Starting phenix.real_space_refine
on Wed Jun  3 21:29:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9px9_71962/06_2026/9px9_71962.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9px9_71962/06_2026/9px9_71962.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9px9_71962/06_2026/9px9_71962.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9px9_71962/06_2026/9px9_71962.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9px9_71962/06_2026/9px9_71962.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9px9_71962/06_2026/9px9_71962.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=   0.003 sd=   0.019
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: 5
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2784      2.51       5
     N     702      2.21       5
     O     798      1.98       5
     H    4308      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8598
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1433
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 4, 'TRANS': 86}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 1.31, per 1000 atoms: 0.15
  Number of scatterers: 8598
  At special positions: 0
  Unit cell: (72.38, 87.42, 45.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       6     16.00
     O     798      8.00
     N     702      7.00
     C    2784      6.00
     H    4308      1.00
    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: 0.65
  Conformation dependent library (CDL) restraints added in 193.3 milliseconds
  

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1044

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 40.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
      removed outlier: 6.679A  pdb=" N   MET C  13 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   VAL D  16 " --> pdb=" O   MET C  13 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   LYS C  15 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   MET E  13 " --> pdb=" O   VAL F  14 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   VAL F  16 " --> pdb=" O   MET E  13 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   LYS E  15 " --> pdb=" O   VAL F  16 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27
    Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 34
      removed outlier: 6.559A  pdb=" N   HIS A  31 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 8.468A  pdb=" N   ARG B  34 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   PHE A  33 " --> pdb=" O   ARG B  34 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   HIS D  31 " --> pdb=" O   VAL E  32 " (cutoff:3.500A)
      removed outlier: 8.433A  pdb=" N   ARG E  34 " --> pdb=" O   HIS D  31 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   PHE D  33 " --> pdb=" O   ARG E  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 65
      removed outlier: 6.962A  pdb=" N   PHE A  64 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   VAL B  65 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   PHE B  64 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL C  65 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   PHE C  64 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   VAL D  65 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   PHE D  64 " --> pdb=" O   GLU E  63 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   VAL E  65 " --> pdb=" O   PHE D  64 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   PHE E  64 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   VAL F  65 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 73
    Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 80
      removed outlier: 7.039A  pdb=" N   SER A  77 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   TYR B  78 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   SER B  77 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   TYR C  78 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   SER C  77 " --> pdb=" O   LYS D  76 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   TYR D  78 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   SER D  77 " --> pdb=" O   LYS E  76 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   TYR E  78 " --> pdb=" O   SER D  77 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   SER E  77 " --> pdb=" O   LYS F  76 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   TYR F  78 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 89 through 97
      removed outlier: 7.042A  pdb=" N   HIS B  90 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A  91 " --> pdb=" O   HIS B  90 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   GLU B  89 " --> pdb=" O   HIS C  90 " (cutoff:3.500A)
      removed outlier: 7.986A  pdb=" N   GLU C  92 " --> pdb=" O   GLU B  89 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   ALA B  91 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   VAL C  94 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   VAL B  93 " --> pdb=" O   VAL C  94 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   THR C  96 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   PHE B  95 " --> pdb=" O   THR C  96 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   GLU C  89 " --> pdb=" O   HIS D  90 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   GLU D  92 " --> pdb=" O   GLU C  89 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   ALA C  91 " --> pdb=" O   GLU D  92 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   VAL D  94 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   VAL C  93 " --> pdb=" O   VAL D  94 " (cutoff:3.500A)
      removed outlier: 8.172A  pdb=" N   THR D  96 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   PHE C  95 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   HIS E  90 " --> pdb=" O   GLU D  89 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA D  91 " --> pdb=" O   HIS E  90 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   HIS F  90 " --> pdb=" O   GLU E  89 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA E  91 " --> pdb=" O   HIS F  90 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 103 through 110
      removed outlier: 6.992A  pdb=" N   ALA A 109 " --> pdb=" O   ALA B 108 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   LEU B 110 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ALA B 109 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   LEU C 110 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   ALA C 109 " --> pdb=" O   ALA D 108 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   LEU D 110 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   ALA D 109 " --> pdb=" O   ALA E 108 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LEU E 110 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   ALA E 109 " --> pdb=" O   ALA F 108 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   LEU F 110 " --> pdb=" O   ALA E 109 " (cutoff:3.500A)

    117 hydrogen bonds defined for protein.
    351 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: 1.90

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4308
        1.03 -     1.22: 0
        1.22 -     1.41: 1804
        1.41 -     1.61: 2576
        1.61 -     1.80: 12
  Bond restraints: 8700
  Sorted by residual:
  bond pdb=" CG  LEU F 110 "
       pdb=" CD1 LEU F 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.43e+00
  bond pdb=" CG  LEU C 110 "
       pdb=" CD1 LEU C 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.36e+00
  bond pdb=" CG  LEU E 110 "
       pdb=" CD1 LEU E 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.32e+00
  bond pdb=" CG  LEU B 110 "
       pdb=" CD1 LEU B 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.29e+00
  bond pdb=" CG  LEU A 110 "
       pdb=" CD1 LEU A 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.27e+00
  ... (remaining 8695 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 15622
        2.29 -     4.59: 87
        4.59 -     6.88: 11
        6.88 -     9.17: 7
        9.17 -    11.47: 11
  Bond angle restraints: 15738
  Sorted by residual:
  angle pdb=" CB  LEU A 110 "
        pdb=" CG  LEU A 110 "
        pdb=" CD2 LEU A 110 "
      ideal   model   delta    sigma   weight residual
     110.70  122.17  -11.47 3.00e+00 1.11e-01 1.46e+01
  angle pdb=" CB  LEU B 110 "
        pdb=" CG  LEU B 110 "
        pdb=" CD2 LEU B 110 "
      ideal   model   delta    sigma   weight residual
     110.70  122.16  -11.46 3.00e+00 1.11e-01 1.46e+01
  angle pdb=" CB  LEU D 110 "
        pdb=" CG  LEU D 110 "
        pdb=" CD2 LEU D 110 "
      ideal   model   delta    sigma   weight residual
     110.70  122.15  -11.45 3.00e+00 1.11e-01 1.46e+01
  angle pdb=" CB  LEU C 110 "
        pdb=" CG  LEU C 110 "
        pdb=" CD2 LEU C 110 "
      ideal   model   delta    sigma   weight residual
     110.70  122.11  -11.41 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" CB  LEU E 110 "
        pdb=" CG  LEU E 110 "
        pdb=" CD2 LEU E 110 "
      ideal   model   delta    sigma   weight residual
     110.70  122.11  -11.41 3.00e+00 1.11e-01 1.45e+01
  ... (remaining 15733 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 3712
       17.74 -    35.49: 278
       35.49 -    53.23: 96
       53.23 -    70.97: 30
       70.97 -    88.71: 12
  Dihedral angle restraints: 4128
    sinusoidal: 2190
      harmonic: 1938
  Sorted by residual:
  dihedral pdb=" CB  GLU D  72 "
           pdb=" CG  GLU D  72 "
           pdb=" CD  GLU D  72 "
           pdb=" OE1 GLU D  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.71  -88.71     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CB  GLU E  72 "
           pdb=" CG  GLU E  72 "
           pdb=" CD  GLU E  72 "
           pdb=" OE1 GLU E  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.70  -88.70     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CB  GLU F  72 "
           pdb=" CG  GLU F  72 "
           pdb=" CD  GLU F  72 "
           pdb=" OE1 GLU F  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.70  -88.70     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 4125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 537
       0.052 -    0.105: 96
       0.105 -    0.157: 57
       0.157 -    0.210: 7
       0.210 -    0.262: 11
  Chirality restraints: 708
  Sorted by residual:
  chirality pdb=" CB  ILE C 122 "
            pdb=" CA  ILE C 122 "
            pdb=" CG1 ILE C 122 "
            pdb=" CG2 ILE C 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.91   -0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CB  ILE A 122 "
            pdb=" CA  ILE A 122 "
            pdb=" CG1 ILE A 122 "
            pdb=" CG2 ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.90   -0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CB  ILE B 122 "
            pdb=" CA  ILE B 122 "
            pdb=" CG1 ILE B 122 "
            pdb=" CG2 ILE B 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.90   -0.26 2.00e-01 2.50e+01 1.65e+00
  ... (remaining 705 not shown)

  Planarity restraints: 1242
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D  23 "   -0.021 5.00e-02 4.00e+02   3.16e-02 1.60e+00
        pdb=" N   PRO D  24 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO D  24 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D  24 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  23 "   -0.021 5.00e-02 4.00e+02   3.14e-02 1.58e+00
        pdb=" N   PRO C  24 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C  24 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C  24 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E  23 "   -0.021 5.00e-02 4.00e+02   3.14e-02 1.58e+00
        pdb=" N   PRO E  24 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO E  24 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO E  24 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1239 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.44: 5014
        2.44 -     2.98: 19739
        2.98 -     3.52: 22405
        3.52 -     4.06: 32687
        4.06 -     4.60: 43472
  Nonbonded interactions: 123317
  Sorted by model distance:
  nonbonded pdb="HG12 ILE D 122 "
            pdb="HG22 ILE E 122 "
     model   vdw
     1.900 2.440
  nonbonded pdb="HG12 ILE A 122 "
            pdb="HG22 ILE B 122 "
     model   vdw
     1.901 2.440
  nonbonded pdb="HG12 ILE C 122 "
            pdb="HG22 ILE D 122 "
     model   vdw
     1.929 2.440
  nonbonded pdb="HG12 ILE B 122 "
            pdb="HG22 ILE C 122 "
     model   vdw
     1.954 2.440
  nonbonded pdb=" HG  SER D 117 "
            pdb=" H   SER E 117 "
     model   vdw
     1.974 2.100
  ... (remaining 123312 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             1.690
  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:             0.050
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.460
  Find NCS groups from input model:        0.060
  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:6.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4392  Z= 0.125
  Angle     :  0.775  11.468   5976  Z= 0.339
  Chirality :  0.061   0.262    708
  Planarity :  0.004   0.032    732
  Dihedral  : 17.456  88.712   1554
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 27.56 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.39 (0.29), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.22), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  21 
 TYR   0.003   0.001   TYR A  78 
 PHE   0.004   0.001   PHE C  33 
 TRP   0.001   0.000   TRP D  79 
 HIS   0.002   0.000   HIS D  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 ( 4392)
  covalent geometry    : angle       0.77538 /  0.34 ( 5976)
  hydrogen bonds       : bond        0.19504 / 13.52 (  117)
  hydrogen bonds       : angle       6.94180 /  4.93 (  351)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 110
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.8077 (ttt180) cc_final: 0.7338 (pmt170)
REVERT: A   62 GLU cc_start: 0.8064 (pt0) cc_final: 0.6303 (tp30)
REVERT: A   63 GLU cc_start: 0.8528 (tt0) cc_final: 0.8304 (tt0)
REVERT: A   70 LYS cc_start: 0.8712 (tttt) cc_final: 0.7629 (pmtt)
REVERT: A   80 LYS cc_start: 0.8384 (tttp) cc_final: 0.7041 (pmtt)
REVERT: B   20 VAL cc_start: 0.8121 (p) cc_final: 0.7913 (p)
REVERT: B   80 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8393 (tttp)
REVERT: C   80 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8281 (tttm)
REVERT: D   20 VAL cc_start: 0.8154 (p) cc_final: 0.7946 (p)
REVERT: F   34 ARG cc_start: 0.8233 (ttt180) cc_final: 0.7633 (tpp-160)
REVERT: F   70 LYS cc_start: 0.8830 (tttt) cc_final: 0.8113 (tppt)
  outliers start: 3
  outliers final: 0
  residues processed: 110
  average time/residue: 1.2158
  time to fit residues: 138.5204
Evaluate side-chains
  87 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain C residue   80 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0980
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    2.3986

-------------------------------------------------------------------------------
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 = 0.4564 r_free = 0.4564 target = 0.144027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.133772 restraints weight = 23286.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.4464 rms_B_bonded: 3.12
r_work: 0.4361 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   4392  Z= 0.155
  Angle     :  0.570   4.082   5976  Z= 0.303
  Chirality :  0.050   0.136    708
  Planarity :  0.005   0.038    732
  Dihedral  :  5.847  33.057    596
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 21.15 %
    Favored  : 72.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.31), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.24), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  34 
 TYR   0.007   0.001   TYR C  78 
 PHE   0.008   0.001   PHE F  95 
 TRP   0.004   0.001   TRP F  79 
 HIS   0.001   0.000   HIS B  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.15 ( 4392)
  covalent geometry    : angle       0.56970 /  0.30 ( 5976)
  hydrogen bonds       : bond        0.03889 /  2.62 (  117)
  hydrogen bonds       : angle       5.38889 /  3.79 (  351)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.8104 (ttt180) cc_final: 0.6842 (pmt170)
REVERT: A   63 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7874 (tt0)
REVERT: A   65 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8564 (p)
REVERT: A   70 LYS cc_start: 0.8582 (tttt) cc_final: 0.7360 (pmtt)
REVERT: A   80 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.7023 (pmtt)
REVERT: B   63 GLU cc_start: 0.8200 (tt0) cc_final: 0.7983 (tt0)
REVERT: B   65 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8298 (p)
REVERT: C   65 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8335 (p)
REVERT: D   65 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8401 (p)
REVERT: E   63 GLU cc_start: 0.8389 (tt0) cc_final: 0.8179 (tt0)
REVERT: E   65 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8435 (p)
REVERT: F   34 ARG cc_start: 0.7689 (ttt180) cc_final: 0.6873 (tpm170)
REVERT: F   65 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8642 (p)
REVERT: F   70 LYS cc_start: 0.8696 (tttt) cc_final: 0.7773 (tppt)
  outliers start: 28
  outliers final: 11
  residues processed: 111
  average time/residue: 1.0531
  time to fit residues: 121.7556
Evaluate side-chains
  101 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 GLU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue   99 ASP
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 47 optimal weight:    7.9990
   chunk 25 optimal weight:    0.7980
   chunk 44 optimal weight:    7.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
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 = 0.4566 r_free = 0.4566 target = 0.142583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.132655 restraints weight = 23217.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.4460 rms_B_bonded: 3.01
r_work: 0.4352 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4392  Z= 0.163
  Angle     :  0.545   4.109   5976  Z= 0.294
  Chirality :  0.050   0.132    708
  Planarity :  0.005   0.038    732
  Dihedral  :  5.043  17.600    588
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 22.22 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.30), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.23), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  21 
 TYR   0.007   0.001   TYR B 105 
 PHE   0.008   0.001   PHE E  95 
 TRP   0.001   0.000   TRP E  79 
 HIS   0.002   0.000   HIS B  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.16 ( 4392)
  covalent geometry    : angle       0.54526 /  0.29 ( 5976)
  hydrogen bonds       : bond        0.03685 /  2.51 (  117)
  hydrogen bonds       : angle       5.25698 /  3.69 (  351)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.8147 (ttt180) cc_final: 0.6893 (pmt170)
REVERT: A   65 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8527 (p)
REVERT: A   70 LYS cc_start: 0.8576 (tttt) cc_final: 0.7422 (pmtt)
REVERT: A   80 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7084 (pmtt)
REVERT: B   13 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7216 (tmt)
REVERT: B   63 GLU cc_start: 0.8235 (tt0) cc_final: 0.8009 (tt0)
REVERT: B   65 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8254 (p)
REVERT: C   65 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8334 (p)
REVERT: C   66 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8076 (pt0)
REVERT: D   65 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8451 (p)
REVERT: E   65 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8435 (p)
REVERT: F   34 ARG cc_start: 0.7763 (ttt180) cc_final: 0.7001 (tpm170)
REVERT: F   65 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8651 (p)
REVERT: F   70 LYS cc_start: 0.8731 (tttt) cc_final: 0.7813 (tppt)
REVERT: F   80 LYS cc_start: 0.8441 (tttp) cc_final: 0.7716 (tppt)
  outliers start: 26
  outliers final: 11
  residues processed: 106
  average time/residue: 1.1627
  time to fit residues: 127.8481
Evaluate side-chains
  102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue   99 ASP
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0980
   chunk 34 optimal weight:    4.9990
   chunk 10 optimal weight:    0.4980
   chunk 7 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.4580 r_free = 0.4580 target = 0.143057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.132607 restraints weight = 23309.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.4461 rms_B_bonded: 3.05
r_work: 0.4358 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4392  Z= 0.125
  Angle     :  0.519   3.799   5976  Z= 0.278
  Chirality :  0.049   0.128    708
  Planarity :  0.005   0.038    732
  Dihedral  :  5.010  17.227    588
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 22.86 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.18 (0.30), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.41 (0.23), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  21 
 TYR   0.007   0.001   TYR B  78 
 PHE   0.007   0.001   PHE E  95 
 TRP   0.001   0.000   TRP E  79 
 HIS   0.003   0.001   HIS B  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 4392)
  covalent geometry    : angle       0.51873 /  0.28 ( 5976)
  hydrogen bonds       : bond        0.03034 /  2.07 (  117)
  hydrogen bonds       : angle       5.06795 /  3.57 (  351)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ARG cc_start: 0.8118 (ttt180) cc_final: 0.6885 (pmt170)
REVERT: A   65 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8553 (p)
REVERT: A   70 LYS cc_start: 0.8575 (tttt) cc_final: 0.7447 (pmtt)
REVERT: A   80 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.7071 (pmtt)
REVERT: B   13 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7158 (tmt)
REVERT: B   63 GLU cc_start: 0.8241 (tt0) cc_final: 0.7938 (tt0)
REVERT: B   65 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8273 (p)
REVERT: C   65 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8265 (p)
REVERT: C   66 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7936 (pt0)
REVERT: D   18 ASP cc_start: 0.7363 (t70) cc_final: 0.7034 (t0)
REVERT: D   65 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8385 (p)
REVERT: E   13 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7565 (tmt)
REVERT: E   65 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8387 (p)
REVERT: F   34 ARG cc_start: 0.7771 (ttt180) cc_final: 0.6982 (tpm170)
REVERT: F   65 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8671 (p)
REVERT: F   70 LYS cc_start: 0.8742 (tttt) cc_final: 0.7772 (tppt)
REVERT: F   80 LYS cc_start: 0.8492 (tttp) cc_final: 0.7748 (tppt)
  outliers start: 24
  outliers final: 11
  residues processed: 114
  average time/residue: 1.1709
  time to fit residues: 138.4265
Evaluate side-chains
  111 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  122 ILE
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue   66 GLU
Chi-restraints excluded: chain F residue   99 ASP
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 4 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0000
   chunk 1 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    2.7992

-------------------------------------------------------------------------------
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 = 0.4557 r_free = 0.4557 target = 0.144406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.134366 restraints weight = 23478.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.4478 rms_B_bonded: 3.11
r_work: 0.4384 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.4384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4392  Z= 0.167
  Angle     :  0.559   6.403   5976  Z= 0.300
  Chirality :  0.050   0.131    708
  Planarity :  0.005   0.038    732
  Dihedral  :  5.141  18.091    588
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 22.65 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.30), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.23), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  21 
 TYR   0.008   0.001   TYR B  78 
 PHE   0.008   0.001   PHE E  95 
 TRP   0.002   0.001   TRP F  79 
 HIS   0.004   0.001   HIS A  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.17 ( 4392)
  covalent geometry    : angle       0.55915 /  0.30 ( 5976)
  hydrogen bonds       : bond        0.03026 /  2.10 (  117)
  hydrogen bonds       : angle       5.12554 /  3.60 (  351)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7320 (ptt180) cc_final: 0.6892 (tpp-160)
REVERT: A   34 ARG cc_start: 0.8118 (ttt180) cc_final: 0.6904 (pmt170)
REVERT: A   65 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8673 (p)
REVERT: A   70 LYS cc_start: 0.8598 (tttt) cc_final: 0.7467 (pmtt)
REVERT: A   80 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.7209 (pmtt)
REVERT: A   92 GLU cc_start: 0.4769 (pm20) cc_final: 0.4535 (pm20)
REVERT: B   13 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7190 (tmt)
REVERT: B   63 GLU cc_start: 0.8287 (tt0) cc_final: 0.8054 (tt0)
REVERT: B   65 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8318 (p)
REVERT: C   65 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8293 (p)
REVERT: C   66 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8058 (pt0)
REVERT: D   65 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8337 (p)
REVERT: E   13 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7561 (tmt)
REVERT: E   65 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8413 (p)
REVERT: F   34 ARG cc_start: 0.7806 (ttt180) cc_final: 0.7022 (tpm170)
REVERT: F   70 LYS cc_start: 0.8793 (tttt) cc_final: 0.7796 (tppt)
REVERT: F   80 LYS cc_start: 0.8661 (tttp) cc_final: 0.7860 (tppt)
  outliers start: 30
  outliers final: 16
  residues processed: 112
  average time/residue: 1.2405
  time to fit residues: 143.6875
Evaluate side-chains
  112 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   62 GLU
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  122 ILE
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   66 GLU
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   66 GLU
Chi-restraints excluded: chain F residue   99 ASP
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 20 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 42 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 = 0.4621 r_free = 0.4621 target = 0.153478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.142300 restraints weight = 22972.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.4473 rms_B_bonded: 3.23
r_work: 0.4371 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4392  Z= 0.164
  Angle     :  0.546   6.171   5976  Z= 0.293
  Chirality :  0.049   0.131    708
  Planarity :  0.005   0.037    732
  Dihedral  :  5.149  18.033    588
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 23.08 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.13 (0.30), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.23), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  21 
 TYR   0.008   0.001   TYR B  78 
 PHE   0.008   0.001   PHE E  95 
 TRP   0.001   0.000   TRP E  79 
 HIS   0.003   0.001   HIS B  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.16 ( 4392)
  covalent geometry    : angle       0.54630 /  0.29 ( 5976)
  hydrogen bonds       : bond        0.02895 /  2.01 (  117)
  hydrogen bonds       : angle       5.08028 /  3.57 (  351)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7713 (ptt180) cc_final: 0.6780 (mmp80)
REVERT: A   34 ARG cc_start: 0.8139 (ttt180) cc_final: 0.6880 (pmt170)
REVERT: A   70 LYS cc_start: 0.8735 (tttt) cc_final: 0.7485 (pmtt)
REVERT: A   80 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.7162 (pmtt)
REVERT: A   92 GLU cc_start: 0.4795 (pm20) cc_final: 0.4542 (pm20)
REVERT: A  122 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7662 (pt)
REVERT: B   13 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7076 (tmt)
REVERT: B   63 GLU cc_start: 0.8253 (tt0) cc_final: 0.7987 (tt0)
REVERT: B   65 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8215 (p)
REVERT: C   65 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8186 (p)
REVERT: C   66 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8060 (pt0)
REVERT: D   65 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8225 (p)
REVERT: E   13 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7440 (tmt)
REVERT: E   65 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8297 (p)
REVERT: F   34 ARG cc_start: 0.7662 (ttt180) cc_final: 0.6885 (tpm170)
REVERT: F   70 LYS cc_start: 0.8675 (tttt) cc_final: 0.7700 (tppt)
REVERT: F   80 LYS cc_start: 0.8542 (tttp) cc_final: 0.7779 (tppt)
  outliers start: 27
  outliers final: 14
  residues processed: 104
  average time/residue: 1.2327
  time to fit residues: 132.7197
Evaluate side-chains
  114 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  122 ILE
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   66 GLU
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   66 GLU
Chi-restraints excluded: chain F residue   99 ASP
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   overall best weight:    3.3186

-------------------------------------------------------------------------------
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 = 0.4535 r_free = 0.4535 target = 0.143496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 21)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.133567 restraints weight = 23934.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.4458 rms_B_bonded: 3.11
r_work: 0.4362 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4392  Z= 0.190
  Angle     :  0.548   3.943   5976  Z= 0.297
  Chirality :  0.049   0.134    708
  Planarity :  0.004   0.038    732
  Dihedral  :  5.266  18.665    588
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 23.08 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.30), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.23), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  21 
 TYR   0.009   0.001   TYR B  78 
 PHE   0.008   0.001   PHE E  95 
 TRP   0.002   0.001   TRP F  79 
 HIS   0.004   0.001   HIS A  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00444 /  0.19 ( 4392)
  covalent geometry    : angle       0.54809 /  0.30 ( 5976)
  hydrogen bonds       : bond        0.03000 /  2.09 (  117)
  hydrogen bonds       : angle       5.13217 /  3.61 (  351)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6781 (tmt)
REVERT: A   21 ARG cc_start: 0.7925 (ptt180) cc_final: 0.7380 (tpm170)
REVERT: A   34 ARG cc_start: 0.8196 (ttt180) cc_final: 0.6954 (pmt170)
REVERT: A   63 GLU cc_start: 0.8432 (tt0) cc_final: 0.8128 (tt0)
REVERT: A   70 LYS cc_start: 0.8781 (tttt) cc_final: 0.7492 (pmtt)
REVERT: A   80 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.7272 (pmtt)
REVERT: A   92 GLU cc_start: 0.4903 (pm20) cc_final: 0.4621 (pm20)
REVERT: B   13 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7051 (tmt)
REVERT: B   63 GLU cc_start: 0.8308 (tt0) cc_final: 0.8040 (tt0)
REVERT: B   65 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8350 (p)
REVERT: C   21 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7242 (pmm-80)
REVERT: C   65 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8312 (p)
REVERT: C   66 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8156 (pt0)
REVERT: D   65 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8324 (p)
REVERT: E   13 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7536 (tmt)
REVERT: E   65 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8411 (p)
REVERT: F   34 ARG cc_start: 0.7848 (ttt180) cc_final: 0.7003 (tpm170)
REVERT: F   70 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.7785 (tppt)
REVERT: F   80 LYS cc_start: 0.8697 (tttp) cc_final: 0.7848 (tppt)
  outliers start: 28
  outliers final: 11
  residues processed: 108
  average time/residue: 1.2715
  time to fit residues: 142.1348
Evaluate side-chains
  108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   21 ARG
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   66 GLU
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   70 LYS
Chi-restraints excluded: chain F residue   99 ASP
Chi-restraints excluded: chain F residue  117 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0370
   chunk 48 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    1.7664

-------------------------------------------------------------------------------
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 = 0.4594 r_free = 0.4594 target = 0.147801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.137899 restraints weight = 22918.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.4464 rms_B_bonded: 3.00
r_work: 0.4357 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.4357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4392  Z= 0.116
  Angle     :  0.522   4.022   5976  Z= 0.279
  Chirality :  0.049   0.127    708
  Planarity :  0.004   0.036    732
  Dihedral  :  5.201  17.730    588
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 24.57 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.04 (0.30), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.23), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  21 
 TYR   0.008   0.001   TYR B  78 
 PHE   0.008   0.001   PHE E  95 
 TRP   0.001   0.000   TRP E  79 
 HIS   0.008   0.001   HIS A  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 4392)
  covalent geometry    : angle       0.52229 /  0.28 ( 5976)
  hydrogen bonds       : bond        0.02664 /  1.86 (  117)
  hydrogen bonds       : angle       4.91383 /  3.47 (  351)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7896 (ptt180) cc_final: 0.7245 (tpm170)
REVERT: A   34 ARG cc_start: 0.8130 (ttt180) cc_final: 0.6858 (pmt170)
REVERT: A   63 GLU cc_start: 0.8414 (tt0) cc_final: 0.8141 (tt0)
REVERT: A   70 LYS cc_start: 0.8762 (tttt) cc_final: 0.7484 (pmtt)
REVERT: A   80 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7219 (pmtt)
REVERT: A   92 GLU cc_start: 0.4707 (pm20) cc_final: 0.4451 (pm20)
REVERT: B   13 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7131 (tmt)
REVERT: B   63 GLU cc_start: 0.8256 (tt0) cc_final: 0.7961 (tt0)
REVERT: B   65 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8266 (p)
REVERT: C   65 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8192 (p)
REVERT: C   66 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8029 (pt0)
REVERT: D   65 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8210 (p)
REVERT: E   13 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7521 (tmt)
REVERT: E   21 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7591 (pmm-80)
REVERT: E   65 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8316 (p)
REVERT: F   34 ARG cc_start: 0.7738 (ttt180) cc_final: 0.6927 (tpm170)
REVERT: F   70 LYS cc_start: 0.8761 (tttt) cc_final: 0.7775 (tppt)
REVERT: F   80 LYS cc_start: 0.8647 (tttp) cc_final: 0.7827 (tppt)
  outliers start: 19
  outliers final: 7
  residues processed: 104
  average time/residue: 1.2728
  time to fit residues: 137.0210
Evaluate side-chains
  106 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   21 ARG
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 27 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0570
   chunk 53 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.7102

-------------------------------------------------------------------------------
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 = 0.4613 r_free = 0.4613 target = 0.150068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.139987 restraints weight = 22841.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.4512 rms_B_bonded: 3.14
r_work: 0.4407 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4392  Z= 0.083
  Angle     :  0.492   4.001   5976  Z= 0.261
  Chirality :  0.049   0.123    708
  Planarity :  0.004   0.035    732
  Dihedral  :  4.961  16.290    588
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 26.28 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.91 (0.31), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.23), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  21 
 TYR   0.005   0.001   TYR B  78 
 PHE   0.007   0.001   PHE D  95 
 TRP   0.002   0.000   TRP C  79 
 HIS   0.007   0.001   HIS A  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00196 /  0.08 ( 4392)
  covalent geometry    : angle       0.49216 /  0.26 ( 5976)
  hydrogen bonds       : bond        0.02237 /  1.55 (  117)
  hydrogen bonds       : angle       4.59443 /  3.26 (  351)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7753 (ptt180) cc_final: 0.7165 (tpm170)
REVERT: A   34 ARG cc_start: 0.8028 (ttt180) cc_final: 0.6805 (pmt170)
REVERT: A   70 LYS cc_start: 0.8554 (tttt) cc_final: 0.7405 (pmtt)
REVERT: A   80 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7104 (pmtt)
REVERT: A   92 GLU cc_start: 0.5178 (pm20) cc_final: 0.4961 (pm20)
REVERT: B   63 GLU cc_start: 0.8376 (tt0) cc_final: 0.8027 (tt0)
REVERT: B   65 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8259 (p)
REVERT: C   21 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7078 (pmm-80)
REVERT: C   65 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8305 (p)
REVERT: E   21 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7603 (pmm-80)
REVERT: E   65 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8318 (p)
REVERT: F   34 ARG cc_start: 0.7743 (ttt180) cc_final: 0.7001 (tpm170)
REVERT: F   70 LYS cc_start: 0.8744 (tttt) cc_final: 0.7723 (tppt)
REVERT: F   80 LYS cc_start: 0.8609 (tttp) cc_final: 0.8348 (tttp)
  outliers start: 11
  outliers final: 4
  residues processed: 100
  average time/residue: 1.3450
  time to fit residues: 139.0015
Evaluate side-chains
  97 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   21 ARG
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain E residue   21 ARG
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   66 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 46 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 42 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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 = 0.4543 r_free = 0.4543 target = 0.143548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.133928 restraints weight = 23512.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.4463 rms_B_bonded: 3.04
r_work: 0.4368 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   4392  Z= 0.191
  Angle     :  0.540   4.193   5976  Z= 0.292
  Chirality :  0.049   0.133    708
  Planarity :  0.004   0.038    732
  Dihedral  :  5.112  18.563    588
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 26.28 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.31), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.25 (0.23), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  21 
 TYR   0.009   0.001   TYR B  78 
 PHE   0.008   0.001   PHE E  95 
 TRP   0.003   0.001   TRP F  79 
 HIS   0.010   0.001   HIS A  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.19 ( 4392)
  covalent geometry    : angle       0.54019 /  0.29 ( 5976)
  hydrogen bonds       : bond        0.02774 /  1.95 (  117)
  hydrogen bonds       : angle       4.90880 /  3.45 (  351)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7923 (ptt180) cc_final: 0.7380 (tpm170)
REVERT: A   34 ARG cc_start: 0.8211 (ttt180) cc_final: 0.7048 (pmt170)
REVERT: A   70 LYS cc_start: 0.8798 (tttt) cc_final: 0.7541 (pmtt)
REVERT: A   80 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8436 (tttm)
REVERT: A   92 GLU cc_start: 0.4867 (pm20) cc_final: 0.4621 (pm20)
REVERT: B   63 GLU cc_start: 0.8339 (tt0) cc_final: 0.8084 (tt0)
REVERT: B   65 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8385 (p)
REVERT: C   21 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7236 (pmm-80)
REVERT: C   65 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8459 (p)
REVERT: E   21 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7811 (pmm-80)
REVERT: E   65 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8450 (p)
REVERT: F   34 ARG cc_start: 0.7896 (ttt180) cc_final: 0.7052 (tpm170)
REVERT: F   70 LYS cc_start: 0.8827 (tttt) cc_final: 0.7856 (tppt)
REVERT: F   80 LYS cc_start: 0.8750 (tttp) cc_final: 0.8508 (tttp)
  outliers start: 11
  outliers final: 5
  residues processed: 96
  average time/residue: 1.4485
  time to fit residues: 143.3677
Evaluate side-chains
  99 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   21 ARG
Chi-restraints excluded: chain C residue   65 VAL
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   21 ARG
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue   66 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 18 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 38 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.9784

-------------------------------------------------------------------------------
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 = 0.4553 r_free = 0.4553 target = 0.144603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.134856 restraints weight = 23153.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.4483 rms_B_bonded: 3.03
r_work: 0.4383 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.4383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.3911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4392  Z= 0.124
  Angle     :  0.515   4.343   5976  Z= 0.274
  Chirality :  0.049   0.128    708
  Planarity :  0.004   0.037    732
  Dihedral  :  5.122  17.878    588
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 25.21 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.30), residues: 522
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.23), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  21 
 TYR   0.007   0.001   TYR B  78 
 PHE   0.007   0.001   PHE E  95 
 TRP   0.002   0.000   TRP F  79 
 HIS   0.008   0.001   HIS A  88 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.12 ( 4392)
  covalent geometry    : angle       0.51498 /  0.27 ( 5976)
  hydrogen bonds       : bond        0.02558 /  1.79 (  117)
  hydrogen bonds       : angle       4.75570 /  3.35 (  351)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3611.50 seconds
wall clock time: 61 minutes 54.19 seconds (3714.19 seconds total)