Starting phenix.real_space_refine
on Wed Jul 30 14:56:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xzy_33534/07_2025/7xzy_33534.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xzy_33534/07_2025/7xzy_33534.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xzy_33534/07_2025/7xzy_33534.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xzy_33534/07_2025/7xzy_33534.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xzy_33534/07_2025/7xzy_33534.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xzy_33534/07_2025/7xzy_33534.cif"
  }
  resolution = 3.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     330      5.49       5
     S      14      5.16       5
     C    7015      2.51       5
     N    2417      2.21       5
     O    3045      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12821
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 844
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 3372
          Classifications: {'DNA': 165}
          Link IDs: {'rna3p': 164}
    Chain: "J"
      Number of atoms: 3393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 3393
          Classifications: {'DNA': 165}
          Link IDs: {'rna3p': 164}
  Time building chain proxies: 7.12, per 1000 atoms: 0.56
  Number of scatterers: 12821
  At special positions: 0
  Unit cell: (127.6, 151.8, 105.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     330     15.00
     O    3045      8.00
     N    2417      7.00
     C    7015      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: 2.80
  Conformation dependent library (CDL) restraints added in 866.3 milliseconds
  

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1420

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      73.5% alpha, 2.4% beta
      163 base pairs and 262 stacking pairs defined.
    Time for finding SS restraints: 5.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.654A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.345A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.175A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 4.127A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
      removed outlier: 3.536A  pdb=" N   ALA D 121 " --> pdb=" O   LYS D 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.519A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 23 through 29
      removed outlier: 4.152A  pdb=" N   ILE F  26 " --> pdb=" O   ARG F  23 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.723A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.306A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 122
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.699A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.602A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
      removed outlier: 4.222A  pdb=" N   ILE C  78 " --> pdb=" O   GLY D  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101
      removed outlier: 3.639A  pdb=" N   THR C 101 " --> pdb=" O   THR F  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.771A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.555A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
      removed outlier: 3.735A  pdb=" N   ILE G  78 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    410 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      423 hydrogen bonds
      842 hydrogen bond angles
      0 basepair planarities
      163 basepair parallelities
      262 stacking parallelities
  Total time for adding SS restraints: 4.40

  Time building geometry restraints manager: 3.40 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2094
        1.33 -     1.45: 4796
        1.45 -     1.57: 6152
        1.57 -     1.69: 658
        1.69 -     1.81: 24
  Bond restraints: 13724
  Sorted by residual:
  bond pdb=" N   ILE H  66 "
       pdb=" CA  ILE H  66 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.038 1.17e-02 7.31e+03 1.04e+01
  bond pdb=" N   ASN H  81 "
       pdb=" CA  ASN H  81 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.26e-02 6.30e+03 8.21e+00
  bond pdb=" N   ILE G  87 "
       pdb=" CA  ILE G  87 "
    ideal  model  delta    sigma   weight residual
    1.460  1.491 -0.031 1.21e-02 6.83e+03 6.56e+00
  bond pdb=" N   ILE D  66 "
       pdb=" CA  ILE D  66 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 1.17e-02 7.31e+03 6.21e+00
  bond pdb=" N   LYS C 118 "
       pdb=" CA  LYS C 118 "
    ideal  model  delta    sigma   weight residual
    1.454  1.480 -0.026 1.23e-02 6.61e+03 4.51e+00
  ... (remaining 13719 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 19164
        1.62 -     3.24: 711
        3.24 -     4.87: 51
        4.87 -     6.49: 15
        6.49 -     8.11: 7
  Bond angle restraints: 19948
  Sorted by residual:
  angle pdb=" CA  ILE D  66 "
        pdb=" C   ILE D  66 "
        pdb=" O   ILE D  66 "
      ideal   model   delta    sigma   weight residual
     121.17  117.11    4.06 1.06e+00 8.90e-01 1.47e+01
  angle pdb=" N   ILE D  66 "
        pdb=" CA  ILE D  66 "
        pdb=" C   ILE D  66 "
      ideal   model   delta    sigma   weight residual
     110.42  107.00    3.42 9.60e-01 1.09e+00 1.27e+01
  angle pdb=" C   THR A  80 "
        pdb=" N   ASP A  81 "
        pdb=" CA  ASP A  81 "
      ideal   model   delta    sigma   weight residual
     121.54  128.31   -6.77 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" CA  GLU A  73 "
        pdb=" CB  GLU A  73 "
        pdb=" CG  GLU A  73 "
      ideal   model   delta    sigma   weight residual
     114.10  121.03   -6.93 2.00e+00 2.50e-01 1.20e+01
  angle pdb=" C   ALA C  86 "
        pdb=" N   ILE C  87 "
        pdb=" CA  ILE C  87 "
      ideal   model   delta    sigma   weight residual
     120.56  116.25    4.31 1.28e+00 6.10e-01 1.14e+01
  ... (remaining 19943 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4731
       17.96 -    35.91: 1186
       35.91 -    53.87: 1116
       53.87 -    71.82: 317
       71.82 -    89.78: 23
  Dihedral angle restraints: 7373
    sinusoidal: 5169
      harmonic: 2204
  Sorted by residual:
  dihedral pdb=" CA  ILE B  29 "
           pdb=" C   ILE B  29 "
           pdb=" N   THR B  30 "
           pdb=" CA  THR B  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.93  -16.07     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CA  ILE G  87 "
           pdb=" CB  ILE G  87 "
           pdb=" CG1 ILE G  87 "
           pdb=" CD1 ILE G  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  124.96   55.04     3      1.50e+01 4.44e-03 9.32e+00
  dihedral pdb=" CG  ARG E 128 "
           pdb=" CD  ARG E 128 "
           pdb=" NE  ARG E 128 "
           pdb=" CZ  ARG E 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.82  -41.18     2      1.50e+01 4.44e-03 9.25e+00
  ... (remaining 7370 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 2042
       0.061 -    0.123: 209
       0.123 -    0.184: 10
       0.184 -    0.245: 1
       0.245 -    0.306: 2
  Chirality restraints: 2264
  Sorted by residual:
  chirality pdb=" CB  ILE B  29 "
            pdb=" CA  ILE B  29 "
            pdb=" CG1 ILE B  29 "
            pdb=" CG2 ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.35e+00
  chirality pdb=" CB  ILE F  29 "
            pdb=" CA  ILE F  29 "
            pdb=" CG1 ILE F  29 "
            pdb=" CG2 ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  ILE C  87 "
            pdb=" N   ILE C  87 "
            pdb=" C   ILE C  87 "
            pdb=" CB  ILE C  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 2261 not shown)

  Planarity restraints: 1381
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  64 "    0.016 2.00e-02 2.50e+03   3.15e-02 9.90e+00
        pdb=" C   ASN B  64 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   ASN B  64 "    0.020 2.00e-02 2.50e+03
        pdb=" N   VAL B  65 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  62 "   -0.014 2.00e-02 2.50e+03   2.79e-02 7.76e+00
        pdb=" C   LEU B  62 "    0.048 2.00e-02 2.50e+03
        pdb=" O   LEU B  62 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLU B  63 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  69 "   -0.012 2.00e-02 2.50e+03   2.38e-02 5.67e+00
        pdb=" C   ALA B  69 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ALA B  69 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL B  70 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1378 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 199
        2.63 -     3.20: 10916
        3.20 -     3.76: 24685
        3.76 -     4.33: 30688
        4.33 -     4.90: 43141
  Nonbonded interactions: 109629
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C  39 "
            pdb=" OE1 GLU D  68 "
     model   vdw
     2.062 3.040
  nonbonded pdb=" O   ARG C  20 "
            pdb=" NZ  LYS D 117 "
     model   vdw
     2.080 3.120
  nonbonded pdb=" OG  SER B  47 "
            pdb=" OP1  DC J 105 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" O2   DC I  73 "
            pdb=" N2   DG J 121 "
     model   vdw
     2.162 2.496
  nonbonded pdb=" NH2 ARG H  30 "
            pdb=" OP2  DA I 146 "
     model   vdw
     2.222 3.120
  ... (remaining 109624 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 23 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 13 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 28 through 121)
  selection = (chain 'H' and resid 28 through 121)
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  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:          0.440
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     32.630
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
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   0.041  13724  Z= 0.200
  Angle     :  0.688   8.112  19948  Z= 0.424
  Chirality :  0.039   0.306   2264
  Planarity :  0.005   0.039   1381
  Dihedral  : 27.844  89.778   5953
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.79 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.28), residues: 746
  helix:  1.20 (0.20), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.54 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS E 113 
 PHE   0.018   0.002   PHE G  25 
 TYR   0.023   0.002   TYR C  50 
 ARG   0.005   0.001   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10071 (  833)
  hydrogen bonds       : angle       3.78212 ( 2048)
  covalent geometry    : bond        0.00398 (13724)
  covalent geometry    : angle       0.68759 (19948)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.874 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.9316 (mp) cc_final: 0.9116 (mp)
REVERT: B   59 LYS cc_start: 0.8792 (tttm) cc_final: 0.8221 (tttm)
REVERT: B   63 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7947 (mp0)
REVERT: C   64 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8299 (mm-30)
REVERT: C   92 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7633 (mt-10)
REVERT: G   39 TYR cc_start: 0.7474 (m-10) cc_final: 0.7231 (m-80)
REVERT: G   92 GLU cc_start: 0.8786 (mp0) cc_final: 0.8585 (mp0)
REVERT: H   31 LYS cc_start: 0.8302 (mmmm) cc_final: 0.7980 (mmmt)
REVERT: H   73 GLU cc_start: 0.8204 (tp30) cc_final: 0.7912 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2314
  time to fit residues: 61.0634
Evaluate side-chains
  144 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:   20.0000
   chunk 78 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0670
   chunk 53 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 94 optimal weight:    7.9990
   overall best weight:    0.7320

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
B  75 HIS
D  81 ASN
E  93 GLN
H  81 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.107226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.087353 restraints weight = 86420.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.088695 restraints weight = 48080.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.089537 restraints weight = 33350.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13724  Z= 0.157
  Angle     :  0.576   6.620  19948  Z= 0.342
  Chirality :  0.034   0.152   2264
  Planarity :  0.005   0.051   1381
  Dihedral  : 31.131  89.050   4432
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  :  9.45 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.30), residues: 746
  helix:  2.07 (0.21), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.56 (0.41), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 113 
 PHE   0.018   0.001   PHE E  67 
 TYR   0.017   0.002   TYR F  88 
 ARG   0.006   0.001   ARG C  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04344 (  833)
  hydrogen bonds       : angle       2.92732 ( 2048)
  covalent geometry    : bond        0.00329 (13724)
  covalent geometry    : angle       0.57558 (19948)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 169
  time to evaluate  : 0.936 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7276 (mt-10)
REVERT: B   73 THR cc_start: 0.9314 (m) cc_final: 0.8934 (t)
REVERT: E   67 PHE cc_start: 0.8572 (t80) cc_final: 0.8314 (t80)
REVERT: F   81 VAL cc_start: 0.8803 (t) cc_final: 0.8593 (m)
REVERT: F   93 GLN cc_start: 0.8438 (tp40) cc_final: 0.8134 (tp40)
REVERT: G   33 LEU cc_start: 0.9083 (mm) cc_final: 0.8831 (mm)
REVERT: G   92 GLU cc_start: 0.8961 (mp0) cc_final: 0.8598 (mp0)
REVERT: H   39 TYR cc_start: 0.8404 (t80) cc_final: 0.7949 (t80)
REVERT: H   42 LEU cc_start: 0.9516 (tp) cc_final: 0.9244 (tp)
REVERT: H   65 ASP cc_start: 0.8745 (t70) cc_final: 0.8460 (t0)
  outliers start: 18
  outliers final: 3
  residues processed: 177
  average time/residue: 0.2235
  time to fit residues: 58.8650
Evaluate side-chains
  144 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 141
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain F residue   59 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 103 optimal weight:   20.0000
   chunk 42 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0470
   chunk 38 optimal weight:    0.0070
   chunk 66 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   overall best weight:    0.6102

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.103072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.082643 restraints weight = 86643.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.083924 restraints weight = 48007.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.084716 restraints weight = 33372.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13724  Z= 0.154
  Angle     :  0.563   7.100  19948  Z= 0.333
  Chirality :  0.032   0.147   2264
  Planarity :  0.004   0.052   1381
  Dihedral  : 31.189  89.101   4432
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.44 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.30), residues: 746
  helix:  2.25 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.62 (0.39), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.014   0.001   PHE E  67 
 TYR   0.011   0.002   TYR H  37 
 ARG   0.006   0.001   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04091 (  833)
  hydrogen bonds       : angle       2.79253 ( 2048)
  covalent geometry    : bond        0.00319 (13724)
  covalent geometry    : angle       0.56256 (19948)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 164
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
REVERT: B   73 THR cc_start: 0.9280 (m) cc_final: 0.8926 (t)
REVERT: B   84 MET cc_start: 0.8466 (mmm) cc_final: 0.8237 (mmm)
REVERT: E   50 GLU cc_start: 0.8426 (pt0) cc_final: 0.7955 (pt0)
REVERT: E   67 PHE cc_start: 0.8771 (t80) cc_final: 0.8471 (t80)
REVERT: F   34 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9013 (mp)
REVERT: F   93 GLN cc_start: 0.8683 (tp40) cc_final: 0.8469 (tp40)
REVERT: G   36 LYS cc_start: 0.9126 (tppt) cc_final: 0.8837 (tppt)
REVERT: G   56 GLU cc_start: 0.8513 (tt0) cc_final: 0.8255 (tt0)
REVERT: G   92 GLU cc_start: 0.8863 (mp0) cc_final: 0.8463 (mp0)
REVERT: H   65 ASP cc_start: 0.8777 (t70) cc_final: 0.8376 (t0)
  outliers start: 9
  outliers final: 4
  residues processed: 170
  average time/residue: 0.2156
  time to fit residues: 54.3468
Evaluate side-chains
  147 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 142
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 103 optimal weight:   20.0000
   chunk 23 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 88 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0170
   chunk 21 optimal weight:    4.9990
   chunk 89 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 29 optimal weight:    6.9990
   overall best weight:    1.1624

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
F  75 HIS
H  81 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.090324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.068409 restraints weight = 84204.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.069517 restraints weight = 46961.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.070240 restraints weight = 33199.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.5279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  13724  Z= 0.172
  Angle     :  0.601   9.581  19948  Z= 0.350
  Chirality :  0.034   0.172   2264
  Planarity :  0.005   0.084   1381
  Dihedral  : 31.135  89.318   4432
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.17 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.30), residues: 746
  helix:  2.24 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.72 (0.40), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  79 
 PHE   0.013   0.001   PHE E  67 
 TYR   0.027   0.002   TYR D  80 
 ARG   0.005   0.001   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04975 (  833)
  hydrogen bonds       : angle       2.89577 ( 2048)
  covalent geometry    : bond        0.00367 (13724)
  covalent geometry    : angle       0.60053 (19948)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   63 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8295 (pt0)
REVERT: C   36 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8747 (tppp)
REVERT: F   34 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9346 (mp)
REVERT: F   93 GLN cc_start: 0.9002 (tp40) cc_final: 0.8783 (tp40)
REVERT: G   50 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8176 (m-80)
REVERT: G   56 GLU cc_start: 0.8529 (tt0) cc_final: 0.8326 (tt0)
REVERT: G   92 GLU cc_start: 0.8790 (mp0) cc_final: 0.8487 (mp0)
REVERT: H   39 TYR cc_start: 0.8423 (t80) cc_final: 0.8057 (t80)
REVERT: H   65 ASP cc_start: 0.8972 (t70) cc_final: 0.8621 (t0)
REVERT: H   73 GLU cc_start: 0.8671 (tp30) cc_final: 0.8402 (tp30)
  outliers start: 19
  outliers final: 10
  residues processed: 160
  average time/residue: 0.2523
  time to fit residues: 57.5783
Evaluate side-chains
  139 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain G residue   50 TYR
Chi-restraints excluded: chain G residue   87 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 58 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 55 optimal weight:    0.1980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.079840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.057586 restraints weight = 84484.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.058602 restraints weight = 46657.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.059275 restraints weight = 32904.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.7472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13724  Z= 0.180
  Angle     :  0.630   9.707  19948  Z= 0.365
  Chirality :  0.034   0.193   2264
  Planarity :  0.005   0.054   1381
  Dihedral  : 31.143  88.467   4432
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 17.48 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.30), residues: 746
  helix:  2.18 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.17 (0.38), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS F  75 
 PHE   0.015   0.001   PHE C  25 
 TYR   0.032   0.002   TYR B  88 
 ARG   0.005   0.001   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04710 (  833)
  hydrogen bonds       : angle       2.98066 ( 2048)
  covalent geometry    : bond        0.00389 (13724)
  covalent geometry    : angle       0.63030 (19948)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8812 (mt-10)
REVERT: C   38 ASN cc_start: 0.8688 (t0) cc_final: 0.8457 (t0)
REVERT: D   90 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8029 (pm20)
REVERT: E   59 GLU cc_start: 0.7900 (pm20) cc_final: 0.7528 (pm20)
REVERT: F   53 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8333 (mp0)
REVERT: G   56 GLU cc_start: 0.8537 (tt0) cc_final: 0.8256 (mt-10)
REVERT: G   92 GLU cc_start: 0.8829 (mp0) cc_final: 0.8550 (mp0)
REVERT: H   39 TYR cc_start: 0.8432 (t80) cc_final: 0.8167 (t80)
REVERT: H   65 ASP cc_start: 0.8962 (t70) cc_final: 0.8646 (t0)
REVERT: H   73 GLU cc_start: 0.8819 (tp30) cc_final: 0.8495 (tp30)
  outliers start: 24
  outliers final: 8
  residues processed: 156
  average time/residue: 0.2683
  time to fit residues: 59.2370
Evaluate side-chains
  131 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 103 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 62 optimal weight:    8.9990
   chunk 102 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 72 optimal weight:   30.0000
   chunk 51 optimal weight:    0.0570
   overall best weight:    4.1904

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
E  93 GLN
F  25 ASN
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  81 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.064563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.041621 restraints weight = 85595.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.042388 restraints weight = 47984.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.042939 restraints weight = 34053.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          1.0907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  13724  Z= 0.271
  Angle     :  0.768  12.986  19948  Z= 0.442
  Chirality :  0.040   0.187   2264
  Planarity :  0.006   0.057   1381
  Dihedral  : 31.575  89.992   4432
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 18.11 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.29), residues: 746
  helix:  1.68 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop : -1.32 (0.39), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS H  79 
 PHE   0.007   0.001   PHE A 104 
 TYR   0.041   0.002   TYR D  80 
 ARG   0.007   0.001   ARG H  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08179 (  833)
  hydrogen bonds       : angle       3.87726 ( 2048)
  covalent geometry    : bond        0.00598 (13724)
  covalent geometry    : angle       0.76772 (19948)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8503 (tptp) cc_final: 0.8276 (tppt)
REVERT: B   50 ILE cc_start: 0.8965 (mm) cc_final: 0.8601 (mm)
REVERT: C   75 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8212 (mmmm)
REVERT: D   90 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8267 (pm20)
REVERT: D   98 LEU cc_start: 0.9360 (mm) cc_final: 0.9154 (mt)
REVERT: E  118 THR cc_start: 0.9492 (m) cc_final: 0.9136 (p)
REVERT: H   81 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8577 (t0)
  outliers start: 26
  outliers final: 11
  residues processed: 152
  average time/residue: 0.2784
  time to fit residues: 58.3879
Evaluate side-chains
  121 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain C residue   50 TYR
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain H residue   81 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 54 optimal weight:    0.4980
   chunk 7 optimal weight:    1.9990
   chunk 93 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 70 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 101 optimal weight:    8.9990
   chunk 100 optimal weight:   10.0000
   overall best weight:    3.8986

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

Flipped N/Q/H residues before XYZ refinement:
D  46 HIS
E 125 GLN
F  75 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.063658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.040971 restraints weight = 84007.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.041895 restraints weight = 45170.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.042533 restraints weight = 31340.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          1.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13724  Z= 0.234
  Angle     :  0.688  13.031  19948  Z= 0.396
  Chirality :  0.036   0.181   2264
  Planarity :  0.005   0.052   1381
  Dihedral  : 31.210  88.994   4432
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 21.57 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.30), residues: 746
  helix:  2.19 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.54 (0.39), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B  75 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.022   0.002   TYR H  80 
 ARG   0.010   0.001   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05651 (  833)
  hydrogen bonds       : angle       3.29174 ( 2048)
  covalent geometry    : bond        0.00522 (13724)
  covalent geometry    : angle       0.68765 (19948)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8286 (tptp) cc_final: 0.8012 (tppt)
REVERT: C   50 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8752 (m-80)
REVERT: C   75 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8258 (mmmm)
REVERT: D   90 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8147 (pm20)
REVERT: E   73 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8751 (tm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 124
  average time/residue: 0.2502
  time to fit residues: 44.4346
Evaluate side-chains
  120 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain C residue   50 TYR
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  118 LYS
Chi-restraints excluded: chain H residue   80 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 102 optimal weight:   10.0000
   chunk 44 optimal weight:    0.4980
   chunk 75 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 72 optimal weight:   40.0000
   chunk 21 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
D  46 HIS
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.065213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.042974 restraints weight = 84540.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.043815 restraints weight = 45083.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.044455 restraints weight = 30735.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          1.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13724  Z= 0.166
  Angle     :  0.645  15.951  19948  Z= 0.369
  Chirality :  0.034   0.174   2264
  Planarity :  0.004   0.055   1381
  Dihedral  : 30.946  89.647   4432
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 23.31 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.31), residues: 746
  helix:  2.37 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.45 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS D  46 
 PHE   0.007   0.001   PHE E  67 
 TYR   0.013   0.001   TYR F  88 
 ARG   0.007   0.000   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04485 (  833)
  hydrogen bonds       : angle       2.92094 ( 2048)
  covalent geometry    : bond        0.00360 (13724)
  covalent geometry    : angle       0.64461 (19948)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8710 (m-10) cc_final: 0.8325 (m-10)
REVERT: C   75 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8190 (mmmm)
REVERT: E   73 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8806 (tm-30)
REVERT: F   91 LYS cc_start: 0.9447 (tttt) cc_final: 0.9209 (tttm)
REVERT: H   90 GLU cc_start: 0.8870 (pm20) cc_final: 0.8477 (pm20)
  outliers start: 10
  outliers final: 2
  residues processed: 130
  average time/residue: 0.2600
  time to fit residues: 48.1638
Evaluate side-chains
  114 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 96 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 83 optimal weight:   10.0000
   overall best weight:    2.1784

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

Flipped N/Q/H residues before XYZ refinement:
D  46 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.063695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.041259 restraints weight = 84506.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.042092 restraints weight = 44669.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.042657 restraints weight = 30598.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          1.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13724  Z= 0.185
  Angle     :  0.669  15.318  19948  Z= 0.380
  Chirality :  0.034   0.179   2264
  Planarity :  0.004   0.050   1381
  Dihedral  : 30.889  89.611   4432
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 23.78 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.32), residues: 746
  helix:  2.44 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -1.53 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS B  75 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.023   0.001   TYR D  80 
 ARG   0.007   0.000   ARG H  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05048 (  833)
  hydrogen bonds       : angle       2.98565 ( 2048)
  covalent geometry    : bond        0.00407 (13724)
  covalent geometry    : angle       0.66851 (19948)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8613 (m-10) cc_final: 0.8094 (m-10)
REVERT: E   73 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8832 (tm-30)
REVERT: E   79 LYS cc_start: 0.8366 (tptp) cc_final: 0.7866 (tttp)
REVERT: E   81 ASP cc_start: 0.8951 (p0) cc_final: 0.8482 (p0)
REVERT: F   53 GLU cc_start: 0.8338 (mp0) cc_final: 0.8125 (mp0)
  outliers start: 11
  outliers final: 7
  residues processed: 117
  average time/residue: 0.2523
  time to fit residues: 42.5622
Evaluate side-chains
  113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  118 LYS
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   80 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0870
   chunk 60 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   overall best weight:    3.4166

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

Flipped N/Q/H residues before XYZ refinement:
D  46 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.061511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.038794 restraints weight = 84979.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.039682 restraints weight = 45595.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.040287 restraints weight = 31384.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          1.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13724  Z= 0.225
  Angle     :  0.723  12.513  19948  Z= 0.409
  Chirality :  0.036   0.193   2264
  Planarity :  0.005   0.048   1381
  Dihedral  : 30.876  89.969   4432
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 23.46 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.32), residues: 746
  helix:  2.37 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -1.70 (0.41), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.021   0.002   HIS D  46 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.031   0.002   TYR D  80 
 ARG   0.007   0.001   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06160 (  833)
  hydrogen bonds       : angle       3.28719 ( 2048)
  covalent geometry    : bond        0.00501 (13724)
  covalent geometry    : angle       0.72332 (19948)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
REVERT: C   64 GLU cc_start: 0.9025 (tt0) cc_final: 0.8704 (tm-30)
REVERT: E   73 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8924 (tm-30)
REVERT: E   79 LYS cc_start: 0.8502 (tptp) cc_final: 0.8204 (tttm)
REVERT: E   81 ASP cc_start: 0.8902 (p0) cc_final: 0.8689 (p0)
REVERT: F   31 LYS cc_start: 0.8783 (tttt) cc_final: 0.8559 (ttpp)
REVERT: H   90 GLU cc_start: 0.8953 (pm20) cc_final: 0.8647 (pm20)
  outliers start: 9
  outliers final: 6
  residues processed: 112
  average time/residue: 0.2545
  time to fit residues: 40.9453
Evaluate side-chains
  110 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  118 LYS
Chi-restraints excluded: chain H residue   80 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0000
   chunk 26 optimal weight:   20.0000
   chunk 3 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 71 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   overall best weight:    2.1992

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

Flipped N/Q/H residues before XYZ refinement:
D  46 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.062496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.040053 restraints weight = 84544.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.040961 restraints weight = 45042.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.041598 restraints weight = 30727.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start:          1.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13724  Z= 0.186
  Angle     :  0.685  17.443  19948  Z= 0.387
  Chirality :  0.034   0.177   2264
  Planarity :  0.004   0.050   1381
  Dihedral  : 30.758  89.664   4432
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 23.78 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.32), residues: 746
  helix:  2.45 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.68 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.008   0.001   PHE C  25 
 TYR   0.033   0.002   TYR D  80 
 ARG   0.006   0.000   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05029 (  833)
  hydrogen bonds       : angle       3.00076 ( 2048)
  covalent geometry    : bond        0.00411 (13724)
  covalent geometry    : angle       0.68540 (19948)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4117.28 seconds
wall clock time: 71 minutes 49.20 seconds (4309.20 seconds total)