Starting phenix.real_space_refine
on Wed Sep 17 20:47:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c4c_45181/09_2025/9c4c_45181.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c4c_45181/09_2025/9c4c_45181.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c4c_45181/09_2025/9c4c_45181.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c4c_45181/09_2025/9c4c_45181.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c4c_45181/09_2025/9c4c_45181.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c4c_45181/09_2025/9c4c_45181.map"
  }
  resolution = 3.09
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.023
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: 7
    Type Number    sf(0)   Gaussians
     Mn      8      7.51       5
     P      77      5.49       5
     S      12      5.16       5
     C    3622      2.51       5
     N    1028      2.21       5
     O    1329      1.98       5
     H    5414      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11490
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 1241
          Classifications: {'DNA': 39}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 38}
    Chain: "B"
      Number of atoms: 1215
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 1215
          Classifications: {'DNA': 38}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 37}
    Chain: "E"
      Number of atoms: 2264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 2264
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 2, 'TRANS': 133}
    Chain: "F"
      Number of atoms: 2249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 2249
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "G"
      Number of atoms: 2249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 2249
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "H"
      Number of atoms: 2264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 2264
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 2, 'TRANS': 133}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "G"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "H"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.52, per 1000 atoms: 0.22
  Number of scatterers: 11490
  At special positions: 0
  Unit cell: (78.8768, 78.8768, 146.771, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Mn      8     24.99
     S      12     16.00
     P      77     15.00
     O    1329      8.00
     N    1028      7.00
     C    3622      6.00
     H    5414      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.26
  Conformation dependent library (CDL) restraints added in 208.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1028

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 4 sheets defined
      81.2% alpha, 4.2% beta
      33 base pairs and 66 stacking pairs defined.
    Time for finding SS restraints: 1.94
  Creating SS restraints...
    Processing helix  chain 'E' and resid 3 through 21
      removed outlier: 4.556A  pdb=" N   TYR E   9 " --> pdb=" O   SER E   5 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ILE E  10 " --> pdb=" O   MET E   6 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 24 through 33
      removed outlier: 3.525A  pdb=" N   ILE E  28 " --> pdb=" O   ARG E  24 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 35 through 48
      removed outlier: 3.596A  pdb=" N   VAL E  39 " --> pdb=" O   HIS E  35 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LYS E  45 " --> pdb=" O   LYS E  41 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LYS E  48 " --> pdb=" O   GLN E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 87
      removed outlier: 3.854A  pdb=" N   LYS E  68 " --> pdb=" O   SER E  64 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE E  69 " --> pdb=" O   LYS E  65 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LYS E  71 " --> pdb=" O   LYS E  67 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG E  72 " --> pdb=" O   LYS E  68 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 92
      No H-bonds generated for 'chain 'E' and resid 90 through 92'
    Processing helix  chain 'E' and resid 93 through 102
    Processing helix  chain 'E' and resid 106 through 122
    Processing helix  chain 'E' and resid 123 through 137
      removed outlier: 4.214A  pdb=" N   LYS E 127 " --> pdb=" O   ASP E 123 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LYS E 135 " --> pdb=" O   LYS E 131 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   THR E 137 " --> pdb=" O   ILE E 133 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 4 through 21
      removed outlier: 3.527A  pdb=" N   ASP F   8 " --> pdb=" O   PRO F   4 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   TYR F   9 " --> pdb=" O   SER F   5 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ILE F  10 " --> pdb=" O   MET F   6 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 33
    Processing helix  chain 'F' and resid 35 through 47
      removed outlier: 3.533A  pdb=" N   VAL F  39 " --> pdb=" O   HIS F  35 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS F  45 " --> pdb=" O   LYS F  41 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 63 through 88
      removed outlier: 3.529A  pdb=" N   LYS F  68 " --> pdb=" O   SER F  64 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ARG F  72 " --> pdb=" O   LYS F  68 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY F  88 " --> pdb=" O   LEU F  84 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 93 through 102
    Processing helix  chain 'F' and resid 106 through 122
    Processing helix  chain 'F' and resid 124 through 135
      removed outlier: 3.561A  pdb=" N   LYS F 128 " --> pdb=" O   ASP F 124 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 4 through 21
      removed outlier: 4.082A  pdb=" N   TYR G   9 " --> pdb=" O   SER G   5 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 24 through 33
      removed outlier: 3.816A  pdb=" N   GLU G  30 " --> pdb=" O   SER G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 35 through 47
      removed outlier: 3.683A  pdb=" N   VAL G  39 " --> pdb=" O   HIS G  35 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LYS G  45 " --> pdb=" O   LYS G  41 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 63 through 88
      removed outlier: 3.595A  pdb=" N   LYS G  68 " --> pdb=" O   SER G  64 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ILE G  69 " --> pdb=" O   LYS G  65 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ARG G  72 " --> pdb=" O   LYS G  68 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 92
      No H-bonds generated for 'chain 'G' and resid 90 through 92'
    Processing helix  chain 'G' and resid 93 through 102
      removed outlier: 3.565A  pdb=" N   GLU G  99 " --> pdb=" O   TYR G  95 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY G 100 " --> pdb=" O   ASN G  96 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 103 through 105
      No H-bonds generated for 'chain 'G' and resid 103 through 105'
    Processing helix  chain 'G' and resid 106 through 122
      removed outlier: 3.733A  pdb=" N   GLN G 118 " --> pdb=" O   GLY G 114 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   PHE G 120 " --> pdb=" O   LEU G 116 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 123 through 136
      removed outlier: 4.047A  pdb=" N   LYS G 127 " --> pdb=" O   ASP G 123 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LYS G 128 " --> pdb=" O   ASP G 124 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LYS G 131 " --> pdb=" O   LYS G 127 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LYS G 136 " --> pdb=" O   SER G 132 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 3 through 5
      No H-bonds generated for 'chain 'H' and resid 3 through 5'
    Processing helix  chain 'H' and resid 6 through 21
      removed outlier: 4.518A  pdb=" N   ILE H  10 " --> pdb=" O   MET H   6 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 26 through 31
      removed outlier: 3.919A  pdb=" N   GLU H  30 " --> pdb=" O   SER H  26 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA H  31 " --> pdb=" O   ASP H  27 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 26 through 31'
    Processing helix  chain 'H' and resid 35 through 48
      removed outlier: 3.888A  pdb=" N   VAL H  39 " --> pdb=" O   HIS H  35 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   LYS H  48 " --> pdb=" O   GLN H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 63 through 88
      removed outlier: 3.955A  pdb=" N   LYS H  68 " --> pdb=" O   SER H  64 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.778A  pdb=" N   ILE H  94 " --> pdb=" O   ASP H  90 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   TYR H  95 " --> pdb=" O   GLU H  91 " (cutoff:3.500A)
      removed outlier: 5.723A  pdb=" N   ASN H  96 " --> pdb=" O   GLU H  92 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 106 through 120
      removed outlier: 3.514A  pdb=" N   GLY H 114 " --> pdb=" O   ILE H 110 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP H 115 " --> pdb=" O   ASP H 111 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU H 116 " --> pdb=" O   ARG H 112 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   PHE H 120 " --> pdb=" O   LEU H 116 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 124 through 137
      removed outlier: 3.889A  pdb=" N   LYS H 128 " --> pdb=" O   ASP H 124 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR H 137 " --> pdb=" O   ILE H 133 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 52 through 54
    Processing sheet with id=AA2, first strand: chain 'F' and resid 52 through 55
    Processing sheet with id=AA3, first strand: chain 'G' and resid 52 through 55
    Processing sheet with id=AA4, first strand: chain 'H' and resid 52 through 55
      removed outlier: 6.470A  pdb=" N   ILE H  53 " --> pdb=" O   LEU H  60 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   LEU H  60 " --> pdb=" O   ILE H  53 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   GLU H  55 " --> pdb=" O   ARG H  58 " (cutoff:3.500A)

    275 hydrogen bonds defined for protein.
    816 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      75 hydrogen bonds
      150 hydrogen bond angles
      0 basepair planarities
      33 basepair parallelities
      66 stacking parallelities
  Total time for adding SS restraints: 2.50

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 5414
        1.03 -     1.22: 32
        1.22 -     1.42: 2651
        1.42 -     1.61: 3621
        1.61 -     1.81: 26
  Bond restraints: 11744
  Sorted by residual:
  bond pdb=" N   THR H   3 "
       pdb=" CA  THR H   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.03e+00
  bond pdb=" N   THR F   3 "
       pdb=" CA  THR F   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.92e+00
  bond pdb=" N   THR E   3 "
       pdb=" CA  THR E   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.86e+00
  bond pdb=" N   THR G   3 "
       pdb=" CA  THR G   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.56e+00
  bond pdb=" N   THR E   3 "
       pdb=" H   THR E   3 "
    ideal  model  delta    sigma   weight residual
    0.860  0.891 -0.031 2.00e-02 2.50e+03 2.47e+00
  ... (remaining 11739 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 20627
        1.74 -     3.47: 668
        3.47 -     5.21: 23
        5.21 -     6.94: 2
        6.94 -     8.68: 1
  Bond angle restraints: 21321
  Sorted by residual:
  angle pdb=" CA  MET H   6 "
        pdb=" CB  MET H   6 "
        pdb=" CG  MET H   6 "
      ideal   model   delta    sigma   weight residual
     114.10  120.17   -6.07 2.00e+00 2.50e-01 9.20e+00
  angle pdb=" CB  MET H   6 "
        pdb=" CG  MET H   6 "
        pdb=" SD  MET H   6 "
      ideal   model   delta    sigma   weight residual
     112.70  121.38   -8.68 3.00e+00 1.11e-01 8.36e+00
  angle pdb=" C3'  DA A  56 "
        pdb=" C2'  DA A  56 "
        pdb=" C1'  DA A  56 "
      ideal   model   delta    sigma   weight residual
     101.60  105.64   -4.04 1.50e+00 4.44e-01 7.27e+00
  angle pdb=" C3'  DC B -47 "
        pdb=" C2'  DC B -47 "
        pdb=" C1'  DC B -47 "
      ideal   model   delta    sigma   weight residual
     101.60  105.57   -3.97 1.50e+00 4.44e-01 7.02e+00
  angle pdb=" N   GLY F  59 "
        pdb=" CA  GLY F  59 "
        pdb=" C   GLY F  59 "
      ideal   model   delta    sigma   weight residual
     110.38  113.68   -3.30 1.28e+00 6.10e-01 6.66e+00
  ... (remaining 21316 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.82: 4686
       34.82 -    69.65: 492
       69.65 -   104.47: 11
      104.47 -   139.29: 0
      139.29 -   174.11: 4
  Dihedral angle restraints: 5193
    sinusoidal: 3335
      harmonic: 1858
  Sorted by residual:
  dihedral pdb=" CA  LYS H  93 "
           pdb=" C   LYS H  93 "
           pdb=" N   ILE H  94 "
           pdb=" CA  ILE H  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.35  -24.65     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" C4'  DT B -43 "
           pdb=" C3'  DT B -43 "
           pdb=" O3'  DT B -43 "
           pdb=" P    DA B -42 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   45.89  174.11     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DA B -44 "
           pdb=" C3'  DA B -44 "
           pdb=" O3'  DA B -44 "
           pdb=" P    DT B -43 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   56.76  163.24     1      3.50e+01 8.16e-04 1.53e+01
  ... (remaining 5190 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 554
       0.030 -    0.060: 248
       0.060 -    0.089: 135
       0.089 -    0.119: 35
       0.119 -    0.149: 6
  Chirality restraints: 978
  Sorted by residual:
  chirality pdb=" CA  ILE H  53 "
            pdb=" N   ILE H  53 "
            pdb=" C   ILE H  53 "
            pdb=" CB  ILE H  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.55e-01
  chirality pdb=" CA  ILE G  53 "
            pdb=" N   ILE G  53 "
            pdb=" C   ILE G  53 "
            pdb=" CB  ILE G  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CA  ILE F  53 "
            pdb=" N   ILE F  53 "
            pdb=" C   ILE F  53 "
            pdb=" CB  ILE F  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.11e-01
  ... (remaining 975 not shown)

  Planarity restraints: 1427
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC A  59 "    0.025 2.00e-02 2.50e+03   2.61e-02 1.87e+01
        pdb=" N1   DC A  59 "   -0.014 2.00e-02 2.50e+03
        pdb=" C2   DC A  59 "    0.057 2.00e-02 2.50e+03
        pdb=" O2   DC A  59 "   -0.055 2.00e-02 2.50e+03
        pdb=" N3   DC A  59 "    0.010 2.00e-02 2.50e+03
        pdb=" C4   DC A  59 "    0.004 2.00e-02 2.50e+03
        pdb=" N4   DC A  59 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DC A  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DC A  59 "   -0.008 2.00e-02 2.50e+03
        pdb=" H5   DC A  59 "   -0.008 2.00e-02 2.50e+03
        pdb=" H6   DC A  59 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT A  32 "    0.026 2.00e-02 2.50e+03   1.12e-02 3.77e+00
        pdb=" N1   DT A  32 "   -0.025 2.00e-02 2.50e+03
        pdb=" C2   DT A  32 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2   DT A  32 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DT A  32 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DT A  32 "    0.005 2.00e-02 2.50e+03
        pdb=" O4   DT A  32 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DT A  32 "    0.003 2.00e-02 2.50e+03
        pdb=" C7   DT A  32 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DT A  32 "   -0.010 2.00e-02 2.50e+03
        pdb=" H3   DT A  32 "    0.002 2.00e-02 2.50e+03
        pdb=" H6   DT A  32 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT A  25 "    0.021 2.00e-02 2.50e+03   9.34e-03 2.62e+00
        pdb=" N1   DT A  25 "   -0.023 2.00e-02 2.50e+03
        pdb=" C2   DT A  25 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2   DT A  25 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DT A  25 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DT A  25 "    0.003 2.00e-02 2.50e+03
        pdb=" O4   DT A  25 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DT A  25 "    0.002 2.00e-02 2.50e+03
        pdb=" C7   DT A  25 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DT A  25 "   -0.002 2.00e-02 2.50e+03
        pdb=" H3   DT A  25 "    0.002 2.00e-02 2.50e+03
        pdb=" H6   DT A  25 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1424 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.09: 161
        2.09 -     2.72: 17757
        2.72 -     3.35: 31233
        3.35 -     3.97: 40782
        3.97 -     4.60: 63110
  Nonbonded interactions: 153043
  Sorted by model distance:
  nonbonded pdb=" OP2  DT A  44 "
            pdb=" HG  SER G  26 "
     model   vdw
     1.467 2.450
  nonbonded pdb=" O   ASP G 129 "
            pdb=" HG  SER G 132 "
     model   vdw
     1.490 2.450
  nonbonded pdb=" OE1 GLU H  30 "
            pdb=" H   GLU H  30 "
     model   vdw
     1.688 2.450
  nonbonded pdb=" OE1 GLU F  55 "
            pdb=" HH  TYR G  22 "
     model   vdw
     1.689 2.450
  nonbonded pdb=" OD2 ASP G  97 "
            pdb=" HG  SER H 109 "
     model   vdw
     1.700 2.450
  ... (remaining 153038 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 'E' and (resid 3 through 137 or resid 201 through 202))
  selection = chain 'F'
  selection = chain 'G'
  selection = (chain 'H' and (resid 3 through 137 or resid 201 through 202))
}

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:             1.150
  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:             0.070
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.450
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
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   0.047   6330  Z= 0.188
  Angle     :  0.711   8.675   8844  Z= 0.426
  Chirality :  0.043   0.149    978
  Planarity :  0.004   0.028    849
  Dihedral  : 22.353 174.115   2660
  Min Nonbonded Distance : 1.733

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  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 aren not related in a simple way.
  whole: -1.20 (0.35), residues: 534
  helix: -0.80 (0.24), residues: 406
  sheet:  None (None), residues: 0
  loop : -0.09 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 112 
 TYR   0.017   0.002   TYR F  57 
 PHE   0.008   0.001   PHE H  83 
 TRP   0.002   0.001   TRP F 107 
 HIS   0.003   0.001   HIS F 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 6330)
  covalent geometry    : angle       0.71129 ( 8844)
  hydrogen bonds       : bond        0.13436 (  350)
  hydrogen bonds       : angle       6.20372 (  966)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: H   95 TYR cc_start: 0.7437 (t80) cc_final: 0.7216 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.2285
  time to fit residues: 20.3900
Evaluate side-chains
  53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** F  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.213828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.203382 restraints weight = 13133.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.4349 rms_B_bonded: 0.54
r_work: 0.4089 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.4034 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   6330  Z= 0.260
  Angle     :  0.691   5.167   8844  Z= 0.412
  Chirality :  0.044   0.154    978
  Planarity :  0.004   0.031    849
  Dihedral  : 25.727 172.089   1478
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.32 %
    Favored  : 88.46 %
  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 aren not related in a simple way.
  whole: -0.25 (0.36), residues: 534
  helix:  0.03 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop : -0.33 (0.59), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG F 112 
 TYR   0.015   0.002   TYR F  57 
 PHE   0.009   0.002   PHE H  83 
 TRP   0.008   0.002   TRP G 107 
 HIS   0.005   0.001   HIS F  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00595 ( 6330)
  covalent geometry    : angle       0.69072 ( 8844)
  hydrogen bonds       : bond        0.07234 (  350)
  hydrogen bonds       : angle       4.74830 (  966)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 4
  residues processed: 53
  average time/residue: 0.1359
  time to fit residues: 10.3749
Evaluate side-chains
  48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain F residue    8 ASP
Chi-restraints excluded: chain F residue   61 VAL
Chi-restraints excluded: chain F residue  124 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 = 0.4420 r_free = 0.4420 target = 0.213814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.202799 restraints weight = 13302.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.4336 rms_B_bonded: 0.49
r_work: 0.4012 rms_B_bonded: 1.23 restraints_weight: 0.5000
r_work: 0.3882 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work: 0.3769 rms_B_bonded: 4.86 restraints_weight: 0.1250
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   6330  Z= 0.211
  Angle     :  0.615   4.694   8844  Z= 0.370
  Chirality :  0.041   0.154    978
  Planarity :  0.004   0.029    849
  Dihedral  : 25.625 174.559   1478
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.54 %
    Favored  : 87.25 %
  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 aren not related in a simple way.
  whole:  0.40 (0.37), residues: 534
  helix:  0.52 (0.26), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.23 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 112 
 TYR   0.012   0.001   TYR H  14 
 PHE   0.005   0.001   PHE E  83 
 TRP   0.006   0.002   TRP F 107 
 HIS   0.003   0.001   HIS F  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 6330)
  covalent geometry    : angle       0.61479 ( 8844)
  hydrogen bonds       : bond        0.05704 (  350)
  hydrogen bonds       : angle       4.44568 (  966)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: G   30 GLU cc_start: 0.8102 (tt0) cc_final: 0.7879 (tt0)
REVERT: H   95 TYR cc_start: 0.7685 (t80) cc_final: 0.7457 (t80)
  outliers start: 6
  outliers final: 4
  residues processed: 51
  average time/residue: 0.1563
  time to fit residues: 11.0031
Evaluate side-chains
  47 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain F residue   61 VAL
Chi-restraints excluded: chain F residue  124 ASP
Chi-restraints excluded: chain G residue  117 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4441 r_free = 0.4441 target = 0.219755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.210294 restraints weight = 13024.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.4381 rms_B_bonded: 0.40
r_work: 0.4096 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.4033 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6330  Z= 0.153
  Angle     :  0.557   5.856   8844  Z= 0.338
  Chirality :  0.038   0.152    978
  Planarity :  0.003   0.026    849
  Dihedral  : 25.502 175.649   1478
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 13.16 %
    Favored  : 86.44 %
  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 aren not related in a simple way.
  whole:  1.17 (0.39), residues: 534
  helix:  1.11 (0.27), residues: 420
  sheet:  None (None), residues: 0
  loop : -0.23 (0.61), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 112 
 TYR   0.012   0.001   TYR H  14 
 PHE   0.004   0.001   PHE E  83 
 TRP   0.006   0.001   TRP F 107 
 HIS   0.002   0.001   HIS E  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6330)
  covalent geometry    : angle       0.55689 ( 8844)
  hydrogen bonds       : bond        0.04276 (  350)
  hydrogen bonds       : angle       4.07280 (  966)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: H   95 TYR cc_start: 0.7475 (t80) cc_final: 0.7273 (t80)
  outliers start: 2
  outliers final: 2
  residues processed: 52
  average time/residue: 0.1648
  time to fit residues: 11.6967
Evaluate side-chains
  47 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain G residue  117 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 46 optimal weight:   10.0000
   chunk 41 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
H 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.219571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.210481 restraints weight = 13101.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.4380 rms_B_bonded: 0.40
r_work: 0.4108 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.4061 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.4061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6330  Z= 0.151
  Angle     :  0.550   4.935   8844  Z= 0.333
  Chirality :  0.038   0.150    978
  Planarity :  0.003   0.026    849
  Dihedral  : 25.476 176.371   1478
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 13.77 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.39), residues: 534
  helix:  1.36 (0.27), residues: 426
  sheet:  None (None), residues: 0
  loop : -0.17 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 112 
 TYR   0.014   0.001   TYR H  14 
 PHE   0.005   0.001   PHE E 120 
 TRP   0.007   0.001   TRP F 107 
 HIS   0.002   0.001   HIS F  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6330)
  covalent geometry    : angle       0.55032 ( 8844)
  hydrogen bonds       : bond        0.04254 (  350)
  hydrogen bonds       : angle       3.97582 (  966)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: H   95 TYR cc_start: 0.7475 (t80) cc_final: 0.7268 (t80)
  outliers start: 5
  outliers final: 5
  residues processed: 51
  average time/residue: 0.1608
  time to fit residues: 11.3008
Evaluate side-chains
  50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain F residue  124 ASP
Chi-restraints excluded: chain G residue   18 GLU
Chi-restraints excluded: chain G residue   37 SER
Chi-restraints excluded: chain G residue  117 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.4394 r_free = 0.4394 target = 0.213405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.203929 restraints weight = 13264.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.4355 rms_B_bonded: 0.46
r_work: 0.4074 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.4014 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   6330  Z= 0.209
  Angle     :  0.595   5.085   8844  Z= 0.358
  Chirality :  0.041   0.150    978
  Planarity :  0.004   0.030    849
  Dihedral  : 25.550 174.999   1478
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.97 %
    Favored  : 84.41 %
  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 aren not related in a simple way.
  whole:  1.23 (0.38), residues: 534
  helix:  1.15 (0.27), residues: 426
  sheet:  None (None), residues: 0
  loop : -0.23 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 112 
 TYR   0.015   0.001   TYR H  14 
 PHE   0.008   0.002   PHE E 120 
 TRP   0.006   0.002   TRP G 107 
 HIS   0.003   0.001   HIS F  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 6330)
  covalent geometry    : angle       0.59499 ( 8844)
  hydrogen bonds       : bond        0.05580 (  350)
  hydrogen bonds       : angle       4.21518 (  966)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.224 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 51
  average time/residue: 0.1518
  time to fit residues: 10.9329
Evaluate side-chains
  49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain F residue   61 VAL
Chi-restraints excluded: chain F residue  124 ASP
Chi-restraints excluded: chain G residue   18 GLU
Chi-restraints excluded: chain G residue   37 SER
Chi-restraints excluded: chain G residue  117 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.217345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.207761 restraints weight = 12973.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.4336 rms_B_bonded: 0.45
r_work: 0.4055 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.4001 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   6330  Z= 0.228
  Angle     :  0.608   4.520   8844  Z= 0.365
  Chirality :  0.042   0.150    978
  Planarity :  0.004   0.030    849
  Dihedral  : 25.610 173.782   1478
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.57 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.38), residues: 534
  helix:  0.99 (0.26), residues: 426
  sheet:  None (None), residues: 0
  loop : -0.21 (0.61), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 112 
 TYR   0.013   0.001   TYR H 119 
 PHE   0.007   0.002   PHE E 120 
 TRP   0.006   0.002   TRP G 107 
 HIS   0.004   0.001   HIS F  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 6330)
  covalent geometry    : angle       0.60761 ( 8844)
  hydrogen bonds       : bond        0.05819 (  350)
  hydrogen bonds       : angle       4.28039 (  966)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.293 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 50
  average time/residue: 0.1370
  time to fit residues: 9.8393
Evaluate side-chains
  49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain F residue   61 VAL
Chi-restraints excluded: chain F residue  124 ASP
Chi-restraints excluded: chain G residue   18 GLU
Chi-restraints excluded: chain G residue   37 SER
Chi-restraints excluded: chain G residue  117 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.9580

-------------------------------------------------------------------------------
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 = 0.4428 r_free = 0.4428 target = 0.218754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.209793 restraints weight = 13005.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.4353 rms_B_bonded: 0.73
r_work: 0.4073 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.4013 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6330  Z= 0.159
  Angle     :  0.555   4.792   8844  Z= 0.336
  Chirality :  0.039   0.147    978
  Planarity :  0.003   0.029    849
  Dihedral  : 25.504 176.002   1478
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 15.18 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.39), residues: 534
  helix:  1.34 (0.27), residues: 426
  sheet:  None (None), residues: 0
  loop : -0.14 (0.62), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 112 
 TYR   0.016   0.001   TYR H  14 
 PHE   0.005   0.001   PHE E 120 
 TRP   0.006   0.001   TRP F 107 
 HIS   0.002   0.001   HIS F  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6330)
  covalent geometry    : angle       0.55501 ( 8844)
  hydrogen bonds       : bond        0.04308 (  350)
  hydrogen bonds       : angle       4.01449 (  966)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.282 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 51
  average time/residue: 0.1511
  time to fit residues: 10.6844
Evaluate side-chains
  49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain F residue   61 VAL
Chi-restraints excluded: chain F residue  124 ASP
Chi-restraints excluded: chain G residue   37 SER
Chi-restraints excluded: chain G residue  117 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 0 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4431 r_free = 0.4431 target = 0.219059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.209528 restraints weight = 12944.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.4368 rms_B_bonded: 0.40
r_work: 0.4095 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.4008 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6330  Z= 0.158
  Angle     :  0.550   4.584   8844  Z= 0.333
  Chirality :  0.038   0.146    978
  Planarity :  0.003   0.029    849
  Dihedral  : 25.487 176.104   1478
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 14.98 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.39), residues: 534
  helix:  1.47 (0.27), residues: 426
  sheet:  None (None), residues: 0
  loop : -0.18 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 112 
 TYR   0.015   0.001   TYR H  14 
 PHE   0.005   0.001   PHE E 120 
 TRP   0.006   0.001   TRP F 107 
 HIS   0.002   0.001   HIS F  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6330)
  covalent geometry    : angle       0.55000 ( 8844)
  hydrogen bonds       : bond        0.04361 (  350)
  hydrogen bonds       : angle       3.98853 (  966)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.311 
Fit side-chains
REVERT: H  112 ARG cc_start: 0.7151 (tpp-160) cc_final: 0.6871 (mmp80)
  outliers start: 6
  outliers final: 6
  residues processed: 49
  average time/residue: 0.1346
  time to fit residues: 9.3984
Evaluate side-chains
  50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain F residue   61 VAL
Chi-restraints excluded: chain F residue  124 ASP
Chi-restraints excluded: chain G residue   18 GLU
Chi-restraints excluded: chain G residue   37 SER
Chi-restraints excluded: chain G residue  117 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0870
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.8960

-------------------------------------------------------------------------------
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 = 0.4432 r_free = 0.4432 target = 0.218972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.210566 restraints weight = 13041.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.4373 rms_B_bonded: 0.49
r_work: 0.4074 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.4021 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6330  Z= 0.153
  Angle     :  0.544   4.617   8844  Z= 0.330
  Chirality :  0.038   0.144    978
  Planarity :  0.003   0.029    849
  Dihedral  : 25.481 176.272   1478
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 15.38 %
    Favored  : 83.60 %
  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 aren not related in a simple way.
  whole:  1.79 (0.39), residues: 534
  helix:  1.55 (0.27), residues: 426
  sheet:  None (None), residues: 0
  loop : -0.09 (0.64), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 112 
 TYR   0.018   0.001   TYR H  14 
 PHE   0.005   0.001   PHE E 120 
 TRP   0.006   0.001   TRP F 107 
 HIS   0.002   0.001   HIS F  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6330)
  covalent geometry    : angle       0.54445 ( 8844)
  hydrogen bonds       : bond        0.04138 (  350)
  hydrogen bonds       : angle       3.95046 (  966)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.174 
Fit side-chains
REVERT: H  112 ARG cc_start: 0.7061 (tpp-160) cc_final: 0.6815 (mmp80)
  outliers start: 5
  outliers final: 5
  residues processed: 50
  average time/residue: 0.1351
  time to fit residues: 9.3227
Evaluate side-chains
  50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain F residue  124 ASP
Chi-restraints excluded: chain G residue   18 GLU
Chi-restraints excluded: chain G residue   37 SER
Chi-restraints excluded: chain G residue  117 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 3 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.4416 r_free = 0.4416 target = 0.217972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.208401 restraints weight = 12943.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.4325 rms_B_bonded: 0.42
r_work: 0.4052 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3954 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6330  Z= 0.190
  Angle     :  0.573   4.424   8844  Z= 0.345
  Chirality :  0.040   0.145    978
  Planarity :  0.003   0.030    849
  Dihedral  : 25.545 175.856   1478
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 15.38 %
    Favored  : 83.60 %
  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 aren not related in a simple way.
  whole:  1.58 (0.39), residues: 534
  helix:  1.41 (0.27), residues: 426
  sheet:  None (None), residues: 0
  loop : -0.19 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 112 
 TYR   0.017   0.001   TYR H  14 
 PHE   0.006   0.001   PHE E 120 
 TRP   0.006   0.002   TRP G 107 
 HIS   0.003   0.001   HIS F  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 6330)
  covalent geometry    : angle       0.57271 ( 8844)
  hydrogen bonds       : bond        0.05144 (  350)
  hydrogen bonds       : angle       4.11405 (  966)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2895.52 seconds
wall clock time: 49 minutes 47.55 seconds (2987.55 seconds total)