Starting phenix.real_space_refine
on Thu Feb 13 07:23:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vfj_31956/02_2025/7vfj_31956.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vfj_31956/02_2025/7vfj_31956.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vfj_31956/02_2025/7vfj_31956.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vfj_31956/02_2025/7vfj_31956.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vfj_31956/02_2025/7vfj_31956.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vfj_31956/02_2025/7vfj_31956.cif"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.032
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      46      5.16       5
     C    5745      2.51       5
     N    1504      2.21       5
     O    1485      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8780
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1586
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 6, 'TRANS': 195}
    Chain: "B"
      Number of atoms: 1663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1663
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 16, 'TRANS': 203}
    Chain: "C"
      Number of atoms: 1848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1848
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 11, 'TRANS': 219}
    Chain: "D"
      Number of atoms: 434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 434
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1586
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 6, 'TRANS': 195}
    Chain: "F"
      Number of atoms: 1663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1663
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 16, 'TRANS': 203}
  Time building chain proxies: 5.97, per 1000 atoms: 0.68
  Number of scatterers: 8780
  At special positions: 0
  Unit cell: (102.336, 99.84, 114.816, 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      46     16.00
     O    1485      8.00
     N    1504      7.00
     C    5745      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.28
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2084

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 6 sheets defined
      65.1% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 48
      removed outlier: 3.668A  pdb=" N   LEU A  44 " --> pdb=" O   LYS A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 69
    Processing helix  chain 'A' and resid 90 through 99
      removed outlier: 3.561A  pdb=" N   ASN A  94 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 115
      removed outlier: 3.708A  pdb=" N   GLU A 109 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 138
      removed outlier: 3.574A  pdb=" N   GLN A 132 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 3.793A  pdb=" N   GLN A 171 " --> pdb=" O   GLN A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 176
      removed outlier: 4.063A  pdb=" N   GLN A 175 " --> pdb=" O   GLN A 171 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLY A 176 " --> pdb=" O   HIS A 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 171 through 176'
    Processing helix  chain 'A' and resid 190 through 194
      removed outlier: 3.844A  pdb=" N   LYS A 193 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 15
      removed outlier: 3.585A  pdb=" N   ILE B   6 " --> pdb=" O   MET B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 40
      removed outlier: 3.785A  pdb=" N   LEU B  25 " --> pdb=" O   ILE B  21 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   PHE B  35 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      Proline residue:  B  36  - end of helix
    Processing helix  chain 'B' and resid 42 through 75
      removed outlier: 3.838A  pdb=" N   LEU B  46 " --> pdb=" O   GLU B  42 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ARG B  48 " --> pdb=" O   GLN B  44 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA B  50 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      Proline residue:  B  51  - end of helix
      removed outlier: 3.747A  pdb=" N   GLU B  67 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ARG B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE B  70 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ASP B  72 " --> pdb=" O   ARG B  68 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   ASP B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   GLN B  75 " --> pdb=" O   ARG B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 84
    Processing helix  chain 'B' and resid 88 through 120
      removed outlier: 3.663A  pdb=" N   ALA B  95 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS B  96 " --> pdb=" O   VAL B  92 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   LEU B 106 " --> pdb=" O   MET B 102 " (cutoff:3.500A)
      Proline residue:  B 107  - end of helix
      Proline residue:  B 113  - end of helix
      removed outlier: 3.531A  pdb=" N   MET B 117 " --> pdb=" O   PRO B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 134
      removed outlier: 3.525A  pdb=" N   VAL B 128 " --> pdb=" O   TYR B 124 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   MET B 129 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 149
      Proline residue:  B 146  - end of helix
      removed outlier: 4.322A  pdb=" N   ALA B 149 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 162
      removed outlier: 3.765A  pdb=" N   SER B 162 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 185
      removed outlier: 3.807A  pdb=" N   LEU B 168 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
      Proline residue:  B 171  - end of helix
      removed outlier: 4.103A  pdb=" N   PHE B 175 " --> pdb=" O   PRO B 171 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   ASP B 181 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ALA B 182 " --> pdb=" O   ALA B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 204
      removed outlier: 4.197A  pdb=" N   LEU B 196 " --> pdb=" O   TYR B 192 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA B 198 " --> pdb=" O   ALA B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 220
    Processing helix  chain 'C' and resid 13 through 18
    Processing helix  chain 'C' and resid 21 through 32
      removed outlier: 3.544A  pdb=" N   ALA C  28 " --> pdb=" O   TRP C  24 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   SER C  29 " --> pdb=" O   LEU C  25 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL C  30 " --> pdb=" O   ALA C  26 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   VAL C  31 " --> pdb=" O   ILE C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 32 through 37
    Processing helix  chain 'C' and resid 56 through 61
    Processing helix  chain 'C' and resid 61 through 80
      removed outlier: 3.728A  pdb=" N   SER C  67 " --> pdb=" O   ALA C  63 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   MET C  68 " --> pdb=" O   ALA C  64 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   TYR C  71 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA C  75 " --> pdb=" O   TYR C  71 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   VAL C  76 " --> pdb=" O   ALA C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 96
      removed outlier: 3.659A  pdb=" N   ALA C  92 " --> pdb=" O   MET C  88 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   VAL C  93 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ALA C  94 " --> pdb=" O   ASN C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 120
      removed outlier: 3.523A  pdb=" N   LYS C 116 " --> pdb=" O   SER C 112 " (cutoff:3.500A)
      Proline residue:  C 117  - end of helix
    Processing helix  chain 'C' and resid 126 through 147
      removed outlier: 4.589A  pdb=" N   GLU C 132 " --> pdb=" O   ARG C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 185
      Proline residue:  C 171  - end of helix
      removed outlier: 3.830A  pdb=" N   TRP C 179 " --> pdb=" O   TYR C 175 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 197
      No H-bonds generated for 'chain 'C' and resid 195 through 197'
    Processing helix  chain 'C' and resid 198 through 229
      removed outlier: 3.979A  pdb=" N   LEU C 202 " --> pdb=" O   MET C 198 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU C 226 " --> pdb=" O   ARG C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 237
      removed outlier: 4.186A  pdb=" N   GLU C 237 " --> pdb=" O   TRP C 234 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 54
      Proline residue:  D  31  - end of helix
      removed outlier: 3.522A  pdb=" N   LEU D  47 " --> pdb=" O   HIS D  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 40 through 49
    Processing helix  chain 'E' and resid 70 through 75
      removed outlier: 3.734A  pdb=" N   GLN E  74 " --> pdb=" O   ASP E  70 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ASN E  75 " --> pdb=" O   SER E  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 70 through 75'
    Processing helix  chain 'E' and resid 90 through 98
      removed outlier: 3.942A  pdb=" N   TYR E  98 " --> pdb=" O   ASN E  94 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 106 through 114
    Processing helix  chain 'E' and resid 123 through 127
    Processing helix  chain 'E' and resid 128 through 138
      removed outlier: 3.953A  pdb=" N   ARG E 134 " --> pdb=" O   GLY E 130 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA E 136 " --> pdb=" O   GLN E 132 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 139 through 142
    Processing helix  chain 'E' and resid 158 through 176
      removed outlier: 4.116A  pdb=" N   ASP E 163 " --> pdb=" O   VAL E 159 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ARG E 164 " --> pdb=" O   ASN E 160 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   ALA E 170 " --> pdb=" O   THR E 166 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   GLU E 174 " --> pdb=" O   ALA E 170 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 16
      removed outlier: 3.774A  pdb=" N   ARG F  16 " --> pdb=" O   ARG F  12 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 22 through 40
      Proline residue:  F  36  - end of helix
    Processing helix  chain 'F' and resid 42 through 67
      Proline residue:  F  51  - end of helix
      removed outlier: 3.516A  pdb=" N   TRP F  55 " --> pdb=" O   PRO F  51 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLU F  67 " --> pdb=" O   LEU F  63 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 88 through 111
      removed outlier: 4.038A  pdb=" N   LEU F 106 " --> pdb=" O   MET F 102 " (cutoff:3.500A)
      Proline residue:  F 107  - end of helix
      removed outlier: 3.868A  pdb=" N   LEU F 111 " --> pdb=" O   PRO F 107 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 111 through 120
    Processing helix  chain 'F' and resid 122 through 152
      Proline residue:  F 138  - end of helix
      Proline residue:  F 146  - end of helix
    Processing helix  chain 'F' and resid 158 through 166
    Processing helix  chain 'F' and resid 169 through 185
      removed outlier: 4.437A  pdb=" N   MET F 185 " --> pdb=" O   ASP F 181 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 190 through 220
      removed outlier: 3.525A  pdb=" N   ILE F 195 " --> pdb=" O   GLY F 191 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER F 207 " --> pdb=" O   THR F 203 " (cutoff:3.500A)
      Proline residue:  F 208  - end of helix
      removed outlier: 3.607A  pdb=" N   GLN F 220 " --> pdb=" O   ARG F 216 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20
      removed outlier: 6.004A  pdb=" N   SER A  18 " --> pdb=" O   CYS A   9 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   CYS A   9 " --> pdb=" O   SER A  18 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LEU A   7 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   ALA A  55 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79
      removed outlier: 6.358A  pdb=" N   LEU A  77 " --> pdb=" O   ILE A 149 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASP A 151 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   ILE A  79 " --> pdb=" O   ASP A 151 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 60
    Processing sheet with id=AA4, first strand: chain 'E' and resid 15 through 20
      removed outlier: 6.213A  pdb=" N   SER E  18 " --> pdb=" O   CYS E   9 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   CYS E   9 " --> pdb=" O   SER E  18 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   GLU E   6 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   GLU E  57 " --> pdb=" O   GLU E   6 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 79
      removed outlier: 5.953A  pdb=" N   LEU E  77 " --> pdb=" O   ILE E 149 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   TRP E  29 " --> pdb=" O   ARG E 195 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   ILE E 197 " --> pdb=" O   TRP E  29 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   GLN E  31 " --> pdb=" O   ILE E 197 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 59 through 60

    456 hydrogen bonds defined for protein.
    1332 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: 2.44

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2784
        1.34 -     1.46: 1833
        1.46 -     1.58: 4289
        1.58 -     1.69: 1
        1.69 -     1.81: 87
  Bond restraints: 8994
  Sorted by residual:
  bond pdb=" CB  PRO E 186 "
       pdb=" CG  PRO E 186 "
    ideal  model  delta    sigma   weight residual
    1.492  1.670 -0.178 5.00e-02 4.00e+02 1.26e+01
  bond pdb=" CG  PRO E 186 "
       pdb=" CD  PRO E 186 "
    ideal  model  delta    sigma   weight residual
    1.503  1.422  0.081 3.40e-02 8.65e+02 5.67e+00
  bond pdb=" C   ASN B  23 "
       pdb=" N   PRO B  24 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.28e-02 6.10e+03 3.63e+00
  bond pdb=" N   PRO E 186 "
       pdb=" CD  PRO E 186 "
    ideal  model  delta    sigma   weight residual
    1.473  1.498 -0.025 1.40e-02 5.10e+03 3.08e+00
  bond pdb=" CG  LEU E  50 "
       pdb=" CD1 LEU E  50 "
    ideal  model  delta    sigma   weight residual
    1.521  1.472  0.049 3.30e-02 9.18e+02 2.22e+00
  ... (remaining 8989 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.19: 12132
        3.19 -     6.38: 131
        6.38 -     9.57: 7
        9.57 -    12.77: 2
       12.77 -    15.96: 1
  Bond angle restraints: 12273
  Sorted by residual:
  angle pdb=" CA  PRO E 186 "
        pdb=" N   PRO E 186 "
        pdb=" CD  PRO E 186 "
      ideal   model   delta    sigma   weight residual
     112.00   96.04   15.96 1.40e+00 5.10e-01 1.30e+02
  angle pdb=" N   PRO E 186 "
        pdb=" CD  PRO E 186 "
        pdb=" CG  PRO E 186 "
      ideal   model   delta    sigma   weight residual
     103.20   94.96    8.24 1.50e+00 4.44e-01 3.02e+01
  angle pdb=" C   ASP A  12 "
        pdb=" CA  ASP A  12 "
        pdb=" CB  ASP A  12 "
      ideal   model   delta    sigma   weight residual
     117.23  110.44    6.79 1.36e+00 5.41e-01 2.49e+01
  angle pdb=" CA  MET F 129 "
        pdb=" CB  MET F 129 "
        pdb=" CG  MET F 129 "
      ideal   model   delta    sigma   weight residual
     114.10  122.00   -7.90 2.00e+00 2.50e-01 1.56e+01
  angle pdb=" N   MET F 129 "
        pdb=" CA  MET F 129 "
        pdb=" CB  MET F 129 "
      ideal   model   delta    sigma   weight residual
     110.30  116.05   -5.75 1.54e+00 4.22e-01 1.39e+01
  ... (remaining 12268 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 4763
       17.43 -    34.86: 434
       34.86 -    52.29: 62
       52.29 -    69.72: 7
       69.72 -    87.15: 4
  Dihedral angle restraints: 5270
    sinusoidal: 2046
      harmonic: 3224
  Sorted by residual:
  dihedral pdb=" CA  TRP C  39 "
           pdb=" C   TRP C  39 "
           pdb=" N   GLY C  40 "
           pdb=" CA  GLY C  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.96   26.04     0      5.00e+00 4.00e-02 2.71e+01
  dihedral pdb=" CA  THR E 166 "
           pdb=" C   THR E 166 "
           pdb=" N   GLN E 167 "
           pdb=" CA  GLN E 167 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.12   23.88     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" CA  LEU B 131 "
           pdb=" C   LEU B 131 "
           pdb=" N   THR B 132 "
           pdb=" CA  THR B 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.12   22.88     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 5267 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1187
       0.057 -    0.114: 242
       0.114 -    0.171: 22
       0.171 -    0.228: 2
       0.228 -    0.285: 1
  Chirality restraints: 1454
  Sorted by residual:
  chirality pdb=" CB  ILE B 163 "
            pdb=" CA  ILE B 163 "
            pdb=" CG1 ILE B 163 "
            pdb=" CG2 ILE B 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CA  PRO E 186 "
            pdb=" N   PRO E 186 "
            pdb=" C   PRO E 186 "
            pdb=" CB  PRO E 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CB  THR E 182 "
            pdb=" CA  THR E 182 "
            pdb=" OG1 THR E 182 "
            pdb=" CG2 THR E 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 1451 not shown)

  Planarity restraints: 1519
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN E 185 "    0.081 5.00e-02 4.00e+02   1.10e-01 1.94e+01
        pdb=" N   PRO E 186 "   -0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO E 186 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO E 186 "    0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  29 "   -0.020 2.00e-02 2.50e+03   1.82e-02 8.24e+00
        pdb=" CG  TRP A  29 "    0.050 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  29 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  29 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  29 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  29 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  29 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  29 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  29 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  29 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 141 "    0.010 2.00e-02 2.50e+03   1.63e-02 6.67e+00
        pdb=" CG  TRP E 141 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 141 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 141 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 141 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 141 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 141 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 141 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 141 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 141 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1516 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 171
        2.69 -     3.24: 9180
        3.24 -     3.79: 13914
        3.79 -     4.35: 17839
        4.35 -     4.90: 28499
  Nonbonded interactions: 69603
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 122 "
            pdb=" N   VAL B 123 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" OG1 THR A  90 "
            pdb=" OE1 GLU A  93 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OG1 THR A 146 "
            pdb=" O   GLY A 176 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" O   VAL F 159 "
            pdb=" OG  SER F 162 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" NE2 HIS E  99 "
            pdb=" O   ASP E 101 "
     model   vdw
     2.239 3.120
  ... (remaining 69598 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}

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:             1.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.840
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
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   0.178   8994  Z= 0.228
  Angle     :  0.833  15.957  12273  Z= 0.451
  Chirality :  0.045   0.285   1454
  Planarity :  0.005   0.110   1519
  Dihedral  : 13.075  87.155   3186
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.98 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.26), residues: 1118
  helix:  0.37 (0.22), residues: 649
  sheet: -1.22 (0.68), residues: 58
  loop : -2.09 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP A  29 
 HIS   0.018   0.001   HIS A  96 
 PHE   0.026   0.002   PHE B 142 
 TYR   0.029   0.002   TYR C 139 
 ARG   0.004   0.000   ARG B  68 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 325
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 ASP cc_start: 0.6921 (t0) cc_final: 0.6446 (t0)
REVERT: B  122 ASP cc_start: 0.8236 (t0) cc_final: 0.7935 (t0)
REVERT: B  135 LEU cc_start: 0.9039 (mt) cc_final: 0.8446 (tp)
REVERT: B  177 THR cc_start: 0.8289 (p) cc_final: 0.8034 (p)
REVERT: B  185 MET cc_start: 0.8138 (ppp) cc_final: 0.7791 (ppp)
REVERT: D    1 MET cc_start: -0.0994 (tpt) cc_final: -0.3193 (pmm)
REVERT: F    7 PHE cc_start: 0.8585 (t80) cc_final: 0.7826 (t80)
REVERT: F   11 LEU cc_start: 0.9158 (mt) cc_final: 0.8759 (mt)
REVERT: F   17 HIS cc_start: 0.7772 (t-90) cc_final: 0.7524 (t-90)
REVERT: F  181 ASP cc_start: 0.8554 (m-30) cc_final: 0.8004 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 325
  average time/residue: 0.1856
  time to fit residues: 86.2585
Evaluate side-chains
  267 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 65 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.088607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.073239 restraints weight = 35040.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.075294 restraints weight = 19966.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.076666 restraints weight = 13613.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   8994  Z= 0.244
  Angle     :  0.764   9.052  12273  Z= 0.375
  Chirality :  0.046   0.299   1454
  Planarity :  0.005   0.051   1519
  Dihedral  :  4.924  28.188   1206
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  8.59 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.03 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.26), residues: 1118
  helix:  0.31 (0.21), residues: 674
  sheet: -0.84 (0.75), residues: 52
  loop : -2.29 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  29 
 HIS   0.005   0.001   HIS E  99 
 PHE   0.027   0.002   PHE A  97 
 TYR   0.019   0.002   TYR C 139 
 ARG   0.011   0.001   ARG F 156 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 282
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8707 (tp) cc_final: 0.8395 (mp)
REVERT: A  169 MET cc_start: 0.7676 (tpt) cc_final: 0.7394 (tpp)
REVERT: B  122 ASP cc_start: 0.8212 (t0) cc_final: 0.7945 (t0)
REVERT: B  135 LEU cc_start: 0.9143 (mt) cc_final: 0.8561 (tt)
REVERT: C   70 ILE cc_start: 0.9277 (tp) cc_final: 0.9038 (tp)
REVERT: C  139 TYR cc_start: 0.8614 (m-10) cc_final: 0.8378 (m-10)
REVERT: D    1 MET cc_start: -0.0924 (tpt) cc_final: -0.3111 (pmm)
REVERT: D   41 MET cc_start: 0.8522 (ppp) cc_final: 0.8272 (ppp)
REVERT: E  121 ASP cc_start: 0.8537 (t0) cc_final: 0.8235 (t0)
REVERT: F   17 HIS cc_start: 0.7763 (t-90) cc_final: 0.7506 (t-90)
REVERT: F   83 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8162 (pmm)
REVERT: F  181 ASP cc_start: 0.8648 (m-30) cc_final: 0.7938 (t0)
REVERT: F  192 TYR cc_start: 0.8629 (m-80) cc_final: 0.8061 (m-80)
  outliers start: 23
  outliers final: 17
  residues processed: 292
  average time/residue: 0.1697
  time to fit residues: 72.0137
Evaluate side-chains
  280 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 262
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ASP
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain E residue   18 SER
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain F residue   81 GLN
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain F residue  106 LEU
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  114 LEU
Chi-restraints excluded: chain F residue  131 LEU
Chi-restraints excluded: chain F residue  172 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 109 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   chunk 30 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0170
   chunk 3 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 108 optimal weight:    6.9990
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.089446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.074090 restraints weight = 35676.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.076192 restraints weight = 19952.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.077636 restraints weight = 13460.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8994  Z= 0.185
  Angle     :  0.732  11.872  12273  Z= 0.347
  Chirality :  0.046   0.294   1454
  Planarity :  0.004   0.053   1519
  Dihedral  :  4.800  24.778   1206
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.16 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 18.76 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.26), residues: 1118
  helix:  0.45 (0.20), residues: 680
  sheet: -0.71 (0.76), residues: 52
  loop : -2.21 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  29 
 HIS   0.003   0.001   HIS A  81 
 PHE   0.021   0.001   PHE A  97 
 TYR   0.017   0.001   TYR C  15 
 ARG   0.004   0.000   ARG F 216 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 298
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8710 (tp) cc_final: 0.8443 (mp)
REVERT: B  100 HIS cc_start: 0.8368 (t70) cc_final: 0.8004 (t70)
REVERT: B  135 LEU cc_start: 0.9101 (mt) cc_final: 0.8572 (tt)
REVERT: B  177 THR cc_start: 0.7886 (p) cc_final: 0.7525 (t)
REVERT: B  185 MET cc_start: 0.8133 (ppp) cc_final: 0.7715 (ppp)
REVERT: C   54 TYR cc_start: 0.7617 (t80) cc_final: 0.7184 (t80)
REVERT: C   70 ILE cc_start: 0.9275 (tp) cc_final: 0.8967 (tp)
REVERT: D    1 MET cc_start: -0.0490 (tpt) cc_final: -0.2705 (pmm)
REVERT: D   41 MET cc_start: 0.8477 (ppp) cc_final: 0.8203 (ppp)
REVERT: E  121 ASP cc_start: 0.8486 (t0) cc_final: 0.8141 (t0)
REVERT: F   71 ARG cc_start: 0.8311 (tpt90) cc_final: 0.8023 (tpm170)
REVERT: F   83 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8106 (pmm)
REVERT: F   98 MET cc_start: 0.8584 (tmm) cc_final: 0.8211 (tmm)
REVERT: F  181 ASP cc_start: 0.8568 (m-30) cc_final: 0.7944 (t0)
REVERT: F  185 MET cc_start: 0.8557 (ptp) cc_final: 0.8151 (ppp)
REVERT: F  192 TYR cc_start: 0.8589 (m-80) cc_final: 0.8194 (m-80)
  outliers start: 39
  outliers final: 24
  residues processed: 314
  average time/residue: 0.1730
  time to fit residues: 78.4215
Evaluate side-chains
  300 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 275
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  121 ASP
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain E residue   18 SER
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain F residue   29 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   81 GLN
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  114 LEU
Chi-restraints excluded: chain F residue  131 LEU
Chi-restraints excluded: chain F residue  172 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 82 optimal weight:    0.9980
   chunk 50 optimal weight:    8.9990
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 24 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:
A  31 GLN
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 127 GLN
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.089214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.073880 restraints weight = 35557.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.075902 restraints weight = 20286.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.077329 restraints weight = 13957.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8994  Z= 0.194
  Angle     :  0.751  14.060  12273  Z= 0.354
  Chirality :  0.047   0.321   1454
  Planarity :  0.004   0.054   1519
  Dihedral  :  4.769  24.137   1206
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.42 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 21.37 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.26), residues: 1118
  helix:  0.49 (0.20), residues: 679
  sheet: -0.62 (0.79), residues: 52
  loop : -2.19 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C 123 
 HIS   0.006   0.001   HIS A  96 
 PHE   0.027   0.001   PHE F  28 
 TYR   0.027   0.001   TYR C 139 
 ARG   0.004   0.000   ARG F 216 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 276
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8736 (tp) cc_final: 0.8435 (mp)
REVERT: A   78 TRP cc_start: 0.8202 (t60) cc_final: 0.7885 (t60)
REVERT: B   31 VAL cc_start: 0.9402 (t) cc_final: 0.9128 (p)
REVERT: B  100 HIS cc_start: 0.8434 (t70) cc_final: 0.8093 (t70)
REVERT: B  122 ASP cc_start: 0.8126 (t0) cc_final: 0.7882 (t70)
REVERT: B  135 LEU cc_start: 0.9102 (mt) cc_final: 0.8622 (tt)
REVERT: B  177 THR cc_start: 0.7872 (p) cc_final: 0.7507 (t)
REVERT: C   54 TYR cc_start: 0.7622 (t80) cc_final: 0.7262 (t80)
REVERT: C   70 ILE cc_start: 0.9263 (tp) cc_final: 0.8955 (tp)
REVERT: C   74 MET cc_start: 0.8565 (mmm) cc_final: 0.8283 (mtt)
REVERT: D    1 MET cc_start: -0.0384 (tpt) cc_final: -0.2568 (pmm)
REVERT: D   41 MET cc_start: 0.8485 (ppp) cc_final: 0.8190 (ppp)
REVERT: E  121 ASP cc_start: 0.8489 (t0) cc_final: 0.8134 (t0)
REVERT: F   71 ARG cc_start: 0.8319 (tpt90) cc_final: 0.7992 (tpm170)
REVERT: F   83 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8074 (pmm)
REVERT: F   98 MET cc_start: 0.8423 (tmm) cc_final: 0.8178 (tmm)
REVERT: F  181 ASP cc_start: 0.8599 (m-30) cc_final: 0.7980 (t0)
REVERT: F  185 MET cc_start: 0.8530 (ptp) cc_final: 0.8152 (ppp)
  outliers start: 41
  outliers final: 30
  residues processed: 292
  average time/residue: 0.1654
  time to fit residues: 69.9805
Evaluate side-chains
  295 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 264
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  121 ASP
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  175 PHE
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain E residue   18 SER
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   81 HIS
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   81 GLN
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  114 LEU
Chi-restraints excluded: chain F residue  129 MET
Chi-restraints excluded: chain F residue  131 LEU
Chi-restraints excluded: chain F residue  155 LYS
Chi-restraints excluded: chain F residue  172 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  99 HIS
C  85 GLN
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.087310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.072266 restraints weight = 35880.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.074219 restraints weight = 20632.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.075579 restraints weight = 14230.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8994  Z= 0.224
  Angle     :  0.750  12.173  12273  Z= 0.361
  Chirality :  0.047   0.336   1454
  Planarity :  0.005   0.053   1519
  Dihedral  :  4.802  24.079   1206
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.68 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 23.56 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.26), residues: 1118
  helix:  0.46 (0.20), residues: 678
  sheet: -0.74 (0.78), residues: 52
  loop : -2.22 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 123 
 HIS   0.005   0.001   HIS A  96 
 PHE   0.019   0.002   PHE F  28 
 TYR   0.026   0.002   TYR C 139 
 ARG   0.003   0.000   ARG F 156 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 265
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8848 (tp) cc_final: 0.8585 (mp)
REVERT: A  181 LEU cc_start: 0.9266 (mp) cc_final: 0.9010 (mp)
REVERT: B   31 VAL cc_start: 0.9431 (t) cc_final: 0.9207 (p)
REVERT: B  100 HIS cc_start: 0.8506 (t70) cc_final: 0.8219 (t70)
REVERT: B  127 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7705 (tm130)
REVERT: B  135 LEU cc_start: 0.9181 (mt) cc_final: 0.8704 (tt)
REVERT: B  177 THR cc_start: 0.7928 (p) cc_final: 0.7636 (t)
REVERT: C   54 TYR cc_start: 0.7688 (t80) cc_final: 0.7174 (t80)
REVERT: C   70 ILE cc_start: 0.9282 (tp) cc_final: 0.9016 (tp)
REVERT: C  219 MET cc_start: 0.7590 (tpp) cc_final: 0.7380 (tpp)
REVERT: C  230 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8757 (pttm)
REVERT: D    1 MET cc_start: -0.0403 (tpt) cc_final: -0.2516 (pmm)
REVERT: D   41 MET cc_start: 0.8520 (ppp) cc_final: 0.8190 (ppp)
REVERT: F   17 HIS cc_start: 0.7516 (t-90) cc_final: 0.7298 (t-90)
REVERT: F   83 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8228 (pmm)
REVERT: F   98 MET cc_start: 0.8338 (tmm) cc_final: 0.8067 (tmm)
REVERT: F  132 THR cc_start: 0.8839 (t) cc_final: 0.8572 (p)
REVERT: F  181 ASP cc_start: 0.8655 (m-30) cc_final: 0.8061 (t0)
REVERT: F  185 MET cc_start: 0.8546 (ptp) cc_final: 0.8149 (ppp)
  outliers start: 47
  outliers final: 35
  residues processed: 287
  average time/residue: 0.1709
  time to fit residues: 70.7805
Evaluate side-chains
  288 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 250
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   99 HIS
Chi-restraints excluded: chain A residue  121 ASP
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  175 PHE
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain C residue  230 LYS
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain E residue   -1 MET
Chi-restraints excluded: chain E residue   18 SER
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   81 HIS
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   81 GLN
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  114 LEU
Chi-restraints excluded: chain F residue  123 VAL
Chi-restraints excluded: chain F residue  129 MET
Chi-restraints excluded: chain F residue  131 LEU
Chi-restraints excluded: chain F residue  155 LYS
Chi-restraints excluded: chain F residue  172 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 64 optimal weight:    0.0370
   chunk 49 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 87 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 39 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 105 optimal weight:    4.9990
   overall best weight:    1.9662

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 100 HIS
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 HIS
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.085002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.069839 restraints weight = 35043.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.071713 restraints weight = 20446.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.073034 restraints weight = 14255.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.3421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8994  Z= 0.247
  Angle     :  0.771  13.774  12273  Z= 0.365
  Chirality :  0.047   0.317   1454
  Planarity :  0.005   0.056   1519
  Dihedral  :  4.907  26.379   1206
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.96 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 25.08 %
    Favored  : 70.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.26), residues: 1118
  helix:  0.43 (0.20), residues: 679
  sheet: -0.91 (0.77), residues: 52
  loop : -2.20 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 123 
 HIS   0.005   0.001   HIS A  99 
 PHE   0.033   0.002   PHE B 142 
 TYR   0.023   0.001   TYR C 139 
 ARG   0.004   0.000   ARG F 216 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 252
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8830 (tp) cc_final: 0.8518 (mp)
REVERT: A  181 LEU cc_start: 0.9239 (mp) cc_final: 0.8957 (mp)
REVERT: B   31 VAL cc_start: 0.9480 (t) cc_final: 0.9234 (p)
REVERT: B   75 GLN cc_start: 0.9361 (pm20) cc_final: 0.9106 (pm20)
REVERT: B  135 LEU cc_start: 0.9323 (mt) cc_final: 0.8835 (tt)
REVERT: C   54 TYR cc_start: 0.7782 (t80) cc_final: 0.7313 (t80)
REVERT: C   70 ILE cc_start: 0.9193 (tp) cc_final: 0.8852 (tp)
REVERT: C  219 MET cc_start: 0.7740 (tpp) cc_final: 0.7469 (tpp)
REVERT: D    1 MET cc_start: -0.0208 (tpt) cc_final: -0.2252 (pmm)
REVERT: D   41 MET cc_start: 0.8515 (ppp) cc_final: 0.8090 (ppp)
REVERT: F   15 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7701 (m-80)
REVERT: F   17 HIS cc_start: 0.7716 (t-90) cc_final: 0.7433 (t-90)
REVERT: F   83 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8246 (pmm)
REVERT: F   98 MET cc_start: 0.8399 (tmm) cc_final: 0.7981 (tmm)
REVERT: F  132 THR cc_start: 0.8968 (t) cc_final: 0.8685 (p)
REVERT: F  181 ASP cc_start: 0.8739 (m-30) cc_final: 0.8154 (t0)
REVERT: F  185 MET cc_start: 0.8562 (ptp) cc_final: 0.8141 (ppp)
REVERT: F  192 TYR cc_start: 0.8798 (m-80) cc_final: 0.8502 (m-80)
  outliers start: 45
  outliers final: 33
  residues processed: 278
  average time/residue: 0.1659
  time to fit residues: 67.5965
Evaluate side-chains
  279 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 244
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  121 ASP
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  175 PHE
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain E residue   -1 MET
Chi-restraints excluded: chain E residue   18 SER
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   81 HIS
Chi-restraints excluded: chain E residue   89 LEU
Chi-restraints excluded: chain F residue   15 PHE
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   81 GLN
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  114 LEU
Chi-restraints excluded: chain F residue  123 VAL
Chi-restraints excluded: chain F residue  129 MET
Chi-restraints excluded: chain F residue  131 LEU
Chi-restraints excluded: chain F residue  155 LYS
Chi-restraints excluded: chain F residue  172 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 89 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0980
   chunk 97 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0770
   overall best weight:    1.8344

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 HIS
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 131 GLN
F 100 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.084347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.069337 restraints weight = 35388.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.071271 restraints weight = 20382.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.072580 restraints weight = 14024.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8994  Z= 0.237
  Angle     :  0.779  12.927  12273  Z= 0.368
  Chirality :  0.047   0.287   1454
  Planarity :  0.005   0.055   1519
  Dihedral  :  4.895  23.945   1206
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.05 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 27.04 %
    Favored  : 68.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.26), residues: 1118
  helix:  0.38 (0.20), residues: 684
  sheet: -0.95 (0.76), residues: 52
  loop : -2.19 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 123 
 HIS   0.007   0.001   HIS B 100 
 PHE   0.027   0.002   PHE F  28 
 TYR   0.016   0.001   TYR C 139 
 ARG   0.003   0.000   ARG F 216 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 257
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8764 (tp) cc_final: 0.8452 (mp)
REVERT: A  181 LEU cc_start: 0.9246 (mp) cc_final: 0.9031 (tp)
REVERT: B    5 ARG cc_start: 0.8855 (mtm180) cc_final: 0.8084 (mtm180)
REVERT: B   75 GLN cc_start: 0.9341 (pm20) cc_final: 0.9103 (pm20)
REVERT: B  135 LEU cc_start: 0.9330 (mt) cc_final: 0.8867 (tt)
REVERT: B  170 ILE cc_start: 0.9317 (mm) cc_final: 0.9111 (mm)
REVERT: C   54 TYR cc_start: 0.7835 (t80) cc_final: 0.7319 (t80)
REVERT: C   70 ILE cc_start: 0.9214 (tp) cc_final: 0.8929 (tp)
REVERT: C  219 MET cc_start: 0.7832 (tpp) cc_final: 0.7474 (tpp)
REVERT: D    1 MET cc_start: -0.0115 (tpt) cc_final: -0.1977 (pmm)
REVERT: D   41 MET cc_start: 0.8552 (ppp) cc_final: 0.8094 (ppp)
REVERT: F   17 HIS cc_start: 0.7841 (t-90) cc_final: 0.7555 (t-90)
REVERT: F   83 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8246 (pmm)
REVERT: F   98 MET cc_start: 0.8383 (tmm) cc_final: 0.8067 (tmm)
REVERT: F  132 THR cc_start: 0.9000 (t) cc_final: 0.8746 (p)
REVERT: F  181 ASP cc_start: 0.8752 (m-30) cc_final: 0.8171 (t0)
REVERT: F  185 MET cc_start: 0.8580 (ptp) cc_final: 0.8161 (ppp)
REVERT: F  192 TYR cc_start: 0.8806 (m-80) cc_final: 0.8505 (m-80)
  outliers start: 42
  outliers final: 36
  residues processed: 279
  average time/residue: 0.1751
  time to fit residues: 70.2694
Evaluate side-chains
  279 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 242
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  175 PHE
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain E residue   -1 MET
Chi-restraints excluded: chain E residue   18 SER
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   81 HIS
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   81 GLN
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  114 LEU
Chi-restraints excluded: chain F residue  123 VAL
Chi-restraints excluded: chain F residue  129 MET
Chi-restraints excluded: chain F residue  131 LEU
Chi-restraints excluded: chain F residue  155 LYS
Chi-restraints excluded: chain F residue  172 LEU
Chi-restraints excluded: chain F residue  220 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 76 optimal weight:    0.0060
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:    7.9990
   chunk 71 optimal weight:    0.0970
   chunk 107 optimal weight:    0.3980
   chunk 96 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 68 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  99 HIS
C  50 GLN
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 HIS
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  96 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.088187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.073118 restraints weight = 36035.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.075136 restraints weight = 20477.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.076551 restraints weight = 14017.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8994  Z= 0.178
  Angle     :  0.786  14.277  12273  Z= 0.360
  Chirality :  0.048   0.334   1454
  Planarity :  0.004   0.054   1519
  Dihedral  :  4.799  23.743   1206
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.33 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 27.81 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.26), residues: 1118
  helix:  0.38 (0.20), residues: 690
  sheet: -0.60 (0.77), residues: 52
  loop : -2.14 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  60 
 HIS   0.006   0.001   HIS E  96 
 PHE   0.029   0.001   PHE F  28 
 TYR   0.017   0.001   TYR C 139 
 ARG   0.005   0.000   ARG F 216 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 262
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8724 (tp) cc_final: 0.8466 (mp)
REVERT: A  181 LEU cc_start: 0.9261 (mp) cc_final: 0.8970 (tp)
REVERT: B    5 ARG cc_start: 0.8787 (mtm180) cc_final: 0.8080 (mtm180)
REVERT: B   75 GLN cc_start: 0.9258 (pm20) cc_final: 0.9002 (pm20)
REVERT: B   98 MET cc_start: 0.8676 (mtt) cc_final: 0.8411 (mtt)
REVERT: B  135 LEU cc_start: 0.9240 (mt) cc_final: 0.8840 (tt)
REVERT: B  170 ILE cc_start: 0.9300 (mm) cc_final: 0.9089 (mm)
REVERT: C   50 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.8025 (mm-40)
REVERT: C   54 TYR cc_start: 0.7649 (t80) cc_final: 0.7223 (t80)
REVERT: C   70 ILE cc_start: 0.9236 (tp) cc_final: 0.8921 (tp)
REVERT: D    1 MET cc_start: 0.0255 (tpt) cc_final: -0.1872 (pmm)
REVERT: D   41 MET cc_start: 0.8585 (ppp) cc_final: 0.8133 (ppp)
REVERT: E  121 ASP cc_start: 0.8302 (t0) cc_final: 0.8079 (t0)
REVERT: F   15 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7582 (m-80)
REVERT: F   83 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8112 (pmm)
REVERT: F   98 MET cc_start: 0.8416 (tmm) cc_final: 0.8116 (tmm)
REVERT: F  132 THR cc_start: 0.8796 (t) cc_final: 0.8548 (p)
REVERT: F  181 ASP cc_start: 0.8654 (m-30) cc_final: 0.8101 (t0)
REVERT: F  185 MET cc_start: 0.8443 (ptp) cc_final: 0.8100 (ppp)
  outliers start: 37
  outliers final: 30
  residues processed: 279
  average time/residue: 0.1716
  time to fit residues: 69.0959
Evaluate side-chains
  284 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 251
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   99 HIS
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  175 PHE
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue   50 GLN
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain E residue   -1 MET
Chi-restraints excluded: chain E residue   18 SER
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   66 HIS
Chi-restraints excluded: chain E residue   81 HIS
Chi-restraints excluded: chain F residue   15 PHE
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   81 GLN
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  114 LEU
Chi-restraints excluded: chain F residue  129 MET
Chi-restraints excluded: chain F residue  155 LYS
Chi-restraints excluded: chain F residue  172 LEU
Chi-restraints excluded: chain F residue  220 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 36 optimal weight:    0.0040
   chunk 111 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0980
   chunk 99 optimal weight:    0.9990
   chunk 2 optimal weight:   20.0000
   chunk 48 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  99 HIS
C  50 GLN
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 HIS
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.088433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.073483 restraints weight = 35907.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.075524 restraints weight = 20280.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.076893 restraints weight = 13788.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8994  Z= 0.191
  Angle     :  0.822  14.598  12273  Z= 0.379
  Chirality :  0.049   0.345   1454
  Planarity :  0.004   0.055   1519
  Dihedral  :  4.801  23.293   1206
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.96 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 28.79 %
    Favored  : 67.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.26), residues: 1118
  helix:  0.40 (0.20), residues: 689
  sheet: -0.58 (0.77), residues: 52
  loop : -2.12 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A  29 
 HIS   0.008   0.001   HIS A  99 
 PHE   0.029   0.001   PHE F  28 
 TYR   0.017   0.001   TYR B 124 
 ARG   0.004   0.000   ARG F 216 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 263
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8725 (tp) cc_final: 0.8430 (mp)
REVERT: B    5 ARG cc_start: 0.8729 (mtm180) cc_final: 0.7976 (mtm180)
REVERT: B   75 GLN cc_start: 0.9212 (pm20) cc_final: 0.8936 (pm20)
REVERT: B  127 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7826 (tm130)
REVERT: B  135 LEU cc_start: 0.9222 (mt) cc_final: 0.8827 (tt)
REVERT: C   54 TYR cc_start: 0.7612 (t80) cc_final: 0.7209 (t80)
REVERT: D    1 MET cc_start: 0.0223 (tpt) cc_final: -0.1921 (pmm)
REVERT: D   41 MET cc_start: 0.8549 (ppp) cc_final: 0.8091 (ppp)
REVERT: E  121 ASP cc_start: 0.8271 (t0) cc_final: 0.8048 (t0)
REVERT: F   15 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7593 (m-80)
REVERT: F   83 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8099 (pmm)
REVERT: F   98 MET cc_start: 0.8465 (tmm) cc_final: 0.8139 (tmm)
REVERT: F  132 THR cc_start: 0.8814 (t) cc_final: 0.8549 (p)
REVERT: F  181 ASP cc_start: 0.8635 (m-30) cc_final: 0.8089 (t0)
REVERT: F  185 MET cc_start: 0.8380 (ptp) cc_final: 0.8061 (ppp)
  outliers start: 37
  outliers final: 30
  residues processed: 282
  average time/residue: 0.1710
  time to fit residues: 69.7359
Evaluate side-chains
  284 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 251
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   99 HIS
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  175 PHE
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain E residue   -1 MET
Chi-restraints excluded: chain E residue   18 SER
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   66 HIS
Chi-restraints excluded: chain E residue   81 HIS
Chi-restraints excluded: chain F residue   15 PHE
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   81 GLN
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  114 LEU
Chi-restraints excluded: chain F residue  129 MET
Chi-restraints excluded: chain F residue  155 LYS
Chi-restraints excluded: chain F residue  172 LEU
Chi-restraints excluded: chain F residue  220 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 102 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 68 optimal weight:    0.0270
   chunk 59 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 90 optimal weight:    0.0980
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.2242

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  99 HIS
C  50 GLN
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 HIS
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.085563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.070397 restraints weight = 35205.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.072345 restraints weight = 20400.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.073680 restraints weight = 14093.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8994  Z= 0.214
  Angle     :  0.856  14.115  12273  Z= 0.395
  Chirality :  0.049   0.361   1454
  Planarity :  0.005   0.058   1519
  Dihedral  :  4.898  23.911   1206
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.69 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 29.99 %
    Favored  : 66.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.26), residues: 1118
  helix:  0.38 (0.20), residues: 690
  sheet: -0.80 (0.76), residues: 52
  loop : -2.07 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  29 
 HIS   0.011   0.001   HIS E  99 
 PHE   0.029   0.001   PHE F  28 
 TYR   0.013   0.001   TYR C 139 
 ARG   0.004   0.000   ARG F 216 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 249
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 LEU cc_start: 0.8728 (tp) cc_final: 0.8372 (mp)
REVERT: B    2 MET cc_start: 0.6686 (ttm) cc_final: 0.6434 (ptp)
REVERT: B    5 ARG cc_start: 0.8762 (mtm180) cc_final: 0.7991 (mtm180)
REVERT: B   75 GLN cc_start: 0.9271 (pm20) cc_final: 0.8938 (pm20)
REVERT: B   96 LYS cc_start: 0.9351 (ttpt) cc_final: 0.9085 (tttt)
REVERT: B  127 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7727 (tm130)
REVERT: B  135 LEU cc_start: 0.9285 (mt) cc_final: 0.8884 (tt)
REVERT: C   54 TYR cc_start: 0.7724 (t80) cc_final: 0.7305 (t80)
REVERT: C   86 MET cc_start: 0.7775 (mmt) cc_final: 0.7572 (mmt)
REVERT: D    1 MET cc_start: 0.0136 (tpt) cc_final: -0.1760 (pmm)
REVERT: D   41 MET cc_start: 0.8557 (ppp) cc_final: 0.8090 (ppp)
REVERT: E  121 ASP cc_start: 0.8344 (t0) cc_final: 0.8117 (t0)
REVERT: F   15 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7598 (m-80)
REVERT: F   83 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8180 (pmm)
REVERT: F   98 MET cc_start: 0.8462 (tmm) cc_final: 0.8100 (tmm)
REVERT: F  132 THR cc_start: 0.8935 (t) cc_final: 0.8685 (p)
REVERT: F  181 ASP cc_start: 0.8726 (m-30) cc_final: 0.8152 (t0)
REVERT: F  185 MET cc_start: 0.8461 (ptp) cc_final: 0.8051 (ppp)
REVERT: F  192 TYR cc_start: 0.8729 (m-80) cc_final: 0.8376 (m-80)
  outliers start: 34
  outliers final: 28
  residues processed: 267
  average time/residue: 0.1795
  time to fit residues: 68.7132
Evaluate side-chains
  276 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 245
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 HIS
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  175 PHE
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain E residue   -1 MET
Chi-restraints excluded: chain E residue   18 SER
Chi-restraints excluded: chain E residue   44 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   66 HIS
Chi-restraints excluded: chain F residue   15 PHE
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   81 GLN
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue  103 VAL
Chi-restraints excluded: chain F residue  112 SER
Chi-restraints excluded: chain F residue  114 LEU
Chi-restraints excluded: chain F residue  129 MET
Chi-restraints excluded: chain F residue  155 LYS
Chi-restraints excluded: chain F residue  172 LEU
Chi-restraints excluded: chain F residue  220 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 95 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 36 optimal weight:   20.0000
   chunk 100 optimal weight:    0.1980
   chunk 40 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 HIS
** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.089065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.073808 restraints weight = 35633.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.075849 restraints weight = 20407.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.077216 restraints weight = 14053.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.4138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8994  Z= 0.194
  Angle     :  0.849  14.552  12273  Z= 0.391
  Chirality :  0.049   0.374   1454
  Planarity :  0.005   0.059   1519
  Dihedral  :  4.888  23.190   1206
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.60 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 29.88 %
    Favored  : 66.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.26), residues: 1118
  helix:  0.41 (0.21), residues: 689
  sheet: -0.60 (0.77), residues: 52
  loop : -2.03 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  29 
 HIS   0.006   0.001   HIS E  99 
 PHE   0.028   0.001   PHE F  28 
 TYR   0.011   0.001   TYR C 139 
 ARG   0.005   0.000   ARG F 216 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2800.98 seconds
wall clock time: 50 minutes 57.34 seconds (3057.34 seconds total)