Starting phenix.real_space_refine
on Wed Mar  4 04:00:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rpw_24624/03_2026/7rpw_24624.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rpw_24624/03_2026/7rpw_24624.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rpw_24624/03_2026/7rpw_24624.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rpw_24624/03_2026/7rpw_24624.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rpw_24624/03_2026/7rpw_24624.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rpw_24624/03_2026/7rpw_24624.cif"
  }
  resolution = 4.38
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.101
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: 6
    Type Number    sf(0)   Gaussians
     Mn      4      7.51       5
     P      63      5.49       5
     S      25      5.16       5
     C    6567      2.51       5
     N    1750      2.21       5
     O    2185      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10594
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 1953
          Classifications: {'peptide': 252}
          Link IDs: {'PTRANS': 8, 'TRANS': 243}
    Chain: "B"
      Number of atoms: 1922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1922
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 9, 'TRANS': 233}
    Chain: "C"
      Number of atoms: 1941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1941
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 5, 'TRANS': 239}
    Chain: "X"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 409
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "Y"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 229
          Classifications: {'DNA': 11}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 10}
    Chain: "Z"
      Number of atoms: 634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 634
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "E"
      Number of atoms: 3480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3480
          Classifications: {'peptide': 439}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 13, 'TRANS': 425}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "X"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "Y"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'AMP%rna2p': 1}
          Classifications: {'RNA_mixed': 1}
          Modifications used: {'rna2p': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.59, per 1000 atoms: 0.24
  Number of scatterers: 10594
  At special positions: 0
  Unit cell: (117, 106.5, 123, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      4     24.99
     S      25     16.00
     P      63     15.00
     O    2185      8.00
     N    1750      7.00
     C    6567      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 511.0 milliseconds
  

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2218

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 15 sheets defined
      28.1% alpha, 16.5% beta
      30 base pairs and 46 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 21
    Processing helix  chain 'A' and resid 74 through 80
      removed outlier: 3.712A  pdb=" N   ILE A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 151
      removed outlier: 3.864A  pdb=" N   ASN A 144 " --> pdb=" O   GLU A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 165
    Processing helix  chain 'A' and resid 202 through 210
    Processing helix  chain 'B' and resid 10 through 20
    Processing helix  chain 'B' and resid 72 through 81
      removed outlier: 3.501A  pdb=" N   VAL B  76 " --> pdb=" O   LYS B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 147
      removed outlier: 4.131A  pdb=" N   LEU B 147 " --> pdb=" O   ILE B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 204
      removed outlier: 3.584A  pdb=" N   VAL B 202 " --> pdb=" O   GLY B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 207
      No H-bonds generated for 'chain 'B' and resid 205 through 207'
    Processing helix  chain 'C' and resid 9 through 20
      removed outlier: 3.705A  pdb=" N   ASP C  13 " --> pdb=" O   ARG C   9 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE C  14 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   ILE C  15 " --> pdb=" O   LEU C  11 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LEU C  18 " --> pdb=" O   ILE C  14 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ARG C  20 " --> pdb=" O   GLN C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 79
      removed outlier: 3.662A  pdb=" N   ILE C  77 " --> pdb=" O   TYR C  73 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU C  78 " --> pdb=" O   LEU C  74 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LYS C  79 " --> pdb=" O   MET C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 147
      removed outlier: 4.070A  pdb=" N   LYS C 140 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER C 141 " --> pdb=" O   ASP C 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 12
      removed outlier: 4.706A  pdb=" N   ILE E   6 " --> pdb=" O   GLU E   2 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 33
      removed outlier: 3.804A  pdb=" N   THR E  23 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ALA E  24 " --> pdb=" O   LEU E  20 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 37 through 47
    Processing helix  chain 'E' and resid 51 through 55
      removed outlier: 3.522A  pdb=" N   LEU E  54 " --> pdb=" O   PRO E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 75
    Processing helix  chain 'E' and resid 77 through 88
    Processing helix  chain 'E' and resid 90 through 97
      removed outlier: 3.840A  pdb=" N   ARG E  97 " --> pdb=" O   GLU E  93 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 133
      removed outlier: 4.304A  pdb=" N   LEU E 133 " --> pdb=" O   SER E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 138 through 153
      removed outlier: 4.557A  pdb=" N   LEU E 142 " --> pdb=" O   GLY E 138 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 168
      removed outlier: 4.067A  pdb=" N   ARG E 164 " --> pdb=" O   LYS E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 175 through 189
      removed outlier: 3.514A  pdb=" N   VAL E 179 " --> pdb=" O   GLY E 175 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 192 through 204
      removed outlier: 4.544A  pdb=" N   ILE E 196 " --> pdb=" O   SER E 192 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE E 197 " --> pdb=" O   ALA E 193 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG E 204 " --> pdb=" O   ALA E 200 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 207 through 217
    Processing helix  chain 'E' and resid 246 through 252
    Processing helix  chain 'E' and resid 291 through 300
      removed outlier: 4.118A  pdb=" N   TYR E 295 " --> pdb=" O   ASP E 291 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   VAL E 296 " --> pdb=" O   VAL E 292 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   SER E 297 " --> pdb=" O   VAL E 293 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS E 298 " --> pdb=" O   ASP E 294 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 323 through 331
      removed outlier: 4.102A  pdb=" N   HIS E 329 " --> pdb=" O   GLN E 325 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ARG E 330 " --> pdb=" O   GLU E 326 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS E 331 " --> pdb=" O   LEU E 327 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 366 through 375
      removed outlier: 3.636A  pdb=" N   GLU E 373 " --> pdb=" O   ARG E 369 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER E 374 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE E 375 " --> pdb=" O   LEU E 371 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 392 through 407
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
      removed outlier: 3.646A  pdb=" N   ILE A  89 " --> pdb=" O   TYR A   6 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   THR A  92 " --> pdb=" O   LYS A  99 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   LYS A  99 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU C 175 " --> pdb=" O   LYS A 110 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   THR A 112 " --> pdb=" O   GLU C 173 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLU C 173 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52
      removed outlier: 4.116A  pdb=" N   ILE A  35 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ARG A  38 " --> pdb=" O   ILE A  27 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   ILE A  27 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   LEU A  40 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 9.028A  pdb=" N   SER A  25 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A  70 " --> pdb=" O   ILE A  26 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   LEU A  28 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 138
      removed outlier: 3.622A  pdb=" N   VAL A 134 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 181
      removed outlier: 3.603A  pdb=" N   ALA A 179 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.670A  pdb=" N   THR B  99 " --> pdb=" O   SER B  92 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 30
    Processing sheet with id=AA7, first strand: chain 'B' and resid 37 through 40
      removed outlier: 3.630A  pdb=" N   ASP B  49 " --> pdb=" O   ASP B 238 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   PHE B  51 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   TYR B 236 " --> pdb=" O   PHE B  51 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 190
      removed outlier: 3.694A  pdb=" N   SER B 189 " --> pdb=" O   LYS B 132 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS B 132 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 159
    Processing sheet with id=AB1, first strand: chain 'B' and resid 165 through 168
      removed outlier: 3.620A  pdb=" N   PHE B 165 " --> pdb=" O   VAL B 176 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL C  97 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ILE C  87 " --> pdb=" O   TYR C   5 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   TYR C   5 " --> pdb=" O   ILE C  87 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 26 through 29
      removed outlier: 4.749A  pdb=" N   VAL C  26 " --> pdb=" O   VAL C  37 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   VAL C  37 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU C  51 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE C  47 " --> pdb=" O   ALA C  38 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU C  46 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 131
      removed outlier: 3.516A  pdb=" N   PHE C 218 " --> pdb=" O   ILE C 130 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 162 through 165
      removed outlier: 3.890A  pdb=" N   SER C 192 " --> pdb=" O   GLY C 157 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 239 through 241
      removed outlier: 6.364A  pdb=" N   GLU E 239 " --> pdb=" O   LYS E 433 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 275 through 278
      removed outlier: 4.203A  pdb=" N   ILE E 307 " --> pdb=" O   ILE E 268 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ILE E 306 " --> pdb=" O   MET E 353 " (cutoff:3.500A)

    311 hydrogen bonds defined for protein.
    852 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      77 hydrogen bonds
      154 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      46 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 1.17 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: 2810
        1.33 -     1.45: 1960
        1.45 -     1.57: 5949
        1.57 -     1.69: 122
        1.69 -     1.81: 50
  Bond restraints: 10891
  Sorted by residual:
  bond pdb=" C3'  DA Z  22 "
       pdb=" O3'  DA Z  22 "
    ideal  model  delta    sigma   weight residual
    1.422  1.474 -0.052 3.00e-02 1.11e+03 3.02e+00
  bond pdb=" C3'  DA Z  13 "
       pdb=" O3'  DA Z  13 "
    ideal  model  delta    sigma   weight residual
    1.422  1.464 -0.042 3.00e-02 1.11e+03 1.92e+00
  bond pdb=" C   ILE E 285 "
       pdb=" O   ILE E 285 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 1.19e-02 7.06e+03 1.20e+00
  bond pdb=" C3'  DT Z  30 "
       pdb=" O3'  DT Z  30 "
    ideal  model  delta    sigma   weight residual
    1.422  1.455 -0.033 3.00e-02 1.11e+03 1.18e+00
  bond pdb=" C4'  DG Y   4 "
       pdb=" C3'  DG Y   4 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.021 2.00e-02 2.50e+03 1.07e+00
  ... (remaining 10886 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 14372
        1.25 -     2.50: 464
        2.50 -     3.75: 93
        3.75 -     5.00: 17
        5.00 -     6.25: 8
  Bond angle restraints: 14954
  Sorted by residual:
  angle pdb=" N   GLU E 366 "
        pdb=" CA  GLU E 366 "
        pdb=" C   GLU E 366 "
      ideal   model   delta    sigma   weight residual
     113.18  109.01    4.17 1.33e+00 5.65e-01 9.81e+00
  angle pdb=" N   ALA E 132 "
        pdb=" CA  ALA E 132 "
        pdb=" C   ALA E 132 "
      ideal   model   delta    sigma   weight residual
     111.02  114.02   -3.00 1.22e+00 6.72e-01 6.04e+00
  angle pdb=" C3'  DA Z  22 "
        pdb=" O3'  DA Z  22 "
        pdb=" P    DC Z  23 "
      ideal   model   delta    sigma   weight residual
     120.20  123.80   -3.60 1.50e+00 4.44e-01 5.77e+00
  angle pdb=" N   SER B  24 "
        pdb=" CA  SER B  24 "
        pdb=" C   SER B  24 "
      ideal   model   delta    sigma   weight residual
     114.09  110.45    3.64 1.55e+00 4.16e-01 5.51e+00
  angle pdb=" C   LYS C 243 "
        pdb=" N   VAL C 244 "
        pdb=" CA  VAL C 244 "
      ideal   model   delta    sigma   weight residual
     121.97  125.94   -3.97 1.80e+00 3.09e-01 4.86e+00
  ... (remaining 14949 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.68: 6066
       34.68 -    69.36: 385
       69.36 -   104.04: 5
      104.04 -   138.72: 0
      138.72 -   173.39: 5
  Dihedral angle restraints: 6461
    sinusoidal: 3029
      harmonic: 3432
  Sorted by residual:
  dihedral pdb=" CA  SER E 139 "
           pdb=" C   SER E 139 "
           pdb=" N   ARG E 140 "
           pdb=" CA  ARG E 140 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.45  -24.55     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  LEU C 205 "
           pdb=" C   LEU C 205 "
           pdb=" N   SER C 206 "
           pdb=" CA  SER C 206 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.66   22.34     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  LEU C  11 "
           pdb=" C   LEU C  11 "
           pdb=" N   LYS C  12 "
           pdb=" CA  LYS C  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.44   20.56     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 6458 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1174
       0.035 -    0.069: 371
       0.069 -    0.104: 120
       0.104 -    0.139: 57
       0.139 -    0.173: 2
  Chirality restraints: 1724
  Sorted by residual:
  chirality pdb=" CB  VAL C 244 "
            pdb=" CA  VAL C 244 "
            pdb=" CG1 VAL C 244 "
            pdb=" CG2 VAL C 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.50e-01
  chirality pdb=" P    DG Z  27 "
            pdb=" OP1  DG Z  27 "
            pdb=" OP2  DG Z  27 "
            pdb=" O5'  DG Z  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.49   -0.14 2.00e-01 2.50e+01 5.13e-01
  chirality pdb=" CA  ILE E 231 "
            pdb=" N   ILE E 231 "
            pdb=" C   ILE E 231 "
            pdb=" CB  ILE E 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.77e-01
  ... (remaining 1721 not shown)

  Planarity restraints: 1681
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  93 "    0.019 5.00e-02 4.00e+02   2.94e-02 1.39e+00
        pdb=" N   PRO C  94 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C  94 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  94 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 226 "   -0.019 5.00e-02 4.00e+02   2.92e-02 1.37e+00
        pdb=" N   PRO E 227 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO E 227 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO E 227 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 121 "   -0.019 5.00e-02 4.00e+02   2.89e-02 1.33e+00
        pdb=" N   PRO B 122 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 122 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 122 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1678 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.38: 62
        2.38 -     3.01: 6110
        3.01 -     3.64: 17020
        3.64 -     4.27: 23587
        4.27 -     4.90: 36833
  Nonbonded interactions: 83612
  Sorted by model distance:
  nonbonded pdb=" O   GLY E  60 "
            pdb="MN    MN X 101 "
     model   vdw
     1.756 2.320
  nonbonded pdb=" OP1  DG X  22 "
            pdb="MN    MN E 701 "
     model   vdw
     1.835 2.320
  nonbonded pdb=" O3'  DG X  20 "
            pdb="MN    MN X 101 "
     model   vdw
     1.913 2.320
  nonbonded pdb=" O   LYS E 130 "
            pdb=" OG1 THR E 134 "
     model   vdw
     2.077 3.040
  nonbonded pdb=" OP1  DC X  21 "
            pdb="MN    MN X 102 "
     model   vdw
     2.146 2.320
  ... (remaining 83607 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.520
  Find NCS groups from input model:        0.050
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10892  Z= 0.161
  Angle     :  0.570   6.255  14954  Z= 0.310
  Chirality :  0.042   0.173   1724
  Planarity :  0.003   0.029   1681
  Dihedral  : 19.290 173.395   4243
  Min Nonbonded Distance : 1.756

Molprobity Statistics.
  All-atom Clashscore : 18.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.27 %
    Favored  : 88.64 %
  Rotamer:
    Outliers :  9.97 %
    Allowed  : 13.46 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.24), residues: 1171
  helix: -0.42 (0.30), residues: 300
  sheet: -1.68 (0.31), residues: 304
  loop : -2.82 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 265 
 TYR   0.010   0.001   TYR C 196 
 PHE   0.018   0.001   PHE E  53 
 TRP   0.003   0.001   TRP E  50 
 HIS   0.005   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (10891)
  covalent geometry    : angle       0.57022 (14954)
  hydrogen bonds       : bond        0.21083 (  388)
  hydrogen bonds       : angle       9.19799 ( 1006)
  Misc. bond           : bond        0.05188 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 103
    poor density    : 153
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 SER cc_start: 0.8093 (t) cc_final: 0.7566 (m)
REVERT: A   80 SER cc_start: 0.9022 (t) cc_final: 0.8779 (p)
REVERT: A  137 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8102 (t)
REVERT: B   21 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7684 (t0)
REVERT: B   89 LEU cc_start: 0.5247 (OUTLIER) cc_final: 0.4884 (tp)
REVERT: C   44 ILE cc_start: 0.9077 (mt) cc_final: 0.8816 (mm)
REVERT: C   75 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7341 (tpp)
REVERT: C  146 VAL cc_start: 0.7875 (t) cc_final: 0.6797 (t)
REVERT: E  123 GLU cc_start: 0.7720 (pp20) cc_final: 0.7429 (mp0)
REVERT: E  142 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7176 (mp)
REVERT: E  164 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7697 (tpt170)
REVERT: E  328 MET cc_start: 0.8600 (mtm) cc_final: 0.7994 (tmm)
REVERT: E  360 TYR cc_start: 0.4794 (OUTLIER) cc_final: 0.4463 (t80)
REVERT: E  372 LEU cc_start: 0.6464 (tp) cc_final: 0.6179 (tp)
  outliers start: 103
  outliers final: 40
  residues processed: 239
  average time/residue: 0.0992
  time to fit residues: 33.5201
Evaluate side-chains
  149 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 103
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    0.2980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:   20.0000
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  21 ASN
A 240 HIS
E 391 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.114537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.096647 restraints weight = 46923.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.097741 restraints weight = 42762.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.098265 restraints weight = 34789.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.098427 restraints weight = 26333.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.099186 restraints weight = 24367.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3940 r_free = 0.3940    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3938 r_free = 0.3938    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6758
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10892  Z= 0.172
  Angle     :  0.670   6.163  14954  Z= 0.360
  Chirality :  0.047   0.237   1724
  Planarity :  0.004   0.033   1681
  Dihedral  : 22.085 175.034   1931
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.44 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.26 %
    Favored  : 95.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.74 (0.24), residues: 1171
  helix: -0.53 (0.29), residues: 301
  sheet: -1.54 (0.31), residues: 309
  loop : -2.75 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 330 
 TYR   0.018   0.002   TYR B  56 
 PHE   0.023   0.002   PHE E  53 
 TRP   0.020   0.002   TRP E  50 
 HIS   0.005   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10891)
  covalent geometry    : angle       0.67005 (14954)
  hydrogen bonds       : bond        0.04925 (  388)
  hydrogen bonds       : angle       6.86364 ( 1006)
  Misc. bond           : bond        0.00031 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 156
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.7326 (mp) cc_final: 0.6593 (mp)
REVERT: A   80 SER cc_start: 0.9015 (t) cc_final: 0.8760 (p)
REVERT: B  146 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6334 (tt0)
REVERT: B  216 GLU cc_start: 0.3798 (mm-30) cc_final: 0.3509 (mm-30)
REVERT: C    1 MET cc_start: 0.7787 (tpt) cc_final: 0.7360 (tpp)
REVERT: C   44 ILE cc_start: 0.8851 (mt) cc_final: 0.8610 (mm)
REVERT: C   80 VAL cc_start: 0.7549 (m) cc_final: 0.6139 (m)
REVERT: C  146 VAL cc_start: 0.7428 (t) cc_final: 0.7177 (t)
REVERT: E    8 GLU cc_start: 0.7814 (tm-30) cc_final: 0.6813 (pt0)
REVERT: E   63 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7527 (mt-10)
REVERT: E  133 LEU cc_start: 0.7608 (mp) cc_final: 0.7262 (mt)
REVERT: E  280 ARG cc_start: 0.6375 (tmt170) cc_final: 0.6076 (tpt-90)
REVERT: E  360 TYR cc_start: 0.6214 (m-10) cc_final: 0.5860 (t80)
REVERT: E  372 LEU cc_start: 0.6421 (tp) cc_final: 0.6146 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 157
  average time/residue: 0.0992
  time to fit residues: 22.1886
Evaluate side-chains
  98 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 78 optimal weight:    8.9990
   chunk 116 optimal weight:    7.9990
   chunk 115 optimal weight:    5.9990
   chunk 101 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 58 optimal weight:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.110814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.092875 restraints weight = 47042.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.093795 restraints weight = 40875.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.094304 restraints weight = 35643.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.094963 restraints weight = 27181.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.095162 restraints weight = 24811.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3861
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3861 r_free = 0.3861    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3860 r_free = 0.3860    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.3069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10892  Z= 0.224
  Angle     :  0.715   9.175  14954  Z= 0.379
  Chirality :  0.048   0.207   1724
  Planarity :  0.004   0.035   1681
  Dihedral  : 22.251 172.461   1931
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 20.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 13.24 %
    Favored  : 86.68 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  5.13 %
    Favored  : 94.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.05 (0.23), residues: 1171
  helix: -0.68 (0.29), residues: 292
  sheet: -1.78 (0.29), residues: 315
  loop : -2.93 (0.23), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 145 
 TYR   0.036   0.002   TYR C  59 
 PHE   0.020   0.002   PHE B 129 
 TRP   0.016   0.002   TRP E  50 
 HIS   0.004   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 (10891)
  covalent geometry    : angle       0.71507 (14954)
  hydrogen bonds       : bond        0.05723 (  388)
  hydrogen bonds       : angle       6.76215 ( 1006)
  Misc. bond           : bond        0.00048 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9039 (t) cc_final: 0.8770 (p)
REVERT: B   36 ARG cc_start: 0.7270 (mmt90) cc_final: 0.7056 (mmt90)
REVERT: B   47 PHE cc_start: 0.5927 (t80) cc_final: 0.5496 (t80)
REVERT: B  146 GLU cc_start: 0.6823 (mt-10) cc_final: 0.5933 (mt-10)
REVERT: B  216 GLU cc_start: 0.4924 (mm-30) cc_final: 0.4592 (mm-30)
REVERT: C    1 MET cc_start: 0.7740 (tpt) cc_final: 0.7349 (tpp)
REVERT: C   44 ILE cc_start: 0.8716 (mt) cc_final: 0.8466 (mm)
REVERT: C   80 VAL cc_start: 0.7707 (m) cc_final: 0.7395 (m)
REVERT: C  140 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8154 (tmtt)
REVERT: C  150 THR cc_start: 0.8614 (p) cc_final: 0.8370 (t)
REVERT: E    8 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7077 (pt0)
REVERT: E   22 LEU cc_start: 0.7707 (pp) cc_final: 0.7464 (pp)
REVERT: E   25 LEU cc_start: 0.9117 (mm) cc_final: 0.8895 (pp)
REVERT: E   63 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7356 (mt-10)
REVERT: E  123 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7398 (mm-30)
REVERT: E  133 LEU cc_start: 0.7758 (mp) cc_final: 0.7507 (mt)
REVERT: E  280 ARG cc_start: 0.6301 (tmt170) cc_final: 0.5858 (tpt-90)
REVERT: E  360 TYR cc_start: 0.5925 (m-10) cc_final: 0.5030 (t80)
REVERT: E  372 LEU cc_start: 0.6514 (tp) cc_final: 0.6247 (tp)
REVERT: E  381 TYR cc_start: 0.7353 (m-80) cc_final: 0.7107 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 120
  average time/residue: 0.0998
  time to fit residues: 17.1151
Evaluate side-chains
  92 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 120 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 2 optimal weight:    7.9990
   chunk 83 optimal weight:    8.9990
   chunk 91 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
E  21 GLN
E 392 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.105177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.086449 restraints weight = 47224.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.087262 restraints weight = 38110.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.087696 restraints weight = 35551.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.087982 restraints weight = 26922.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.088300 restraints weight = 25096.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058  10892  Z= 0.303
  Angle     :  0.826  10.676  14954  Z= 0.437
  Chirality :  0.051   0.191   1724
  Planarity :  0.005   0.046   1681
  Dihedral  : 22.447 170.289   1931
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 24.75
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 15.54 %
    Favored  : 84.37 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  6.00 %
    Favored  : 93.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.55 (0.22), residues: 1171
  helix: -1.28 (0.28), residues: 288
  sheet: -2.05 (0.29), residues: 323
  loop : -3.16 (0.23), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 204 
 TYR   0.040   0.003   TYR C  59 
 PHE   0.024   0.003   PHE E 165 
 TRP   0.027   0.003   TRP E  50 
 HIS   0.011   0.002   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00671 (10891)
  covalent geometry    : angle       0.82643 (14954)
  hydrogen bonds       : bond        0.07227 (  388)
  hydrogen bonds       : angle       7.16730 ( 1006)
  Misc. bond           : bond        0.00039 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9127 (t) cc_final: 0.8792 (p)
REVERT: A  163 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8063 (mp0)
REVERT: B    2 MET cc_start: 0.7154 (tmm) cc_final: 0.6869 (tmm)
REVERT: B   78 ASP cc_start: 0.7833 (m-30) cc_final: 0.7624 (m-30)
REVERT: B  208 MET cc_start: 0.9011 (mmm) cc_final: 0.8787 (tpt)
REVERT: B  216 GLU cc_start: 0.4928 (mm-30) cc_final: 0.4621 (mm-30)
REVERT: C   44 ILE cc_start: 0.8766 (mt) cc_final: 0.8507 (mm)
REVERT: C   75 MET cc_start: 0.8681 (tpp) cc_final: 0.8150 (tpp)
REVERT: C  140 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8238 (tmtt)
REVERT: E    8 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7151 (pt0)
REVERT: E   63 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7527 (mt-10)
REVERT: E  133 LEU cc_start: 0.7650 (mp) cc_final: 0.7260 (mt)
REVERT: E  280 ARG cc_start: 0.6326 (tmt170) cc_final: 0.5977 (tpt-90)
REVERT: E  360 TYR cc_start: 0.6462 (m-10) cc_final: 0.5037 (t80)
REVERT: E  372 LEU cc_start: 0.6367 (tp) cc_final: 0.6031 (tp)
REVERT: E  381 TYR cc_start: 0.7485 (m-80) cc_final: 0.7250 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 106
  average time/residue: 0.1106
  time to fit residues: 16.5371
Evaluate side-chains
  85 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 101 optimal weight:    0.0170
   chunk 42 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 117 optimal weight:   20.0000
   chunk 73 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 75 optimal weight:    8.9990
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    4.6026

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

Flipped N/Q/H residues before XYZ refinement:
E  21 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.105851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.087114 restraints weight = 47138.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.087831 restraints weight = 38466.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.088353 restraints weight = 35544.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.088637 restraints weight = 26916.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.089144 restraints weight = 25107.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.3923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  10892  Z= 0.268
  Angle     :  0.790  10.014  14954  Z= 0.419
  Chirality :  0.050   0.175   1724
  Planarity :  0.005   0.047   1681
  Dihedral  : 22.514 170.733   1931
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 22.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 14.18 %
    Favored  : 85.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.67 (0.22), residues: 1171
  helix: -1.37 (0.28), residues: 285
  sheet: -2.12 (0.29), residues: 323
  loop : -3.22 (0.23), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 210 
 TYR   0.039   0.003   TYR C  59 
 PHE   0.022   0.003   PHE C 228 
 TRP   0.043   0.004   TRP E  50 
 HIS   0.009   0.002   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 (10891)
  covalent geometry    : angle       0.79003 (14954)
  hydrogen bonds       : bond        0.06652 (  388)
  hydrogen bonds       : angle       7.11597 ( 1006)
  Misc. bond           : bond        0.00021 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9108 (t) cc_final: 0.8773 (p)
REVERT: A  163 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8163 (mp0)
REVERT: B   78 ASP cc_start: 0.7919 (m-30) cc_final: 0.7653 (m-30)
REVERT: B  146 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6698 (mt-10)
REVERT: B  216 GLU cc_start: 0.4912 (mm-30) cc_final: 0.4520 (mm-30)
REVERT: C   44 ILE cc_start: 0.8808 (mt) cc_final: 0.8571 (mm)
REVERT: C  140 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8158 (tmtt)
REVERT: E    8 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7141 (pt0)
REVERT: E   63 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7468 (mt-10)
REVERT: E  133 LEU cc_start: 0.7311 (mp) cc_final: 0.7100 (mt)
REVERT: E  183 MET cc_start: 0.8515 (pmm) cc_final: 0.8190 (pmm)
REVERT: E  280 ARG cc_start: 0.6491 (tmt170) cc_final: 0.6218 (tpt-90)
REVERT: E  360 TYR cc_start: 0.5731 (m-10) cc_final: 0.4834 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1055
  time to fit residues: 15.6998
Evaluate side-chains
  86 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 102 optimal weight:    0.0970
   chunk 47 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 31 optimal weight:    0.3980
   chunk 104 optimal weight:    0.0050
   chunk 107 optimal weight:    0.9980
   chunk 117 optimal weight:   20.0000
   chunk 83 optimal weight:    0.0770
   overall best weight:    0.3150

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

Flipped N/Q/H residues before XYZ refinement:
E 202 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.116067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.098013 restraints weight = 47037.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.098997 restraints weight = 38463.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.099491 restraints weight = 33743.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.099810 restraints weight = 25043.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.100385 restraints weight = 23188.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3965 r_free = 0.3965    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3965 r_free = 0.3965    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6692
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10892  Z= 0.128
  Angle     :  0.620   6.429  14954  Z= 0.331
  Chirality :  0.045   0.171   1724
  Planarity :  0.004   0.046   1681
  Dihedral  : 22.259 173.345   1931
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.05 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.85 (0.24), residues: 1171
  helix: -0.61 (0.29), residues: 299
  sheet: -1.58 (0.31), residues: 297
  loop : -2.81 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 145 
 TYR   0.019   0.001   TYR C  59 
 PHE   0.015   0.001   PHE C 228 
 TRP   0.025   0.002   TRP E  50 
 HIS   0.003   0.001   HIS E 386 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (10891)
  covalent geometry    : angle       0.61963 (14954)
  hydrogen bonds       : bond        0.03541 (  388)
  hydrogen bonds       : angle       5.78048 ( 1006)
  Misc. bond           : bond        0.00020 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9030 (t) cc_final: 0.8742 (m)
REVERT: B  216 GLU cc_start: 0.4250 (mm-30) cc_final: 0.4024 (mm-30)
REVERT: C    1 MET cc_start: 0.7836 (tpp) cc_final: 0.7466 (tpp)
REVERT: C   44 ILE cc_start: 0.8762 (mt) cc_final: 0.8353 (mm)
REVERT: E    8 GLU cc_start: 0.7822 (tm-30) cc_final: 0.6876 (pt0)
REVERT: E  150 LEU cc_start: 0.9042 (mm) cc_final: 0.8829 (tp)
REVERT: E  360 TYR cc_start: 0.4943 (m-10) cc_final: 0.4400 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1016
  time to fit residues: 18.6045
Evaluate side-chains
  91 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 76 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 87 optimal weight:    3.9990
   chunk 118 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 115 optimal weight:    0.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
E 267 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.115307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.097143 restraints weight = 46730.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.098534 restraints weight = 39274.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.099161 restraints weight = 31578.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.099718 restraints weight = 23457.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.099938 restraints weight = 21513.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3965 r_free = 0.3965    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3965 r_free = 0.3965    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6710
moved from start:          0.4335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10892  Z= 0.124
  Angle     :  0.612   8.237  14954  Z= 0.323
  Chirality :  0.043   0.144   1724
  Planarity :  0.004   0.038   1681
  Dihedral  : 22.170 174.617   1931
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.22 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.79 (0.24), residues: 1171
  helix: -0.57 (0.29), residues: 307
  sheet: -1.43 (0.31), residues: 301
  loop : -2.87 (0.24), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  82 
 TYR   0.016   0.001   TYR A 200 
 PHE   0.016   0.001   PHE C 228 
 TRP   0.023   0.002   TRP E  50 
 HIS   0.003   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10891)
  covalent geometry    : angle       0.61194 (14954)
  hydrogen bonds       : bond        0.03589 (  388)
  hydrogen bonds       : angle       5.66280 ( 1006)
  Misc. bond           : bond        0.00018 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9029 (t) cc_final: 0.8718 (m)
REVERT: B   36 ARG cc_start: 0.6718 (mpt180) cc_final: 0.6376 (mpt180)
REVERT: B  216 GLU cc_start: 0.4068 (mm-30) cc_final: 0.3800 (mm-30)
REVERT: C    1 MET cc_start: 0.7676 (tpp) cc_final: 0.7344 (tpp)
REVERT: C   44 ILE cc_start: 0.8752 (mt) cc_final: 0.8450 (mm)
REVERT: C   75 MET cc_start: 0.7755 (tpp) cc_final: 0.7515 (tpp)
REVERT: E    8 GLU cc_start: 0.7906 (tm-30) cc_final: 0.6944 (pt0)
REVERT: E  150 LEU cc_start: 0.9091 (mm) cc_final: 0.8848 (tp)
REVERT: E  183 MET cc_start: 0.8313 (pmm) cc_final: 0.8054 (pmm)
REVERT: E  372 LEU cc_start: 0.6678 (pp) cc_final: 0.6350 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0855
  time to fit residues: 14.4055
Evaluate side-chains
  89 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 106 optimal weight:    0.0370
   chunk 85 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 12 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 98 optimal weight:    0.0570
   chunk 0 optimal weight:   10.0000
   chunk 118 optimal weight:    0.6980
   overall best weight:    1.1378

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

Flipped N/Q/H residues before XYZ refinement:
E 267 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.115713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.097980 restraints weight = 46141.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.098421 restraints weight = 40938.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.099162 restraints weight = 35162.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.099969 restraints weight = 26499.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.100215 restraints weight = 23578.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3967
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3967 r_free = 0.3967    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3967 r_free = 0.3967    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3967
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6706
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10892  Z= 0.124
  Angle     :  0.601   9.192  14954  Z= 0.317
  Chirality :  0.043   0.204   1724
  Planarity :  0.003   0.039   1681
  Dihedral  : 22.088 173.859   1931
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.80 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.73 (0.24), residues: 1171
  helix: -0.45 (0.30), residues: 307
  sheet: -1.35 (0.31), residues: 302
  loop : -2.92 (0.23), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 158 
 TYR   0.013   0.001   TYR E 360 
 PHE   0.016   0.001   PHE A  15 
 TRP   0.023   0.002   TRP E  50 
 HIS   0.004   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10891)
  covalent geometry    : angle       0.60146 (14954)
  hydrogen bonds       : bond        0.03524 (  388)
  hydrogen bonds       : angle       5.53947 ( 1006)
  Misc. bond           : bond        0.00019 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8076 (ttm) cc_final: 0.7668 (ttm)
REVERT: A   80 SER cc_start: 0.9044 (t) cc_final: 0.8692 (p)
REVERT: B   36 ARG cc_start: 0.6835 (mpt180) cc_final: 0.6424 (mpt180)
REVERT: B  121 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8272 (tm-30)
REVERT: B  216 GLU cc_start: 0.4599 (mm-30) cc_final: 0.4278 (mm-30)
REVERT: C    1 MET cc_start: 0.7386 (tpp) cc_final: 0.7013 (tpp)
REVERT: C   44 ILE cc_start: 0.8689 (mt) cc_final: 0.8407 (mm)
REVERT: C   75 MET cc_start: 0.7657 (tpp) cc_final: 0.7309 (tpp)
REVERT: E    8 GLU cc_start: 0.7803 (tm-30) cc_final: 0.6933 (pt0)
REVERT: E   25 LEU cc_start: 0.9066 (mm) cc_final: 0.8861 (pp)
REVERT: E  150 LEU cc_start: 0.9086 (mm) cc_final: 0.8836 (tp)
REVERT: E  183 MET cc_start: 0.8294 (pmm) cc_final: 0.8014 (pmm)
REVERT: E  372 LEU cc_start: 0.6753 (pp) cc_final: 0.6372 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0883
  time to fit residues: 15.0707
Evaluate side-chains
  83 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 63 optimal weight:    0.7980
   chunk 77 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 121 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 16 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 115 optimal weight:    0.2980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** E 267 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 = 0.4262 r_free = 0.4262 target = 0.115827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.098040 restraints weight = 46328.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.098989 restraints weight = 40429.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.099490 restraints weight = 34986.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.099930 restraints weight = 25324.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.100528 restraints weight = 23180.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3973
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3973 r_free = 0.3973    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3973 r_free = 0.3973    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3973
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6707
moved from start:          0.4597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10892  Z= 0.125
  Angle     :  0.594   7.615  14954  Z= 0.314
  Chirality :  0.043   0.178   1724
  Planarity :  0.004   0.081   1681
  Dihedral  : 22.064 174.524   1931
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.71 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.68 (0.24), residues: 1171
  helix: -0.40 (0.30), residues: 308
  sheet: -1.27 (0.31), residues: 302
  loop : -2.93 (0.23), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 330 
 TYR   0.010   0.001   TYR E 360 
 PHE   0.015   0.001   PHE E  53 
 TRP   0.023   0.002   TRP E  50 
 HIS   0.004   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10891)
  covalent geometry    : angle       0.59381 (14954)
  hydrogen bonds       : bond        0.03491 (  388)
  hydrogen bonds       : angle       5.43314 ( 1006)
  Misc. bond           : bond        0.00021 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8116 (ttm) cc_final: 0.7801 (ttm)
REVERT: A   80 SER cc_start: 0.9025 (t) cc_final: 0.8678 (p)
REVERT: B  121 GLN cc_start: 0.8458 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: B  126 ASN cc_start: 0.7515 (t0) cc_final: 0.6879 (m-40)
REVERT: B  216 GLU cc_start: 0.4446 (mm-30) cc_final: 0.4137 (mm-30)
REVERT: C    1 MET cc_start: 0.7307 (tpp) cc_final: 0.7015 (tpp)
REVERT: C   44 ILE cc_start: 0.8692 (mt) cc_final: 0.8435 (mm)
REVERT: C   75 MET cc_start: 0.7556 (tpp) cc_final: 0.7241 (tpp)
REVERT: E    8 GLU cc_start: 0.7856 (tm-30) cc_final: 0.6973 (pt0)
REVERT: E   25 LEU cc_start: 0.9161 (mm) cc_final: 0.8902 (pp)
REVERT: E  150 LEU cc_start: 0.9037 (mm) cc_final: 0.8818 (tp)
REVERT: E  183 MET cc_start: 0.8343 (pmm) cc_final: 0.8058 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0805
  time to fit residues: 13.6213
Evaluate side-chains
  84 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 111 optimal weight:    7.9990
   chunk 116 optimal weight:    5.9990
   chunk 92 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
B 157 HIS
E  21 GLN
** E 202 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 = 0.4202 r_free = 0.4202 target = 0.111811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.093876 restraints weight = 46618.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.094171 restraints weight = 38805.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.094821 restraints weight = 36960.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.095302 restraints weight = 26805.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.095790 restraints weight = 24600.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6858
moved from start:          0.4539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10892  Z= 0.180
  Angle     :  0.662   8.197  14954  Z= 0.349
  Chirality :  0.045   0.182   1724
  Planarity :  0.004   0.077   1681
  Dihedral  : 22.160 173.990   1931
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.96 %
    Favored  : 87.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.23), residues: 1171
  helix: -0.66 (0.29), residues: 297
  sheet: -1.53 (0.31), residues: 304
  loop : -3.02 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 330 
 TYR   0.018   0.002   TYR B  14 
 PHE   0.028   0.002   PHE C 228 
 TRP   0.029   0.002   TRP E  50 
 HIS   0.008   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (10891)
  covalent geometry    : angle       0.66220 (14954)
  hydrogen bonds       : bond        0.04623 (  388)
  hydrogen bonds       : angle       5.80707 ( 1006)
  Misc. bond           : bond        0.00014 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9124 (t) cc_final: 0.8743 (p)
REVERT: B    2 MET cc_start: 0.6582 (tmm) cc_final: 0.6298 (tmm)
REVERT: B  121 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7829 (tm-30)
REVERT: B  216 GLU cc_start: 0.4679 (mm-30) cc_final: 0.4343 (mm-30)
REVERT: C    1 MET cc_start: 0.7237 (tpp) cc_final: 0.6855 (tpp)
REVERT: C   44 ILE cc_start: 0.8710 (mt) cc_final: 0.8461 (mm)
REVERT: C  213 TYR cc_start: 0.7847 (m-80) cc_final: 0.7393 (m-80)
REVERT: E    8 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7093 (pt0)
REVERT: E   25 LEU cc_start: 0.9196 (mm) cc_final: 0.8895 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0809
  time to fit residues: 12.8355
Evaluate side-chains
  82 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 86 optimal weight:    9.9990
   chunk 21 optimal weight:    0.8980
   chunk 43 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 12 optimal weight:    0.0470
   overall best weight:    1.1682

-------------------------------------------------------------------------------
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 = 0.4256 r_free = 0.4256 target = 0.115333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.097408 restraints weight = 46488.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.097495 restraints weight = 44225.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.098581 restraints weight = 33894.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.098883 restraints weight = 25595.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.099209 restraints weight = 25423.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6746
moved from start:          0.4737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10892  Z= 0.126
  Angle     :  0.605   7.370  14954  Z= 0.319
  Chirality :  0.044   0.206   1724
  Planarity :  0.004   0.076   1681
  Dihedral  : 22.099 174.317   1931
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.97 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.81 (0.23), residues: 1171
  helix: -0.54 (0.30), residues: 307
  sheet: -1.30 (0.31), residues: 297
  loop : -3.01 (0.23), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 330 
 TYR   0.011   0.001   TYR E 360 
 PHE   0.017   0.001   PHE C 228 
 TRP   0.021   0.001   TRP E  50 
 HIS   0.003   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10891)
  covalent geometry    : angle       0.60479 (14954)
  hydrogen bonds       : bond        0.03541 (  388)
  hydrogen bonds       : angle       5.43311 ( 1006)
  Misc. bond           : bond        0.00016 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1488.64 seconds
wall clock time: 26 minutes 35.40 seconds (1595.40 seconds total)