Starting phenix.real_space_refine
on Fri Dec 27 08:35:01 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tdn_41171/12_2024/8tdn_41171.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tdn_41171/12_2024/8tdn_41171.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tdn_41171/12_2024/8tdn_41171.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tdn_41171/12_2024/8tdn_41171.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tdn_41171/12_2024/8tdn_41171.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tdn_41171/12_2024/8tdn_41171.cif"
  }
  resolution = 3.1
  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       5      5.16       5
     C    2330      2.51       5
     N     600      2.21       5
     O     685      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 3620
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 724
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 1.99, per 1000 atoms: 0.55
  Number of scatterers: 3620
  At special positions: 0
  Unit cell: (70.55, 83.83, 40.67, 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       5     16.00
     O     685      8.00
     N     600      7.00
     C    2330      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: 0.83
  Conformation dependent library (CDL) restraints added in 458.3 milliseconds
  

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  880

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 49.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16
      removed outlier: 6.590A  pdb=" N   MET A  13 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 8.010A  pdb=" N   VAL C  16 " --> pdb=" O   MET A  13 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   LYS A  15 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   MET C  13 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   VAL E  16 " --> pdb=" O   MET C  13 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   LYS C  15 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 21
      removed outlier: 6.255A  pdb=" N   VAL B  20 " --> pdb=" O   ARG D  21 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   VAL A  20 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 32
      removed outlier: 6.349A  pdb=" N   ALA A  25 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   VAL C  28 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ASN A  27 " --> pdb=" O   VAL C  28 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   VAL C  30 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ALA A  29 " --> pdb=" O   VAL C  30 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   VAL C  32 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   HIS A  31 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   ALA C  25 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   VAL E  28 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ASN C  27 " --> pdb=" O   VAL E  28 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   VAL E  30 " --> pdb=" O   ASN C  27 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ALA C  29 " --> pdb=" O   VAL E  30 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   VAL E  32 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   HIS C  31 " --> pdb=" O   VAL E  32 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 66
      removed outlier: 6.375A  pdb=" N   THR B  59 " --> pdb=" O   THR D  60 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   GLU D  62 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   GLU B  61 " --> pdb=" O   GLU D  62 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   PHE D  64 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   GLU B  63 " --> pdb=" O   PHE D  64 " (cutoff:3.500A)
      removed outlier: 10.236A  pdb=" N   GLU D  66 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 8.993A  pdb=" N   VAL B  65 " --> pdb=" O   GLU D  66 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   THR A  59 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
      removed outlier: 8.053A  pdb=" N   GLU B  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   GLU A  61 " --> pdb=" O   GLU B  62 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   PHE B  64 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   GLU A  63 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 10.203A  pdb=" N   GLU B  66 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
      removed outlier: 8.959A  pdb=" N   VAL A  65 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   PHE A  64 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL C  65 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   GLU A  66 " --> pdb=" O   VAL C  65 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   PHE C  64 " --> pdb=" O   GLU E  63 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   VAL E  65 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   GLU C  66 " --> pdb=" O   VAL E  65 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 75
      removed outlier: 7.078A  pdb=" N   ASP B  74 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   THR D  75 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   ASP A  74 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   THR B  75 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   TYR A  69 " --> pdb=" O   LYS C  70 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   GLU C  72 " --> pdb=" O   TYR A  69 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VAL A  71 " --> pdb=" O   GLU C  72 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   ASP C  74 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 8.561A  pdb=" N   ILE A  73 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   TYR C  69 " --> pdb=" O   LYS E  70 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   GLU E  72 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   VAL C  71 " --> pdb=" O   GLU E  72 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   ASP E  74 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 8.583A  pdb=" N   ILE C  73 " --> pdb=" O   ASP E  74 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 78 through 80
      removed outlier: 6.904A  pdb=" N   LYS D  80 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   LYS B  80 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   TYR A  78 " --> pdb=" O   TRP C  79 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   TYR C  78 " --> pdb=" O   TRP E  79 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 96
      removed outlier: 3.501A  pdb=" N   ALA D  91 " --> pdb=" O   HIS B  90 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ALA A  91 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   VAL C  94 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL A  93 " --> pdb=" O   VAL C  94 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   THR C  96 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   PHE A  95 " --> pdb=" O   THR C  96 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ALA C  91 " --> pdb=" O   GLU E  92 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   VAL E  94 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   VAL C  93 " --> pdb=" O   VAL E  94 " (cutoff:3.500A)
      removed outlier: 7.772A  pdb=" N   THR E  96 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   PHE C  95 " --> pdb=" O   THR E  96 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 110
      removed outlier: 6.643A  pdb=" N   ARG B 104 " --> pdb=" O   TYR D 105 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ILE D 107 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   THR B 106 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   ALA D 109 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   ALA B 108 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   ARG A 104 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   ILE B 107 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   THR A 106 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   ALA B 109 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   ALA A 108 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   LEU C 110 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   LEU E 110 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 115
      removed outlier: 7.031A  pdb=" N   TYR B 114 " --> pdb=" O   SER D 115 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   TYR A 114 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 123
      removed outlier: 6.878A  pdb=" N   THR B 119 " --> pdb=" O   ALA D 120 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   VAL D 122 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL B 121 " --> pdb=" O   VAL D 122 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   THR A 119 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   VAL B 122 " --> pdb=" O   THR A 119 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   VAL A 121 " --> pdb=" O   VAL B 122 " (cutoff:3.500A)

    77 hydrogen bonds defined for protein.
    231 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: 0.88

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1140
        1.34 -     1.45: 536
        1.45 -     1.57: 2019
        1.57 -     1.68: 0
        1.68 -     1.80: 10
  Bond restraints: 3705
  Sorted by residual:
  bond pdb=" CG  PRO E  24 "
       pdb=" CD  PRO E  24 "
    ideal  model  delta    sigma   weight residual
    1.503  1.481  0.022 3.40e-02 8.65e+02 4.11e-01
  bond pdb=" CG  PRO C  24 "
       pdb=" CD  PRO C  24 "
    ideal  model  delta    sigma   weight residual
    1.503  1.482  0.021 3.40e-02 8.65e+02 3.95e-01
  bond pdb=" CG  PRO A  24 "
       pdb=" CD  PRO A  24 "
    ideal  model  delta    sigma   weight residual
    1.503  1.482  0.021 3.40e-02 8.65e+02 3.93e-01
  bond pdb=" CG  PRO D  24 "
       pdb=" CD  PRO D  24 "
    ideal  model  delta    sigma   weight residual
    1.503  1.482  0.021 3.40e-02 8.65e+02 3.88e-01
  bond pdb=" CG  PRO B  24 "
       pdb=" CD  PRO B  24 "
    ideal  model  delta    sigma   weight residual
    1.503  1.482  0.021 3.40e-02 8.65e+02 3.81e-01
  ... (remaining 3700 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.87: 4640
        0.87 -     1.75: 330
        1.75 -     2.62: 35
        2.62 -     3.49: 30
        3.49 -     4.37: 5
  Bond angle restraints: 5040
  Sorted by residual:
  angle pdb=" CA  TYR C  78 "
        pdb=" CB  TYR C  78 "
        pdb=" CG  TYR C  78 "
      ideal   model   delta    sigma   weight residual
     113.90  116.91   -3.01 1.80e+00 3.09e-01 2.80e+00
  angle pdb=" CA  TYR D  78 "
        pdb=" CB  TYR D  78 "
        pdb=" CG  TYR D  78 "
      ideal   model   delta    sigma   weight residual
     113.90  116.89   -2.99 1.80e+00 3.09e-01 2.76e+00
  angle pdb=" CA  TYR E  78 "
        pdb=" CB  TYR E  78 "
        pdb=" CG  TYR E  78 "
      ideal   model   delta    sigma   weight residual
     113.90  116.88   -2.98 1.80e+00 3.09e-01 2.74e+00
  angle pdb=" CA  TYR A  78 "
        pdb=" CB  TYR A  78 "
        pdb=" CG  TYR A  78 "
      ideal   model   delta    sigma   weight residual
     113.90  116.86   -2.96 1.80e+00 3.09e-01 2.71e+00
  angle pdb=" CA  TYR B  78 "
        pdb=" CB  TYR B  78 "
        pdb=" CG  TYR B  78 "
      ideal   model   delta    sigma   weight residual
     113.90  116.84   -2.94 1.80e+00 3.09e-01 2.68e+00
  ... (remaining 5035 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.74: 1801
       13.74 -    27.48: 274
       27.48 -    41.22: 85
       41.22 -    54.96: 20
       54.96 -    68.70: 5
  Dihedral angle restraints: 2185
    sinusoidal: 825
      harmonic: 1360
  Sorted by residual:
  dihedral pdb=" CA  ALA C  25 "
           pdb=" C   ALA C  25 "
           pdb=" N   ILE C  26 "
           pdb=" CA  ILE C  26 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.88  -15.12     0      5.00e+00 4.00e-02 9.15e+00
  dihedral pdb=" CA  ALA E  25 "
           pdb=" C   ALA E  25 "
           pdb=" N   ILE E  26 "
           pdb=" CA  ILE E  26 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.90  -15.10     0      5.00e+00 4.00e-02 9.12e+00
  dihedral pdb=" CA  GLU E  62 "
           pdb=" CB  GLU E  62 "
           pdb=" CG  GLU E  62 "
           pdb=" CD  GLU E  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  127.60   52.40     3      1.50e+01 4.44e-03 9.11e+00
  ... (remaining 2182 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 262
       0.025 -    0.049: 192
       0.049 -    0.073: 51
       0.073 -    0.098: 32
       0.098 -    0.122: 53
  Chirality restraints: 590
  Sorted by residual:
  chirality pdb=" CA  VAL D  65 "
            pdb=" N   VAL D  65 "
            pdb=" C   VAL D  65 "
            pdb=" CB  VAL D  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.74e-01
  chirality pdb=" CA  VAL B  65 "
            pdb=" N   VAL B  65 "
            pdb=" C   VAL B  65 "
            pdb=" CB  VAL B  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.73e-01
  chirality pdb=" CA  VAL A  65 "
            pdb=" N   VAL A  65 "
            pdb=" C   VAL A  65 "
            pdb=" CB  VAL A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.72e-01
  ... (remaining 587 not shown)

  Planarity restraints: 625
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  78 "    0.007 2.00e-02 2.50e+03   5.57e-03 6.20e-01
        pdb=" CG  TYR A  78 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  78 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  78 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  78 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  78 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  78 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A  78 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E  78 "    0.007 2.00e-02 2.50e+03   5.53e-03 6.12e-01
        pdb=" CG  TYR E  78 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TYR E  78 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR E  78 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR E  78 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR E  78 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR E  78 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR E  78 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  78 "    0.007 2.00e-02 2.50e+03   5.53e-03 6.11e-01
        pdb=" CG  TYR B  78 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  78 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  78 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  78 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  78 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  78 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B  78 "    0.001 2.00e-02 2.50e+03
  ... (remaining 622 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 739
        2.80 -     3.32: 3073
        3.32 -     3.85: 6288
        3.85 -     4.37: 7035
        4.37 -     4.90: 13646
  Nonbonded interactions: 30781
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 114 "
            pdb=" OG1 THR B 119 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG1 THR A 119 "
            pdb=" OH  TYR C 114 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG1 THR C 119 "
            pdb=" OH  TYR E 114 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OH  TYR B 114 "
            pdb=" OG1 THR D 119 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OD1 ASP A  99 "
            pdb=" NH1 ARG C 103 "
     model   vdw
     2.421 3.120
  ... (remaining 30776 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'
  selection = chain 'E'
}

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:             0.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.230
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
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   0.022   3705  Z= 0.242
  Angle     :  0.540   4.368   5040  Z= 0.293
  Chirality :  0.047   0.122    590
  Planarity :  0.003   0.016    625
  Dihedral  : 15.568  68.705   1305
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 18.99 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.34), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.26), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B  79 
 HIS   0.002   0.001   HIS B  31 
 PHE   0.013   0.002   PHE B  64 
 TYR   0.014   0.002   TYR A  78 
 ARG   0.001   0.000   ARG E  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7747 (mp0)
REVERT: B   62 GLU cc_start: 0.8148 (tt0) cc_final: 0.7578 (tt0)
REVERT: C   61 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7455 (mp0)
REVERT: D   62 GLU cc_start: 0.8140 (tt0) cc_final: 0.7896 (tt0)
REVERT: E   61 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7789 (mp0)
REVERT: E   66 GLU cc_start: 0.7819 (tt0) cc_final: 0.7388 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.2457
  time to fit residues: 14.9342
Evaluate side-chains
  50 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    0.4980
   chunk 18 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0770
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
B  27 ASN
C  27 ASN
D  27 ASN
E  27 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.0868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3705  Z= 0.199
  Angle     :  0.497   3.678   5040  Z= 0.271
  Chirality :  0.047   0.125    590
  Planarity :  0.003   0.019    625
  Dihedral  :  5.202  15.738    500
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.44 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.35), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP E  79 
 HIS   0.002   0.001   HIS B  88 
 PHE   0.010   0.001   PHE A  64 
 TYR   0.015   0.002   TYR C 114 
 ARG   0.003   0.000   ARG A 103 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7901 (mp0)
REVERT: B   62 GLU cc_start: 0.8206 (tt0) cc_final: 0.7741 (tt0)
REVERT: D   62 GLU cc_start: 0.8180 (tt0) cc_final: 0.7653 (tt0)
REVERT: E   13 MET cc_start: 0.7954 (tpt) cc_final: 0.7735 (tmm)
REVERT: E   66 GLU cc_start: 0.7832 (tt0) cc_final: 0.7343 (tt0)
REVERT: E   80 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7817 (tttp)
  outliers start: 10
  outliers final: 7
  residues processed: 51
  average time/residue: 0.2050
  time to fit residues: 12.5951
Evaluate side-chains
  53 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   80 LYS
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0670
   chunk 36 optimal weight:    0.0170
   chunk 13 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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: 0.8266
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3705  Z= 0.178
  Angle     :  0.479   3.759   5040  Z= 0.259
  Chirality :  0.046   0.123    590
  Planarity :  0.003   0.018    625
  Dihedral  :  5.038  15.388    500
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.18 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.84 (0.35), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP E  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.010   0.001   PHE A  64 
 TYR   0.014   0.002   TYR C 114 
 ARG   0.001   0.000   ARG A 103 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7855 (mp0)
REVERT: B   62 GLU cc_start: 0.8164 (tt0) cc_final: 0.7723 (tt0)
REVERT: C   61 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7486 (mp0)
REVERT: D   62 GLU cc_start: 0.8195 (tt0) cc_final: 0.7701 (tt0)
REVERT: D   99 ASP cc_start: 0.8294 (t70) cc_final: 0.7904 (t70)
REVERT: E   66 GLU cc_start: 0.7812 (tt0) cc_final: 0.7353 (tt0)
REVERT: E   80 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7868 (tttp)
  outliers start: 12
  outliers final: 7
  residues processed: 55
  average time/residue: 0.2075
  time to fit residues: 13.6602
Evaluate side-chains
  56 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   80 LYS
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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: 0.8353
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.056   3705  Z= 0.746
  Angle     :  0.740   4.397   5040  Z= 0.403
  Chirality :  0.054   0.137    590
  Planarity :  0.004   0.023    625
  Dihedral  :  6.116  19.194    500
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 10.63 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.33), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.25), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  79 
 HIS   0.004   0.001   HIS E  31 
 PHE   0.011   0.003   PHE B  95 
 TYR   0.027   0.003   TYR C  78 
 ARG   0.002   0.000   ARG E  21 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 48
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7874 (mp0)
REVERT: C   66 GLU cc_start: 0.8113 (tt0) cc_final: 0.7551 (tt0)
REVERT: D   62 GLU cc_start: 0.8170 (tt0) cc_final: 0.7655 (tt0)
REVERT: E   66 GLU cc_start: 0.8042 (tt0) cc_final: 0.7477 (tt0)
REVERT: E   78 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8772 (m-80)
REVERT: E   80 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7867 (tttp)
  outliers start: 23
  outliers final: 8
  residues processed: 66
  average time/residue: 0.1915
  time to fit residues: 15.1716
Evaluate side-chains
  54 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   78 TYR
Chi-restraints excluded: chain E residue   80 LYS
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 32 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 30 optimal weight:    0.8980
   chunk 0 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 39 optimal weight:    0.3980
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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: 0.8312
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3705  Z= 0.188
  Angle     :  0.506   3.838   5040  Z= 0.275
  Chirality :  0.047   0.125    590
  Planarity :  0.003   0.019    625
  Dihedral  :  5.465  17.195    500
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.67 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.34), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.26), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP D  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.010   0.001   PHE B  64 
 TYR   0.020   0.002   TYR B  78 
 ARG   0.003   0.000   ARG A 103 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7965 (mp0)
REVERT: B   62 GLU cc_start: 0.8175 (tt0) cc_final: 0.7706 (tt0)
REVERT: C   66 GLU cc_start: 0.7919 (tt0) cc_final: 0.7601 (tt0)
REVERT: D   62 GLU cc_start: 0.8216 (tt0) cc_final: 0.7712 (tt0)
REVERT: E   66 GLU cc_start: 0.7930 (tt0) cc_final: 0.7498 (tt0)
  outliers start: 6
  outliers final: 3
  residues processed: 49
  average time/residue: 0.1753
  time to fit residues: 10.6746
Evaluate side-chains
  47 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0770
   overall best weight:    0.8740

-------------------------------------------------------------------------------
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: 0.8326
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3705  Z= 0.252
  Angle     :  0.509   3.632   5040  Z= 0.275
  Chirality :  0.047   0.127    590
  Planarity :  0.003   0.016    625
  Dihedral  :  5.302  16.374    500
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 14.43 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.34), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.26), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.011   0.001   PHE B  64 
 TYR   0.018   0.002   TYR B  78 
 ARG   0.001   0.000   ARG B 103 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7976 (mp0)
REVERT: B   62 GLU cc_start: 0.8184 (tt0) cc_final: 0.7767 (tt0)
REVERT: D   62 GLU cc_start: 0.8215 (tt0) cc_final: 0.7741 (tt0)
REVERT: E   66 GLU cc_start: 0.7908 (tt0) cc_final: 0.7262 (tt0)
  outliers start: 5
  outliers final: 4
  residues processed: 48
  average time/residue: 0.1729
  time to fit residues: 10.3231
Evaluate side-chains
  49 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 43 optimal weight:    0.2980
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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: 0.8331
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3705  Z= 0.294
  Angle     :  0.520   3.783   5040  Z= 0.281
  Chirality :  0.047   0.127    590
  Planarity :  0.003   0.018    625
  Dihedral  :  5.310  16.499    500
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.18 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.34), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.26), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP E  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.011   0.002   PHE A  64 
 TYR   0.019   0.002   TYR B  78 
 ARG   0.001   0.000   ARG B 103 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8020 (mp0)
REVERT: B   62 GLU cc_start: 0.8191 (tt0) cc_final: 0.7803 (tt0)
REVERT: C   66 GLU cc_start: 0.7994 (tt0) cc_final: 0.7693 (tt0)
REVERT: D   62 GLU cc_start: 0.8206 (tt0) cc_final: 0.7732 (tt0)
REVERT: E   66 GLU cc_start: 0.7930 (tt0) cc_final: 0.7438 (tt0)
REVERT: E   80 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7851 (tttp)
  outliers start: 8
  outliers final: 5
  residues processed: 51
  average time/residue: 0.1858
  time to fit residues: 11.6729
Evaluate side-chains
  52 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain E residue   80 LYS
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 34 optimal weight:    0.1980
   chunk 39 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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: 0.8325
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3705  Z= 0.250
  Angle     :  0.503   3.672   5040  Z= 0.272
  Chirality :  0.047   0.126    590
  Planarity :  0.003   0.016    625
  Dihedral  :  5.221  16.086    500
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.18 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.34), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.26), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP E  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.010   0.002   PHE B  64 
 TYR   0.018   0.002   TYR B  78 
 ARG   0.001   0.000   ARG B 103 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7512 (mp0)
REVERT: B   62 GLU cc_start: 0.8223 (tt0) cc_final: 0.7861 (tt0)
REVERT: D   62 GLU cc_start: 0.8207 (tt0) cc_final: 0.7614 (tt0)
REVERT: E   66 GLU cc_start: 0.7927 (tt0) cc_final: 0.7279 (tt0)
  outliers start: 7
  outliers final: 5
  residues processed: 52
  average time/residue: 0.1896
  time to fit residues: 12.0414
Evaluate side-chains
  50 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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: 0.8326
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3705  Z= 0.259
  Angle     :  0.508   3.679   5040  Z= 0.274
  Chirality :  0.047   0.126    590
  Planarity :  0.003   0.017    625
  Dihedral  :  5.219  16.067    500
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.16 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.34), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.26), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP E  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.010   0.002   PHE A  64 
 TYR   0.021   0.002   TYR C  78 
 ARG   0.001   0.000   ARG B 103 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7527 (mp0)
REVERT: B   62 GLU cc_start: 0.8185 (tt0) cc_final: 0.7866 (tt0)
REVERT: D   62 GLU cc_start: 0.8192 (tt0) cc_final: 0.7629 (tt0)
REVERT: E   66 GLU cc_start: 0.7935 (tt0) cc_final: 0.7285 (tt0)
  outliers start: 7
  outliers final: 7
  residues processed: 49
  average time/residue: 0.1928
  time to fit residues: 11.5550
Evaluate side-chains
  53 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 36 optimal weight:    0.4980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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: 0.8337
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   3705  Z= 0.337
  Angle     :  0.541   3.759   5040  Z= 0.291
  Chirality :  0.048   0.127    590
  Planarity :  0.003   0.016    625
  Dihedral  :  5.371  16.274    500
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.16 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (0.33), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.25), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.011   0.002   PHE A  64 
 TYR   0.021   0.002   TYR C  78 
 ARG   0.001   0.000   ARG B 103 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7531 (mp0)
REVERT: B   62 GLU cc_start: 0.8182 (tt0) cc_final: 0.7868 (tt0)
REVERT: C   62 GLU cc_start: 0.8188 (tt0) cc_final: 0.7952 (tt0)
REVERT: D   62 GLU cc_start: 0.8152 (tt0) cc_final: 0.7558 (tt0)
REVERT: E   66 GLU cc_start: 0.7962 (tt0) cc_final: 0.7318 (tt0)
  outliers start: 6
  outliers final: 5
  residues processed: 51
  average time/residue: 0.1879
  time to fit residues: 11.7379
Evaluate side-chains
  54 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4125 r_free = 0.4125 target = 0.139951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.118959 restraints weight = 4201.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 2.87
r_work: 0.3762 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3633 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   3705  Z= 0.237
  Angle     :  0.503   3.694   5040  Z= 0.271
  Chirality :  0.047   0.125    590
  Planarity :  0.003   0.017    625
  Dihedral  :  5.227  16.891    500
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.67 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.34), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.26), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP E  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.010   0.002   PHE B  64 
 TYR   0.017   0.002   TYR B  78 
 ARG   0.001   0.000   ARG B 103 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1402.00 seconds
wall clock time: 25 minutes 59.44 seconds (1559.44 seconds total)