Starting phenix.real_space_refine
on Tue Jun 10 03:08:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c4c_45181/06_2025/9c4c_45181.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c4c_45181/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c4c_45181/06_2025/9c4c_45181.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c4c_45181/06_2025/9c4c_45181.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c4c_45181/06_2025/9c4c_45181.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c4c_45181/06_2025/9c4c_45181.cif"
  }
  resolution = 3.09
  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=   0.023
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.20, per 1000 atoms: 0.71
  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: 3.73
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 6.65
  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: 4.52

  Time building geometry restraints manager: 4.71 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:             42.810
  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:             0.210
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     41.660
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.050
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   88.920
-------------------------------------------------------------------------------
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 (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: -1.20 (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
 TRP   0.002   0.001   TRP F 107 
 HIS   0.003   0.001   HIS F 103 
 PHE   0.008   0.001   PHE H  83 
 TYR   0.017   0.002   TYR F  57 
 ARG   0.003   0.000   ARG F 112 

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

*********************** 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  : 0.887 
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: 0.5132
  time to fit residues: 46.3893
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  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.215545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.205898 restraints weight = 13088.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.4376 rms_B_bonded: 0.48
r_work: 0.4058 rms_B_bonded: 1.19 restraints_weight: 0.5000
r_work: 0.3911 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.1805

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= 0.191
  Angle     :  0.629   5.220   8844  Z= 0.378
  Chirality :  0.041   0.153    978
  Planarity :  0.004   0.024    849
  Dihedral  : 25.589 173.804   1478
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  8.50 %
    Favored  : 90.49 %
  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:  0.14 (0.37), residues: 534
  helix:  0.31 (0.26), residues: 412
  sheet:  None (None), residues: 0
  loop : -0.22 (0.60), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP F 107 
 HIS   0.003   0.001   HIS F  77 
 PHE   0.007   0.001   PHE H  83 
 TYR   0.013   0.001   TYR F  57 
 ARG   0.002   0.000   ARG E 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05686 (  350)
  hydrogen bonds       : angle       4.57272 (  966)
  covalent geometry    : bond        0.00428 ( 6330)
  covalent geometry    : angle       0.62872 ( 8844)

*********************** 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
  56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.906 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 56
  average time/residue: 0.3516
  time to fit residues: 27.1880
Evaluate side-chains
  48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain F residue   61 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0170
   chunk 52 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.8022

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.216604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.205079 restraints weight = 13285.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.4370 rms_B_bonded: 0.48
r_work: 0.4065 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.3915 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6330  Z= 0.153
  Angle     :  0.567   4.911   8844  Z= 0.343
  Chirality :  0.038   0.153    978
  Planarity :  0.003   0.023    849
  Dihedral  : 25.470 175.677   1478
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 10.12 %
    Favored  : 89.47 %
  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:  1.13 (0.38), residues: 534
  helix:  1.05 (0.27), residues: 414
  sheet:  None (None), residues: 0
  loop : -0.01 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 107 
 HIS   0.002   0.001   HIS F  77 
 PHE   0.004   0.001   PHE H  83 
 TYR   0.011   0.001   TYR H  14 
 ARG   0.002   0.000   ARG H 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04476 (  350)
  hydrogen bonds       : angle       4.15303 (  966)
  covalent geometry    : bond        0.00341 ( 6330)
  covalent geometry    : angle       0.56654 ( 8844)

*********************** 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: 2
    poor density    : 49
  time to evaluate  : 0.815 
Fit side-chains
REVERT: H   95 TYR cc_start: 0.7583 (t80) cc_final: 0.7317 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 51
  average time/residue: 0.3386
  time to fit residues: 24.2100
Evaluate side-chains
  43 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 51 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.214844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.201617 restraints weight = 13256.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.4329 rms_B_bonded: 0.47
r_work: 0.4003 rms_B_bonded: 1.09 restraints_weight: 0.5000
r_work: 0.3822 rms_B_bonded: 2.57 restraints_weight: 0.2500
r_work: 0.3739 rms_B_bonded: 3.87 restraints_weight: 0.1250
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6330  Z= 0.185
  Angle     :  0.589   5.309   8844  Z= 0.355
  Chirality :  0.040   0.153    978
  Planarity :  0.003   0.025    849
  Dihedral  : 25.463 175.707   1478
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 11.13 %
    Favored  : 88.06 %
  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:  1.19 (0.39), residues: 534
  helix:  1.11 (0.27), residues: 418
  sheet:  None (None), residues: 0
  loop : -0.10 (0.61), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G 107 
 HIS   0.003   0.001   HIS F  77 
 PHE   0.006   0.001   PHE E 120 
 TYR   0.013   0.001   TYR H  14 
 ARG   0.003   0.000   ARG F 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05159 (  350)
  hydrogen bonds       : angle       4.19725 (  966)
  covalent geometry    : bond        0.00419 ( 6330)
  covalent geometry    : angle       0.58866 ( 8844)

*********************** 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
  51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.892 
Fit side-chains
REVERT: H   95 TYR cc_start: 0.7655 (t80) cc_final: 0.7387 (t80)
  outliers start: 4
  outliers final: 4
  residues processed: 51
  average time/residue: 0.3433
  time to fit residues: 24.5190
Evaluate side-chains
  52 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 9 optimal weight:    0.0170
   chunk 35 optimal weight:    0.5980
   chunk 48 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.7224

-------------------------------------------------------------------------------
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 = 0.4452 r_free = 0.4452 target = 0.220726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.210606 restraints weight = 12952.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.4389 rms_B_bonded: 0.41
r_work: 0.4098 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.4033 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.2930

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= 0.142
  Angle     :  0.539   4.946   8844  Z= 0.328
  Chirality :  0.038   0.151    978
  Planarity :  0.003   0.025    849
  Dihedral  : 25.362 176.749   1478
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 12.35 %
    Favored  : 87.04 %
  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:  1.79 (0.39), residues: 534
  helix:  1.53 (0.27), residues: 422
  sheet:  None (None), residues: 0
  loop :  0.07 (0.62), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 107 
 HIS   0.001   0.001   HIS E  77 
 PHE   0.003   0.001   PHE E 120 
 TYR   0.014   0.001   TYR H  14 
 ARG   0.002   0.000   ARG F 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03829 (  350)
  hydrogen bonds       : angle       3.92183 (  966)
  covalent geometry    : bond        0.00318 ( 6330)
  covalent geometry    : angle       0.53934 ( 8844)

*********************** 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
  51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 1.529 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 51
  average time/residue: 0.4313
  time to fit residues: 31.6855
Evaluate side-chains
  49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   40 THR
Chi-restraints excluded: chain F residue    8 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.4440 r_free = 0.4440 target = 0.220050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.210917 restraints weight = 13079.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.4385 rms_B_bonded: 0.40
r_work: 0.4117 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.4057 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.3084

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= 0.156
  Angle     :  0.550   5.241   8844  Z= 0.333
  Chirality :  0.038   0.148    978
  Planarity :  0.003   0.027    849
  Dihedral  : 25.370 176.800   1478
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.35 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.78 (0.39), residues: 534
  helix:  1.53 (0.27), residues: 426
  sheet:  None (None), residues: 0
  loop : -0.02 (0.65), residues: 108

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04370 (  350)
  hydrogen bonds       : angle       3.96792 (  966)
  covalent geometry    : bond        0.00351 ( 6330)
  covalent geometry    : angle       0.54984 ( 8844)

*********************** 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
  51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.817 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 51
  average time/residue: 0.2876
  time to fit residues: 21.1323
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  : 0.801 
-------------------------------------------------------------------------------
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  124 ASP
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 18 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.4418 r_free = 0.4418 target = 0.215377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.207500 restraints weight = 13341.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.4384 rms_B_bonded: 0.41
r_work: 0.4113 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.4039 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.3187

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= 0.160
  Angle     :  0.550   4.742   8844  Z= 0.333
  Chirality :  0.039   0.148    978
  Planarity :  0.003   0.028    849
  Dihedral  : 25.373 176.488   1478
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.15 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.84 (0.39), residues: 534
  helix:  1.56 (0.27), residues: 424
  sheet:  None (None), residues: 0
  loop :  0.05 (0.63), residues: 110

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04327 (  350)
  hydrogen bonds       : angle       3.97466 (  966)
  covalent geometry    : bond        0.00360 ( 6330)
  covalent geometry    : angle       0.55047 ( 8844)

*********************** 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: 6
    poor density    : 45
  time to evaluate  : 0.828 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 51
  average time/residue: 0.2800
  time to fit residues: 20.8229
Evaluate side-chains
  48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
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
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 11 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4424 r_free = 0.4424 target = 0.215892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.206877 restraints weight = 13280.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.4370 rms_B_bonded: 0.78
r_work: 0.4080 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.4019 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6330  Z= 0.145
  Angle     :  0.535   4.588   8844  Z= 0.325
  Chirality :  0.038   0.147    978
  Planarity :  0.003   0.028    849
  Dihedral  : 25.371 176.397   1478
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 12.75 %
    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 (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:  2.08 (0.39), residues: 534
  helix:  1.74 (0.27), residues: 424
  sheet:  None (None), residues: 0
  loop :  0.09 (0.63), residues: 110

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03909 (  350)
  hydrogen bonds       : angle       3.87081 (  966)
  covalent geometry    : bond        0.00325 ( 6330)
  covalent geometry    : angle       0.53499 ( 8844)

*********************** 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
  48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.853 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 48
  average time/residue: 0.2984
  time to fit residues: 21.7950
Evaluate side-chains
  46 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
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  124 ASP
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 37 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 46 optimal weight:    8.9990
   chunk 24 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.4402 r_free = 0.4402 target = 0.214148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.205313 restraints weight = 13166.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.4346 rms_B_bonded: 0.75
r_work: 0.4062 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.4006 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6330  Z= 0.186
  Angle     :  0.568   4.267   8844  Z= 0.343
  Chirality :  0.040   0.147    978
  Planarity :  0.003   0.029    849
  Dihedral  : 25.445 176.150   1478
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.75 %
    Favored  : 86.23 %
  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:  1.73 (0.39), residues: 534
  helix:  1.51 (0.27), residues: 426
  sheet:  None (None), residues: 0
  loop : -0.12 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP G 107 
 HIS   0.003   0.001   HIS F  77 
 PHE   0.007   0.001   PHE E 120 
 TYR   0.017   0.001   TYR H  14 
 ARG   0.002   0.000   ARG F 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04927 (  350)
  hydrogen bonds       : angle       4.06560 (  966)
  covalent geometry    : bond        0.00423 ( 6330)
  covalent geometry    : angle       0.56792 ( 8844)

*********************** 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
  48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.822 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 47
  average time/residue: 0.2809
  time to fit residues: 19.6770
Evaluate side-chains
  46 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
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  124 ASP
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain H residue  108 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.0186

-------------------------------------------------------------------------------
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 = 0.4425 r_free = 0.4425 target = 0.218950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.209387 restraints weight = 12974.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.4364 rms_B_bonded: 0.43
r_work: 0.4077 rms_B_bonded: 1.72 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: 0.7249
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.147   6330  Z= 0.191
  Angle     :  0.963  59.200   8844  Z= 0.587
  Chirality :  0.039   0.144    978
  Planarity :  0.003   0.029    849
  Dihedral  : 25.445 176.035   1478
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 13.56 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.74 (0.39), residues: 534
  helix:  1.52 (0.27), residues: 426
  sheet:  None (None), residues: 0
  loop : -0.12 (0.63), residues: 108

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04881 (  350)
  hydrogen bonds       : angle       4.06312 (  966)
  covalent geometry    : bond        0.00434 ( 6330)
  covalent geometry    : angle       0.96309 ( 8844)

********************** 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
  45 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 1.297 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 45
  average time/residue: 0.2860
  time to fit residues: 20.0270
Evaluate side-chains
  44 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
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  124 ASP
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 23 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 22 optimal weight:    0.4980
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.218865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.209303 restraints weight = 13025.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.4363 rms_B_bonded: 0.43
r_work: 0.4085 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.4023 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.147   6330  Z= 0.191
  Angle     :  0.963  59.200   8844  Z= 0.587
  Chirality :  0.039   0.144    978
  Planarity :  0.003   0.029    849
  Dihedral  : 25.445 176.035   1478
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 13.36 %
    Favored  : 85.83 %
  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:  1.74 (0.39), residues: 534
  helix:  1.52 (0.27), residues: 426
  sheet:  None (None), residues: 0
  loop : -0.12 (0.63), residues: 108

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04881 (  350)
  hydrogen bonds       : angle       4.06312 (  966)
  covalent geometry    : bond        0.00434 ( 6330)
  covalent geometry    : angle       0.96309 ( 8844)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6106.77 seconds
wall clock time: 105 minutes 50.40 seconds (6350.40 seconds total)