Starting phenix.real_space_refine
on Sat Aug 23 15:54:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t9h_41111/08_2025/8t9h_41111.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t9h_41111/08_2025/8t9h_41111.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t9h_41111/08_2025/8t9h_41111.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t9h_41111/08_2025/8t9h_41111.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t9h_41111/08_2025/8t9h_41111.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t9h_41111/08_2025/8t9h_41111.cif"
  }
  resolution = 3.37
  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=  -0.001 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1622 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     201      5.49       5
     S      29      5.16       5
     C    6930      2.51       5
     N    2237      2.21       5
     O    2642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12039
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 693
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
    Chain: "C"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 811
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 750
          Classifications: {'peptide': 92}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 811
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
    Chain: "H"
      Number of atoms: 709
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 709
          Classifications: {'peptide': 91}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 2012
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 2012
          Classifications: {'DNA': 99}
          Link IDs: {'rna3p': 98}
    Chain: "J"
      Number of atoms: 2110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 2110
          Classifications: {'DNA': 102}
          Link IDs: {'rna3p': 101}
    Chain: "K"
      Number of atoms: 1969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 1969
          Classifications: {'peptide': 249}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 5, 'TRANS': 243}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 40
  Time building chain proxies: 2.27, per 1000 atoms: 0.19
  Number of scatterers: 12039
  At special positions: 0
  Unit cell: (92.064, 118.368, 127.136, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      29     16.00
     P     201     15.00
     O    2642      8.00
     N    2237      7.00
     C    6930      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 293.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1880

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 13 sheets defined
      65.9% alpha, 5.5% beta
      96 base pairs and 141 stacking pairs defined.
    Time for finding SS restraints: 1.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.990A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.523A  pdb=" N   ARG A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.569A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.530A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.511A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.505A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 45 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 4.173A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS E  79 " --> pdb=" O   ALA E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 77
      removed outlier: 3.669A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.492A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 39 through 50
      removed outlier: 3.524A  pdb=" N   TYR H  43 " --> pdb=" O   ALA H  39 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 56 through 85
    Processing helix  chain 'H' and resid 91 through 103
    Processing helix  chain 'H' and resid 104 through 124
      removed outlier: 3.609A  pdb=" N   ALA H 108 " --> pdb=" O   PRO H 104 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 88
    Processing helix  chain 'K' and resid 88 through 94
    Processing helix  chain 'K' and resid 134 through 148
      removed outlier: 3.697A  pdb=" N   LYS K 138 " --> pdb=" O   GLN K 134 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU K 142 " --> pdb=" O   LYS K 138 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 149 through 158
    Processing helix  chain 'K' and resid 160 through 169
      removed outlier: 3.652A  pdb=" N   LEU K 168 " --> pdb=" O   ARG K 164 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASN K 169 " --> pdb=" O   HIS K 165 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 171 through 188
      removed outlier: 3.509A  pdb=" N   ILE K 184 " --> pdb=" O   GLU K 180 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   TYR K 185 " --> pdb=" O   HIS K 181 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 235 through 243
      removed outlier: 3.709A  pdb=" N   ASN K 240 " --> pdb=" O   GLU K 236 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   MET K 241 " --> pdb=" O   ILE K 237 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 266 through 270
      removed outlier: 3.683A  pdb=" N   PHE K 270 " --> pdb=" O   PRO K 267 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 321 through 328
    Processing helix  chain 'K' and resid 329 through 333
    Processing helix  chain 'K' and resid 354 through 361
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.154A  pdb=" N   ARG A  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22
      removed outlier: 3.570A  pdb=" N   CYS K 260 " --> pdb=" O   SER K 255 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   ALA K 261 " --> pdb=" O   LEU K 234 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA K 232 " --> pdb=" O   LEU K 263 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU K 265 " --> pdb=" O   CYS K 230 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 46
      removed outlier: 7.652A  pdb=" N   ARG B  45 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81
    Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.453A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.049A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.287A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB3, first strand: chain 'K' and resid 195 through 199
      removed outlier: 3.697A  pdb=" N   GLU K 301 " --> pdb=" O   ALA K 214 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'K' and resid 279 through 283

    483 hydrogen bonds defined for protein.
    1419 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      247 hydrogen bonds
      486 hydrogen bond angles
      0 basepair planarities
      96 basepair parallelities
      141 stacking parallelities
  Total time for adding SS restraints: 1.90

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2831
        1.33 -     1.45: 3313
        1.45 -     1.57: 6062
        1.57 -     1.69: 400
        1.69 -     1.81: 44
  Bond restraints: 12650
  Sorted by residual:
  bond pdb=" C3'  DG I  94 "
       pdb=" O3'  DG I  94 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.64e+00
  bond pdb=" C3'  DA J  44 "
       pdb=" O3'  DA J  44 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.38e+00
  bond pdb=" CA  ILE C  79 "
       pdb=" CB  ILE C  79 "
    ideal  model  delta    sigma   weight residual
    1.546  1.536  0.010 8.80e-03 1.29e+04 1.23e+00
  bond pdb=" O5'  DA I  49 "
       pdb=" C5'  DA I  49 "
    ideal  model  delta    sigma   weight residual
    1.423  1.455 -0.032 3.00e-02 1.11e+03 1.15e+00
  bond pdb=" C3'  DT I  48 "
       pdb=" O3'  DT I  48 "
    ideal  model  delta    sigma   weight residual
    1.422  1.452 -0.030 3.00e-02 1.11e+03 9.75e-01
  ... (remaining 12645 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 17096
        1.11 -     2.23: 695
        2.23 -     3.34: 119
        3.34 -     4.46: 10
        4.46 -     5.57: 8
  Bond angle restraints: 17928
  Sorted by residual:
  angle pdb=" N   GLY D 104 "
        pdb=" CA  GLY D 104 "
        pdb=" C   GLY D 104 "
      ideal   model   delta    sigma   weight residual
     111.02  116.36   -5.34 1.86e+00 2.89e-01 8.23e+00
  angle pdb=" C3'  DT I  48 "
        pdb=" C2'  DT I  48 "
        pdb=" C1'  DT I  48 "
      ideal   model   delta    sigma   weight residual
     101.60   97.33    4.27 1.50e+00 4.44e-01 8.12e+00
  angle pdb=" C   ASN G  73 "
        pdb=" N   LYS G  74 "
        pdb=" CA  LYS G  74 "
      ideal   model   delta    sigma   weight residual
     121.54  126.03   -4.49 1.91e+00 2.74e-01 5.52e+00
  angle pdb=" C4'  DA I  49 "
        pdb=" C3'  DA I  49 "
        pdb=" C2'  DA I  49 "
      ideal   model   delta    sigma   weight residual
     102.40   98.93    3.47 1.50e+00 4.44e-01 5.36e+00
  angle pdb=" N   PRO D 103 "
        pdb=" CA  PRO D 103 "
        pdb=" C   PRO D 103 "
      ideal   model   delta    sigma   weight residual
     110.21  113.95   -3.74 1.64e+00 3.72e-01 5.21e+00
  ... (remaining 17923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.17: 6152
       35.17 -    70.34: 927
       70.34 -   105.50: 42
      105.50 -   140.67: 0
      140.67 -   175.84: 3
  Dihedral angle restraints: 7124
    sinusoidal: 4214
      harmonic: 2910
  Sorted by residual:
  dihedral pdb=" C4'  DA J  44 "
           pdb=" C3'  DA J  44 "
           pdb=" O3'  DA J  44 "
           pdb=" P    DT J  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.16  175.84     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG I  94 "
           pdb=" C3'  DG I  94 "
           pdb=" O3'  DG I  94 "
           pdb=" P    DC I  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   51.01  168.99     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" C4'  DG I  85 "
           pdb=" C3'  DG I  85 "
           pdb=" O3'  DG I  85 "
           pdb=" P    DT I  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   55.01  164.99     1      3.50e+01 8.16e-04 1.54e+01
  ... (remaining 7121 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1456
       0.031 -    0.063: 428
       0.063 -    0.094: 89
       0.094 -    0.125: 53
       0.125 -    0.156: 5
  Chirality restraints: 2031
  Sorted by residual:
  chirality pdb=" C3'  DT I  48 "
            pdb=" C4'  DT I  48 "
            pdb=" O3'  DT I  48 "
            pdb=" C2'  DT I  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.82    0.16 2.00e-01 2.50e+01 6.11e-01
  chirality pdb=" P    DT I  86 "
            pdb=" OP1  DT I  86 "
            pdb=" OP2  DT I  86 "
            pdb=" O5'  DT I  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.49   -0.14 2.00e-01 2.50e+01 5.01e-01
  chirality pdb=" CA  ILE F  29 "
            pdb=" N   ILE F  29 "
            pdb=" C   ILE F  29 "
            pdb=" CB  ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  ... (remaining 2028 not shown)

  Planarity restraints: 1592
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  49 "    0.031 2.00e-02 2.50e+03   1.38e-02 5.22e+00
        pdb=" N9   DA I  49 "   -0.029 2.00e-02 2.50e+03
        pdb=" C8   DA I  49 "    0.000 2.00e-02 2.50e+03
        pdb=" N7   DA I  49 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5   DA I  49 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DA I  49 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  49 "    0.011 2.00e-02 2.50e+03
        pdb=" N1   DA I  49 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2   DA I  49 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DA I  49 "   -0.008 2.00e-02 2.50e+03
        pdb=" C4   DA I  49 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  98 "    0.001 2.00e-02 2.50e+03   1.40e-02 4.44e+00
        pdb=" N1   DC J  98 "    0.005 2.00e-02 2.50e+03
        pdb=" C2   DC J  98 "   -0.034 2.00e-02 2.50e+03
        pdb=" O2   DC J  98 "    0.017 2.00e-02 2.50e+03
        pdb=" N3   DC J  98 "    0.008 2.00e-02 2.50e+03
        pdb=" C4   DC J  98 "   -0.013 2.00e-02 2.50e+03
        pdb=" N4   DC J  98 "    0.008 2.00e-02 2.50e+03
        pdb=" C5   DC J  98 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DC J  98 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  88 "   -0.024 2.00e-02 2.50e+03   1.15e-02 3.31e+00
        pdb=" N1   DT I  88 "    0.024 2.00e-02 2.50e+03
        pdb=" C2   DT I  88 "    0.003 2.00e-02 2.50e+03
        pdb=" O2   DT I  88 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DT I  88 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DT I  88 "   -0.004 2.00e-02 2.50e+03
        pdb=" O4   DT I  88 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DT I  88 "   -0.001 2.00e-02 2.50e+03
        pdb=" C7   DT I  88 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DT I  88 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1589 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 2498
        2.78 -     3.31: 11748
        3.31 -     3.84: 23449
        3.84 -     4.37: 25860
        4.37 -     4.90: 39469
  Nonbonded interactions: 103024
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  85 "
            pdb=" OH  TYR D  83 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" NE2 GLN K 262 "
            pdb=" O   LEU K 263 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   GLU K 236 "
            pdb=" ND2 ASN K 240 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" O   ILE K 271 "
            pdb=" OH  TYR K 307 "
     model   vdw
     2.264 3.040
  ... (remaining 103019 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 44 through 135)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 23 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 35 through 125)
  selection = chain 'H'
}

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:             2.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.150
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12650  Z= 0.149
  Angle     :  0.519   5.574  17928  Z= 0.317
  Chirality :  0.035   0.156   2031
  Planarity :  0.004   0.034   1592
  Dihedral  : 24.898 175.838   5244
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  6.18 %
    Favored  : 92.85 %
  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:  1.98 (0.27), residues: 981
  helix:  2.29 (0.21), residues: 624
  sheet: -0.80 (0.82), residues: 44
  loop : -0.37 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 100 
 TYR   0.008   0.001   TYR G  57 
 PHE   0.008   0.001   PHE E  78 
 TRP   0.004   0.001   TRP K 218 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (12650)
  covalent geometry    : angle       0.51903 (17928)
  hydrogen bonds       : bond        0.11301 (  730)
  hydrogen bonds       : angle       4.85681 ( 1905)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 196
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8624 (tp-100)
REVERT: C   90 ASP cc_start: 0.8267 (t70) cc_final: 0.7652 (t0)
REVERT: C   92 GLU cc_start: 0.8607 (mp0) cc_final: 0.7966 (mp0)
REVERT: C  104 GLN cc_start: 0.8060 (mp10) cc_final: 0.7564 (mp10)
REVERT: D   51 ASP cc_start: 0.8292 (p0) cc_final: 0.7962 (p0)
REVERT: D   68 ASP cc_start: 0.8875 (t70) cc_final: 0.8551 (t0)
REVERT: D   93 GLU cc_start: 0.8430 (mp0) cc_final: 0.7859 (mp0)
REVERT: D  123 SER cc_start: 0.7785 (m) cc_final: 0.7510 (p)
REVERT: G   92 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8398 (mm-30)
REVERT: K  185 TYR cc_start: 0.9105 (m-80) cc_final: 0.8396 (m-80)
  outliers start: 8
  outliers final: 2
  residues processed: 202
  average time/residue: 0.0813
  time to fit residues: 24.0248
Evaluate side-chains
  173 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 171
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain G residue   27 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:   40.0000
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    9.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C 112 GLN
G 112 GLN
H  50 HIS
K 134 GLN
K 174 GLN
K 240 ASN
K 262 GLN
K 346 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.068830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.045910 restraints weight = 56143.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 3.39
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12650  Z= 0.158
  Angle     :  0.547   5.720  17928  Z= 0.321
  Chirality :  0.036   0.151   2031
  Planarity :  0.004   0.036   1592
  Dihedral  : 29.628 176.268   3315
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.52 %
    Favored  : 87.27 %
  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:  2.16 (0.27), residues: 981
  helix:  2.46 (0.20), residues: 635
  sheet: -0.85 (0.82), residues: 44
  loop : -0.47 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  99 
 TYR   0.018   0.001   TYR H  84 
 PHE   0.007   0.001   PHE A  67 
 TRP   0.006   0.001   TRP K 218 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (12650)
  covalent geometry    : angle       0.54701 (17928)
  hydrogen bonds       : bond        0.03962 (  730)
  hydrogen bonds       : angle       3.65200 ( 1905)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 187
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9328 (tt0) cc_final: 0.9106 (tt0)
REVERT: A   76 GLN cc_start: 0.8974 (tp-100) cc_final: 0.8521 (tp-100)
REVERT: B   84 MET cc_start: 0.8753 (mmm) cc_final: 0.8254 (mmm)
REVERT: B   88 TYR cc_start: 0.8535 (m-80) cc_final: 0.7922 (m-80)
REVERT: B   93 GLN cc_start: 0.8698 (mp10) cc_final: 0.8398 (mm-40)
REVERT: C   64 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: C   90 ASP cc_start: 0.8148 (t70) cc_final: 0.7216 (t70)
REVERT: C   92 GLU cc_start: 0.8824 (mp0) cc_final: 0.8148 (mp0)
REVERT: C  104 GLN cc_start: 0.8148 (mp10) cc_final: 0.7566 (mp10)
REVERT: D   37 TYR cc_start: 0.8975 (m-10) cc_final: 0.8769 (m-10)
REVERT: D   51 ASP cc_start: 0.8972 (p0) cc_final: 0.8208 (p0)
REVERT: D   68 ASP cc_start: 0.9188 (t70) cc_final: 0.8863 (t0)
REVERT: D   93 GLU cc_start: 0.8893 (mp0) cc_final: 0.8061 (mp0)
REVERT: D  123 SER cc_start: 0.8375 (m) cc_final: 0.7968 (p)
REVERT: E   50 GLU cc_start: 0.9582 (tt0) cc_final: 0.9324 (tt0)
REVERT: E  125 GLN cc_start: 0.9246 (pt0) cc_final: 0.8686 (pm20)
REVERT: F   44 LYS cc_start: 0.9053 (mmtp) cc_final: 0.8631 (mmtp)
REVERT: G   90 ASP cc_start: 0.8702 (t0) cc_final: 0.8284 (t0)
REVERT: H   69 ASP cc_start: 0.9386 (t70) cc_final: 0.8983 (t0)
REVERT: K  185 TYR cc_start: 0.9116 (m-80) cc_final: 0.8454 (m-80)
  outliers start: 10
  outliers final: 6
  residues processed: 189
  average time/residue: 0.0826
  time to fit residues: 22.5324
Evaluate side-chains
  177 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 171
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain H residue   77 GLU
Chi-restraints excluded: chain K residue   88 VAL
Chi-restraints excluded: chain K residue  149 HIS
Chi-restraints excluded: chain K residue  188 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 109 optimal weight:   10.0000
   chunk 93 optimal weight:    8.9990
   chunk 95 optimal weight:   10.0000
   chunk 86 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
D 109 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.067431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.044388 restraints weight = 57089.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 3.39
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  12650  Z= 0.211
  Angle     :  0.563   5.751  17928  Z= 0.330
  Chirality :  0.037   0.153   2031
  Planarity :  0.004   0.033   1592
  Dihedral  : 29.766 177.753   3313
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.88 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.18 (0.27), residues: 981
  helix:  2.48 (0.20), residues: 636
  sheet: -0.97 (0.80), residues: 44
  loop : -0.45 (0.33), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  99 
 TYR   0.016   0.001   TYR H  84 
 PHE   0.006   0.001   PHE A  78 
 TRP   0.007   0.002   TRP K 264 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (12650)
  covalent geometry    : angle       0.56267 (17928)
  hydrogen bonds       : bond        0.04259 (  730)
  hydrogen bonds       : angle       3.57783 ( 1905)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 174
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8470 (tp-100)
REVERT: A  133 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8374 (mt-10)
REVERT: B   88 TYR cc_start: 0.8790 (m-80) cc_final: 0.8520 (m-80)
REVERT: B   93 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8352 (mm-40)
REVERT: C   29 ARG cc_start: 0.8554 (ttm170) cc_final: 0.8204 (ttm170)
REVERT: C   64 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7998 (tm-30)
REVERT: C   90 ASP cc_start: 0.8240 (t70) cc_final: 0.7317 (t70)
REVERT: C   92 GLU cc_start: 0.8868 (mp0) cc_final: 0.8096 (mp0)
REVERT: C   99 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7980 (mmm-85)
REVERT: C  104 GLN cc_start: 0.8203 (mp10) cc_final: 0.7637 (mp10)
REVERT: D   51 ASP cc_start: 0.9012 (p0) cc_final: 0.8253 (p0)
REVERT: D   68 ASP cc_start: 0.9162 (t70) cc_final: 0.8835 (t0)
REVERT: D   93 GLU cc_start: 0.8963 (mp0) cc_final: 0.8100 (mp0)
REVERT: D  123 SER cc_start: 0.8397 (m) cc_final: 0.7990 (p)
REVERT: E   50 GLU cc_start: 0.9596 (tt0) cc_final: 0.8905 (tm-30)
REVERT: E  125 GLN cc_start: 0.9252 (pt0) cc_final: 0.8970 (pt0)
REVERT: F   44 LYS cc_start: 0.9077 (mmtp) cc_final: 0.8633 (mmtp)
REVERT: G   90 ASP cc_start: 0.8740 (t0) cc_final: 0.8354 (t0)
REVERT: K  185 TYR cc_start: 0.8991 (m-80) cc_final: 0.8370 (m-80)
REVERT: K  253 MET cc_start: 0.8450 (mpp) cc_final: 0.8060 (mpp)
  outliers start: 14
  outliers final: 10
  residues processed: 178
  average time/residue: 0.0936
  time to fit residues: 23.8096
Evaluate side-chains
  182 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 171
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain H residue   40 ILE
Chi-restraints excluded: chain H residue   77 GLU
Chi-restraints excluded: chain K residue   88 VAL
Chi-restraints excluded: chain K residue  149 HIS
Chi-restraints excluded: chain K residue  188 MET
Chi-restraints excluded: chain K residue  291 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 81 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 106 optimal weight:    9.9990
   chunk 7 optimal weight:    4.9990
   chunk 91 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 105 optimal weight:   20.0000
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
F  93 GLN
K 316 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.064808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.041519 restraints weight = 57805.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 3.37
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.045  12650  Z= 0.363
  Angle     :  0.677   6.922  17928  Z= 0.389
  Chirality :  0.041   0.194   2031
  Planarity :  0.004   0.042   1592
  Dihedral  : 30.299 179.139   3313
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.09 %
    Favored  : 84.36 %
  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:  1.83 (0.27), residues: 981
  helix:  2.18 (0.20), residues: 640
  sheet: -1.26 (0.77), residues: 44
  loop : -0.55 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  39 
 TYR   0.015   0.002   TYR C  57 
 PHE   0.008   0.001   PHE A  78 
 TRP   0.008   0.002   TRP K 218 
 HIS   0.006   0.001   HIS D 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00806 (12650)
  covalent geometry    : angle       0.67714 (17928)
  hydrogen bonds       : bond        0.05819 (  730)
  hydrogen bonds       : angle       3.89453 ( 1905)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 165
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8259 (mt-10)
REVERT: B   23 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7902 (mmm-85)
REVERT: B   84 MET cc_start: 0.8719 (mmm) cc_final: 0.8360 (tpp)
REVERT: B   88 TYR cc_start: 0.8835 (m-80) cc_final: 0.8126 (m-80)
REVERT: B   93 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7575 (mp10)
REVERT: C   64 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7866 (tm-30)
REVERT: C   90 ASP cc_start: 0.8362 (t70) cc_final: 0.7563 (t0)
REVERT: C   92 GLU cc_start: 0.8890 (mp0) cc_final: 0.8144 (mp0)
REVERT: C  104 GLN cc_start: 0.8421 (mp10) cc_final: 0.7633 (mp10)
REVERT: D   51 ASP cc_start: 0.9066 (p0) cc_final: 0.8434 (p0)
REVERT: D   68 ASP cc_start: 0.9239 (t70) cc_final: 0.8933 (t0)
REVERT: D   83 TYR cc_start: 0.8340 (t80) cc_final: 0.7876 (t80)
REVERT: E   73 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8506 (tm-30)
REVERT: E  125 GLN cc_start: 0.9235 (pt0) cc_final: 0.8939 (pt0)
REVERT: F   44 LYS cc_start: 0.9020 (mmtp) cc_final: 0.8618 (mmtp)
REVERT: G   90 ASP cc_start: 0.8737 (t0) cc_final: 0.8379 (t0)
REVERT: G   92 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8577 (mm-30)
  outliers start: 21
  outliers final: 15
  residues processed: 172
  average time/residue: 0.0878
  time to fit residues: 21.6889
Evaluate side-chains
  175 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain H residue   40 ILE
Chi-restraints excluded: chain K residue   88 VAL
Chi-restraints excluded: chain K residue  149 HIS
Chi-restraints excluded: chain K residue  188 MET
Chi-restraints excluded: chain K residue  224 ILE
Chi-restraints excluded: chain K residue  291 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 112 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 102 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3608 r_free = 0.3608 target = 0.067288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.044262 restraints weight = 56284.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 3.37
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12650  Z= 0.161
  Angle     :  0.568   7.843  17928  Z= 0.330
  Chirality :  0.037   0.169   2031
  Planarity :  0.004   0.036   1592
  Dihedral  : 29.995 179.583   3313
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.15 %
    Favored  : 83.52 %
  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:  2.10 (0.27), residues: 981
  helix:  2.41 (0.20), residues: 636
  sheet: -1.14 (0.75), residues: 44
  loop : -0.46 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.021   0.001   TYR H  41 
 PHE   0.008   0.001   PHE H  71 
 TRP   0.010   0.002   TRP K 218 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (12650)
  covalent geometry    : angle       0.56792 (17928)
  hydrogen bonds       : bond        0.03900 (  730)
  hydrogen bonds       : angle       3.40063 ( 1905)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 176
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9204 (tt0) cc_final: 0.8812 (tt0)
REVERT: A   76 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8444 (tp-100)
REVERT: A  133 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8201 (mt-10)
REVERT: B   84 MET cc_start: 0.8739 (mmm) cc_final: 0.8367 (mmm)
REVERT: B   88 TYR cc_start: 0.8667 (m-80) cc_final: 0.8159 (m-80)
REVERT: B   93 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7537 (mp10)
REVERT: C   64 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: C   90 ASP cc_start: 0.8239 (t70) cc_final: 0.7420 (t0)
REVERT: C   92 GLU cc_start: 0.8890 (mp0) cc_final: 0.7988 (mp0)
REVERT: C  104 GLN cc_start: 0.8269 (mp10) cc_final: 0.7592 (mp10)
REVERT: D   51 ASP cc_start: 0.8961 (p0) cc_final: 0.8273 (p0)
REVERT: D   68 ASP cc_start: 0.9155 (t70) cc_final: 0.8853 (t0)
REVERT: D   83 TYR cc_start: 0.8282 (t80) cc_final: 0.7971 (t80)
REVERT: D   93 GLU cc_start: 0.8979 (mp0) cc_final: 0.8041 (mp0)
REVERT: E   50 GLU cc_start: 0.9566 (tt0) cc_final: 0.9361 (tt0)
REVERT: E  125 GLN cc_start: 0.9243 (pt0) cc_final: 0.9001 (pt0)
REVERT: F   44 LYS cc_start: 0.8970 (mmtp) cc_final: 0.8551 (mmtp)
REVERT: G   90 ASP cc_start: 0.8726 (t0) cc_final: 0.8295 (t0)
REVERT: H   69 ASP cc_start: 0.9406 (t70) cc_final: 0.9052 (t0)
REVERT: K  188 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8875 (ppp)
REVERT: K  253 MET cc_start: 0.8188 (mpp) cc_final: 0.7861 (mpp)
  outliers start: 11
  outliers final: 7
  residues processed: 179
  average time/residue: 0.0875
  time to fit residues: 22.6592
Evaluate side-chains
  181 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 172
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain K residue   88 VAL
Chi-restraints excluded: chain K residue  149 HIS
Chi-restraints excluded: chain K residue  188 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 91 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3617 r_free = 0.3617 target = 0.067660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.044677 restraints weight = 56455.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 3.40
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12650  Z= 0.159
  Angle     :  0.561   8.827  17928  Z= 0.323
  Chirality :  0.036   0.160   2031
  Planarity :  0.004   0.040   1592
  Dihedral  : 29.861 179.808   3313
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.52 %
    Favored  : 82.91 %
  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:  2.22 (0.27), residues: 981
  helix:  2.48 (0.20), residues: 636
  sheet: -0.96 (0.75), residues: 44
  loop : -0.37 (0.33), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  99 
 TYR   0.008   0.001   TYR G  57 
 PHE   0.007   0.001   PHE H  71 
 TRP   0.009   0.002   TRP K 218 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (12650)
  covalent geometry    : angle       0.56074 (17928)
  hydrogen bonds       : bond        0.03757 (  730)
  hydrogen bonds       : angle       3.29978 ( 1905)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 178
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9177 (tt0) cc_final: 0.8728 (tt0)
REVERT: A   76 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8387 (tp-100)
REVERT: A  133 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8130 (mt-10)
REVERT: B   20 MET cc_start: 0.8809 (mmm) cc_final: 0.8567 (mmm)
REVERT: B   23 ARG cc_start: 0.8377 (mmt90) cc_final: 0.8172 (mmt90)
REVERT: B   53 GLU cc_start: 0.8987 (tp30) cc_final: 0.8766 (tp30)
REVERT: B   68 ASP cc_start: 0.9092 (m-30) cc_final: 0.8828 (m-30)
REVERT: B   84 MET cc_start: 0.8737 (mmm) cc_final: 0.8431 (mmm)
REVERT: B   88 TYR cc_start: 0.8711 (m-80) cc_final: 0.8220 (m-80)
REVERT: B   93 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7434 (mp10)
REVERT: C   29 ARG cc_start: 0.8633 (ttm170) cc_final: 0.8196 (ttm170)
REVERT: C   64 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7925 (tm-30)
REVERT: C   72 ASP cc_start: 0.8788 (m-30) cc_final: 0.8484 (m-30)
REVERT: C   90 ASP cc_start: 0.8266 (t70) cc_final: 0.7705 (t0)
REVERT: C   92 GLU cc_start: 0.8862 (mp0) cc_final: 0.8272 (mp0)
REVERT: C  104 GLN cc_start: 0.8253 (mp10) cc_final: 0.7590 (mp10)
REVERT: D   51 ASP cc_start: 0.8963 (p0) cc_final: 0.8241 (p0)
REVERT: D   68 ASP cc_start: 0.9176 (t70) cc_final: 0.8880 (t0)
REVERT: D   83 TYR cc_start: 0.8301 (t80) cc_final: 0.7949 (t80)
REVERT: D   93 GLU cc_start: 0.8941 (mp0) cc_final: 0.8058 (mp0)
REVERT: D  123 SER cc_start: 0.8351 (m) cc_final: 0.8000 (p)
REVERT: E   50 GLU cc_start: 0.9581 (tt0) cc_final: 0.9335 (tt0)
REVERT: E  125 GLN cc_start: 0.9238 (pt0) cc_final: 0.9005 (pt0)
REVERT: F   44 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8594 (mmtp)
REVERT: G   90 ASP cc_start: 0.8739 (t0) cc_final: 0.8334 (t0)
REVERT: H   69 ASP cc_start: 0.9403 (t70) cc_final: 0.9039 (t0)
REVERT: K  188 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8842 (ppp)
REVERT: K  253 MET cc_start: 0.8221 (mpp) cc_final: 0.7924 (mpp)
  outliers start: 13
  outliers final: 10
  residues processed: 181
  average time/residue: 0.0957
  time to fit residues: 24.8194
Evaluate side-chains
  181 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 169
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain H residue   40 ILE
Chi-restraints excluded: chain H residue   77 GLU
Chi-restraints excluded: chain K residue   88 VAL
Chi-restraints excluded: chain K residue  149 HIS
Chi-restraints excluded: chain K residue  188 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 95 optimal weight:   20.0000
   chunk 80 optimal weight:    4.9990
   chunk 4 optimal weight:    0.4980
   chunk 114 optimal weight:    0.0980
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 97 optimal weight:   40.0000
   chunk 63 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3612 r_free = 0.3612 target = 0.067454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.044458 restraints weight = 56418.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 3.39
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12650  Z= 0.170
  Angle     :  0.561   7.959  17928  Z= 0.324
  Chirality :  0.036   0.169   2031
  Planarity :  0.003   0.035   1592
  Dihedral  : 29.826 179.604   3313
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.88 %
    Favored  : 82.55 %
  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:  2.26 (0.27), residues: 981
  helix:  2.51 (0.20), residues: 637
  sheet: -0.91 (0.76), residues: 44
  loop : -0.36 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  71 
 TYR   0.008   0.001   TYR G  57 
 PHE   0.007   0.001   PHE E  78 
 TRP   0.010   0.001   TRP K 218 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (12650)
  covalent geometry    : angle       0.56144 (17928)
  hydrogen bonds       : bond        0.03772 (  730)
  hydrogen bonds       : angle       3.28272 ( 1905)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 175
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9177 (tt0) cc_final: 0.8748 (tt0)
REVERT: A   76 GLN cc_start: 0.8947 (tp-100) cc_final: 0.8388 (tp-100)
REVERT: A  133 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8104 (mt-10)
REVERT: B   20 MET cc_start: 0.8916 (mmm) cc_final: 0.8659 (mmm)
REVERT: B   23 ARG cc_start: 0.8390 (mmt90) cc_final: 0.8094 (mmt90)
REVERT: B   84 MET cc_start: 0.8775 (mmm) cc_final: 0.8483 (mmm)
REVERT: B   88 TYR cc_start: 0.8735 (m-80) cc_final: 0.8236 (m-80)
REVERT: B   93 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7432 (mp10)
REVERT: C   64 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7916 (tm-30)
REVERT: C   72 ASP cc_start: 0.8822 (m-30) cc_final: 0.8523 (m-30)
REVERT: C   90 ASP cc_start: 0.8250 (t70) cc_final: 0.7694 (t0)
REVERT: C   92 GLU cc_start: 0.8869 (mp0) cc_final: 0.8260 (mp0)
REVERT: C  104 GLN cc_start: 0.8204 (mp10) cc_final: 0.7527 (mp10)
REVERT: D   51 ASP cc_start: 0.8931 (p0) cc_final: 0.8211 (p0)
REVERT: D   68 ASP cc_start: 0.9177 (t70) cc_final: 0.8878 (t0)
REVERT: D   83 TYR cc_start: 0.8228 (t80) cc_final: 0.7886 (t80)
REVERT: D   93 GLU cc_start: 0.8933 (mp0) cc_final: 0.8060 (mp0)
REVERT: D  123 SER cc_start: 0.8368 (m) cc_final: 0.8016 (p)
REVERT: E   50 GLU cc_start: 0.9559 (tt0) cc_final: 0.9308 (tt0)
REVERT: E   73 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8535 (tm-30)
REVERT: E  125 GLN cc_start: 0.9243 (pt0) cc_final: 0.9036 (pt0)
REVERT: F   44 LYS cc_start: 0.8991 (mmtp) cc_final: 0.8604 (mmtp)
REVERT: G   90 ASP cc_start: 0.8714 (t0) cc_final: 0.8294 (t0)
REVERT: K  188 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8835 (ppp)
REVERT: K  253 MET cc_start: 0.8214 (mpp) cc_final: 0.7972 (mpp)
  outliers start: 13
  outliers final: 10
  residues processed: 179
  average time/residue: 0.0910
  time to fit residues: 23.4830
Evaluate side-chains
  184 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain H residue   40 ILE
Chi-restraints excluded: chain H residue   77 GLU
Chi-restraints excluded: chain K residue   88 VAL
Chi-restraints excluded: chain K residue  149 HIS
Chi-restraints excluded: chain K residue  188 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 108 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 96 optimal weight:   20.0000
   chunk 1 optimal weight:    1.9990
   chunk 114 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
E 125 GLN
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.068447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.045611 restraints weight = 56205.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 3.41
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12650  Z= 0.146
  Angle     :  0.558   8.672  17928  Z= 0.318
  Chirality :  0.036   0.157   2031
  Planarity :  0.004   0.037   1592
  Dihedral  : 29.675 179.213   3313
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 16.48 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.34 (0.27), residues: 981
  helix:  2.56 (0.20), residues: 637
  sheet: -0.78 (0.76), residues: 44
  loop : -0.33 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  99 
 TYR   0.008   0.001   TYR H  84 
 PHE   0.007   0.001   PHE H  71 
 TRP   0.012   0.002   TRP K 218 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (12650)
  covalent geometry    : angle       0.55798 (17928)
  hydrogen bonds       : bond        0.03541 (  730)
  hydrogen bonds       : angle       3.19019 ( 1905)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 184
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9145 (tt0) cc_final: 0.8680 (tt0)
REVERT: A   76 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8336 (tp-100)
REVERT: A  133 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8051 (mt-10)
REVERT: B   20 MET cc_start: 0.8928 (mmm) cc_final: 0.8659 (mmm)
REVERT: B   23 ARG cc_start: 0.8412 (mmt90) cc_final: 0.8055 (mmt90)
REVERT: B   84 MET cc_start: 0.8806 (mmm) cc_final: 0.8604 (mmm)
REVERT: B   88 TYR cc_start: 0.8710 (m-80) cc_final: 0.8274 (m-80)
REVERT: B   93 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7461 (mp10)
REVERT: C   29 ARG cc_start: 0.8499 (ttm170) cc_final: 0.8211 (ttm170)
REVERT: C   64 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7884 (tm-30)
REVERT: C   90 ASP cc_start: 0.8336 (t70) cc_final: 0.7616 (t70)
REVERT: C   92 GLU cc_start: 0.8867 (mp0) cc_final: 0.8221 (mp0)
REVERT: D   51 ASP cc_start: 0.8928 (p0) cc_final: 0.8198 (p0)
REVERT: D   68 ASP cc_start: 0.9168 (t70) cc_final: 0.8884 (t0)
REVERT: D   83 TYR cc_start: 0.8300 (t80) cc_final: 0.7961 (t80)
REVERT: D   93 GLU cc_start: 0.8907 (mp0) cc_final: 0.8104 (mp0)
REVERT: D  123 SER cc_start: 0.8444 (m) cc_final: 0.8086 (p)
REVERT: E   50 GLU cc_start: 0.9543 (tt0) cc_final: 0.9293 (tt0)
REVERT: E   73 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8490 (tm-30)
REVERT: F   44 LYS cc_start: 0.8981 (mmtp) cc_final: 0.8560 (mmtp)
REVERT: G   90 ASP cc_start: 0.8697 (t0) cc_final: 0.8183 (t0)
REVERT: H   69 ASP cc_start: 0.9397 (t70) cc_final: 0.9028 (t0)
REVERT: K  188 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8853 (ppp)
REVERT: K  253 MET cc_start: 0.8187 (mpp) cc_final: 0.7949 (mpp)
  outliers start: 12
  outliers final: 8
  residues processed: 186
  average time/residue: 0.0988
  time to fit residues: 25.7138
Evaluate side-chains
  182 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 172
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain H residue   40 ILE
Chi-restraints excluded: chain H residue   77 GLU
Chi-restraints excluded: chain K residue   88 VAL
Chi-restraints excluded: chain K residue  149 HIS
Chi-restraints excluded: chain K residue  188 MET
Chi-restraints excluded: chain K residue  307 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 111 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.067968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.045139 restraints weight = 56115.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 3.36
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12650  Z= 0.167
  Angle     :  0.564   8.960  17928  Z= 0.322
  Chirality :  0.036   0.157   2031
  Planarity :  0.003   0.035   1592
  Dihedral  : 29.693 179.368   3313
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 16.73 %
    Favored  : 81.70 %
  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:  2.34 (0.27), residues: 981
  helix:  2.55 (0.20), residues: 638
  sheet: -0.72 (0.77), residues: 44
  loop : -0.32 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  71 
 TYR   0.008   0.001   TYR E  54 
 PHE   0.006   0.001   PHE H  71 
 TRP   0.011   0.001   TRP K 218 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (12650)
  covalent geometry    : angle       0.56446 (17928)
  hydrogen bonds       : bond        0.03699 (  730)
  hydrogen bonds       : angle       3.23301 ( 1905)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 171
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9179 (tt0) cc_final: 0.8728 (tt0)
REVERT: A   76 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8345 (tp-100)
REVERT: A  133 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8071 (mt-10)
REVERT: B   23 ARG cc_start: 0.8418 (mmt90) cc_final: 0.8052 (mmt90)
REVERT: B   84 MET cc_start: 0.8801 (mmm) cc_final: 0.8596 (mmm)
REVERT: B   88 TYR cc_start: 0.8717 (m-80) cc_final: 0.8257 (m-80)
REVERT: B   93 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7517 (mp10)
REVERT: C   64 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: C   90 ASP cc_start: 0.8321 (t70) cc_final: 0.7669 (t0)
REVERT: C   92 GLU cc_start: 0.8928 (mp0) cc_final: 0.8300 (mp0)
REVERT: C  104 GLN cc_start: 0.8182 (mp10) cc_final: 0.7586 (mp10)
REVERT: D   51 ASP cc_start: 0.8920 (p0) cc_final: 0.8233 (p0)
REVERT: D   68 ASP cc_start: 0.9186 (t70) cc_final: 0.8894 (t0)
REVERT: D   83 TYR cc_start: 0.8302 (t80) cc_final: 0.7925 (t80)
REVERT: D   93 GLU cc_start: 0.8937 (mp0) cc_final: 0.8047 (mp0)
REVERT: D  123 SER cc_start: 0.8318 (m) cc_final: 0.7965 (p)
REVERT: E   50 GLU cc_start: 0.9554 (tt0) cc_final: 0.9292 (tt0)
REVERT: E   73 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8493 (tm-30)
REVERT: F   44 LYS cc_start: 0.9003 (mmtp) cc_final: 0.8596 (mmtp)
REVERT: G   90 ASP cc_start: 0.8694 (t0) cc_final: 0.8238 (t0)
REVERT: H   69 ASP cc_start: 0.9395 (t70) cc_final: 0.9021 (t0)
REVERT: K  188 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8823 (ppp)
  outliers start: 13
  outliers final: 11
  residues processed: 176
  average time/residue: 0.1107
  time to fit residues: 28.1037
Evaluate side-chains
  183 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain H residue   40 ILE
Chi-restraints excluded: chain H residue   77 GLU
Chi-restraints excluded: chain K residue   88 VAL
Chi-restraints excluded: chain K residue  149 HIS
Chi-restraints excluded: chain K residue  188 MET
Chi-restraints excluded: chain K residue  307 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   chunk 41 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
F  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.068447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.045561 restraints weight = 56462.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 3.42
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12650  Z= 0.155
  Angle     :  0.576  10.534  17928  Z= 0.325
  Chirality :  0.036   0.159   2031
  Planarity :  0.004   0.045   1592
  Dihedral  : 29.618 179.145   3313
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 16.97 %
    Favored  : 81.33 %
  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:  2.36 (0.27), residues: 981
  helix:  2.57 (0.20), residues: 638
  sheet: -0.73 (0.76), residues: 44
  loop : -0.31 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  99 
 TYR   0.009   0.001   TYR D  37 
 PHE   0.007   0.001   PHE H  71 
 TRP   0.012   0.002   TRP K 218 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (12650)
  covalent geometry    : angle       0.57607 (17928)
  hydrogen bonds       : bond        0.03583 (  730)
  hydrogen bonds       : angle       3.18154 ( 1905)

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 177
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9188 (tt0) cc_final: 0.8759 (tt0)
REVERT: A   76 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8341 (tp-100)
REVERT: A  133 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8084 (mt-10)
REVERT: B   23 ARG cc_start: 0.8456 (mmt90) cc_final: 0.8076 (mmt90)
REVERT: B   88 TYR cc_start: 0.8711 (m-80) cc_final: 0.8296 (m-80)
REVERT: B   93 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7513 (mp10)
REVERT: C   64 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7902 (tm-30)
REVERT: C   90 ASP cc_start: 0.8329 (t70) cc_final: 0.7740 (t0)
REVERT: C   92 GLU cc_start: 0.8947 (mp0) cc_final: 0.8372 (mp0)
REVERT: C  104 GLN cc_start: 0.8203 (mp10) cc_final: 0.7667 (mp10)
REVERT: D   51 ASP cc_start: 0.8942 (p0) cc_final: 0.8260 (p0)
REVERT: D   68 ASP cc_start: 0.9183 (t70) cc_final: 0.8896 (t0)
REVERT: D   83 TYR cc_start: 0.8320 (t80) cc_final: 0.8017 (t80)
REVERT: D   93 GLU cc_start: 0.8922 (mp0) cc_final: 0.8104 (mp0)
REVERT: D  123 SER cc_start: 0.8446 (m) cc_final: 0.8085 (p)
REVERT: E   50 GLU cc_start: 0.9554 (tt0) cc_final: 0.9288 (tt0)
REVERT: E   73 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8458 (tm-30)
REVERT: F   44 LYS cc_start: 0.9005 (mmtp) cc_final: 0.8598 (mmtp)
REVERT: G   90 ASP cc_start: 0.8699 (t0) cc_final: 0.8243 (t0)
REVERT: H   69 ASP cc_start: 0.9397 (t70) cc_final: 0.9024 (t0)
REVERT: K  188 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8830 (ppp)
REVERT: K  253 MET cc_start: 0.8069 (mpp) cc_final: 0.7719 (mpp)
  outliers start: 14
  outliers final: 11
  residues processed: 182
  average time/residue: 0.1266
  time to fit residues: 32.5093
Evaluate side-chains
  183 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain H residue   40 ILE
Chi-restraints excluded: chain H residue   77 GLU
Chi-restraints excluded: chain K residue   88 VAL
Chi-restraints excluded: chain K residue  149 HIS
Chi-restraints excluded: chain K residue  188 MET
Chi-restraints excluded: chain K residue  307 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 112 optimal weight:    9.9990
   chunk 66 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0770
   chunk 76 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
F  93 GLN
** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.068891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.046265 restraints weight = 56212.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 3.40
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12650  Z= 0.144
  Angle     :  0.570  10.626  17928  Z= 0.322
  Chirality :  0.036   0.159   2031
  Planarity :  0.003   0.037   1592
  Dihedral  : 29.530 178.981   3313
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 17.09 %
    Favored  : 81.21 %
  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:  2.41 (0.27), residues: 981
  helix:  2.57 (0.20), residues: 645
  sheet: -0.69 (0.77), residues: 44
  loop : -0.25 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.012   0.001   TYR D  37 
 PHE   0.007   0.001   PHE H  71 
 TRP   0.011   0.001   TRP K 218 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (12650)
  covalent geometry    : angle       0.57043 (17928)
  hydrogen bonds       : bond        0.03549 (  730)
  hydrogen bonds       : angle       3.14424 ( 1905)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1818.79 seconds
wall clock time: 32 minutes 10.48 seconds (1930.48 seconds total)