal weight:   20.0000
   chunk 54 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 92 optimal weight:    8.9990
   chunk 77 optimal weight:    0.7980
   chunk 43 optimal weight:   20.0000
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0000
   chunk 48 optimal weight:    3.9990
   chunk 89 optimal weight:   20.0000
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
B  91 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.1853

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= 0.160
  Angle     :  0.455   6.179  10064  Z= 0.242
  Chirality :  0.045   0.150   1192
  Planarity :  0.004   0.042   1292
  Dihedral  :  4.240  59.601   1030
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.38 %
    Favored  : 82.05 %
  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:  0.28 (0.26), residues: 972
  helix:  1.65 (0.69), residues: 56
  sheet:  0.79 (0.23), residues: 508
  loop : -0.77 (0.27), residues: 408

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 106 

*********************** 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
  98 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8059 (ttt90)
REVERT: A  140 THR cc_start: 0.9014 (m) cc_final: 0.8773 (m)
REVERT: A  212 MET cc_start: 0.5715 (OUTLIER) cc_final: 0.5345 (tpt)
REVERT: B   11 LYS cc_start: 0.8770 (mmmm) cc_final: 0.7151 (mmpt)
REVERT: B   41 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8611 (mttp)
REVERT: C   31 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8862 (mm)
REVERT: C   43 LYS cc_start: 0.8890 (mtpp) cc_final: 0.7627 (mmtt)
REVERT: C  134 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8391 (mtpm)
REVERT: C  148 ARG cc_start: 0.8353 (ttt180) cc_final: 0.6656 (tpp-160)
REVERT: D    5 ASN cc_start: 0.7781 (t0) cc_final: 0.7440 (t0)
REVERT: D   29 ASN cc_start: 0.8805 (t0) cc_final: 0.8575 (t0)
REVERT: D   43 LYS cc_start: 0.8687 (mtpp) cc_final: 0.7732 (mmtm)
REVERT: D   53 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7662 (pt0)
REVERT: D  135 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7959 (mt-10)
  outliers start: 20
  outliers final: 7
  residues processed: 89
  average time/residue: 1.4542
  time to fit residues: 135.6256
Evaluate side-chains
  90 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
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  136 VAL
Chi-restraints excluded: chain A residue  212 MET
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   53 GLU
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 92 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 36 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
B  91 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7368  Z= 0.201
  Angle     :  0.478   7.237  10064  Z= 0.252
  Chirality :  0.046   0.152   1192
  Planarity :  0.004   0.043   1292
  Dihedral  :  4.286  59.586   1030
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.64 %
    Favored  : 81.67 %
  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:  0.33 (0.26), residues: 972
  helix:  1.65 (0.69), residues: 56
  sheet:  0.85 (0.24), residues: 494
  loop : -0.73 (0.26), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  18 
 PHE   0.015   0.002   PHE A 120 
 TYR   0.009   0.001   TYR B 108 
 ARG   0.001   0.000   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 fitting.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.802 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8031 (ttt90)
REVERT: A  140 THR cc_start: 0.9029 (m) cc_final: 0.8828 (m)
REVERT: B   11 LYS cc_start: 0.8780 (mmmm) cc_final: 0.7175 (mmpt)
REVERT: B   41 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8596 (mttp)
REVERT: C   31 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8872 (mm)
REVERT: C   43 LYS cc_start: 0.8899 (mtpp) cc_final: 0.7726 (mmtt)
REVERT: C  134 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8399 (mtpm)
REVERT: C  148 ARG cc_start: 0.8330 (ttt180) cc_final: 0.6653 (tpp-160)
REVERT: D    5 ASN cc_start: 0.7742 (t0) cc_final: 0.7401 (t0)
REVERT: D   29 ASN cc_start: 0.8862 (t0) cc_final: 0.8620 (t0)
REVERT: D   43 LYS cc_start: 0.8694 (mtpp) cc_final: 0.7738 (mmtm)
REVERT: D   53 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7723 (pt0)
REVERT: D  135 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7970 (mt-10)
  outliers start: 21
  outliers final: 12
  residues processed: 92
  average time/residue: 1.4159
  time to fit residues: 136.5862
Evaluate side-chains
  97 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
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  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   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   50 LEU
Chi-restraints excluded: chain D residue   53 GLU
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 27 optimal weight:    0.9980
   chunk 18 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 88 optimal weight:   20.0000
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
B  91 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7368  Z= 0.182
  Angle     :  0.462   6.804  10064  Z= 0.244
  Chirality :  0.045   0.151   1192
  Planarity :  0.004   0.044   1292
  Dihedral  :  4.191  58.629   1030
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.77 %
    Favored  : 81.28 %
  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:  1.70 (0.69), residues: 56
  sheet:  0.86 (0.24), residues: 494
  loop : -0.69 (0.26), residues: 422

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   0.008   0.001   TYR B 108 
 ARG   0.002   0.000   ARG D 121 

*********************** 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
  102 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8123 (ttt90)
REVERT: A  135 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8375 (mt-10)
REVERT: A  140 THR cc_start: 0.9011 (m) cc_final: 0.8770 (m)
REVERT: B   11 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.7166 (mmpt)
REVERT: B   41 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8564 (mttp)
REVERT: C   31 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8858 (mm)
REVERT: C   43 LYS cc_start: 0.8863 (mtpp) cc_final: 0.7672 (mmtt)
REVERT: C  134 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8403 (mtpm)
REVERT: C  148 ARG cc_start: 0.8331 (ttt180) cc_final: 0.6680 (tpp-160)
REVERT: D    5 ASN cc_start: 0.7776 (t0) cc_final: 0.7401 (t0)
REVERT: D   29 ASN cc_start: 0.8832 (t0) cc_final: 0.8573 (t0)
REVERT: D   43 LYS cc_start: 0.8698 (mtpp) cc_final: 0.7730 (mmtm)
REVERT: D   53 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7661 (pt0)
REVERT: D  135 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7956 (mt-10)
  outliers start: 23
  outliers final: 10
  residues processed: 93
  average time/residue: 1.4076
  time to fit residues: 137.1258
Evaluate side-chains
  94 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
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  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   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   53 GLU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 81 optimal weight:    0.4980
   chunk 85 optimal weight:    0.0270
   chunk 56 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    2.7044

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

Flipped N/Q/H residues before XYZ refinement:
B  91 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6983
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   7368  Z= 0.297
  Angle     :  0.524   7.292  10064  Z= 0.277
  Chirality :  0.047   0.159   1192
  Planarity :  0.005   0.064   1292
  Dihedral  :  4.473  59.243   1030
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.90 %
    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:  0.24 (0.26), residues: 972
  helix:  1.45 (0.69), residues: 56
  sheet:  0.80 (0.24), residues: 496
  loop : -0.78 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D  18 
 PHE   0.019   0.002   PHE A 120 
 TYR   0.010   0.001   TYR B 108 
 ARG   0.003   0.000   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
  99 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8015 (ttt90)
REVERT: B   11 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7146 (mmpt)
REVERT: B   41 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8600 (mttp)
REVERT: C   31 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8866 (mm)
REVERT: C   43 LYS cc_start: 0.8864 (mtpp) cc_final: 0.7703 (mmtt)
REVERT: C  134 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8404 (mtpm)
REVERT: C  148 ARG cc_start: 0.8353 (ttt180) cc_final: 0.6673 (tpp-160)
REVERT: D    5 ASN cc_start: 0.7776 (t0) cc_final: 0.7431 (t0)
REVERT: D   29 ASN cc_start: 0.8874 (t0) cc_final: 0.8601 (t0)
REVERT: D   43 LYS cc_start: 0.8721 (mtpp) cc_final: 0.7760 (mmtm)
REVERT: D   53 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7802 (pt0)
REVERT: D  135 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7956 (mt-10)
  outliers start: 23
  outliers final: 13
  residues processed: 91
  average time/residue: 1.4655
  time to fit residues: 139.8760
Evaluate side-chains
  98 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
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  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   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   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
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 43 optimal weight:   20.0000
   chunk 63 optimal weight:    2.9990
   chunk 95 optimal weight:   30.0000
   chunk 88 optimal weight:   30.0000
   chunk 76 optimal weight:    0.1980
   chunk 7 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
B  91 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7368  Z= 0.245
  Angle     :  0.497   7.034  10064  Z= 0.264
  Chirality :  0.047   0.155   1192
  Planarity :  0.005   0.057   1292
  Dihedral  :  4.377  58.878   1030
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.03 %
    Favored  : 81.28 %
  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:  0.25 (0.26), residues: 972
  helix:  1.48 (0.68), residues: 56
  sheet:  0.81 (0.24), residues: 496
  loop : -0.79 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  18 
 PHE   0.017   0.002   PHE A 120 
 TYR   0.009   0.001   TYR B 108 
 ARG   0.002   0.000   ARG D 121 

********************** 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
  96 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8057 (ttt90)
REVERT: B   11 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.7107 (mmpt)
REVERT: B   41 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8634 (mttp)
REVERT: C   31 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8870 (mm)
REVERT: C   43 LYS cc_start: 0.8877 (mtpp) cc_final: 0.7687 (mmtt)
REVERT: C  134 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8401 (mtpm)
REVERT: C  148 ARG cc_start: 0.8331 (ttt180) cc_final: 0.6687 (tpp-160)
REVERT: D    5 ASN cc_start: 0.7775 (t0) cc_final: 0.7411 (t0)
REVERT: D   43 LYS cc_start: 0.8706 (mtpp) cc_final: 0.7756 (mmtm)
REVERT: D   53 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7771 (pt0)
REVERT: D  135 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7950 (mt-10)
  outliers start: 21
  outliers final: 14
  residues processed: 89
  average time/residue: 1.4484
  time to fit residues: 135.1113
Evaluate side-chains
  94 residues out of total 780 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
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  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   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   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
Chi-restraints excluded: chain D residue  135 GLU
Chi-restraints excluded: chain D residue  191 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:   30.0000
   chunk 70 optimal weight:   20.0000
   chunk 11 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   chunk 76 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0570
   chunk 78 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 66 optimal weight:   20.0000
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.4193 r_free = 0.4193 target = 0.195138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.109778 restraints weight = 7769.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.39
r_work: 0.3167 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1945

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= 0.110
  Angle     :  0.418   6.143  10064  Z= 0.222
  Chirality :  0.044   0.145   1192
  Planarity :  0.004   0.057   1292
  Dihedral  :  3.946  57.186   1030
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 17.44 %
    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:  0.42 (0.26), residues: 972
  helix:  1.82 (0.68), residues: 56
  sheet:  0.90 (0.24), residues: 494
  loop : -0.67 (0.26), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  18 
 PHE   0.010   0.001   PHE B  82 
 TYR   0.007   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: 2971.28 seconds
wall clock time: 52 minutes 43.81 seconds (3163.81 seconds total)