Starting phenix.real_space_refine
on Tue Feb 11 08:29:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mmv_48404/02_2025/9mmv_48404.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mmv_48404/02_2025/9mmv_48404.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mmv_48404/02_2025/9mmv_48404.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mmv_48404/02_2025/9mmv_48404.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mmv_48404/02_2025/9mmv_48404.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mmv_48404/02_2025/9mmv_48404.cif"
  }
  resolution = 3.79
  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=   0.369 sd=   1.521
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      12      5.16       5
     C    2924      2.51       5
     N     961      2.21       5
     O    1071      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4968
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 1253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1253
          Classifications: {'peptide': 210}
          Incomplete info: {'backbone_only': 89}
          Link IDs: {'PTRANS': 11, 'TRANS': 198}
          Chain breaks: 1
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 333
          Unresolved non-hydrogen angles: 495
          Unresolved non-hydrogen dihedrals: 206
          Unresolved non-hydrogen chiralities: 119
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 107
    Chain: "L"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1137
          Classifications: {'peptide': 194}
          Incomplete info: {'backbone_only': 85}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 178}
          Chain breaks: 2
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 331
          Unresolved non-hydrogen angles: 491
          Unresolved non-hydrogen dihedrals: 210
          Unresolved non-hydrogen chiralities: 110
          Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 132
    Chain: "M"
      Number of atoms: 1351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1351
          Classifications: {'peptide': 222}
          Incomplete info: {'backbone_only': 88, 'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 209}
          Chain breaks: 1
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 335
          Unresolved non-hydrogen angles: 497
          Unresolved non-hydrogen dihedrals: 208
          Unresolved non-hydrogen chiralities: 118
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 111
    Chain: "N"
      Number of atoms: 1227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1227
          Classifications: {'peptide': 211}
          Incomplete info: {'backbone_only': 102, 'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 416
          Unresolved non-hydrogen angles: 605
          Unresolved non-hydrogen dihedrals: 263
          Unresolved non-hydrogen chiralities: 129
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 188
  Time building chain proxies: 3.51, per 1000 atoms: 0.71
  Number of scatterers: 4968
  At special positions: 0
  Unit cell: (54, 70.5, 142, 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      12     16.00
     O    1071      8.00
     N     961      7.00
     C    2924      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 745.5 milliseconds
  

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  808

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 21 sheets defined
      6.8% alpha, 50.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.673A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 188 through 190
      No H-bonds generated for 'chain 'H' and resid 188 through 190'
    Processing helix  chain 'L' and resid 77 through 81
      removed outlier: 3.535A  pdb=" N   GLU L  81 " --> pdb=" O   ALA L  78 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 127
    Processing helix  chain 'M' and resid 53 through 57
    Processing helix  chain 'M' and resid 89 through 93
      removed outlier: 3.502A  pdb=" N   THR M  93 " --> pdb=" O   THR M  90 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 196 through 200
      removed outlier: 4.247A  pdb=" N   GLY M 200 " --> pdb=" O   SER M 196 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 196 through 200'
    Processing helix  chain 'N' and resid 121 through 126
      removed outlier: 4.353A  pdb=" N   LYS N 126 " --> pdb=" O   ASP N 122 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 183 through 189
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 7.099A  pdb=" N   LEU H  34 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   GLY H  50 " --> pdb=" O   LEU H  34 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 121 through 125
      removed outlier: 6.038A  pdb=" N   TYR H 177 " --> pdb=" O   ASP H 145 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 121 through 125
      removed outlier: 6.038A  pdb=" N   TYR H 177 " --> pdb=" O   ASP H 145 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 151 through 155
      removed outlier: 3.745A  pdb=" N   TYR H 195 " --> pdb=" O   VAL H 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.662A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 104 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   TRP L  33 " --> pdb=" O   VAL L  45 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.662A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 104 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 21
    Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 116
      removed outlier: 5.038A  pdb=" N   THR L 131 " --> pdb=" O   LEU L 180 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   LEU L 180 " --> pdb=" O   THR L 131 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 178 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   LEU L 178 " --> pdb=" O   VAL L 133 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   LEU L 135 " --> pdb=" O   SER L 176 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   SER L 176 " --> pdb=" O   LEU L 135 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   SER L 137 " --> pdb=" O   ALA L 174 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ALA L 174 " --> pdb=" O   SER L 137 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 114 through 116
      removed outlier: 5.038A  pdb=" N   THR L 131 " --> pdb=" O   LEU L 180 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   LEU L 180 " --> pdb=" O   THR L 131 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 178 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   LEU L 178 " --> pdb=" O   VAL L 133 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   LEU L 135 " --> pdb=" O   SER L 176 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   SER L 176 " --> pdb=" O   LEU L 135 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   SER L 137 " --> pdb=" O   ALA L 174 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ALA L 174 " --> pdb=" O   SER L 137 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 145 through 149
    Processing sheet with id=AB3, first strand: chain 'M' and resid 3 through 7
      removed outlier: 3.571A  pdb=" N   SER M  21 " --> pdb=" O   SER M   7 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'M' and resid 11 through 12
      removed outlier: 3.711A  pdb=" N   ALA M  33 " --> pdb=" O   GLY M 101 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   MET M  34 " --> pdb=" O   PHE M  50 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   PHE M  50 " --> pdb=" O   MET M  34 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   TRP M  36 " --> pdb=" O   ILE M  48 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'M' and resid 11 through 12
      removed outlier: 6.626A  pdb=" N   CYS M  98 " --> pdb=" O   TRP M 117 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   TRP M 117 " --> pdb=" O   CYS M  98 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ARG M 100 " --> pdb=" O   ASP M 115 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   GLY M 113 " --> pdb=" O   ALA M 102 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'M' and resid 134 through 138
      removed outlier: 3.668A  pdb=" N   CYS M 150 " --> pdb=" O   SER M 190 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   TYR M 186 " --> pdb=" O   ASP M 154 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'M' and resid 134 through 138
      removed outlier: 3.668A  pdb=" N   CYS M 150 " --> pdb=" O   SER M 190 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   TYR M 186 " --> pdb=" O   ASP M 154 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'M' and resid 160 through 164
    Processing sheet with id=AB9, first strand: chain 'N' and resid 4 through 7
      removed outlier: 3.540A  pdb=" N   THR N  22 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'N' and resid 10 through 13
      removed outlier: 6.869A  pdb=" N   LEU N  33 " --> pdb=" O   PHE N  49 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   PHE N  49 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'N' and resid 114 through 118
      removed outlier: 4.046A  pdb=" N   SER N 174 " --> pdb=" O   THR N 164 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'N' and resid 153 through 155
      removed outlier: 4.308A  pdb=" N   TRP N 148 " --> pdb=" O   GLN N 155 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TYR N 192 " --> pdb=" O   PHE N 209 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   CYS N 194 " --> pdb=" O   LYS N 207 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LYS N 207 " --> pdb=" O   CYS N 194 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL N 196 " --> pdb=" O   VAL N 205 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   VAL N 205 " --> pdb=" O   VAL N 196 " (cutoff:3.500A)

    286 hydrogen bonds defined for protein.
    708 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: 1.55

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1319
        1.33 -     1.45: 1118
        1.45 -     1.57: 2588
        1.57 -     1.69: 0
        1.69 -     1.82: 16
  Bond restraints: 5041
  Sorted by residual:
  bond pdb=" CA  ASP N  50 "
       pdb=" C   ASP N  50 "
    ideal  model  delta    sigma   weight residual
    1.527  1.479  0.048 1.30e-02 5.92e+03 1.37e+01
  bond pdb=" CA  SER N  10 "
       pdb=" C   SER N  10 "
    ideal  model  delta    sigma   weight residual
    1.523  1.488  0.034 1.23e-02 6.61e+03 7.74e+00
  bond pdb=" C   SER N  10 "
       pdb=" N   LEU N  11 "
    ideal  model  delta    sigma   weight residual
    1.331  1.298  0.032 1.34e-02 5.57e+03 5.76e+00
  bond pdb=" N   PHE N  96 "
       pdb=" CA  PHE N  96 "
    ideal  model  delta    sigma   weight residual
    1.463  1.432  0.031 1.30e-02 5.92e+03 5.62e+00
  bond pdb=" C   ARG N 142 "
       pdb=" O   ARG N 142 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.027 1.17e-02 7.31e+03 5.24e+00
  ... (remaining 5036 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.75: 6643
        4.75 -     9.50: 27
        9.50 -    14.25: 2
       14.25 -    19.01: 1
       19.01 -    23.76: 1
  Bond angle restraints: 6674
  Sorted by residual:
  angle pdb=" C   GLU M 158 "
        pdb=" N   PRO M 159 "
        pdb=" CA  PRO M 159 "
      ideal   model   delta    sigma   weight residual
     119.84  143.60  -23.76 1.25e+00 6.40e-01 3.61e+02
  angle pdb=" N   GLU M 158 "
        pdb=" CA  GLU M 158 "
        pdb=" C   GLU M 158 "
      ideal   model   delta    sigma   weight residual
     108.07  120.12  -12.05 8.90e-01 1.26e+00 1.83e+02
  angle pdb=" N   SER N  52 "
        pdb=" CA  SER N  52 "
        pdb=" C   SER N  52 "
      ideal   model   delta    sigma   weight residual
     111.28  119.43   -8.15 1.09e+00 8.42e-01 5.59e+01
  angle pdb=" C   TYR N 140 "
        pdb=" N   PRO N 141 "
        pdb=" CA  PRO N 141 "
      ideal   model   delta    sigma   weight residual
     127.00  144.88  -17.88 2.40e+00 1.74e-01 5.55e+01
  angle pdb=" C   GLN N  79 "
        pdb=" N   PRO N  80 "
        pdb=" CA  PRO N  80 "
      ideal   model   delta    sigma   weight residual
     119.05  125.68   -6.63 1.11e+00 8.12e-01 3.56e+01
  ... (remaining 6669 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.92: 2195
       21.92 -    43.85: 209
       43.85 -    65.77: 25
       65.77 -    87.69: 2
       87.69 -   109.62: 3
  Dihedral angle restraints: 2434
    sinusoidal: 772
      harmonic: 1662
  Sorted by residual:
  dihedral pdb=" CA  GLU H 149 "
           pdb=" C   GLU H 149 "
           pdb=" N   PRO H 150 "
           pdb=" CA  PRO H 150 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   70.38  109.62     0      5.00e+00 4.00e-02 4.81e+02
  dihedral pdb=" CA  PHE H 147 "
           pdb=" C   PHE H 147 "
           pdb=" N   PRO H 148 "
           pdb=" CA  PRO H 148 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -80.95  -99.05     0      5.00e+00 4.00e-02 3.92e+02
  dihedral pdb=" CA  SER N   7 "
           pdb=" C   SER N   7 "
           pdb=" N   PRO N   8 "
           pdb=" CA  PRO N   8 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -40.41   40.41     0      5.00e+00 4.00e-02 6.53e+01
  ... (remaining 2431 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 474
       0.087 -    0.174: 43
       0.174 -    0.261: 2
       0.261 -    0.348: 2
       0.348 -    0.435: 1
  Chirality restraints: 522
  Sorted by residual:
  chirality pdb=" CA  SER N  53 "
            pdb=" N   SER N  53 "
            pdb=" C   SER N  53 "
            pdb=" CB  SER N  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.44 2.00e-01 2.50e+01 4.73e+00
  chirality pdb=" CA  SER N  52 "
            pdb=" N   SER N  52 "
            pdb=" C   SER N  52 "
            pdb=" CB  SER N  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  LYS H  43 "
            pdb=" N   LYS H  43 "
            pdb=" C   LYS H  43 "
            pdb=" CB  LYS H  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.28 2.00e-01 2.50e+01 1.89e+00
  ... (remaining 519 not shown)

  Planarity restraints: 995
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG M  13 "   -0.074 5.00e-02 4.00e+02   1.10e-01 1.94e+01
        pdb=" N   PRO M  14 "    0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO M  14 "   -0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO M  14 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA N  43 "   -0.047 5.00e-02 4.00e+02   7.16e-02 8.21e+00
        pdb=" N   PRO N  44 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO N  44 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO N  44 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE N  49 "    0.013 2.00e-02 2.50e+03   2.73e-02 7.43e+00
        pdb=" C   PHE N  49 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   PHE N  49 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASP N  50 "    0.016 2.00e-02 2.50e+03
  ... (remaining 992 not shown)

  Histogram of nonbonded interaction distances:
        1.34 -     2.05: 2
        2.05 -     2.76: 807
        2.76 -     3.48: 6176
        3.48 -     4.19: 9974
        4.19 -     4.90: 17756
  Nonbonded interactions: 34715
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU M  61 "
            pdb=" CD2 PHE N  94 "
     model   vdw
     1.340 3.340
  nonbonded pdb=" OE2 GLU M  61 "
            pdb=" CE2 PHE N  94 "
     model   vdw
     1.624 3.340
  nonbonded pdb=" NH2 ARG N  61 "
            pdb=" OE1 GLU N  81 "
     model   vdw
     2.103 3.120
  nonbonded pdb=" OG  SER N  26 "
            pdb=" OE1 GLN N  27 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" OH  TYR M 104 "
            pdb=" OD2 ASP N  50 "
     model   vdw
     2.146 3.040
  ... (remaining 34710 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 'H' and (resid 2 through 12 or resid 14 through 15 or resid 17 through 22 \ 
 or resid 25 through 27 or resid 29 or resid 32 or resid 36 through 47 or resid  \ 
49 or resid 51 or resid 53 or resid 57 or resid 60 through 61 or resid 63 throug \ 
h 73 or resid 75 through 77 or resid 80 through 86 or resid 89 through 96 or res \ 
id 98 through 100 or resid 102 through 108 or resid 110 through 128 or resid 135 \ 
 through 214))
  selection = (chain 'M' and (resid 2 through 12 or resid 14 through 15 or resid 17 through 22 \ 
 or resid 25 through 27 or resid 29 or resid 32 or resid 36 through 47 or resid  \ 
49 or resid 51 or resid 53 or resid 59 or resid 62 through 63 or resid 65 throug \ 
h 75 or resid 77 through 79 or resid 82 through 88 or resid 91 through 98 or res \ 
id 100 or resid 111 through 112 or resid 115 through 121 or resid 123 through 22 \ 
3))
}

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:             0.440
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.170
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
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   0.049   5041  Z= 0.281
  Angle     :  0.815  23.757   6674  Z= 0.532
  Chirality :  0.053   0.435    522
  Planarity :  0.006   0.110    995
  Dihedral  : 15.097 109.619   1614
  Min Nonbonded Distance : 1.340

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  3.41 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 33.69 %
    Favored  : 65.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.31), residues: 821
  helix:  1.90 (1.56), residues: 15
  sheet:  1.70 (0.27), residues: 358
  loop :  0.34 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP M  47 
 HIS   0.003   0.002   HIS H  35 
 PHE   0.010   0.002   PHE H  68 
 TYR   0.015   0.001   TYR M 112 
 ARG   0.008   0.001   ARG M  16 

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 144
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.8449 (mp0) cc_final: 0.8237 (mp0)
REVERT: H   76 LYS cc_start: 0.8928 (tmtt) cc_final: 0.8718 (tmtt)
  outliers start: 4
  outliers final: 1
  residues processed: 145
  average time/residue: 0.1924
  time to fit residues: 34.4621
Evaluate side-chains
  144 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue    7 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 62 optimal weight:    8.9990
   chunk 34 optimal weight:   50.0000
   chunk 21 optimal weight:    0.0770
   chunk 42 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 39 optimal weight:   50.0000
   chunk 48 optimal weight:    1.9990
   chunk 75 optimal weight:    8.9990
   overall best weight:    2.4146

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

Flipped N/Q/H residues before XYZ refinement:
L  77 GLN
N  79 GLN
N  89 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.082646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.068760 restraints weight = 12845.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.070339 restraints weight = 7454.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.071478 restraints weight = 5122.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5041  Z= 0.191
  Angle     :  0.541   5.674   6674  Z= 0.300
  Chirality :  0.042   0.139    522
  Planarity :  0.005   0.073    995
  Dihedral  :  4.450  28.855    876
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.17 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 28.30 %
    Favored  : 66.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.30), residues: 821
  helix:  1.54 (1.48), residues: 16
  sheet:  1.62 (0.27), residues: 361
  loop :  0.32 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP M  47 
 HIS   0.004   0.003   HIS H  35 
 PHE   0.016   0.002   PHE N  96 
 TYR   0.012   0.001   TYR L  47 
 ARG   0.005   0.001   ARG M  16 

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.539 
Fit side-chains
REVERT: H   76 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8218 (tmtt)
REVERT: L   16 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8238 (tm-30)
REVERT: L  101 THR cc_start: 0.8876 (m) cc_final: 0.8561 (p)
REVERT: M  122 THR cc_start: 0.9232 (m) cc_final: 0.8967 (p)
  outliers start: 21
  outliers final: 7
  residues processed: 157
  average time/residue: 0.1944
  time to fit residues: 37.7353
Evaluate side-chains
  154 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   76 LYS
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   30 TYR
Chi-restraints excluded: chain M residue   11 LEU
Chi-restraints excluded: chain M residue   62 TYR
Chi-restraints excluded: chain M residue  116 VAL
Chi-restraints excluded: chain N residue  100 GLN
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   chunk 37 optimal weight:   40.0000
   chunk 60 optimal weight:   50.0000
   chunk 12 optimal weight:   20.0000
   chunk 48 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 80 optimal weight:   40.0000
   chunk 50 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   overall best weight:    6.3988

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

Flipped N/Q/H residues before XYZ refinement:
L  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.079146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.064710 restraints weight = 13268.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.066372 restraints weight = 7544.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.067513 restraints weight = 5156.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   5041  Z= 0.379
  Angle     :  0.641   9.638   6674  Z= 0.352
  Chirality :  0.045   0.187    522
  Planarity :  0.005   0.058    995
  Dihedral  :  4.831  19.377    875
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.51 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 30.19 %
    Favored  : 64.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.30), residues: 821
  helix:  1.18 (1.49), residues: 16
  sheet:  1.55 (0.27), residues: 359
  loop :  0.10 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP M  47 
 HIS   0.006   0.004   HIS H  35 
 PHE   0.029   0.003   PHE N  94 
 TYR   0.020   0.002   TYR L  47 
 ARG   0.006   0.001   ARG H  98 

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.559 
Fit side-chains
REVERT: H   76 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8259 (tmtt)
REVERT: L   16 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8172 (tm-30)
REVERT: L  101 THR cc_start: 0.8921 (m) cc_final: 0.8598 (p)
REVERT: N    4 MET cc_start: 0.8379 (mmm) cc_final: 0.8124 (mmm)
REVERT: N   73 LEU cc_start: 0.8772 (mt) cc_final: 0.8554 (mt)
  outliers start: 20
  outliers final: 11
  residues processed: 155
  average time/residue: 0.1804
  time to fit residues: 34.7825
Evaluate side-chains
  158 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   76 LYS
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   30 TYR
Chi-restraints excluded: chain M residue   75 ASP
Chi-restraints excluded: chain M residue   85 MET
Chi-restraints excluded: chain M residue   99 THR
Chi-restraints excluded: chain M residue  116 VAL
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue  100 GLN
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 75 optimal weight:   40.0000
   chunk 7 optimal weight:    0.9980
   chunk 70 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 46 optimal weight:   20.0000
   chunk 73 optimal weight:    0.0770
   chunk 5 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    2.0142

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
L  36 GLN
L  77 GLN
N  79 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.082033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.067478 restraints weight = 13135.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.069119 restraints weight = 7681.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.070301 restraints weight = 5333.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5041  Z= 0.172
  Angle     :  0.513   5.771   6674  Z= 0.282
  Chirality :  0.042   0.144    522
  Planarity :  0.004   0.049    995
  Dihedral  :  4.176  16.752    875
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.41 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 30.73 %
    Favored  : 64.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.30), residues: 821
  helix:  1.44 (1.47), residues: 16
  sheet:  1.41 (0.26), residues: 369
  loop :  0.24 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP M  47 
 HIS   0.003   0.002   HIS H  35 
 PHE   0.014   0.002   PHE N  94 
 TYR   0.011   0.001   TYR L  47 
 ARG   0.005   0.001   ARG M  16 

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.8039 (mp0) cc_final: 0.7829 (mp0)
REVERT: H   76 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8197 (tmtt)
REVERT: L   16 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: L  101 THR cc_start: 0.8859 (m) cc_final: 0.8540 (p)
REVERT: M  122 THR cc_start: 0.9225 (m) cc_final: 0.9015 (p)
  outliers start: 19
  outliers final: 12
  residues processed: 161
  average time/residue: 0.1896
  time to fit residues: 37.6521
Evaluate side-chains
  163 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   76 LYS
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   30 TYR
Chi-restraints excluded: chain M residue   11 LEU
Chi-restraints excluded: chain M residue   12 VAL
Chi-restraints excluded: chain M residue   62 TYR
Chi-restraints excluded: chain M residue   85 MET
Chi-restraints excluded: chain M residue  116 VAL
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue  100 GLN
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 1 optimal weight:    0.2980
   chunk 68 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 67 optimal weight:    0.6980
   chunk 78 optimal weight:   40.0000
   chunk 45 optimal weight:   10.0000
   chunk 81 optimal weight:   40.0000
   chunk 80 optimal weight:   30.0000
   chunk 47 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    4.9986

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

Flipped N/Q/H residues before XYZ refinement:
L  77 GLN
N  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.080005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.065798 restraints weight = 13151.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.067440 restraints weight = 7608.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.068434 restraints weight = 5279.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5041  Z= 0.308
  Angle     :  0.595   7.736   6674  Z= 0.326
  Chirality :  0.043   0.175    522
  Planarity :  0.005   0.055    995
  Dihedral  :  4.575  18.398    875
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.90 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 32.61 %
    Favored  : 62.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.30), residues: 821
  helix:  1.30 (1.45), residues: 16
  sheet:  1.36 (0.26), residues: 368
  loop :  0.14 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP M  47 
 HIS   0.004   0.002   HIS H  35 
 PHE   0.024   0.003   PHE H  68 
 TYR   0.019   0.002   TYR M 112 
 ARG   0.005   0.001   ARG M  16 

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.556 
Fit side-chains
REVERT: H   76 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8254 (tmtt)
REVERT: L   16 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8321 (tm-30)
REVERT: L  101 THR cc_start: 0.8894 (m) cc_final: 0.8504 (p)
  outliers start: 19
  outliers final: 12
  residues processed: 153
  average time/residue: 0.1780
  time to fit residues: 33.9600
Evaluate side-chains
  159 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   76 LYS
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain M residue   12 VAL
Chi-restraints excluded: chain M residue   53 SER
Chi-restraints excluded: chain M residue   85 MET
Chi-restraints excluded: chain M residue  116 VAL
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue  100 GLN
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 13 optimal weight:   50.0000
   chunk 38 optimal weight:   50.0000
   chunk 69 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0970
   chunk 49 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 35 optimal weight:   50.0000
   overall best weight:    4.8186

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

Flipped N/Q/H residues before XYZ refinement:
N   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.079798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.065518 restraints weight = 13265.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.067088 restraints weight = 7727.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.068208 restraints weight = 5361.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5041  Z= 0.298
  Angle     :  0.595   7.374   6674  Z= 0.325
  Chirality :  0.043   0.180    522
  Planarity :  0.004   0.055    995
  Dihedral  :  4.578  17.618    875
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.38 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 31.00 %
    Favored  : 63.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.95 (0.30), residues: 821
  helix:  1.25 (1.46), residues: 16
  sheet:  1.29 (0.26), residues: 369
  loop :  0.08 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP M  47 
 HIS   0.004   0.002   HIS H  35 
 PHE   0.026   0.003   PHE H  68 
 TYR   0.017   0.002   TYR M 112 
 ARG   0.006   0.001   ARG M  16 

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.552 
Fit side-chains
REVERT: H   76 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8251 (tmtt)
REVERT: L   16 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: L  101 THR cc_start: 0.8881 (m) cc_final: 0.8523 (p)
  outliers start: 22
  outliers final: 15
  residues processed: 152
  average time/residue: 0.1795
  time to fit residues: 33.9699
Evaluate side-chains
  161 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   76 LYS
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  113 SER
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   30 TYR
Chi-restraints excluded: chain M residue   11 LEU
Chi-restraints excluded: chain M residue   12 VAL
Chi-restraints excluded: chain M residue   53 SER
Chi-restraints excluded: chain M residue   62 TYR
Chi-restraints excluded: chain M residue   85 MET
Chi-restraints excluded: chain M residue  116 VAL
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue  100 GLN
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 34 optimal weight:   40.0000
   chunk 28 optimal weight:    6.9990
   chunk 23 optimal weight:   20.0000
   chunk 59 optimal weight:   50.0000
   chunk 50 optimal weight:    9.9990
   chunk 15 optimal weight:   40.0000
   chunk 62 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 52 optimal weight:   20.0000
   chunk 10 optimal weight:    8.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
N   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.077810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.063387 restraints weight = 13267.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.065091 restraints weight = 7533.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.066258 restraints weight = 5161.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   5041  Z= 0.464
  Angle     :  0.702   9.730   6674  Z= 0.385
  Chirality :  0.047   0.207    522
  Planarity :  0.005   0.060    995
  Dihedral  :  5.114  19.014    875
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.60 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 30.73 %
    Favored  : 63.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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 (0.30), residues: 821
  helix:  0.85 (1.45), residues: 16
  sheet:  1.29 (0.26), residues: 369
  loop : -0.07 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP H 104 
 HIS   0.005   0.003   HIS H  35 
 PHE   0.033   0.004   PHE H  68 
 TYR   0.028   0.003   TYR M 112 
 ARG   0.007   0.001   ARG M  16 

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.573 
Fit side-chains
REVERT: H   76 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8285 (tmtt)
REVERT: L   16 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8322 (tm-30)
REVERT: L  101 THR cc_start: 0.8892 (m) cc_final: 0.8555 (p)
  outliers start: 23
  outliers final: 17
  residues processed: 150
  average time/residue: 0.1872
  time to fit residues: 34.8898
Evaluate side-chains
  159 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   76 LYS
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain M residue   11 LEU
Chi-restraints excluded: chain M residue   12 VAL
Chi-restraints excluded: chain M residue   30 ASP
Chi-restraints excluded: chain M residue   43 LYS
Chi-restraints excluded: chain M residue   53 SER
Chi-restraints excluded: chain M residue   79 ASN
Chi-restraints excluded: chain M residue   85 MET
Chi-restraints excluded: chain M residue  116 VAL
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue  100 GLN
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 78 optimal weight:   40.0000
   chunk 68 optimal weight:    5.9990
   chunk 56 optimal weight:   40.0000
   chunk 38 optimal weight:    4.9990
   chunk 52 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   chunk 76 optimal weight:   30.0000
   chunk 73 optimal weight:    9.9990
   chunk 28 optimal weight:    7.9990
   chunk 63 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
N  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.078747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.064344 restraints weight = 13506.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.066003 restraints weight = 7655.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.067176 restraints weight = 5189.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5041  Z= 0.317
  Angle     :  0.619   7.924   6674  Z= 0.340
  Chirality :  0.044   0.183    522
  Planarity :  0.005   0.058    995
  Dihedral  :  4.802  17.955    875
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.63 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 32.35 %
    Favored  : 62.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.82 (0.30), residues: 821
  helix:  0.97 (1.46), residues: 16
  sheet:  1.26 (0.26), residues: 362
  loop : -0.04 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP M  47 
 HIS   0.004   0.002   HIS H  35 
 PHE   0.023   0.003   PHE H  68 
 TYR   0.023   0.002   TYR M 112 
 ARG   0.005   0.001   ARG M  16 

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.532 
Fit side-chains
REVERT: H   76 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8270 (tmtt)
REVERT: L   16 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8324 (tm-30)
REVERT: L  101 THR cc_start: 0.8864 (m) cc_final: 0.8555 (p)
  outliers start: 20
  outliers final: 15
  residues processed: 155
  average time/residue: 0.1942
  time to fit residues: 37.4412
Evaluate side-chains
  162 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   76 LYS
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain M residue   11 LEU
Chi-restraints excluded: chain M residue   12 VAL
Chi-restraints excluded: chain M residue   43 LYS
Chi-restraints excluded: chain M residue   53 SER
Chi-restraints excluded: chain M residue   78 LYS
Chi-restraints excluded: chain M residue   85 MET
Chi-restraints excluded: chain M residue  116 VAL
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue  100 GLN
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 78 optimal weight:   40.0000
   chunk 51 optimal weight:   10.0000
   chunk 55 optimal weight:   30.0000
   chunk 58 optimal weight:   20.0000
   chunk 20 optimal weight:   50.0000
   chunk 23 optimal weight:   20.0000
   chunk 40 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:   50.0000
   chunk 70 optimal weight:    8.9990
   overall best weight:    6.3992

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

Flipped N/Q/H residues before XYZ refinement:
** N   6 GLN ** 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 = 0.3030 r_free = 0.3030 target = 0.078092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.063980 restraints weight = 13252.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.065647 restraints weight = 7469.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.066803 restraints weight = 5092.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   5041  Z= 0.377
  Angle     :  0.664   8.784   6674  Z= 0.363
  Chirality :  0.045   0.193    522
  Planarity :  0.005   0.061    995
  Dihedral  :  4.944  18.534    875
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.60 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 32.08 %
    Favored  : 61.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.73 (0.30), residues: 821
  helix:  0.93 (1.45), residues: 16
  sheet:  1.17 (0.26), residues: 369
  loop : -0.10 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP M  47 
 HIS   0.004   0.002   HIS H  35 
 PHE   0.036   0.003   PHE H  68 
 TYR   0.028   0.002   TYR M 112 
 ARG   0.005   0.001   ARG M  16 

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.655 
Fit side-chains
REVERT: H   76 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8299 (tmtt)
REVERT: L   16 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8321 (tm-30)
REVERT: L  101 THR cc_start: 0.8875 (m) cc_final: 0.8564 (p)
  outliers start: 22
  outliers final: 19
  residues processed: 151
  average time/residue: 0.2003
  time to fit residues: 37.5243
Evaluate side-chains
  161 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   76 LYS
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   30 TYR
Chi-restraints excluded: chain M residue   11 LEU
Chi-restraints excluded: chain M residue   12 VAL
Chi-restraints excluded: chain M residue   43 LYS
Chi-restraints excluded: chain M residue   53 SER
Chi-restraints excluded: chain M residue   75 ASP
Chi-restraints excluded: chain M residue   78 LYS
Chi-restraints excluded: chain M residue   85 MET
Chi-restraints excluded: chain M residue  116 VAL
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue  100 GLN
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 78 optimal weight:   30.0000
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:   40.0000
   chunk 45 optimal weight:    2.9990
   overall best weight:    2.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.080284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.066023 restraints weight = 13199.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.067673 restraints weight = 7498.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.068859 restraints weight = 5151.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5041  Z= 0.213
  Angle     :  0.579   6.614   6674  Z= 0.316
  Chirality :  0.042   0.164    522
  Planarity :  0.004   0.059    995
  Dihedral  :  4.421  17.592    875
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.38 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 33.15 %
    Favored  : 61.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.82 (0.30), residues: 821
  helix:  1.29 (1.46), residues: 16
  sheet:  1.14 (0.26), residues: 368
  loop :  0.05 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP M  47 
 HIS   0.003   0.002   HIS H  35 
 PHE   0.027   0.002   PHE N  49 
 TYR   0.018   0.002   TYR M 112 
 ARG   0.006   0.001   ARG M  19 

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

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

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1642 Ramachandran restraints generated.
    821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.593 
Fit side-chains
REVERT: H   76 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8240 (tmtt)
REVERT: L   16 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8341 (tm-30)
REVERT: L  101 THR cc_start: 0.8834 (m) cc_final: 0.8547 (p)
REVERT: N    4 MET cc_start: 0.8473 (tpp) cc_final: 0.8179 (mmm)
  outliers start: 19
  outliers final: 16
  residues processed: 157
  average time/residue: 0.1904
  time to fit residues: 37.1898
Evaluate side-chains
  162 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   76 LYS
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   99 TYR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   30 TYR
Chi-restraints excluded: chain M residue   11 LEU
Chi-restraints excluded: chain M residue   12 VAL
Chi-restraints excluded: chain M residue   43 LYS
Chi-restraints excluded: chain M residue   53 SER
Chi-restraints excluded: chain M residue   85 MET
Chi-restraints excluded: chain M residue  116 VAL
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue  100 GLN
Chi-restraints excluded: chain N residue  106 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 39 optimal weight:   50.0000
   chunk 37 optimal weight:   50.0000
   chunk 80 optimal weight:   40.0000
   chunk 36 optimal weight:    8.9990
   chunk 12 optimal weight:   20.0000
   chunk 44 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 13 optimal weight:   50.0000
   chunk 25 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    5.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.078759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.064381 restraints weight = 13395.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.066021 restraints weight = 7535.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.067260 restraints weight = 5132.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5041  Z= 0.351
  Angle     :  0.647   8.135   6674  Z= 0.354
  Chirality :  0.044   0.189    522
  Planarity :  0.005   0.061    995
  Dihedral  :  4.767  19.196    875
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.12 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 34.23 %
    Favored  : 60.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.79 (0.30), residues: 821
  helix:  1.28 (1.47), residues: 16
  sheet:  1.18 (0.26), residues: 367
  loop : -0.04 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP M  47 
 HIS   0.003   0.002   HIS H  35 
 PHE   0.024   0.003   PHE H  68 
 TYR   0.027   0.002   TYR M 112 
 ARG   0.008   0.001   ARG M  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1815.39 seconds
wall clock time: 33 minutes 10.67 seconds (1990.67 seconds total)