Starting phenix.real_space_refine
on Tue Feb  3 14:14:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d27_46487/02_2026/9d27_46487.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d27_46487/02_2026/9d27_46487.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d27_46487/02_2026/9d27_46487.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d27_46487/02_2026/9d27_46487.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d27_46487/02_2026/9d27_46487.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d27_46487/02_2026/9d27_46487.cif"
  }
  resolution = 3.19
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       5      5.16       5
     C    2285      2.51       5
     N     580      2.21       5
     O     655      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  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: 3525
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 705
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 4, 'TRANS': 85}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.37, per 1000 atoms: 0.10
  Number of scatterers: 3525
  At special positions: 0
  Unit cell: (76.626, 78.518, 41.624, 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     655      8.00
     N     580      7.00
     C    2285      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: 0.15
  Conformation dependent library (CDL) restraints added in 82.2 milliseconds
  

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  860

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 35.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16
      removed outlier: 6.412A  pdb=" N   VAL A  14 " --> pdb=" O   LYS C  15 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   VAL C  14 " --> pdb=" O   LYS E  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 28 through 32
      removed outlier: 6.463A  pdb=" N   VAL A  28 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 8.172A  pdb=" N   HIS C  31 " --> pdb=" O   VAL A  28 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   VAL A  30 " --> pdb=" O   HIS C  31 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   VAL C  28 " --> pdb=" O   ALA E  29 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   HIS E  31 " --> pdb=" O   VAL C  28 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   VAL C  30 " --> pdb=" O   HIS E  31 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 64 through 68
      removed outlier: 9.221A  pdb=" N   PHE B  64 " --> pdb=" O   VAL D  65 " (cutoff:3.500A)
      removed outlier: 9.251A  pdb=" N   GLY D  67 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 5.805A  pdb=" N   GLU B  66 " --> pdb=" O   GLY D  67 " (cutoff:3.500A)
      removed outlier: 9.225A  pdb=" N   PHE A  64 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
      removed outlier: 9.258A  pdb=" N   GLY B  67 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   GLU A  66 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   VAL A  65 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   GLU C  66 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   VAL C  65 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   GLU E  66 " --> pdb=" O   VAL C  65 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 71 through 75
      removed outlier: 6.561A  pdb=" N   VAL B  71 " --> pdb=" O   GLU D  72 " (cutoff:3.500A)
      removed outlier: 8.225A  pdb=" N   ASP D  74 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 8.444A  pdb=" N   ILE B  73 " --> pdb=" O   ASP D  74 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL A  71 " --> pdb=" O   GLU B  72 " (cutoff:3.500A)
      removed outlier: 8.220A  pdb=" N   ASP B  74 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 8.424A  pdb=" N   ILE A  73 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   THR C  75 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   THR E  75 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 89 through 99
      removed outlier: 6.545A  pdb=" N   GLU B  89 " --> pdb=" O   HIS D  90 " (cutoff:3.500A)
      removed outlier: 8.468A  pdb=" N   GLU D  92 " --> pdb=" O   GLU B  89 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   ALA B  91 " --> pdb=" O   GLU D  92 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   VAL D  94 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   VAL B  93 " --> pdb=" O   VAL D  94 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   THR D  96 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   PHE B  95 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   ASN D  98 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   ALA B  97 " --> pdb=" O   ASN D  98 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   GLU A  89 " --> pdb=" O   HIS B  90 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   GLU B  92 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   ALA A  91 " --> pdb=" O   GLU B  92 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   VAL B  94 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   VAL A  93 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   THR B  96 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   PHE A  95 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   ASN B  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   ALA A  97 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   HIS A  90 " --> pdb=" O   GLU C  89 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA C  91 " --> pdb=" O   HIS A  90 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   HIS C  90 " --> pdb=" O   GLU E  89 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA E  91 " --> pdb=" O   HIS C  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 105 through 107
      removed outlier: 6.315A  pdb=" N   THR A 106 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   THR C 106 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 114 through 115
      removed outlier: 6.957A  pdb=" N   TYR A 114 " --> pdb=" O   SER C 115 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   TYR C 114 " --> pdb=" O   SER E 115 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 122
      removed outlier: 6.850A  pdb=" N   THR A 119 " --> pdb=" O   ALA C 120 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   VAL C 122 " --> pdb=" O   THR A 119 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   VAL A 121 " --> pdb=" O   VAL C 122 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   THR C 119 " --> pdb=" O   ALA E 120 " (cutoff:3.500A)
      removed outlier: 8.315A  pdb=" N   VAL E 122 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   VAL C 121 " --> pdb=" O   VAL E 122 " (cutoff:3.500A)

    54 hydrogen bonds defined for protein.
    162 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: 0.29

  Time building geometry restraints manager: 0.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1100
        1.34 -     1.45: 497
        1.45 -     1.57: 1998
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 3605
  Sorted by residual:
  bond pdb=" CA  ARG B 103 "
       pdb=" CB  ARG B 103 "
    ideal  model  delta    sigma   weight residual
    1.535  1.524  0.011 1.93e-02 2.68e+03 3.46e-01
  bond pdb=" CB  ILE A  26 "
       pdb=" CG2 ILE A  26 "
    ideal  model  delta    sigma   weight residual
    1.521  1.502  0.019 3.30e-02 9.18e+02 3.37e-01
  bond pdb=" CB  ILE D  26 "
       pdb=" CG2 ILE D  26 "
    ideal  model  delta    sigma   weight residual
    1.521  1.502  0.019 3.30e-02 9.18e+02 3.35e-01
  bond pdb=" CB  ILE C  26 "
       pdb=" CG2 ILE C  26 "
    ideal  model  delta    sigma   weight residual
    1.521  1.502  0.019 3.30e-02 9.18e+02 3.34e-01
  bond pdb=" CA  ARG A 103 "
       pdb=" CB  ARG A 103 "
    ideal  model  delta    sigma   weight residual
    1.535  1.524  0.011 1.93e-02 2.68e+03 3.24e-01
  ... (remaining 3600 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.70: 4090
        0.70 -     1.40: 651
        1.40 -     2.10: 109
        2.10 -     2.81: 34
        2.81 -     3.51: 21
  Bond angle restraints: 4905
  Sorted by residual:
  angle pdb=" C   PRO C 113 "
        pdb=" N   TYR C 114 "
        pdb=" CA  TYR C 114 "
      ideal   model   delta    sigma   weight residual
     122.29  119.48    2.81 1.65e+00 3.67e-01 2.90e+00
  angle pdb=" C   PRO E 113 "
        pdb=" N   TYR E 114 "
        pdb=" CA  TYR E 114 "
      ideal   model   delta    sigma   weight residual
     122.29  119.49    2.80 1.65e+00 3.67e-01 2.87e+00
  angle pdb=" C   PRO B 113 "
        pdb=" N   TYR B 114 "
        pdb=" CA  TYR B 114 "
      ideal   model   delta    sigma   weight residual
     122.29  119.50    2.79 1.65e+00 3.67e-01 2.87e+00
  angle pdb=" C   PRO D 113 "
        pdb=" N   TYR D 114 "
        pdb=" CA  TYR D 114 "
      ideal   model   delta    sigma   weight residual
     122.29  119.50    2.79 1.65e+00 3.67e-01 2.86e+00
  angle pdb=" C   PRO A 113 "
        pdb=" N   TYR A 114 "
        pdb=" CA  TYR A 114 "
      ideal   model   delta    sigma   weight residual
     122.29  119.52    2.77 1.65e+00 3.67e-01 2.81e+00
  ... (remaining 4900 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.65: 1825
       15.65 -    31.30: 210
       31.30 -    46.95: 55
       46.95 -    62.59: 30
       62.59 -    78.24: 5
  Dihedral angle restraints: 2125
    sinusoidal: 800
      harmonic: 1325
  Sorted by residual:
  dihedral pdb=" CA  ASP C  99 "
           pdb=" CB  ASP C  99 "
           pdb=" CG  ASP C  99 "
           pdb=" OD1 ASP C  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.23   58.23     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CA  ASP A  99 "
           pdb=" CB  ASP A  99 "
           pdb=" CG  ASP A  99 "
           pdb=" OD1 ASP A  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.19   58.19     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CA  ASP D  99 "
           pdb=" CB  ASP D  99 "
           pdb=" CG  ASP D  99 "
           pdb=" OD1 ASP D  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.18   58.18     1      2.00e+01 2.50e-03 1.13e+01
  ... (remaining 2122 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 266
       0.030 -    0.059: 212
       0.059 -    0.089: 30
       0.089 -    0.118: 58
       0.118 -    0.148: 14
  Chirality restraints: 580
  Sorted by residual:
  chirality pdb=" CA  VAL C  65 "
            pdb=" N   VAL C  65 "
            pdb=" C   VAL C  65 "
            pdb=" CB  VAL C  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.48e-01
  chirality pdb=" CA  VAL D  65 "
            pdb=" N   VAL D  65 "
            pdb=" C   VAL D  65 "
            pdb=" CB  VAL D  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.38e-01
  chirality pdb=" CA  VAL B  65 "
            pdb=" N   VAL B  65 "
            pdb=" C   VAL B  65 "
            pdb=" CB  VAL B  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.28e-01
  ... (remaining 577 not shown)

  Planarity restraints: 605
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 114 "   -0.011 2.00e-02 2.50e+03   8.23e-03 1.36e+00
        pdb=" CG  TYR D 114 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 114 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 114 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 114 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 114 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 114 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR D 114 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D  85 "   -0.019 5.00e-02 4.00e+02   2.86e-02 1.31e+00
        pdb=" N   PRO D  86 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO D  86 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D  86 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 114 "   -0.010 2.00e-02 2.50e+03   8.06e-03 1.30e+00
        pdb=" CG  TYR A 114 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 114 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 114 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 114 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 114 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 114 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 114 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 602 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 50
        2.68 -     3.23: 3070
        3.23 -     3.79: 5144
        3.79 -     4.34: 6664
        4.34 -     4.90: 11542
  Nonbonded interactions: 26470
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D  74 "
            pdb=" OH  TYR D 105 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" OD2 ASP A  74 "
            pdb=" OH  TYR A 105 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OD2 ASP C  74 "
            pdb=" OH  TYR C 105 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OD2 ASP B  74 "
            pdb=" OH  TYR B 105 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" OD2 ASP E  74 "
            pdb=" OH  TYR E 105 "
     model   vdw
     2.125 3.040
  ... (remaining 26465 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:             1.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.690
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.010
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   3605  Z= 0.190
  Angle     :  0.592   3.508   4905  Z= 0.340
  Chirality :  0.051   0.148    580
  Planarity :  0.004   0.029    605
  Dihedral  : 16.576  78.241   1265
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.74 %
    Favored  : 80.26 %
  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: -2.57 (0.32), residues: 430
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.24), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 103 
 TYR   0.020   0.002   TYR D 114 
 PHE   0.010   0.002   PHE B  95 
 TRP   0.004   0.001   TRP B  79 
 HIS   0.006   0.002   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 3605)
  covalent geometry    : angle       0.59151 ( 4905)
  hydrogen bonds       : bond        0.20016 (   54)
  hydrogen bonds       : angle       8.60146 (  162)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.131 
Fit side-chains
REVERT: B   17 LEU cc_start: 0.7879 (mt) cc_final: 0.7492 (mt)
REVERT: B   62 GLU cc_start: 0.7153 (tt0) cc_final: 0.6949 (mt-10)
REVERT: D   23 SER cc_start: 0.8625 (m) cc_final: 0.8136 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0598
  time to fit residues: 3.9942
Evaluate side-chains
  46 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.2980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B  31 HIS
C  31 HIS
E  31 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.171371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.145386 restraints weight = 4019.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.4324 rms_B_bonded: 2.83
r_work: 0.4218 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.4218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   3605  Z= 0.160
  Angle     :  0.582   4.992   4905  Z= 0.312
  Chirality :  0.050   0.139    580
  Planarity :  0.004   0.032    605
  Dihedral  :  5.208  15.642    485
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 15.00 %
    Favored  : 80.79 %
  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: -2.42 (0.34), residues: 430
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.26), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 104 
 TYR   0.029   0.002   TYR B 114 
 PHE   0.009   0.001   PHE E  64 
 TRP   0.003   0.001   TRP D  79 
 HIS   0.003   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 3605)
  covalent geometry    : angle       0.58207 ( 4905)
  hydrogen bonds       : bond        0.03921 (   54)
  hydrogen bonds       : angle       5.69838 (  162)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6958 (mm-30)
REVERT: A  114 TYR cc_start: 0.9298 (p90) cc_final: 0.8999 (p90)
REVERT: B   62 GLU cc_start: 0.6791 (tt0) cc_final: 0.6277 (mt-10)
REVERT: B   82 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7117 (mp)
REVERT: D   23 SER cc_start: 0.8451 (m) cc_final: 0.7896 (p)
REVERT: D   35 LYS cc_start: 0.8101 (tttt) cc_final: 0.7286 (tptp)
  outliers start: 16
  outliers final: 5
  residues processed: 59
  average time/residue: 0.0341
  time to fit residues: 2.6770
Evaluate side-chains
  53 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.171265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.144629 restraints weight = 4024.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.4364 rms_B_bonded: 2.93
r_work: 0.4212 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3605  Z= 0.187
  Angle     :  0.604   7.436   4905  Z= 0.321
  Chirality :  0.052   0.150    580
  Planarity :  0.004   0.033    605
  Dihedral  :  5.177  14.984    485
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.58 %
    Favored  : 80.53 %
  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: -2.52 (0.34), residues: 430
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.26), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 103 
 TYR   0.041   0.002   TYR B 114 
 PHE   0.008   0.001   PHE A  95 
 TRP   0.004   0.001   TRP D  79 
 HIS   0.005   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 3605)
  covalent geometry    : angle       0.60440 ( 4905)
  hydrogen bonds       : bond        0.03840 (   54)
  hydrogen bonds       : angle       5.45927 (  162)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.134 
Fit side-chains
REVERT: B   62 GLU cc_start: 0.7102 (tt0) cc_final: 0.6666 (mt-10)
REVERT: B  114 TYR cc_start: 0.9233 (p90) cc_final: 0.8798 (p90)
REVERT: C   17 LEU cc_start: 0.7556 (mt) cc_final: 0.7316 (mt)
REVERT: C   35 LYS cc_start: 0.7622 (ttmm) cc_final: 0.7059 (tptp)
REVERT: D   23 SER cc_start: 0.8784 (m) cc_final: 0.8258 (p)
REVERT: D   35 LYS cc_start: 0.8156 (tttt) cc_final: 0.7476 (tptp)
REVERT: D   62 GLU cc_start: 0.7347 (tt0) cc_final: 0.7005 (mt-10)
REVERT: E   21 ARG cc_start: 0.7411 (ttp80) cc_final: 0.5796 (mmt180)
  outliers start: 11
  outliers final: 7
  residues processed: 54
  average time/residue: 0.0655
  time to fit residues: 4.5266
Evaluate side-chains
  52 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 24 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4694 r_free = 0.4694 target = 0.178003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.152086 restraints weight = 3959.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.4435 rms_B_bonded: 2.90
r_work: 0.4291 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.4291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3605  Z= 0.112
  Angle     :  0.525   5.599   4905  Z= 0.277
  Chirality :  0.050   0.133    580
  Planarity :  0.004   0.030    605
  Dihedral  :  4.740  14.081    485
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 19.47 %
    Favored  : 78.16 %
  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: -2.44 (0.35), residues: 430
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG D  21 
 TYR   0.030   0.002   TYR B 114 
 PHE   0.008   0.001   PHE A  95 
 TRP   0.002   0.001   TRP D  79 
 HIS   0.003   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3605)
  covalent geometry    : angle       0.52463 ( 4905)
  hydrogen bonds       : bond        0.02611 (   54)
  hydrogen bonds       : angle       4.87847 (  162)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.130 
Fit side-chains
REVERT: B   18 ASP cc_start: 0.8290 (m-30) cc_final: 0.7898 (t0)
REVERT: B   35 LYS cc_start: 0.7446 (tttt) cc_final: 0.6878 (tptp)
REVERT: B   62 GLU cc_start: 0.7071 (tt0) cc_final: 0.6636 (mt-10)
REVERT: B  114 TYR cc_start: 0.9268 (p90) cc_final: 0.8894 (p90)
REVERT: C   35 LYS cc_start: 0.7658 (ttmm) cc_final: 0.6999 (tptp)
REVERT: D   17 LEU cc_start: 0.8166 (mt) cc_final: 0.7873 (mt)
REVERT: D   23 SER cc_start: 0.8682 (m) cc_final: 0.8181 (p)
REVERT: D   35 LYS cc_start: 0.8036 (tttt) cc_final: 0.7443 (tptp)
REVERT: E   21 ARG cc_start: 0.7397 (ttp80) cc_final: 0.5961 (tpm170)
  outliers start: 9
  outliers final: 6
  residues processed: 51
  average time/residue: 0.0630
  time to fit residues: 4.1302
Evaluate side-chains
  50 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0870
   chunk 2 optimal weight:    0.4980
   chunk 32 optimal weight:    0.4980
   chunk 8 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.4687 r_free = 0.4687 target = 0.176848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.150555 restraints weight = 3911.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.4475 rms_B_bonded: 2.92
r_work: 0.4338 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3605  Z= 0.094
  Angle     :  0.505   8.235   4905  Z= 0.264
  Chirality :  0.049   0.131    580
  Planarity :  0.004   0.028    605
  Dihedral  :  4.456  12.868    485
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 18.95 %
    Favored  : 77.63 %
  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: -2.36 (0.35), residues: 430
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E  34 
 TYR   0.025   0.001   TYR B 114 
 PHE   0.008   0.001   PHE A  95 
 TRP   0.002   0.001   TRP A  79 
 HIS   0.003   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 3605)
  covalent geometry    : angle       0.50466 ( 4905)
  hydrogen bonds       : bond        0.02238 (   54)
  hydrogen bonds       : angle       4.59002 (  162)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.139 
Fit side-chains
REVERT: B   35 LYS cc_start: 0.7458 (tttt) cc_final: 0.6909 (tptp)
REVERT: B   62 GLU cc_start: 0.7025 (tt0) cc_final: 0.6651 (mt-10)
REVERT: B  114 TYR cc_start: 0.9297 (p90) cc_final: 0.8903 (p90)
REVERT: C   35 LYS cc_start: 0.7681 (ttmm) cc_final: 0.6981 (tptp)
REVERT: D   17 LEU cc_start: 0.8179 (mt) cc_final: 0.7936 (mt)
REVERT: D   23 SER cc_start: 0.8656 (m) cc_final: 0.8096 (p)
REVERT: D   35 LYS cc_start: 0.7955 (tttt) cc_final: 0.7422 (tptp)
REVERT: E   21 ARG cc_start: 0.7359 (ttp80) cc_final: 0.5980 (tpm170)
  outliers start: 13
  outliers final: 7
  residues processed: 52
  average time/residue: 0.0606
  time to fit residues: 4.1028
Evaluate side-chains
  50 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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 = 0.4628 r_free = 0.4628 target = 0.176003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.148294 restraints weight = 3970.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.4336 rms_B_bonded: 2.95
r_work: 0.4204 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3605  Z= 0.209
  Angle     :  0.599   7.767   4905  Z= 0.315
  Chirality :  0.052   0.146    580
  Planarity :  0.005   0.033    605
  Dihedral  :  4.984  15.504    485
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.95 %
    Favored  : 78.16 %
  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: -2.48 (0.35), residues: 430
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  34 
 TYR   0.026   0.002   TYR B 114 
 PHE   0.009   0.001   PHE A  95 
 TRP   0.004   0.001   TRP A  79 
 HIS   0.004   0.002   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 3605)
  covalent geometry    : angle       0.59917 ( 4905)
  hydrogen bonds       : bond        0.03343 (   54)
  hydrogen bonds       : angle       5.26363 (  162)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.138 
Fit side-chains
REVERT: B   35 LYS cc_start: 0.7464 (tttt) cc_final: 0.6944 (tptp)
REVERT: B   62 GLU cc_start: 0.6992 (tt0) cc_final: 0.6570 (mt-10)
REVERT: C   35 LYS cc_start: 0.7650 (ttmm) cc_final: 0.6945 (tptp)
REVERT: D   23 SER cc_start: 0.8723 (m) cc_final: 0.8285 (p)
REVERT: D   35 LYS cc_start: 0.8118 (tttt) cc_final: 0.7520 (tptp)
REVERT: D   62 GLU cc_start: 0.7253 (tt0) cc_final: 0.6885 (mt-10)
REVERT: E   21 ARG cc_start: 0.7352 (ttp80) cc_final: 0.5878 (tpm170)
  outliers start: 11
  outliers final: 9
  residues processed: 51
  average time/residue: 0.0798
  time to fit residues: 5.0714
Evaluate side-chains
  55 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0010
   chunk 43 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.1390

-------------------------------------------------------------------------------
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 = 0.4659 r_free = 0.4659 target = 0.178794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.151434 restraints weight = 4014.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.4371 rms_B_bonded: 2.94
r_work: 0.4240 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3605  Z= 0.147
  Angle     :  0.557   7.431   4905  Z= 0.293
  Chirality :  0.050   0.137    580
  Planarity :  0.004   0.039    605
  Dihedral  :  4.771  14.677    485
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.26 %
    Favored  : 76.58 %
  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: -2.48 (0.35), residues: 430
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 103 
 TYR   0.046   0.002   TYR B 114 
 PHE   0.009   0.001   PHE A  95 
 TRP   0.003   0.001   TRP D  79 
 HIS   0.004   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3605)
  covalent geometry    : angle       0.55730 ( 4905)
  hydrogen bonds       : bond        0.02986 (   54)
  hydrogen bonds       : angle       4.93399 (  162)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.082 
Fit side-chains
REVERT: B   35 LYS cc_start: 0.7517 (tttt) cc_final: 0.6955 (tptp)
REVERT: B   62 GLU cc_start: 0.7004 (tt0) cc_final: 0.6571 (mt-10)
REVERT: B  114 TYR cc_start: 0.9200 (p90) cc_final: 0.8789 (p90)
REVERT: C   35 LYS cc_start: 0.7676 (ttmm) cc_final: 0.6956 (tptp)
REVERT: D   23 SER cc_start: 0.8678 (m) cc_final: 0.8256 (p)
REVERT: D   35 LYS cc_start: 0.8076 (tttt) cc_final: 0.7525 (tptp)
REVERT: E   21 ARG cc_start: 0.7317 (ttp80) cc_final: 0.5896 (tpm170)
  outliers start: 12
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0474
  time to fit residues: 2.9685
Evaluate side-chains
  53 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    0.1980
   chunk 23 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 11 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.4681 r_free = 0.4681 target = 0.184960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.158286 restraints weight = 3826.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.4399 rms_B_bonded: 2.98
r_work: 0.4267 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3605  Z= 0.108
  Angle     :  0.525   7.209   4905  Z= 0.274
  Chirality :  0.050   0.137    580
  Planarity :  0.004   0.040    605
  Dihedral  :  4.555  14.126    485
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 21.05 %
    Favored  : 76.84 %
  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: -2.43 (0.36), residues: 430
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 104 
 TYR   0.036   0.002   TYR B 114 
 PHE   0.008   0.001   PHE A  95 
 TRP   0.002   0.001   TRP D  79 
 HIS   0.003   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3605)
  covalent geometry    : angle       0.52502 ( 4905)
  hydrogen bonds       : bond        0.02489 (   54)
  hydrogen bonds       : angle       4.66327 (  162)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.080 
Fit side-chains
REVERT: B   35 LYS cc_start: 0.7346 (tttt) cc_final: 0.6831 (tptp)
REVERT: B   62 GLU cc_start: 0.6868 (tt0) cc_final: 0.6454 (mt-10)
REVERT: B  114 TYR cc_start: 0.9191 (p90) cc_final: 0.8817 (p90)
REVERT: C   35 LYS cc_start: 0.7521 (ttmm) cc_final: 0.6870 (tptp)
REVERT: D   23 SER cc_start: 0.8573 (m) cc_final: 0.8158 (p)
REVERT: D   35 LYS cc_start: 0.8036 (tttt) cc_final: 0.7450 (tptp)
REVERT: E   21 ARG cc_start: 0.7149 (ttp80) cc_final: 0.5689 (tpm170)
  outliers start: 8
  outliers final: 8
  residues processed: 47
  average time/residue: 0.0607
  time to fit residues: 3.6658
Evaluate side-chains
  51 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 9 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.4637 r_free = 0.4637 target = 0.176739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.149184 restraints weight = 3957.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.4345 rms_B_bonded: 2.93
r_work: 0.4214 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.4214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3605  Z= 0.187
  Angle     :  0.580   7.172   4905  Z= 0.305
  Chirality :  0.051   0.142    580
  Planarity :  0.005   0.043    605
  Dihedral  :  4.887  14.371    485
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 20.79 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.50 (0.36), residues: 430
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 103 
 TYR   0.040   0.002   TYR B 114 
 PHE   0.009   0.001   PHE A  95 
 TRP   0.004   0.001   TRP B  79 
 HIS   0.004   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 3605)
  covalent geometry    : angle       0.57988 ( 4905)
  hydrogen bonds       : bond        0.03246 (   54)
  hydrogen bonds       : angle       5.05352 (  162)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.136 
Fit side-chains
REVERT: B   35 LYS cc_start: 0.7439 (tttt) cc_final: 0.6935 (tptp)
REVERT: B   62 GLU cc_start: 0.7002 (tt0) cc_final: 0.6591 (mt-10)
REVERT: B  114 TYR cc_start: 0.9245 (p90) cc_final: 0.8828 (p90)
REVERT: C   35 LYS cc_start: 0.7647 (ttmm) cc_final: 0.6968 (tptp)
REVERT: D   23 SER cc_start: 0.8718 (m) cc_final: 0.8300 (p)
REVERT: D   35 LYS cc_start: 0.7989 (tttt) cc_final: 0.7433 (tptp)
REVERT: D   62 GLU cc_start: 0.7189 (tt0) cc_final: 0.6809 (mt-10)
REVERT: E   21 ARG cc_start: 0.7330 (ttp80) cc_final: 0.5894 (tpm170)
  outliers start: 11
  outliers final: 9
  residues processed: 49
  average time/residue: 0.0646
  time to fit residues: 4.0760
Evaluate side-chains
  54 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue  112 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 35 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0030
   chunk 12 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0270
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.4648

-------------------------------------------------------------------------------
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 = 0.4720 r_free = 0.4720 target = 0.186618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.160817 restraints weight = 3879.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.4452 rms_B_bonded: 2.91
r_work: 0.4321 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3605  Z= 0.093
  Angle     :  0.514   7.192   4905  Z= 0.266
  Chirality :  0.049   0.131    580
  Planarity :  0.004   0.039    605
  Dihedral  :  4.464  13.606    485
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 21.32 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.40 (0.36), residues: 430
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 103 
 TYR   0.032   0.001   TYR B 114 
 PHE   0.007   0.001   PHE A  95 
 TRP   0.003   0.001   TRP C  79 
 HIS   0.003   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3605)
  covalent geometry    : angle       0.51387 ( 4905)
  hydrogen bonds       : bond        0.02227 (   54)
  hydrogen bonds       : angle       4.48947 (  162)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.131 
Fit side-chains
REVERT: B   21 ARG cc_start: 0.7391 (ttp80) cc_final: 0.6573 (ttp-110)
REVERT: B   35 LYS cc_start: 0.7351 (tttt) cc_final: 0.6911 (tptp)
REVERT: B   62 GLU cc_start: 0.6916 (tt0) cc_final: 0.6553 (mt-10)
REVERT: B  114 TYR cc_start: 0.9209 (p90) cc_final: 0.8809 (p90)
REVERT: C   35 LYS cc_start: 0.7608 (ttmm) cc_final: 0.6976 (tptp)
REVERT: D   23 SER cc_start: 0.8591 (m) cc_final: 0.8191 (p)
REVERT: D   35 LYS cc_start: 0.7927 (tttt) cc_final: 0.7434 (tptp)
REVERT: E   21 ARG cc_start: 0.7229 (ttp80) cc_final: 0.5783 (tpm170)
  outliers start: 9
  outliers final: 8
  residues processed: 47
  average time/residue: 0.0522
  time to fit residues: 3.1584
Evaluate side-chains
  51 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 20 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0030
   overall best weight:    0.8994

-------------------------------------------------------------------------------
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 = 0.4699 r_free = 0.4699 target = 0.185216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.157883 restraints weight = 3869.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.4409 rms_B_bonded: 2.97
r_work: 0.4275 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3605  Z= 0.126
  Angle     :  0.535   7.064   4905  Z= 0.278
  Chirality :  0.050   0.142    580
  Planarity :  0.004   0.043    605
  Dihedral  :  4.596  13.516    485
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 21.32 %
    Favored  : 76.58 %
  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 (0.36), residues: 430
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 103 
 TYR   0.034   0.002   TYR B 114 
 PHE   0.008   0.001   PHE A  95 
 TRP   0.002   0.001   TRP D  79 
 HIS   0.004   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3605)
  covalent geometry    : angle       0.53464 ( 4905)
  hydrogen bonds       : bond        0.02683 (   54)
  hydrogen bonds       : angle       4.71455 (  162)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 947.36 seconds
wall clock time: 16 minutes 56.47 seconds (1016.47 seconds total)