Starting phenix.real_space_refine
on Tue Feb  3 14:19:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d23_46481/02_2026/9d23_46481.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d23_46481/02_2026/9d23_46481.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d23_46481/02_2026/9d23_46481.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d23_46481/02_2026/9d23_46481.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d23_46481/02_2026/9d23_46481.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d23_46481/02_2026/9d23_46481.cif"
  }
  resolution = 3.18
  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=   0.000 sd=   0.006
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    2320      2.51       5
     N     590      2.21       5
     O     665      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3580
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 716
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 4, 'TRANS': 87}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.58, per 1000 atoms: 0.16
  Number of scatterers: 3580
  At special positions: 0
  Unit cell: (68.112, 89.87, 40.678, 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     665      8.00
     N     590      7.00
     C    2320      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: 0.25
  Conformation dependent library (CDL) restraints added in 132.3 milliseconds
  

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  870

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 46.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 16
      removed outlier: 6.502A  pdb=" N   LEU B  12 " --> pdb=" O   MET D  13 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   LYS D  15 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   VAL B  14 " --> pdb=" O   LYS D  15 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU A  12 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 8.082A  pdb=" N   LYS B  15 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   VAL A  14 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 21
      removed outlier: 6.369A  pdb=" N   ALA A  19 " --> pdb=" O   VAL C  20 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ALA C  19 " --> pdb=" O   VAL E  20 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 32
      removed outlier: 6.554A  pdb=" N   ALA A  25 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
      removed outlier: 7.961A  pdb=" N   VAL C  28 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ASN A  27 " --> pdb=" O   VAL C  28 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   VAL C  30 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ALA A  29 " --> pdb=" O   VAL C  30 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   VAL C  32 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   HIS A  31 " --> pdb=" O   VAL C  32 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ALA C  25 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   VAL E  28 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   ASN C  27 " --> pdb=" O   VAL E  28 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   VAL E  30 " --> pdb=" O   ASN C  27 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ALA C  29 " --> pdb=" O   VAL E  30 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   VAL E  32 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 6.570A  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 62
      removed outlier: 6.507A  pdb=" N   THR B  59 " --> pdb=" O   ALA D  60 " (cutoff:3.500A)
      removed outlier: 8.494A  pdb=" N   GLU D  62 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   GLU B  61 " --> pdb=" O   GLU D  62 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   THR A  59 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 8.498A  pdb=" N   GLU B  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   GLU A  61 " --> pdb=" O   GLU B  62 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 65 through 66
      removed outlier: 6.493A  pdb=" N   VAL A  65 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL C  65 " --> pdb=" O   GLU E  66 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 73
      removed outlier: 6.632A  pdb=" N   TYR A  69 " --> pdb=" O   LYS C  70 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   GLU C  72 " --> pdb=" O   TYR A  69 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   VAL A  71 " --> pdb=" O   GLU C  72 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   TYR C  69 " --> pdb=" O   LYS E  70 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   GLU E  72 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   VAL C  71 " --> pdb=" O   GLU E  72 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 76 through 80
      removed outlier: 9.143A  pdb=" N   LYS B  76 " --> pdb=" O   SER D  77 " (cutoff:3.500A)
      removed outlier: 9.753A  pdb=" N   TRP D  79 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   TYR B  78 " --> pdb=" O   TRP D  79 " (cutoff:3.500A)
      removed outlier: 9.133A  pdb=" N   LYS A  76 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 9.750A  pdb=" N   TRP B  79 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   TYR A  78 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   SER A  77 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   TYR C  78 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   SER C  77 " --> pdb=" O   LYS E  76 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   TYR E  78 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 92 through 98
      removed outlier: 6.569A  pdb=" N   GLU B  92 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   PHE D  95 " --> pdb=" O   GLU B  92 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   VAL B  94 " --> pdb=" O   PHE D  95 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ALA D  97 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   THR B  96 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL A  93 " --> pdb=" O   VAL C  94 " (cutoff:3.500A)
      removed outlier: 8.005A  pdb=" N   THR C  96 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   PHE A  95 " --> pdb=" O   THR C  96 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   ASN C  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   ALA A  97 " --> pdb=" O   ASN C  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 103 through 110
      removed outlier: 6.963A  pdb=" N   LEU B 110 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   LEU A 110 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ARG A 103 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
      removed outlier: 8.183A  pdb=" N   THR C 106 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   TYR A 105 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   ALA C 108 " --> pdb=" O   TYR A 105 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   ILE A 107 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   LEU C 110 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 8.298A  pdb=" N   ALA A 109 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG C 103 " --> pdb=" O   ARG E 104 " (cutoff:3.500A)
      removed outlier: 8.187A  pdb=" N   THR E 106 " --> pdb=" O   ARG C 103 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   TYR C 105 " --> pdb=" O   THR E 106 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   ALA E 108 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   ILE C 107 " --> pdb=" O   ALA E 108 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   LEU E 110 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 8.330A  pdb=" N   ALA C 109 " --> pdb=" O   LEU E 110 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115
      removed outlier: 7.021A  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=AB2, first strand: chain 'D' and resid 118 through 122
      removed outlier: 5.899A  pdb=" N   THR A 118 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   VAL C 121 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   ALA A 120 " --> pdb=" O   VAL C 121 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   THR C 118 " --> pdb=" O   THR E 119 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   VAL E 121 " --> pdb=" O   THR C 118 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA C 120 " --> pdb=" O   VAL E 121 " (cutoff:3.500A)

    80 hydrogen bonds defined for protein.
    240 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: 0.47

  Time building geometry restraints manager: 0.34 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: 1120
        1.34 -     1.46: 649
        1.46 -     1.57: 1886
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 3665
  Sorted by residual:
  bond pdb=" CA  SER C 100 "
       pdb=" C   SER C 100 "
    ideal  model  delta    sigma   weight residual
    1.530  1.517  0.013 1.08e-02 8.57e+03 1.46e+00
  bond pdb=" CA  SER E 100 "
       pdb=" C   SER E 100 "
    ideal  model  delta    sigma   weight residual
    1.530  1.518  0.013 1.08e-02 8.57e+03 1.42e+00
  bond pdb=" CA  SER A 100 "
       pdb=" C   SER A 100 "
    ideal  model  delta    sigma   weight residual
    1.530  1.518  0.013 1.08e-02 8.57e+03 1.41e+00
  bond pdb=" CA  SER B 100 "
       pdb=" C   SER B 100 "
    ideal  model  delta    sigma   weight residual
    1.530  1.518  0.013 1.08e-02 8.57e+03 1.34e+00
  bond pdb=" CA  SER D 100 "
       pdb=" C   SER D 100 "
    ideal  model  delta    sigma   weight residual
    1.530  1.518  0.012 1.08e-02 8.57e+03 1.24e+00
  ... (remaining 3660 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 4625
        1.06 -     2.12: 245
        2.12 -     3.18: 90
        3.18 -     4.24: 10
        4.24 -     5.30: 15
  Bond angle restraints: 4985
  Sorted by residual:
  angle pdb=" N   SER E  23 "
        pdb=" CA  SER E  23 "
        pdb=" C   SER E  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.11   -5.30 2.21e+00 2.05e-01 5.74e+00
  angle pdb=" N   SER C  23 "
        pdb=" CA  SER C  23 "
        pdb=" C   SER C  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.08   -5.27 2.21e+00 2.05e-01 5.68e+00
  angle pdb=" N   SER A  23 "
        pdb=" CA  SER A  23 "
        pdb=" C   SER A  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.06   -5.25 2.21e+00 2.05e-01 5.64e+00
  angle pdb=" N   SER D  23 "
        pdb=" CA  SER D  23 "
        pdb=" C   SER D  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.05   -5.24 2.21e+00 2.05e-01 5.63e+00
  angle pdb=" N   SER B  23 "
        pdb=" CA  SER B  23 "
        pdb=" C   SER B  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.04   -5.23 2.21e+00 2.05e-01 5.59e+00
  ... (remaining 4980 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 1940
       15.94 -    31.88: 175
       31.88 -    47.82: 35
       47.82 -    63.76: 5
       63.76 -    79.70: 5
  Dihedral angle restraints: 2160
    sinusoidal: 815
      harmonic: 1345
  Sorted by residual:
  dihedral pdb=" CA  GLU C  62 "
           pdb=" C   GLU C  62 "
           pdb=" N   GLU C  63 "
           pdb=" CA  GLU C  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.43   16.57     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  GLU E  62 "
           pdb=" C   GLU E  62 "
           pdb=" N   GLU E  63 "
           pdb=" CA  GLU E  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.45   16.55     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  GLU B  62 "
           pdb=" C   GLU B  62 "
           pdb=" N   GLU B  63 "
           pdb=" CA  GLU B  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.47   16.53     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 2157 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 283
       0.031 -    0.061: 192
       0.061 -    0.092: 20
       0.092 -    0.123: 80
       0.123 -    0.153: 10
  Chirality restraints: 585
  Sorted by residual:
  chirality pdb=" CA  SER C  23 "
            pdb=" N   SER C  23 "
            pdb=" C   SER C  23 "
            pdb=" CB  SER C  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.89e-01
  chirality pdb=" CA  SER D  23 "
            pdb=" N   SER D  23 "
            pdb=" C   SER D  23 "
            pdb=" CB  SER D  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.77e-01
  chirality pdb=" CA  SER A  23 "
            pdb=" N   SER A  23 "
            pdb=" C   SER A  23 "
            pdb=" CB  SER A  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.68e-01
  ... (remaining 582 not shown)

  Planarity restraints: 615
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 112 "    0.021 5.00e-02 4.00e+02   3.12e-02 1.55e+00
        pdb=" N   PRO E 113 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO E 113 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO E 113 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 112 "    0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO C 113 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C 113 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 113 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 112 "    0.020 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO D 113 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO D 113 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D 113 "    0.017 5.00e-02 4.00e+02
  ... (remaining 612 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 515
        2.78 -     3.31: 3041
        3.31 -     3.84: 5615
        3.84 -     4.37: 6371
        4.37 -     4.90: 11178
  Nonbonded interactions: 26720
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP E  74 "
            pdb=" OH  TYR E 105 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OD2 ASP D  74 "
            pdb=" OH  TYR D 105 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OD2 ASP A  74 "
            pdb=" OH  TYR A 105 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OD2 ASP B  74 "
            pdb=" OH  TYR B 105 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OD2 ASP C  74 "
            pdb=" OH  TYR C 105 "
     model   vdw
     2.248 3.040
  ... (remaining 26715 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: 0.01
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:             1.000
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.840
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
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   0.017   3665  Z= 0.152
  Angle     :  0.655   5.296   4985  Z= 0.358
  Chirality :  0.053   0.153    585
  Planarity :  0.004   0.031    615
  Dihedral  : 13.139  79.703   1290
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.39 %
    Favored  : 89.61 %
  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: -2.30 (0.36), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 104 
 TYR   0.016   0.002   TYR E 114 
 PHE   0.007   0.001   PHE C  33 
 TRP   0.009   0.002   TRP A  79 
 HIS   0.002   0.000   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3665)
  covalent geometry    : angle       0.65468 ( 4985)
  hydrogen bonds       : bond        0.21188 (   80)
  hydrogen bonds       : angle       8.78007 (  240)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7057 (mt-10)
REVERT: B   62 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7427 (mt-10)
REVERT: C   34 ARG cc_start: 0.8088 (ttt90) cc_final: 0.7470 (ttt90)
REVERT: C   62 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7303 (mm-30)
REVERT: D   62 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7288 (mt-10)
REVERT: D   99 ASP cc_start: 0.7532 (t70) cc_final: 0.7231 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0542
  time to fit residues: 2.6458
Evaluate side-chains
  39 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    0.3980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.3902 r_free = 0.3902 target = 0.120506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.096615 restraints weight = 4284.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.34
r_work: 0.3470 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.1186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3665  Z= 0.159
  Angle     :  0.670   5.926   4985  Z= 0.355
  Chirality :  0.052   0.132    585
  Planarity :  0.004   0.029    615
  Dihedral  :  5.703  19.235    495
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.21 %
    Favored  : 85.97 %
  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: -2.18 (0.38), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 103 
 TYR   0.015   0.002   TYR C 114 
 PHE   0.010   0.002   PHE C  95 
 TRP   0.010   0.002   TRP E  79 
 HIS   0.002   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3665)
  covalent geometry    : angle       0.67027 ( 4985)
  hydrogen bonds       : bond        0.03598 (   80)
  hydrogen bonds       : angle       5.53381 (  240)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7714 (mm-30) cc_final: 0.6958 (mt-10)
REVERT: B   35 LYS cc_start: 0.8270 (tttm) cc_final: 0.8033 (ttmm)
REVERT: B   62 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7444 (mt-10)
REVERT: C   34 ARG cc_start: 0.8359 (ttt90) cc_final: 0.7791 (ttt90)
REVERT: D   62 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7589 (mt-10)
REVERT: E   62 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7675 (mp0)
REVERT: E   63 GLU cc_start: 0.7975 (pt0) cc_final: 0.7735 (pt0)
  outliers start: 7
  outliers final: 1
  residues processed: 46
  average time/residue: 0.0795
  time to fit residues: 4.4039
Evaluate side-chains
  41 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  123 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 2 optimal weight:    0.3980
   chunk 12 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.8788

-------------------------------------------------------------------------------
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 = 0.3868 r_free = 0.3868 target = 0.117433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.093513 restraints weight = 4347.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.33
r_work: 0.3424 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3297 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3665  Z= 0.206
  Angle     :  0.711   6.366   4985  Z= 0.380
  Chirality :  0.053   0.137    585
  Planarity :  0.004   0.034    615
  Dihedral  :  5.913  20.161    495
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.47 %
    Favored  : 86.49 %
  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: -2.31 (0.37), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 104 
 TYR   0.017   0.002   TYR C 114 
 PHE   0.012   0.002   PHE A  95 
 TRP   0.009   0.002   TRP B  79 
 HIS   0.002   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 3665)
  covalent geometry    : angle       0.71076 ( 4985)
  hydrogen bonds       : bond        0.03940 (   80)
  hydrogen bonds       : angle       5.26773 (  240)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A   13 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7435 (tmm)
REVERT: A   62 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7266 (mt-10)
REVERT: B   35 LYS cc_start: 0.8553 (tttm) cc_final: 0.8308 (ttmm)
REVERT: B   62 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7752 (mt-10)
REVERT: C   62 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7056 (mp0)
REVERT: D   62 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7760 (mt-10)
REVERT: D   66 GLU cc_start: 0.7618 (tt0) cc_final: 0.7093 (tm-30)
REVERT: E   13 MET cc_start: 0.8480 (ttt) cc_final: 0.8240 (ttp)
REVERT: E   62 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7686 (mp0)
REVERT: E   63 GLU cc_start: 0.8026 (pt0) cc_final: 0.7768 (pt0)
  outliers start: 4
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0675
  time to fit residues: 3.7334
Evaluate side-chains
  39 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.123079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.099275 restraints weight = 4205.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.21
r_work: 0.3455 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3665  Z= 0.177
  Angle     :  0.673   5.910   4985  Z= 0.358
  Chirality :  0.052   0.136    585
  Planarity :  0.004   0.037    615
  Dihedral  :  5.791  20.102    495
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 13.77 %
    Favored  : 85.19 %
  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: -2.33 (0.37), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 104 
 TYR   0.017   0.002   TYR C 114 
 PHE   0.012   0.002   PHE A  95 
 TRP   0.006   0.001   TRP C  79 
 HIS   0.002   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 3665)
  covalent geometry    : angle       0.67274 ( 4985)
  hydrogen bonds       : bond        0.03249 (   80)
  hydrogen bonds       : angle       5.05061 (  240)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7337 (mt-10)
REVERT: A   70 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7582 (ttpp)
REVERT: B   35 LYS cc_start: 0.8532 (tttm) cc_final: 0.8289 (ttmm)
REVERT: B   62 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7789 (mt-10)
REVERT: C   62 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7191 (mp0)
REVERT: D   62 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7824 (mt-10)
REVERT: E   13 MET cc_start: 0.8484 (ttt) cc_final: 0.8253 (ttp)
REVERT: E   62 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7777 (mp0)
  outliers start: 4
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0988
  time to fit residues: 4.8721
Evaluate side-chains
  38 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
E  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.114724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.090699 restraints weight = 4365.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.31
r_work: 0.3369 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.038   3665  Z= 0.308
  Angle     :  0.785   6.781   4985  Z= 0.426
  Chirality :  0.056   0.146    585
  Planarity :  0.005   0.035    615
  Dihedral  :  6.237  20.580    495
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.03 %
    Favored  : 84.94 %
  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: -2.46 (0.37), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  21 
 TYR   0.018   0.003   TYR C 114 
 PHE   0.014   0.003   PHE E  87 
 TRP   0.010   0.002   TRP D  79 
 HIS   0.003   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00753 ( 3665)
  covalent geometry    : angle       0.78466 ( 4985)
  hydrogen bonds       : bond        0.04233 (   80)
  hydrogen bonds       : angle       5.21706 (  240)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8085 (ttp-170) cc_final: 0.7553 (ttm110)
REVERT: A   62 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7383 (mt-10)
REVERT: A   70 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7764 (ttpp)
REVERT: B   62 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7810 (mt-10)
REVERT: C   34 ARG cc_start: 0.8430 (ttt90) cc_final: 0.7899 (ttt90)
REVERT: C   62 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7095 (mp0)
REVERT: D   62 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7809 (mt-10)
REVERT: D   66 GLU cc_start: 0.7592 (tt0) cc_final: 0.7090 (tm-30)
REVERT: E   13 MET cc_start: 0.8497 (ttt) cc_final: 0.8252 (ttp)
REVERT: E   62 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7657 (mp0)
  outliers start: 4
  outliers final: 2
  residues processed: 46
  average time/residue: 0.1536
  time to fit residues: 8.0482
Evaluate side-chains
  46 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain C residue   70 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 37 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
E  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.125346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.101328 restraints weight = 4140.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.23
r_work: 0.3511 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3665  Z= 0.119
  Angle     :  0.615   5.447   4985  Z= 0.325
  Chirality :  0.051   0.132    585
  Planarity :  0.004   0.033    615
  Dihedral  :  5.592  19.565    495
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.03 %
    Favored  : 84.68 %
  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: -2.37 (0.38), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  21 
 TYR   0.016   0.002   TYR C 114 
 PHE   0.010   0.001   PHE A  95 
 TRP   0.004   0.001   TRP C  79 
 HIS   0.002   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3665)
  covalent geometry    : angle       0.61544 ( 4985)
  hydrogen bonds       : bond        0.02520 (   80)
  hydrogen bonds       : angle       4.80438 (  240)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7376 (mt-10)
REVERT: B   62 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7819 (mt-10)
REVERT: C   34 ARG cc_start: 0.8307 (ttt90) cc_final: 0.7790 (ttt90)
REVERT: C   62 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7151 (mp0)
REVERT: D   62 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7871 (mt-10)
REVERT: E   62 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7688 (mp0)
REVERT: E   63 GLU cc_start: 0.7808 (pt0) cc_final: 0.7249 (tt0)
  outliers start: 5
  outliers final: 2
  residues processed: 50
  average time/residue: 0.1136
  time to fit residues: 6.4821
Evaluate side-chains
  48 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain C residue   70 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0770
   chunk 22 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0770
   chunk 20 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8100

-------------------------------------------------------------------------------
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 = 0.3954 r_free = 0.3954 target = 0.127033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.102850 restraints weight = 4164.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.24
r_work: 0.3530 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3406 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3665  Z= 0.118
  Angle     :  0.610   5.311   4985  Z= 0.322
  Chirality :  0.051   0.132    585
  Planarity :  0.004   0.035    615
  Dihedral  :  5.446  19.307    495
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.03 %
    Favored  : 84.42 %
  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: -2.34 (0.38), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 104 
 TYR   0.017   0.001   TYR C 114 
 PHE   0.009   0.001   PHE A  95 
 TRP   0.003   0.001   TRP C  79 
 HIS   0.002   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3665)
  covalent geometry    : angle       0.61049 ( 4985)
  hydrogen bonds       : bond        0.02479 (   80)
  hydrogen bonds       : angle       4.72637 (  240)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7415 (mt-10)
REVERT: A   70 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7452 (ttpt)
REVERT: C   34 ARG cc_start: 0.8325 (ttt90) cc_final: 0.7819 (ttt90)
REVERT: C   62 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7165 (mp0)
REVERT: C   70 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7818 (ttpt)
REVERT: D   62 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7899 (mt-10)
REVERT: E   62 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7781 (mp0)
REVERT: E   63 GLU cc_start: 0.7844 (pt0) cc_final: 0.7286 (tt0)
  outliers start: 6
  outliers final: 1
  residues processed: 49
  average time/residue: 0.0878
  time to fit residues: 5.0671
Evaluate side-chains
  48 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain C residue   70 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
E  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.115939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.092137 restraints weight = 4403.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.30
r_work: 0.3404 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   3665  Z= 0.252
  Angle     :  0.733   6.465   4985  Z= 0.395
  Chirality :  0.054   0.146    585
  Planarity :  0.004   0.033    615
  Dihedral  :  6.025  20.600    495
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 15.32 %
    Favored  : 83.38 %
  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: -2.47 (0.38), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 104 
 TYR   0.018   0.002   TYR C 114 
 PHE   0.013   0.002   PHE A  95 
 TRP   0.008   0.001   TRP D  79 
 HIS   0.002   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 3665)
  covalent geometry    : angle       0.73295 ( 4985)
  hydrogen bonds       : bond        0.03777 (   80)
  hydrogen bonds       : angle       4.97734 (  240)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   13 MET cc_start: 0.7603 (ttt) cc_final: 0.7324 (tmm)
REVERT: A   62 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7432 (mt-10)
REVERT: A   70 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7711 (ttpp)
REVERT: C   34 ARG cc_start: 0.8416 (ttt90) cc_final: 0.8206 (ttt-90)
REVERT: C   62 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7090 (mp0)
REVERT: D   62 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7939 (mt-10)
REVERT: E   12 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7920 (tt)
REVERT: E   13 MET cc_start: 0.8512 (ttt) cc_final: 0.8274 (ttp)
REVERT: E   62 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7631 (mp0)
REVERT: E   63 GLU cc_start: 0.7851 (pt0) cc_final: 0.7274 (tt0)
  outliers start: 5
  outliers final: 3
  residues processed: 48
  average time/residue: 0.1094
  time to fit residues: 6.1499
Evaluate side-chains
  47 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain C residue   70 LYS
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   28 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0030
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.6792

-------------------------------------------------------------------------------
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 = 0.3969 r_free = 0.3969 target = 0.128382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.104611 restraints weight = 4134.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 2.20
r_work: 0.3538 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3665  Z= 0.110
  Angle     :  0.608   5.194   4985  Z= 0.320
  Chirality :  0.051   0.131    585
  Planarity :  0.004   0.033    615
  Dihedral  :  5.434  19.396    495
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.81 %
    Favored  : 83.90 %
  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: -2.37 (0.38), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 104 
 TYR   0.016   0.001   TYR C 114 
 PHE   0.009   0.001   PHE A  95 
 TRP   0.003   0.001   TRP C  79 
 HIS   0.002   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3665)
  covalent geometry    : angle       0.60839 ( 4985)
  hydrogen bonds       : bond        0.02295 (   80)
  hydrogen bonds       : angle       4.66831 (  240)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   13 MET cc_start: 0.7499 (ttt) cc_final: 0.7231 (tmm)
REVERT: A   62 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7416 (mt-10)
REVERT: C   34 ARG cc_start: 0.8321 (ttt90) cc_final: 0.7845 (ttt90)
REVERT: C   62 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7117 (mp0)
REVERT: C   70 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7788 (ttpt)
REVERT: D   62 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7954 (mt-10)
REVERT: E   62 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7779 (mp0)
REVERT: E   63 GLU cc_start: 0.7784 (pt0) cc_final: 0.7310 (tt0)
  outliers start: 5
  outliers final: 3
  residues processed: 50
  average time/residue: 0.0872
  time to fit residues: 5.1545
Evaluate side-chains
  49 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain C residue   70 LYS
Chi-restraints excluded: chain E residue   28 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0670
   overall best weight:    1.6126

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

Flipped N/Q/H residues before XYZ refinement:
E  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.123146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.099569 restraints weight = 4278.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.20
r_work: 0.3454 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3665  Z= 0.184
  Angle     :  0.689   7.594   4985  Z= 0.366
  Chirality :  0.052   0.143    585
  Planarity :  0.004   0.034    615
  Dihedral  :  5.790  20.354    495
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.58 %
    Favored  : 83.38 %
  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: -2.41 (0.38), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 104 
 TYR   0.018   0.002   TYR C 114 
 PHE   0.011   0.002   PHE A  95 
 TRP   0.005   0.001   TRP D  79 
 HIS   0.002   0.001   HIS E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 3665)
  covalent geometry    : angle       0.68878 ( 4985)
  hydrogen bonds       : bond        0.03181 (   80)
  hydrogen bonds       : angle       4.77194 (  240)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   13 MET cc_start: 0.7519 (ttt) cc_final: 0.7252 (tmm)
REVERT: A   62 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7351 (mt-10)
REVERT: A   70 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7488 (ttpt)
REVERT: C   34 ARG cc_start: 0.8398 (ttt90) cc_final: 0.7890 (ttt90)
REVERT: C   62 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7094 (mp0)
REVERT: C   70 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7921 (ttpt)
REVERT: D   62 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7967 (mt-10)
REVERT: E   13 MET cc_start: 0.8551 (ttt) cc_final: 0.8316 (ttp)
REVERT: E   62 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7774 (mp0)
REVERT: E   63 GLU cc_start: 0.7841 (pt0) cc_final: 0.7395 (tt0)
  outliers start: 4
  outliers final: 2
  residues processed: 45
  average time/residue: 0.1431
  time to fit residues: 7.4312
Evaluate side-chains
  45 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain C residue   70 LYS
Chi-restraints excluded: chain E residue   28 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.124423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.100854 restraints weight = 4201.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.18
r_work: 0.3475 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3665  Z= 0.155
  Angle     :  0.668   7.569   4985  Z= 0.354
  Chirality :  0.052   0.136    585
  Planarity :  0.004   0.033    615
  Dihedral  :  5.656  19.822    495
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 15.06 %
    Favored  : 83.64 %
  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: -2.37 (0.38), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 104 
 TYR   0.017   0.002   TYR C 114 
 PHE   0.010   0.002   PHE A  95 
 TRP   0.004   0.001   TRP C  79 
 HIS   0.002   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 3665)
  covalent geometry    : angle       0.66789 ( 4985)
  hydrogen bonds       : bond        0.02885 (   80)
  hydrogen bonds       : angle       4.70270 (  240)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 983.77 seconds
wall clock time: 17 minutes 30.99 seconds (1050.99 seconds total)