Starting phenix.real_space_refine
on Wed Feb  4 00:56:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9e3j_47485/02_2026/9e3j_47485.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9e3j_47485/02_2026/9e3j_47485.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9e3j_47485/02_2026/9e3j_47485.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9e3j_47485/02_2026/9e3j_47485.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9e3j_47485/02_2026/9e3j_47485.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9e3j_47485/02_2026/9e3j_47485.map"
  }
  resolution = 3.6
  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=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     C    5122      2.51       5
     N    1393      2.21       5
     O    1537      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8113
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1739
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1489
          Classifications: {'peptide': 191}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 182}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 852
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 104}
    Chain: "D"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 830
          Classifications: {'peptide': 109}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 97}
    Chain: "E"
      Number of atoms: 676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 676
          Classifications: {'peptide': 89}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 80}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 742
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 90}
    Chain: "H"
      Number of atoms: 977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 977
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 119}
    Chain: "L"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 808
          Classifications: {'peptide': 104}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97}
  Time building chain proxies: 1.69, per 1000 atoms: 0.21
  Number of scatterers: 8113
  At special positions: 0
  Unit cell: (96.403, 102.873, 123.577, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      61     16.00
     O    1537      8.00
     N    1393      7.00
     C    5122      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  41 " - pdb=" SG  CYS A 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 120 " - pdb=" SG  CYS B 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 192 " - pdb=" SG  CYS B 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 120 " - pdb=" SG  CYS C 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 192 " - pdb=" SG  CYS C 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  31 " - pdb=" SG  CYS D  51 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 103 " - pdb=" SG  CYS D 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  31 " - pdb=" SG  CYS E  51 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 103 " - pdb=" SG  CYS E 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  27 " - pdb=" SG  CYS F  41 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  92 " - pdb=" SG  CYS F  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  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: 0.77
  Conformation dependent library (CDL) restraints added in 326.5 milliseconds
  

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1918

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 12 sheets defined
      19.5% alpha, 23.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 19
    Processing helix  chain 'A' and resid 31 through 37
      removed outlier: 3.726A  pdb=" N   HIS A  35 " --> pdb=" O   ASN A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 42
      removed outlier: 3.563A  pdb=" N   CYS A  41 " --> pdb=" O   GLY A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 77
      removed outlier: 3.640A  pdb=" N   THR A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 111
    Processing helix  chain 'A' and resid 112 through 116
      removed outlier: 3.535A  pdb=" N   ALA A 115 " --> pdb=" O   GLY A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 128
    Processing helix  chain 'A' and resid 137 through 139
      No H-bonds generated for 'chain 'A' and resid 137 through 139'
    Processing helix  chain 'A' and resid 200 through 207
      removed outlier: 4.022A  pdb=" N   GLU A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 22
      removed outlier: 4.256A  pdb=" N   GLY B  21 " --> pdb=" O   SER B  18 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ARG B  22 " --> pdb=" O   PRO B  19 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 18 through 22'
    Processing helix  chain 'B' and resid 31 through 38
      removed outlier: 3.757A  pdb=" N   SER B  38 " --> pdb=" O   GLU B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 49
      removed outlier: 3.524A  pdb=" N   GLN B  42 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   THR B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 82
      removed outlier: 4.001A  pdb=" N   ASP B  81 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 144
      No H-bonds generated for 'chain 'B' and resid 142 through 144'
    Processing helix  chain 'B' and resid 145 through 159
      removed outlier: 5.821A  pdb=" N   LYS B 151 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   MET B 152 " --> pdb=" O   ARG B 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 144
      No H-bonds generated for 'chain 'C' and resid 142 through 144'
    Processing helix  chain 'C' and resid 145 through 159
      removed outlier: 3.758A  pdb=" N   LEU C 152 " --> pdb=" O   ALA C 148 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   MET C 155 " --> pdb=" O   ARG C 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 43 through 47
      removed outlier: 3.531A  pdb=" N   ALA D  46 " --> pdb=" O   SER D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 75
    Processing helix  chain 'E' and resid 62 through 75
      removed outlier: 3.525A  pdb=" N   VAL E  66 " --> pdb=" O   SER E  62 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   MET E  67 " --> pdb=" O   PRO E  63 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 67
      removed outlier: 3.614A  pdb=" N   THR F  55 " --> pdb=" O   THR F  51 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 11
      removed outlier: 3.674A  pdb=" N   PHE A  84 " --> pdb=" O   HIS A 149 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG A 143 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ARG A  92 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ILE A 141 " --> pdb=" O   ARG A  92 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASN A 150 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLU A 155 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24
      removed outlier: 3.871A  pdb=" N   PHE A  23 " --> pdb=" O   ILE A 136 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 52
    Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 199
    Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 29
    Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 56
      removed outlier: 3.936A  pdb=" N   TYR B  62 " --> pdb=" O   PHE B  55 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 93
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 92 through 93
    current: chain 'B' and resid 119 through 125
      removed outlier: 3.535A  pdb=" N   ALA B 133 " --> pdb=" O   ALA B 121 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ILE B 131 " --> pdb=" O   PHE B 123 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   ARG B 125 " --> pdb=" O   PRO B 129 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 128 through 135
    current: chain 'B' and resid 183 through 191
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 183 through 191
    current: chain 'C' and resid 119 through 125
      removed outlier: 6.706A  pdb=" N   LEU C 119 " --> pdb=" O   CYS C 134 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   CYS C 134 " --> pdb=" O   LEU C 119 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ALA C 121 " --> pdb=" O   GLY C 132 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   GLY C 132 " --> pdb=" O   ALA C 121 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   PHE C 123 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 128 through 135
    current: chain 'C' and resid 183 through 191
      removed outlier: 9.449A  pdb=" N   THR C 187 " --> pdb=" O   PRO D  20 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE C 189 " --> pdb=" O   MET D  18 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   VAL D  16 " --> pdb=" O   LEU C 191 " (cutoff:3.500A)
      removed outlier: 5.620A  pdb=" N   VAL D  13 " --> pdb=" O   ALA D  35 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ALA D  35 " --> pdb=" O   VAL D  13 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 48 through 55
    current: chain 'D' and resid 92 through 102
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 92 through 102
    current: chain 'E' and resid 27 through 36
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 48 through 55
    current: chain 'E' and resid 99 through 102
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 99 through 102
    current: chain 'F' and resid 23 through 31
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 37 through 43
    current: chain 'F' and resid 84 through 91
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.967A  pdb=" N   VAL H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   SER H  25 " --> pdb=" O   VAL H   3 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 34 through 39
      removed outlier: 6.673A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.595A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 46 through 51
    current: chain 'H' and resid 109 through 112
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.547A  pdb=" N   GLU L 105 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54
      removed outlier: 5.815A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)

    216 hydrogen bonds defined for protein.
    588 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.96

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2632
        1.35 -     1.48: 2218
        1.48 -     1.61: 3359
        1.61 -     1.74: 0
        1.74 -     1.86: 93
  Bond restraints: 8302
  Sorted by residual:
  bond pdb=" CB  CYS F  27 "
       pdb=" SG  CYS F  27 "
    ideal  model  delta    sigma   weight residual
    1.808  1.744  0.064 3.30e-02 9.18e+02 3.73e+00
  bond pdb=" CB  CYS F  41 "
       pdb=" SG  CYS F  41 "
    ideal  model  delta    sigma   weight residual
    1.808  1.865 -0.057 3.30e-02 9.18e+02 2.98e+00
  bond pdb=" CB  ASN A  28 "
       pdb=" CG  ASN A  28 "
    ideal  model  delta    sigma   weight residual
    1.516  1.552 -0.036 2.50e-02 1.60e+03 2.06e+00
  bond pdb=" CB  MET D  28 "
       pdb=" CG  MET D  28 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.77e+00
  bond pdb=" CG  MET D  28 "
       pdb=" SD  MET D  28 "
    ideal  model  delta    sigma   weight residual
    1.803  1.771  0.032 2.50e-02 1.60e+03 1.64e+00
  ... (remaining 8297 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.46: 11215
        3.46 -     6.91: 40
        6.91 -    10.37: 6
       10.37 -    13.83: 1
       13.83 -    17.29: 1
  Bond angle restraints: 11263
  Sorted by residual:
  angle pdb=" CA  CYS F  27 "
        pdb=" CB  CYS F  27 "
        pdb=" SG  CYS F  27 "
      ideal   model   delta    sigma   weight residual
     114.40  126.93  -12.53 2.30e+00 1.89e-01 2.97e+01
  angle pdb=" CB  ARG E  76 "
        pdb=" CG  ARG E  76 "
        pdb=" CD  ARG E  76 "
      ideal   model   delta    sigma   weight residual
     111.30  103.26    8.04 2.30e+00 1.89e-01 1.22e+01
  angle pdb=" N   CYS F  27 "
        pdb=" CA  CYS F  27 "
        pdb=" C   CYS F  27 "
      ideal   model   delta    sigma   weight residual
     109.07  113.99   -4.92 1.52e+00 4.33e-01 1.05e+01
  angle pdb=" CA  ARG E  76 "
        pdb=" CB  ARG E  76 "
        pdb=" CG  ARG E  76 "
      ideal   model   delta    sigma   weight residual
     114.10  120.36   -6.26 2.00e+00 2.50e-01 9.78e+00
  angle pdb=" CG  ARG E  76 "
        pdb=" CD  ARG E  76 "
        pdb=" NE  ARG E  76 "
      ideal   model   delta    sigma   weight residual
     112.00  118.86   -6.86 2.20e+00 2.07e-01 9.73e+00
  ... (remaining 11258 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 4123
       17.62 -    35.24: 627
       35.24 -    52.86: 168
       52.86 -    70.48: 38
       70.48 -    88.10: 22
  Dihedral angle restraints: 4978
    sinusoidal: 1962
      harmonic: 3016
  Sorted by residual:
  dihedral pdb=" CB  CYS E 103 "
           pdb=" SG  CYS E 103 "
           pdb=" SG  CYS E 109 "
           pdb=" CB  CYS E 109 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   25.07   67.93     1      1.00e+01 1.00e-02 5.99e+01
  dihedral pdb=" CB  CYS F  27 "
           pdb=" SG  CYS F  27 "
           pdb=" SG  CYS F  41 "
           pdb=" CB  CYS F  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   48.35   44.65     1      1.00e+01 1.00e-02 2.77e+01
  dihedral pdb=" CA  TYR H 105 "
           pdb=" C   TYR H 105 "
           pdb=" N   SER H 106 "
           pdb=" CA  SER H 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.71   26.29     0      5.00e+00 4.00e-02 2.77e+01
  ... (remaining 4975 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 939
       0.045 -    0.089: 209
       0.089 -    0.134: 71
       0.134 -    0.179: 5
       0.179 -    0.224: 2
  Chirality restraints: 1226
  Sorted by residual:
  chirality pdb=" CA  CYS F  27 "
            pdb=" N   CYS F  27 "
            pdb=" C   CYS F  27 "
            pdb=" CB  CYS F  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ASN B 105 "
            pdb=" N   ASN B 105 "
            pdb=" C   ASN B 105 "
            pdb=" CB  ASN B 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.41e-01
  chirality pdb=" CA  MET D  28 "
            pdb=" N   MET D  28 "
            pdb=" C   MET D  28 "
            pdb=" CB  MET D  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.60e-01
  ... (remaining 1223 not shown)

  Planarity restraints: 1451
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A  28 "    0.015 2.00e-02 2.50e+03   2.93e-02 8.58e+00
        pdb=" C   ASN A  28 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ASN A  28 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASN A  29 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 107 "   -0.016 2.00e-02 2.50e+03   1.77e-02 6.26e+00
        pdb=" CG  TYR A 107 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 107 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 107 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 107 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 107 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 107 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 107 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA L  43 "   -0.040 5.00e-02 4.00e+02   6.11e-02 5.98e+00
        pdb=" N   PRO L  44 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO L  44 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO L  44 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1448 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 530
        2.73 -     3.27: 7973
        3.27 -     3.82: 13774
        3.82 -     4.36: 15703
        4.36 -     4.90: 27311
  Nonbonded interactions: 65291
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  53 "
            pdb=" O   TYR A 130 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OH  TYR A 104 "
            pdb=" O   ARG A 117 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER C 168 "
            pdb=" OE1 GLU C 170 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OG  SER B 104 "
            pdb=" NH1 ARG B 164 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OH  TYR B 157 "
            pdb=" OE2 GLU D 102 "
     model   vdw
     2.230 3.040
  ... (remaining 65286 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.120
  Find NCS groups from input model:        0.040
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6241
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8316  Z= 0.178
  Angle     :  0.689  17.287  11291  Z= 0.354
  Chirality :  0.043   0.224   1226
  Planarity :  0.005   0.072   1451
  Dihedral  : 18.912  88.096   3018
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 32.91 %
    Favored  : 64.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.25), residues: 1016
  helix: -0.78 (0.37), residues: 168
  sheet: -0.44 (0.31), residues: 262
  loop : -0.68 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E  76 
 TYR   0.042   0.002   TYR A 107 
 PHE   0.020   0.002   PHE B  86 
 TRP   0.029   0.002   TRP L  35 
 HIS   0.004   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 8302)
  covalent geometry    : angle       0.68079 (11263)
  SS BOND              : bond        0.00415 (   14)
  SS BOND              : angle       2.26126 (   28)
  hydrogen bonds       : bond        0.19999 (  216)
  hydrogen bonds       : angle       7.50694 (  588)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.6986 (t0) cc_final: 0.6627 (t0)
REVERT: A   33 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7227 (mp)
REVERT: A   43 VAL cc_start: 0.8484 (t) cc_final: 0.8187 (p)
REVERT: A  145 THR cc_start: 0.8427 (m) cc_final: 0.8003 (p)
REVERT: D   28 MET cc_start: 0.5657 (mmt) cc_final: 0.5328 (mmt)
REVERT: D   86 GLN cc_start: 0.5723 (mp10) cc_final: 0.5519 (mt0)
REVERT: D  106 LYS cc_start: 0.6592 (OUTLIER) cc_final: 0.6260 (ptmm)
REVERT: E   73 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6410 (mtm)
REVERT: H  112 TRP cc_start: 0.7171 (m-10) cc_final: 0.5222 (m-10)
  outliers start: 19
  outliers final: 12
  residues processed: 151
  average time/residue: 0.0863
  time to fit residues: 17.4844
Evaluate side-chains
  155 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  230 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain D residue  102 GLU
Chi-restraints excluded: chain D residue  106 LYS
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   26 THR
Chi-restraints excluded: chain E residue   73 MET
Chi-restraints excluded: chain F residue   56 MET
Chi-restraints excluded: chain F residue   66 LEU
Chi-restraints excluded: chain F residue   86 LEU
Chi-restraints excluded: chain F residue   91 ILE
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   33 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  10 GLN
D  86 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.159347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.142046 restraints weight = 12044.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.146499 restraints weight = 6232.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.149431 restraints weight = 3752.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.151437 restraints weight = 2506.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.152650 restraints weight = 1806.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6525
moved from start:          0.0757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8316  Z= 0.198
  Angle     :  0.653  17.463  11291  Z= 0.334
  Chirality :  0.043   0.199   1226
  Planarity :  0.005   0.072   1451
  Dihedral  :  7.292  84.416   1201
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 29.93 %
    Favored  : 64.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.25), residues: 1016
  helix: -0.11 (0.40), residues: 165
  sheet: -0.39 (0.29), residues: 291
  loop : -0.64 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 118 
 TYR   0.035   0.002   TYR A 107 
 PHE   0.020   0.002   PHE B  86 
 TRP   0.016   0.002   TRP L  35 
 HIS   0.004   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 8302)
  covalent geometry    : angle       0.64938 (11263)
  SS BOND              : bond        0.00334 (   14)
  SS BOND              : angle       1.53839 (   28)
  hydrogen bonds       : bond        0.04657 (  216)
  hydrogen bonds       : angle       6.21903 (  588)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 138
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7180 (t0) cc_final: 0.6944 (t0)
REVERT: A   43 VAL cc_start: 0.8444 (t) cc_final: 0.8175 (p)
REVERT: B   30 LEU cc_start: 0.5933 (OUTLIER) cc_final: 0.5607 (tp)
REVERT: C  124 VAL cc_start: 0.8335 (t) cc_final: 0.8071 (m)
REVERT: D   86 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.5607 (mt0)
REVERT: E   64 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.5527 (ttm)
REVERT: H  112 TRP cc_start: 0.7089 (m-10) cc_final: 0.5120 (m-10)
REVERT: L   91 TYR cc_start: 0.7785 (p90) cc_final: 0.7275 (p90)
  outliers start: 49
  outliers final: 24
  residues processed: 170
  average time/residue: 0.0800
  time to fit residues: 18.5738
Evaluate side-chains
  163 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  199 CYS
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   86 GLN
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   64 MET
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue   91 ILE
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  105 TYR
Chi-restraints excluded: chain H residue  122 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 49 optimal weight:    0.1980
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 44 optimal weight:    0.3980
   chunk 18 optimal weight:    7.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
B  10 GLN
D  86 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.160660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.143516 restraints weight = 11891.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.147996 restraints weight = 6140.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.150943 restraints weight = 3694.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.152918 restraints weight = 2467.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.154149 restraints weight = 1771.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6504
moved from start:          0.0971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8316  Z= 0.154
  Angle     :  0.613  16.438  11291  Z= 0.311
  Chirality :  0.042   0.189   1226
  Planarity :  0.004   0.060   1451
  Dihedral  :  5.711  84.461   1176
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 30.28 %
    Favored  : 63.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.26), residues: 1016
  helix:  0.07 (0.41), residues: 164
  sheet: -0.33 (0.30), residues: 286
  loop : -0.63 (0.25), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 118 
 TYR   0.025   0.001   TYR A 107 
 PHE   0.015   0.001   PHE B  86 
 TRP   0.009   0.002   TRP L  96 
 HIS   0.003   0.001   HIS E  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8302)
  covalent geometry    : angle       0.60973 (11263)
  SS BOND              : bond        0.00350 (   14)
  SS BOND              : angle       1.46072 (   28)
  hydrogen bonds       : bond        0.04016 (  216)
  hydrogen bonds       : angle       5.86932 (  588)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 148
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 VAL cc_start: 0.8430 (t) cc_final: 0.8164 (p)
REVERT: A   68 MET cc_start: 0.6310 (tpp) cc_final: 0.6105 (tpp)
REVERT: B   30 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5602 (tp)
REVERT: B  107 THR cc_start: 0.7556 (m) cc_final: 0.7213 (p)
REVERT: B  115 THR cc_start: 0.7356 (m) cc_final: 0.7011 (p)
REVERT: C  145 MET cc_start: 0.7510 (mmt) cc_final: 0.7301 (tpp)
REVERT: D  106 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6604 (ptmm)
REVERT: E   64 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.5444 (ttm)
REVERT: H   83 MET cc_start: 0.7083 (mmm) cc_final: 0.6616 (mmt)
REVERT: H  112 TRP cc_start: 0.7048 (m-10) cc_final: 0.5297 (m-10)
  outliers start: 51
  outliers final: 27
  residues processed: 184
  average time/residue: 0.0922
  time to fit residues: 23.1252
Evaluate side-chains
  175 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  199 CYS
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  106 LYS
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   64 MET
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue   52 TRP
Chi-restraints excluded: chain F residue   91 ILE
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue  122 SER
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 90 optimal weight:    0.2980
   chunk 67 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0050
   chunk 3 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
B  10 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.160492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.143176 restraints weight = 12196.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.147735 restraints weight = 6265.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.150695 restraints weight = 3753.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.152688 restraints weight = 2497.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.153946 restraints weight = 1793.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6484
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8316  Z= 0.131
  Angle     :  0.594  14.209  11291  Z= 0.299
  Chirality :  0.042   0.190   1226
  Planarity :  0.004   0.058   1451
  Dihedral  :  5.547  84.130   1176
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 30.28 %
    Favored  : 63.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.26), residues: 1016
  helix:  0.19 (0.41), residues: 164
  sheet: -0.36 (0.29), residues: 307
  loop : -0.56 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 148 
 TYR   0.020   0.001   TYR A 107 
 PHE   0.013   0.001   PHE B  86 
 TRP   0.018   0.002   TRP L  35 
 HIS   0.003   0.001   HIS E  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8302)
  covalent geometry    : angle       0.59147 (11263)
  SS BOND              : bond        0.00238 (   14)
  SS BOND              : angle       1.32275 (   28)
  hydrogen bonds       : bond        0.03475 (  216)
  hydrogen bonds       : angle       5.72423 (  588)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 144
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.7144 (t0) cc_final: 0.6870 (t0)
REVERT: A   67 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7505 (ttm110)
REVERT: A  196 PRO cc_start: 0.6772 (Cg_endo) cc_final: 0.6447 (Cg_exo)
REVERT: B   30 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.5471 (tp)
REVERT: B  107 THR cc_start: 0.7563 (m) cc_final: 0.7234 (p)
REVERT: B  115 THR cc_start: 0.7278 (m) cc_final: 0.7014 (p)
REVERT: C  177 GLU cc_start: 0.4608 (OUTLIER) cc_final: 0.4211 (mt-10)
REVERT: D  106 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6578 (ptmm)
REVERT: E   64 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5386 (ttm)
REVERT: H    4 LEU cc_start: 0.8343 (mt) cc_final: 0.8118 (mt)
REVERT: H   53 TYR cc_start: 0.6319 (p90) cc_final: 0.5931 (p90)
REVERT: H   83 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6701 (mmm)
  outliers start: 53
  outliers final: 28
  residues processed: 183
  average time/residue: 0.0849
  time to fit residues: 21.4869
Evaluate side-chains
  175 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 SER
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  199 CYS
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  177 GLU
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  106 LYS
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   64 MET
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain F residue   24 GLN
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  122 SER
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 81 optimal weight:    0.5980
   chunk 78 optimal weight:    5.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  31 ASN
B  10 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.157540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.140083 restraints weight = 12108.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.144589 restraints weight = 6207.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.147536 restraints weight = 3735.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.149465 restraints weight = 2498.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.150853 restraints weight = 1815.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6543
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8316  Z= 0.216
  Angle     :  0.666  16.557  11291  Z= 0.336
  Chirality :  0.044   0.191   1226
  Planarity :  0.005   0.060   1451
  Dihedral  :  5.764  84.043   1174
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 29.59 %
    Favored  : 63.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.26), residues: 1016
  helix:  0.16 (0.42), residues: 164
  sheet: -0.45 (0.30), residues: 294
  loop : -0.65 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 148 
 TYR   0.023   0.002   TYR B 184 
 PHE   0.017   0.002   PHE B  86 
 TRP   0.021   0.002   TRP L  35 
 HIS   0.004   0.001   HIS E  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 8302)
  covalent geometry    : angle       0.66239 (11263)
  SS BOND              : bond        0.00501 (   14)
  SS BOND              : angle       1.47421 (   28)
  hydrogen bonds       : bond        0.04185 (  216)
  hydrogen bonds       : angle       5.80588 (  588)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 150
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 VAL cc_start: 0.8411 (t) cc_final: 0.8144 (p)
REVERT: A   67 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7530 (ttm110)
REVERT: A  196 PRO cc_start: 0.6840 (Cg_endo) cc_final: 0.6518 (Cg_exo)
REVERT: B   30 LEU cc_start: 0.5899 (OUTLIER) cc_final: 0.5654 (tp)
REVERT: B  107 THR cc_start: 0.7759 (m) cc_final: 0.7478 (p)
REVERT: B  115 THR cc_start: 0.7283 (m) cc_final: 0.7041 (p)
REVERT: C  128 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.5787 (pp30)
REVERT: C  177 GLU cc_start: 0.4640 (OUTLIER) cc_final: 0.4256 (mt-10)
REVERT: D  106 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6587 (ptmm)
REVERT: E   64 MET cc_start: 0.5940 (OUTLIER) cc_final: 0.5580 (ttm)
REVERT: H   53 TYR cc_start: 0.6360 (p90) cc_final: 0.5960 (p90)
REVERT: H   83 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6744 (mmm)
REVERT: H  112 TRP cc_start: 0.7231 (m-10) cc_final: 0.5624 (m-10)
  outliers start: 59
  outliers final: 37
  residues processed: 190
  average time/residue: 0.0804
  time to fit residues: 20.9398
Evaluate side-chains
  191 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 148
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ASN
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  230 SER
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  199 CYS
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  177 GLU
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  106 LYS
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   64 MET
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue   86 LEU
Chi-restraints excluded: chain F residue   91 ILE
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  105 TYR
Chi-restraints excluded: chain H residue  122 SER
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 66 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A  31 ASN
B  10 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.158791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.141411 restraints weight = 11905.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.145908 restraints weight = 6148.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.148843 restraints weight = 3705.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.150797 restraints weight = 2485.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.152164 restraints weight = 1796.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6517
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8316  Z= 0.163
  Angle     :  0.650  16.866  11291  Z= 0.322
  Chirality :  0.043   0.189   1226
  Planarity :  0.004   0.061   1451
  Dihedral  :  5.683  84.960   1174
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 30.16 %
    Favored  : 63.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.26), residues: 1016
  helix:  0.22 (0.42), residues: 164
  sheet: -0.38 (0.30), residues: 297
  loop : -0.67 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E  76 
 TYR   0.021   0.002   TYR A 107 
 PHE   0.013   0.001   PHE B  86 
 TRP   0.021   0.002   TRP L  35 
 HIS   0.003   0.001   HIS E  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 8302)
  covalent geometry    : angle       0.64619 (11263)
  SS BOND              : bond        0.00304 (   14)
  SS BOND              : angle       1.49541 (   28)
  hydrogen bonds       : bond        0.03771 (  216)
  hydrogen bonds       : angle       5.74287 (  588)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 143
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ARG cc_start: 0.7377 (ttt90) cc_final: 0.6850 (ttt90)
REVERT: A   29 ASN cc_start: 0.7154 (t0) cc_final: 0.6881 (t0)
REVERT: A  196 PRO cc_start: 0.6775 (Cg_endo) cc_final: 0.6525 (Cg_exo)
REVERT: B   30 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5625 (tp)
REVERT: C  128 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.5751 (pp30)
REVERT: C  177 GLU cc_start: 0.4589 (OUTLIER) cc_final: 0.4214 (mt-10)
REVERT: D  106 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6591 (ptmm)
REVERT: E   64 MET cc_start: 0.5914 (OUTLIER) cc_final: 0.5521 (ttm)
REVERT: E   76 ARG cc_start: 0.6664 (ptt180) cc_final: 0.6440 (ptp90)
REVERT: H   53 TYR cc_start: 0.6354 (p90) cc_final: 0.5961 (p90)
REVERT: H   83 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6714 (mmm)
REVERT: H  112 TRP cc_start: 0.7262 (m-10) cc_final: 0.5626 (m-10)
  outliers start: 53
  outliers final: 38
  residues processed: 182
  average time/residue: 0.0906
  time to fit residues: 22.2638
Evaluate side-chains
  187 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 143
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ASN
Chi-restraints excluded: chain A residue  230 SER
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  199 CYS
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  177 GLU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  106 LYS
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   64 MET
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain F residue   24 GLN
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue   86 LEU
Chi-restraints excluded: chain F residue   91 ILE
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   95 TYR
Chi-restraints excluded: chain H residue  122 SER
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 74 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  31 ASN
B  10 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.158860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.141280 restraints weight = 12112.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.145848 restraints weight = 6240.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.148812 restraints weight = 3749.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.150802 restraints weight = 2509.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.152145 restraints weight = 1810.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6522
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8316  Z= 0.172
  Angle     :  0.649  15.933  11291  Z= 0.323
  Chirality :  0.043   0.189   1226
  Planarity :  0.004   0.060   1451
  Dihedral  :  5.705  85.119   1174
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 30.39 %
    Favored  : 63.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.26), residues: 1016
  helix:  0.23 (0.42), residues: 164
  sheet: -0.35 (0.30), residues: 297
  loop : -0.64 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 148 
 TYR   0.018   0.002   TYR L  91 
 PHE   0.013   0.001   PHE B  86 
 TRP   0.024   0.002   TRP L  35 
 HIS   0.003   0.001   HIS E  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 8302)
  covalent geometry    : angle       0.64505 (11263)
  SS BOND              : bond        0.00343 (   14)
  SS BOND              : angle       1.56797 (   28)
  hydrogen bonds       : bond        0.03762 (  216)
  hydrogen bonds       : angle       5.70896 (  588)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 144
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ARG cc_start: 0.7393 (ttt90) cc_final: 0.6858 (ttt90)
REVERT: A   29 ASN cc_start: 0.7142 (t0) cc_final: 0.6885 (t0)
REVERT: A  196 PRO cc_start: 0.6755 (Cg_endo) cc_final: 0.6514 (Cg_exo)
REVERT: B   30 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5656 (tp)
REVERT: C  128 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.5753 (pp30)
REVERT: C  177 GLU cc_start: 0.4685 (OUTLIER) cc_final: 0.4298 (mt-10)
REVERT: D   29 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6689 (tp)
REVERT: D  106 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6583 (ptmm)
REVERT: E   64 MET cc_start: 0.5926 (OUTLIER) cc_final: 0.5544 (ttm)
REVERT: E   76 ARG cc_start: 0.6659 (ptt180) cc_final: 0.6441 (ptt90)
REVERT: H   53 TYR cc_start: 0.6421 (p90) cc_final: 0.5993 (p90)
REVERT: H   83 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6705 (mmm)
REVERT: H  112 TRP cc_start: 0.7293 (m-10) cc_final: 0.5626 (m-10)
  outliers start: 57
  outliers final: 41
  residues processed: 185
  average time/residue: 0.0765
  time to fit residues: 19.5490
Evaluate side-chains
  191 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 143
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  230 SER
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  199 CYS
Chi-restraints excluded: chain C residue  115 THR
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  177 GLU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  106 LYS
Chi-restraints excluded: chain E residue   11 MET
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   64 MET
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain F residue   24 GLN
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue   86 LEU
Chi-restraints excluded: chain F residue   91 ILE
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   95 TYR
Chi-restraints excluded: chain H residue  122 SER
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 34 optimal weight:    0.0370
   chunk 19 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 44 optimal weight:    0.4980
   chunk 75 optimal weight:    0.0170
   chunk 0 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0070
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.2314

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

Flipped N/Q/H residues before XYZ refinement:
A  31 ASN
B  10 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.160968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.143492 restraints weight = 12103.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.148041 restraints weight = 6168.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.151029 restraints weight = 3701.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.153074 restraints weight = 2451.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.154446 restraints weight = 1754.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6450
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8316  Z= 0.109
  Angle     :  0.612  14.164  11291  Z= 0.302
  Chirality :  0.042   0.185   1226
  Planarity :  0.004   0.060   1451
  Dihedral  :  5.429  85.294   1174
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 31.54 %
    Favored  : 63.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.26), residues: 1016
  helix:  0.22 (0.42), residues: 164
  sheet: -0.17 (0.31), residues: 281
  loop : -0.58 (0.25), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 148 
 TYR   0.015   0.001   TYR A 107 
 PHE   0.009   0.001   PHE C 123 
 TRP   0.032   0.002   TRP L  35 
 HIS   0.003   0.000   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8302)
  covalent geometry    : angle       0.60867 (11263)
  SS BOND              : bond        0.00397 (   14)
  SS BOND              : angle       1.43957 (   28)
  hydrogen bonds       : bond        0.03151 (  216)
  hydrogen bonds       : angle       5.62592 (  588)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 133
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ARG cc_start: 0.7304 (ttt90) cc_final: 0.6761 (ttt90)
REVERT: A   29 ASN cc_start: 0.7100 (t0) cc_final: 0.6843 (t0)
REVERT: A  196 PRO cc_start: 0.6662 (Cg_endo) cc_final: 0.6425 (Cg_exo)
REVERT: B   30 LEU cc_start: 0.5641 (OUTLIER) cc_final: 0.5426 (tp)
REVERT: C  128 GLN cc_start: 0.6623 (OUTLIER) cc_final: 0.5722 (pp30)
REVERT: C  177 GLU cc_start: 0.4679 (OUTLIER) cc_final: 0.4273 (mt-10)
REVERT: D   29 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6570 (tp)
REVERT: D  106 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6542 (ptmm)
REVERT: E   64 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.5066 (ttm)
REVERT: E   67 MET cc_start: 0.7483 (tmm) cc_final: 0.7119 (tmm)
REVERT: H    6 GLU cc_start: 0.6650 (mp0) cc_final: 0.6153 (mp0)
REVERT: H   53 TYR cc_start: 0.6336 (p90) cc_final: 0.6014 (p90)
REVERT: H   83 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6825 (mmm)
REVERT: H  112 TRP cc_start: 0.7293 (m-10) cc_final: 0.5657 (m-10)
  outliers start: 45
  outliers final: 26
  residues processed: 166
  average time/residue: 0.0820
  time to fit residues: 18.5766
Evaluate side-chains
  164 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   36 ARG
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  199 CYS
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  177 GLU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  106 LYS
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   18 MET
Chi-restraints excluded: chain E residue   64 MET
Chi-restraints excluded: chain F residue   10 PHE
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue   86 LEU
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   95 TYR
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  122 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0170
   chunk 28 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 81 optimal weight:    0.1980
   chunk 44 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
B  10 GLN
H  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.158746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.141850 restraints weight = 11985.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.146286 restraints weight = 6173.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.149186 restraints weight = 3685.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.151043 restraints weight = 2436.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.152362 restraints weight = 1755.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6483
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8316  Z= 0.149
  Angle     :  0.634  15.893  11291  Z= 0.313
  Chirality :  0.042   0.187   1226
  Planarity :  0.004   0.059   1451
  Dihedral  :  5.509  84.878   1174
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 31.65 %
    Favored  : 63.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.26), residues: 1016
  helix:  0.22 (0.42), residues: 164
  sheet: -0.19 (0.30), residues: 290
  loop : -0.54 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG E  76 
 TYR   0.017   0.001   TYR C 173 
 PHE   0.011   0.001   PHE B  86 
 TRP   0.033   0.002   TRP L  35 
 HIS   0.003   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8302)
  covalent geometry    : angle       0.62936 (11263)
  SS BOND              : bond        0.00278 (   14)
  SS BOND              : angle       1.66570 (   28)
  hydrogen bonds       : bond        0.03485 (  216)
  hydrogen bonds       : angle       5.58965 (  588)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 127
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ARG cc_start: 0.7333 (ttt90) cc_final: 0.6770 (ttt90)
REVERT: A   29 ASN cc_start: 0.7079 (t0) cc_final: 0.6836 (t0)
REVERT: B   30 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5564 (tp)
REVERT: B  145 MET cc_start: 0.7301 (mmt) cc_final: 0.6907 (mmt)
REVERT: C  128 GLN cc_start: 0.6675 (OUTLIER) cc_final: 0.5743 (pp30)
REVERT: C  177 GLU cc_start: 0.4675 (OUTLIER) cc_final: 0.4273 (mt-10)
REVERT: D   29 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6640 (tp)
REVERT: D  106 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6558 (ptmm)
REVERT: E   64 MET cc_start: 0.5926 (OUTLIER) cc_final: 0.5193 (ttm)
REVERT: H   53 TYR cc_start: 0.6348 (p90) cc_final: 0.6025 (p90)
REVERT: H   83 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6654 (mmm)
REVERT: H  112 TRP cc_start: 0.7341 (m-10) cc_final: 0.5638 (m-10)
  outliers start: 41
  outliers final: 27
  residues processed: 156
  average time/residue: 0.0829
  time to fit residues: 17.5795
Evaluate side-chains
  160 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  199 CYS
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  177 GLU
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  106 LYS
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   18 MET
Chi-restraints excluded: chain E residue   64 MET
Chi-restraints excluded: chain F residue   10 PHE
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain F residue   25 GLU
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue   86 LEU
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   95 TYR
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  122 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 45 optimal weight:    0.4980
   chunk 93 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0470
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
B  10 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.158736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.141781 restraints weight = 12054.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.146200 restraints weight = 6188.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.149069 restraints weight = 3688.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.150851 restraints weight = 2450.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.152217 restraints weight = 1788.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   8316  Z= 0.151
  Angle     :  0.663  19.461  11291  Z= 0.322
  Chirality :  0.043   0.186   1226
  Planarity :  0.005   0.078   1451
  Dihedral  :  5.571  84.850   1174
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 32.34 %
    Favored  : 63.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.26), residues: 1016
  helix:  0.27 (0.42), residues: 158
  sheet: -0.17 (0.30), residues: 290
  loop : -0.50 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG E  76 
 TYR   0.017   0.001   TYR C 173 
 PHE   0.011   0.001   PHE B  86 
 TRP   0.036   0.002   TRP L  35 
 HIS   0.004   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8302)
  covalent geometry    : angle       0.65811 (11263)
  SS BOND              : bond        0.00300 (   14)
  SS BOND              : angle       1.78080 (   28)
  hydrogen bonds       : bond        0.03532 (  216)
  hydrogen bonds       : angle       5.64779 (  588)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 130
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ARG cc_start: 0.7322 (ttt90) cc_final: 0.6817 (ttt90)
REVERT: A   29 ASN cc_start: 0.7068 (t0) cc_final: 0.6822 (t0)
REVERT: B   10 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7419 (tp40)
REVERT: B   30 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5547 (tp)
REVERT: C  128 GLN cc_start: 0.6667 (OUTLIER) cc_final: 0.5728 (pp30)
REVERT: C  177 GLU cc_start: 0.4687 (OUTLIER) cc_final: 0.4297 (mt-10)
REVERT: D  106 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6543 (ptmm)
REVERT: E   64 MET cc_start: 0.5941 (OUTLIER) cc_final: 0.5203 (ttm)
REVERT: H   53 TYR cc_start: 0.6350 (p90) cc_final: 0.6023 (p90)
REVERT: H   83 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6649 (mmm)
REVERT: H  112 TRP cc_start: 0.7358 (m-10) cc_final: 0.5583 (m-10)
  outliers start: 38
  outliers final: 28
  residues processed: 157
  average time/residue: 0.0789
  time to fit residues: 17.2382
Evaluate side-chains
  163 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain B residue   10 GLN
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  199 CYS
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  177 GLU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  106 LYS
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   18 MET
Chi-restraints excluded: chain E residue   64 MET
Chi-restraints excluded: chain F residue   10 PHE
Chi-restraints excluded: chain F residue   20 LYS
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue   86 LEU
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   95 TYR
Chi-restraints excluded: chain H residue  122 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 15 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.158409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.141533 restraints weight = 12091.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.145850 restraints weight = 6236.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.148752 restraints weight = 3749.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.150701 restraints weight = 2485.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.151858 restraints weight = 1780.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6493
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.192   8316  Z= 0.267
  Angle     :  0.985  59.191  11291  Z= 0.554
  Chirality :  0.051   1.001   1226
  Planarity :  0.005   0.075   1451
  Dihedral  :  5.580  84.860   1174
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 32.91 %
    Favored  : 62.84 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 7.84 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.26), residues: 1016
  helix:  0.26 (0.42), residues: 158
  sheet: -0.17 (0.30), residues: 290
  loop : -0.49 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 148 
 TYR   0.014   0.001   TYR C 173 
 PHE   0.010   0.001   PHE D  52 
 TRP   0.028   0.002   TRP L  35 
 HIS   0.003   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 8302)
  covalent geometry    : angle       0.98290 (11263)
  SS BOND              : bond        0.00327 (   14)
  SS BOND              : angle       1.67744 (   28)
  hydrogen bonds       : bond        0.03557 (  216)
  hydrogen bonds       : angle       5.64790 (  588)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1568.48 seconds
wall clock time: 27 minutes 43.13 seconds (1663.13 seconds total)