Starting phenix.real_space_refine
on Thu Feb 13 18:23:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d6x_30595/02_2025/7d6x_30595.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d6x_30595/02_2025/7d6x_30595.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d6x_30595/02_2025/7d6x_30595.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d6x_30595/02_2025/7d6x_30595.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d6x_30595/02_2025/7d6x_30595.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d6x_30595/02_2025/7d6x_30595.cif"
  }
  resolution = 2.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.058
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
     Fe     11      7.16       5
     P       3      5.49       5
     S      63      5.16       5
     C    5510      2.51       5
     N    1527      2.21       5
     O    1597      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8711
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 594, 4531
          Classifications: {'peptide': 594}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 28, 'TRANS': 565}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "B"
      Number of atoms: 1914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1914
          Classifications: {'peptide': 239}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 2141
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2141
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 249}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 19
          Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 53
          Unusual residues: {'FES': 1, 'PEV': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4955  SG  CYS B  54      40.180  50.828  44.564  1.00 47.83           S
  ATOM   4988  SG  CYS B  59      43.330  52.111  45.865  1.00 44.04           S
  ATOM   5004  SG  CYS B  62      40.040  56.787  49.369  1.00 38.59           S
  ATOM   5095  SG  CYS B  74      37.355  54.005  48.548  1.00 44.78           S
  ATOM   5724  SG  CYS B 151      49.821  52.122  59.823  1.00 33.32           S
  ATOM   5676  SG  CYS B 145      48.703  47.346  55.630  1.00 37.11           S
  ATOM   5699  SG  CYS B 148      45.322  53.550  55.841  1.00 34.94           S
  ATOM   6224  SG  CYS B 213      43.207  48.452  59.497  1.00 36.21           S
  ATOM   6151  SG  CYS B 203      52.826  51.709  70.220  1.00 35.58           S
  ATOM   5754  SG  CYS B 155      52.970  56.300  66.188  1.00 35.44           S
  ATOM   6195  SG  CYS B 209      47.472  51.268  66.441  1.00 37.85           S
  ATOM   8037  SG  CYS C 206      48.119  40.050  81.592  1.00 37.27           S
  ATOM   7292  SG  CYS C 114      45.646  46.687  82.164  1.00 36.54           S

  Time building chain proxies: 6.22, per 1000 atoms: 0.71
  Number of scatterers: 8711
  At special positions: 0
  Unit cell: (84.46, 88.56, 124.64, 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)
     Fe     11     26.01
     S      63     16.00
     P       3     15.00
     O    1597      8.00
     N    1527      7.00
     C    5510      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: 2.59
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" F3S B 303 "
        pdb="FE1  F3S B 303 " - pdb=" SG  CYS B 203 "
        pdb="FE3  F3S B 303 " - pdb=" SG  CYS B 155 "
        pdb="FE4  F3S B 303 " - pdb=" SG  CYS B 209 "
      pdb=" FES B 301 "
        pdb="FE1  FES B 301 " - pdb=" SG  CYS B  59 "
        pdb="FE2  FES B 301 " - pdb=" SG  CYS B  62 "
        pdb="FE2  FES B 301 " - pdb=" SG  CYS B  74 "
        pdb="FE1  FES B 301 " - pdb=" SG  CYS B  54 "
      pdb=" FES C 302 "
        pdb="FE1  FES C 302 " - pdb=" NE2 HIS C 155 "
        pdb="FE2  FES C 302 " - pdb=" NE2 HIS C 240 "
        pdb="FE2  FES C 302 " - pdb=" SG  CYS C 114 "
        pdb="FE1  FES C 302 " - pdb=" SG  CYS C 206 "
      pdb=" SF4 B 302 "
        pdb="FE2  SF4 B 302 " - pdb=" SG  CYS B 145 "
        pdb="FE4  SF4 B 302 " - pdb=" SG  CYS B 213 "
        pdb="FE1  SF4 B 302 " - pdb=" SG  CYS B 151 "
        pdb="FE3  SF4 B 302 " - pdb=" SG  CYS B 148 "
      Number of angles added : 29


  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2010

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 10 sheets defined
      46.3% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 31
    Processing helix  chain 'A' and resid 45 through 50
    Processing helix  chain 'A' and resid 66 through 78
    Processing helix  chain 'A' and resid 83 through 102
      Proline residue:  A  95  - end of helix
      removed outlier: 3.617A  pdb=" N   GLU A 102 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 159
      removed outlier: 3.705A  pdb=" N   GLU A 139 " --> pdb=" O   ARG A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 216
      removed outlier: 3.574A  pdb=" N   PHE A 216 " --> pdb=" O   GLY A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 237
    Processing helix  chain 'A' and resid 267 through 271
    Processing helix  chain 'A' and resid 321 through 335
      removed outlier: 3.526A  pdb=" N   ALA A 335 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 361
      removed outlier: 3.979A  pdb=" N   LYS A 358 " --> pdb=" O   ALA A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 372
    Processing helix  chain 'A' and resid 411 through 413
      No H-bonds generated for 'chain 'A' and resid 411 through 413'
    Processing helix  chain 'A' and resid 426 through 449
      removed outlier: 3.943A  pdb=" N   LEU A 432 " --> pdb=" O   SER A 428 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   LEU A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 470
      removed outlier: 3.626A  pdb=" N   VAL A 461 " --> pdb=" O   SER A 457 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ASP A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 473
      No H-bonds generated for 'chain 'A' and resid 471 through 473'
    Processing helix  chain 'A' and resid 480 through 496
    Processing helix  chain 'A' and resid 501 through 506
      removed outlier: 3.605A  pdb=" N   GLN A 506 " --> pdb=" O   GLU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 519
      removed outlier: 3.835A  pdb=" N   GLN A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLU A 514 " --> pdb=" O   ASP A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 522
      No H-bonds generated for 'chain 'A' and resid 520 through 522'
    Processing helix  chain 'A' and resid 531 through 557
      removed outlier: 4.376A  pdb=" N   ARG A 541 " --> pdb=" O   ALA A 537 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ASN A 542 " --> pdb=" O   ILE A 538 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU A 545 " --> pdb=" O   ARG A 541 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLU A 548 " --> pdb=" O   LEU A 544 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN A 556 " --> pdb=" O   LYS A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 619
    Processing helix  chain 'B' and resid 32 through 44
      removed outlier: 3.550A  pdb=" N   ILE B  36 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 111
    Processing helix  chain 'B' and resid 112 through 115
      removed outlier: 3.736A  pdb=" N   ILE B 115 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 112 through 115'
    Processing helix  chain 'B' and resid 125 through 129
      removed outlier: 4.099A  pdb=" N   TYR B 129 " --> pdb=" O   PRO B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 143
      removed outlier: 4.733A  pdb=" N   ARG B 138 " --> pdb=" O   GLU B 134 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   SER B 139 " --> pdb=" O   ASP B 135 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU B 141 " --> pdb=" O   ASN B 137 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   PHE B 142 " --> pdb=" O   ARG B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 155
    Processing helix  chain 'B' and resid 155 through 160
    Processing helix  chain 'B' and resid 161 through 165
      removed outlier: 3.603A  pdb=" N   ASN B 164 " --> pdb=" O   HIS B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.704A  pdb=" N   ILE B 177 " --> pdb=" O   PHE B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 197
      removed outlier: 3.775A  pdb=" N   GLN B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 203
    Processing helix  chain 'B' and resid 218 through 223
    Processing helix  chain 'B' and resid 223 through 236
      removed outlier: 3.631A  pdb=" N   ARG B 234 " --> pdb=" O   ARG B 230 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 32 through 56
      removed outlier: 3.688A  pdb=" N   LEU C  36 " --> pdb=" O   TRP C  32 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   PHE C  54 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   GLY C  56 " --> pdb=" O   ARG C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 72
    Processing helix  chain 'C' and resid 103 through 113
    Processing helix  chain 'C' and resid 114 through 125
      removed outlier: 3.674A  pdb=" N   LYS C 119 " --> pdb=" O   TYR C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 145
    Processing helix  chain 'C' and resid 146 through 151
      removed outlier: 3.803A  pdb=" N   LEU C 151 " --> pdb=" O   PHE C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 176
      removed outlier: 3.581A  pdb=" N   PHE C 158 " --> pdb=" O   ILE C 154 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   TYR C 160 " --> pdb=" O   ARG C 156 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 205
      removed outlier: 3.552A  pdb=" N   ILE C 191 " --> pdb=" O   LEU C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 214
      removed outlier: 3.823A  pdb=" N   GLY C 214 " --> pdb=" O   ARG C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 238
    Processing helix  chain 'C' and resid 239 through 264
      removed outlier: 3.510A  pdb=" N   PHE C 243 " --> pdb=" O   ARG C 239 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   TRP C 245 " --> pdb=" O   MET C 241 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8
      removed outlier: 6.407A  pdb=" N   GLU A   5 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   GLU A 201 " --> pdb=" O   GLU A   5 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   HIS A   7 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   PHE A 188 " --> pdb=" O   THR A 175 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 169
      removed outlier: 6.657A  pdb=" N   VAL A  34 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   PHE A 169 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   VAL A  36 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   VAL A  12 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   VAL A 205 " --> pdb=" O   PHE A 409 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55
    Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 241
      removed outlier: 5.918A  pdb=" N   ILE A 394 " --> pdb=" O   GLY A 416 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 249
      removed outlier: 6.444A  pdb=" N   HIS A 249 " --> pdb=" O   CYS A 387 " (cutoff:3.500A)
      removed outlier: 5.388A  pdb=" N   CYS A 387 " --> pdb=" O   HIS A 249 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 582 through 585
    Processing sheet with id=AA7, first strand: chain 'B' and resid 17 through 27
      removed outlier: 3.548A  pdb=" N   ASP B  14 " --> pdb=" O   GLY B  17 " (cutoff:3.500A)
      removed outlier: 9.279A  pdb=" N   VAL B  87 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LYS B   7 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   VAL B  89 " --> pdb=" O   LYS B   7 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   ARG B   9 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 65
    Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 61
      removed outlier: 3.525A  pdb=" N   TYR C  66 " --> pdb=" O   VAL C  61 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 178 through 179

    336 hydrogen bonds defined for protein.
    948 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.40

  Time building geometry restraints manager: 2.87 seconds

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

  Histogram of bond lengths:
        1.18 -     1.74: 8823
        1.74 -     2.31: 104
        2.31 -     2.87: 0
        2.87 -     3.44: 0
        3.44 -     4.00: 3
  Bond restraints: 8930
  Sorted by residual:
  bond pdb=" S2  F3S B 303 "
       pdb="FE3  F3S B 303 "
    ideal  model  delta    sigma   weight residual
    2.300  4.001 -1.701 2.00e-02 2.50e+03 7.23e+03
  bond pdb=" S1  F3S B 303 "
       pdb="FE4  F3S B 303 "
    ideal  model  delta    sigma   weight residual
    2.258  3.925 -1.667 2.00e-02 2.50e+03 6.95e+03
  bond pdb=" S4  F3S B 303 "
       pdb="FE1  F3S B 303 "
    ideal  model  delta    sigma   weight residual
    2.233  3.729 -1.496 2.00e-02 2.50e+03 5.60e+03
  bond pdb=" S3  F3S B 303 "
       pdb="FE1  F3S B 303 "
    ideal  model  delta    sigma   weight residual
    2.296  2.048  0.248 2.00e-02 2.50e+03 1.54e+02
  bond pdb=" S2  F3S B 303 "
       pdb="FE4  F3S B 303 "
    ideal  model  delta    sigma   weight residual
    2.317  2.083  0.234 2.00e-02 2.50e+03 1.37e+02
  ... (remaining 8925 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.15: 12083
       13.15 -    26.29: 40
       26.29 -    39.44: 7
       39.44 -    52.59: 0
       52.59 -    65.74: 2
  Bond angle restraints: 12132
  Sorted by residual:
  angle pdb=" N   CYS B  54 "
        pdb=" CA  CYS B  54 "
        pdb=" C   CYS B  54 "
      ideal   model   delta    sigma   weight residual
     114.12  148.44  -34.32 1.39e+00 5.18e-01 6.10e+02
  angle pdb=" S1  F3S B 303 "
        pdb="FE4  F3S B 303 "
        pdb=" S3  F3S B 303 "
      ideal   model   delta    sigma   weight residual
     114.75   49.01   65.74 3.00e+00 1.11e-01 4.80e+02
  angle pdb=" S3  F3S B 303 "
        pdb="FE1  F3S B 303 "
        pdb=" S4  F3S B 303 "
      ideal   model   delta    sigma   weight residual
     112.59   50.99   61.60 3.00e+00 1.11e-01 4.22e+02
  angle pdb=" N   LYS B  58 "
        pdb=" CA  LYS B  58 "
        pdb=" CB  LYS B  58 "
      ideal   model   delta    sigma   weight residual
     111.54   83.03   28.51 1.45e+00 4.76e-01 3.87e+02
  angle pdb=" S1  FES B 301 "
        pdb="FE2  FES B 301 "
        pdb=" S2  FES B 301 "
      ideal   model   delta    sigma   weight residual
     104.33   89.91   14.42 1.14e+00 7.69e-01 1.60e+02
  ... (remaining 12127 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.08: 5043
       27.08 -    54.17: 233
       54.17 -    81.25: 22
       81.25 -   108.33: 4
      108.33 -   135.41: 1
  Dihedral angle restraints: 5303
    sinusoidal: 2161
      harmonic: 3142
  Sorted by residual:
  dihedral pdb=" C   CYS B  59 "
           pdb=" N   CYS B  59 "
           pdb=" CA  CYS B  59 "
           pdb=" CB  CYS B  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -158.19   35.59     0      2.50e+00 1.60e-01 2.03e+02
  dihedral pdb=" N   CYS B  59 "
           pdb=" C   CYS B  59 "
           pdb=" CA  CYS B  59 "
           pdb=" CB  CYS B  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  158.28  -35.48     0      2.50e+00 1.60e-01 2.01e+02
  dihedral pdb=" N   LYS B  58 "
           pdb=" C   LYS B  58 "
           pdb=" CA  LYS B  58 "
           pdb=" CB  LYS B  58 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   89.09   33.71     0      2.50e+00 1.60e-01 1.82e+02
  ... (remaining 5300 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    2.902: 1316
       2.902 -    5.804: 0
       5.804 -    8.706: 0
       8.706 -   11.607: 0
      11.607 -   14.509: 1
  Chirality restraints: 1317
  Sorted by residual:
  chirality pdb=" S2  F3S B 303 "
            pdb="FE1  F3S B 303 "
            pdb="FE3  F3S B 303 "
            pdb="FE4  F3S B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     10.77   -3.74   14.51 2.00e-01 2.50e+01 5.26e+03
  chirality pdb=" CA  CYS B  59 "
            pdb=" N   CYS B  59 "
            pdb=" C   CYS B  59 "
            pdb=" CB  CYS B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.85    1.66 2.00e-01 2.50e+01 6.89e+01
  chirality pdb=" CA  LYS B  55 "
            pdb=" N   LYS B  55 "
            pdb=" C   LYS B  55 "
            pdb=" CB  LYS B  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.18    1.33 2.00e-01 2.50e+01 4.45e+01
  ... (remaining 1314 not shown)

  Planarity restraints: 1560
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 606 "   -0.075 5.00e-02 4.00e+02   1.12e-01 2.00e+01
        pdb=" N   PRO A 607 "    0.193 5.00e-02 4.00e+02
        pdb=" CA  PRO A 607 "   -0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO A 607 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 128 "   -0.062 5.00e-02 4.00e+02   9.44e-02 1.43e+01
        pdb=" N   PRO C 129 "    0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO C 129 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO C 129 "   -0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 145 "    0.017 2.00e-02 2.50e+03   3.60e-02 1.30e+01
        pdb=" C   CYS B 145 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   CYS B 145 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ILE B 146 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1557 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 82
        2.57 -     3.15: 7006
        3.15 -     3.74: 13103
        3.74 -     4.32: 20070
        4.32 -     4.90: 33391
  Nonbonded interactions: 73652
  Sorted by model distance:
  nonbonded pdb=" O2' FAD A 701 "
            pdb=" O4' FAD A 701 "
     model   vdw
     1.988 3.040
  nonbonded pdb=" S3  F3S B 303 "
            pdb="FE3  F3S B 303 "
     model   vdw
     2.052 2.688
  nonbonded pdb=" S4  F3S B 303 "
            pdb="FE4  F3S B 303 "
     model   vdw
     2.088 2.688
  nonbonded pdb=" S1  F3S B 303 "
            pdb="FE1  F3S B 303 "
     model   vdw
     2.130 2.688
  nonbonded pdb=" OD1 ASP B 237 "
            pdb=" OH  TYR C 157 "
     model   vdw
     2.202 3.040
  ... (remaining 73647 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.650
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:11.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
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      :  0.032   1.701   8930  Z= 2.276
  Angle     :  1.735  65.736  12132  Z= 0.891
  Chirality :  0.412  14.509   1317
  Planarity :  0.007   0.112   1560
  Dihedral  : 14.906 135.413   3293
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.66 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  5.11 %
    Favored  : 94.67 %
  Cbeta Deviations :  0.40 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.45 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.23), residues: 1089
  helix: -0.81 (0.24), residues: 425
  sheet: -1.32 (0.51), residues: 92
  loop : -3.03 (0.23), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C  55 
 HIS   0.008   0.001   HIS A 170 
 PHE   0.022   0.002   PHE A 530 
 TYR   0.023   0.002   TYR B 202 
 ARG   0.005   0.001   ARG A 606 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A  366 HIS cc_start: 0.7613 (m90) cc_final: 0.7228 (p-80)
  outliers start: 2
  outliers final: 1
  residues processed: 114
  average time/residue: 1.5601
  time to fit residues: 187.9646
Evaluate side-chains
  79 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  592 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.4980
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 63 optimal weight:    0.3980
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 118 GLN
A 330 ASN
A 480 ASN
B 133 GLN
B 174 HIS
B 195 GLN
C  88 GLN
C 237 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.112078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.096295 restraints weight = 12000.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.76
r_work: 0.3077 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.137   8930  Z= 0.236
  Angle     :  1.065  81.679  12132  Z= 0.436
  Chirality :  0.061   1.509   1317
  Planarity :  0.006   0.111   1560
  Dihedral  : 10.478 115.528   1310
  Min Nonbonded Distance : 1.748

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.73 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.00 %
    Favored  : 86.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.25), residues: 1089
  helix:  0.22 (0.26), residues: 432
  sheet: -1.17 (0.58), residues: 76
  loop : -2.70 (0.23), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  52 
 HIS   0.003   0.001   HIS A 170 
 PHE   0.012   0.001   PHE C  96 
 TYR   0.026   0.001   TYR C 121 
 ARG   0.003   0.000   ARG B 172 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 1.040 
Fit side-chains
REVERT: A  324 GLU cc_start: 0.6295 (tm-30) cc_final: 0.6088 (tm-30)
REVERT: A  366 HIS cc_start: 0.7859 (m90) cc_final: 0.7301 (p-80)
REVERT: A  370 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7768 (tm-30)
REVERT: A  441 LEU cc_start: 0.8253 (tt) cc_final: 0.7768 (tt)
REVERT: A  445 ASP cc_start: 0.8226 (m-30) cc_final: 0.7740 (m-30)
REVERT: A  603 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8274 (p)
REVERT: B   69 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8271 (mmm-85)
REVERT: B  211 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8285 (mm-30)
  outliers start: 16
  outliers final: 5
  residues processed: 98
  average time/residue: 1.3684
  time to fit residues: 143.1340
Evaluate side-chains
  85 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain B residue   69 ARG
Chi-restraints excluded: chain B residue  211 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
C 195 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.111293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.095772 restraints weight = 12695.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 1.77
r_work: 0.3039 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.108   8930  Z= 0.304
  Angle     :  1.068  82.206  12132  Z= 0.439
  Chirality :  0.062   1.483   1317
  Planarity :  0.006   0.103   1560
  Dihedral  :  9.493 108.496   1310
  Min Nonbonded Distance : 1.782

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.11 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.25), residues: 1089
  helix:  0.64 (0.27), residues: 425
  sheet: -1.18 (0.51), residues: 99
  loop : -2.62 (0.24), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  95 
 HIS   0.006   0.001   HIS A 170 
 PHE   0.015   0.002   PHE A 435 
 TYR   0.023   0.001   TYR C 121 
 ARG   0.003   0.000   ARG C 239 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A  324 GLU cc_start: 0.6349 (tm-30) cc_final: 0.6029 (tm-30)
REVERT: A  366 HIS cc_start: 0.7846 (m90) cc_final: 0.7347 (p-80)
REVERT: A  441 LEU cc_start: 0.8281 (tt) cc_final: 0.7856 (tt)
REVERT: A  445 ASP cc_start: 0.8216 (m-30) cc_final: 0.7768 (m-30)
REVERT: A  502 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7997 (tm-30)
REVERT: A  572 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5326 (pp-130)
REVERT: A  603 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8335 (p)
REVERT: B   69 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8412 (mmm-85)
REVERT: B  211 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8267 (mm-30)
REVERT: C  269 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5272 (mp)
  outliers start: 23
  outliers final: 8
  residues processed: 96
  average time/residue: 1.3618
  time to fit residues: 139.4205
Evaluate side-chains
  86 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  572 MET
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain B residue   69 ARG
Chi-restraints excluded: chain B residue  208 CYS
Chi-restraints excluded: chain B residue  211 GLU
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  269 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 66 optimal weight:    0.4980
   chunk 81 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 103 optimal weight:    0.3980
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 82 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.114120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.098219 restraints weight = 12497.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 1.81
r_work: 0.3072 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.109   8930  Z= 0.216
  Angle     :  1.028  81.445  12132  Z= 0.414
  Chirality :  0.061   1.534   1317
  Planarity :  0.005   0.096   1560
  Dihedral  :  8.387 100.639   1310
  Min Nonbonded Distance : 1.782

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.89 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.64 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.26), residues: 1089
  helix:  0.81 (0.27), residues: 439
  sheet: -1.18 (0.57), residues: 81
  loop : -2.47 (0.24), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 170 
 PHE   0.012   0.001   PHE C  96 
 TYR   0.021   0.001   TYR C 121 
 ARG   0.002   0.000   ARG C 239 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 1.029 
Fit side-chains
REVERT: A  324 GLU cc_start: 0.6365 (tm-30) cc_final: 0.6006 (tm-30)
REVERT: A  441 LEU cc_start: 0.8204 (tt) cc_final: 0.7769 (tt)
REVERT: A  445 ASP cc_start: 0.8185 (m-30) cc_final: 0.7736 (m-30)
REVERT: A  502 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7977 (tm-30)
REVERT: A  572 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.5457 (pp-130)
REVERT: A  603 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8368 (p)
REVERT: A  612 CYS cc_start: 0.1816 (OUTLIER) cc_final: 0.0231 (m)
REVERT: B   31 GLU cc_start: 0.8320 (pt0) cc_final: 0.8099 (pt0)
REVERT: B   69 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8241 (mmm-85)
REVERT: C   63 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7249 (p0)
REVERT: C  259 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7963 (ttm)
REVERT: C  269 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.5166 (mp)
  outliers start: 24
  outliers final: 6
  residues processed: 105
  average time/residue: 1.3275
  time to fit residues: 148.7715
Evaluate side-chains
  89 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  572 MET
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  612 CYS
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain B residue   69 ARG
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  259 MET
Chi-restraints excluded: chain C residue  269 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 99 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0070
   chunk 42 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   overall best weight:    0.6600

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.114021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.098354 restraints weight = 12512.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.77
r_work: 0.3082 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   8930  Z= 0.230
  Angle     :  1.030  81.355  12132  Z= 0.416
  Chirality :  0.061   1.540   1317
  Planarity :  0.005   0.093   1560
  Dihedral  :  7.935  96.756   1310
  Min Nonbonded Distance : 1.779

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.92 %
    Favored  : 90.08 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 15.11 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.64 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.26), residues: 1089
  helix:  0.92 (0.27), residues: 440
  sheet: -0.94 (0.55), residues: 92
  loop : -2.41 (0.24), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  95 
 HIS   0.004   0.001   HIS A 170 
 PHE   0.013   0.001   PHE A 435 
 TYR   0.021   0.001   TYR C 121 
 ARG   0.003   0.000   ARG C 239 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 78
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A  324 GLU cc_start: 0.6430 (tm-30) cc_final: 0.6036 (tm-30)
REVERT: A  445 ASP cc_start: 0.8234 (m-30) cc_final: 0.7758 (m-30)
REVERT: A  502 GLU cc_start: 0.8490 (tm-30) cc_final: 0.7949 (tm-30)
REVERT: A  559 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8483 (pt0)
REVERT: A  572 MET cc_start: 0.6325 (OUTLIER) cc_final: 0.6005 (ppp)
REVERT: A  603 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8308 (p)
REVERT: A  612 CYS cc_start: 0.1836 (OUTLIER) cc_final: 0.0289 (m)
REVERT: B   69 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8260 (mmm-85)
REVERT: C   63 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7282 (p0)
REVERT: C  235 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8441 (mtmp)
REVERT: C  259 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7959 (ttm)
REVERT: C  269 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5072 (mp)
  outliers start: 29
  outliers final: 11
  residues processed: 103
  average time/residue: 1.2716
  time to fit residues: 140.1655
Evaluate side-chains
  94 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  559 GLU
Chi-restraints excluded: chain A residue  572 MET
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  612 CYS
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain B residue   69 ARG
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  235 LYS
Chi-restraints excluded: chain C residue  259 MET
Chi-restraints excluded: chain C residue  269 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 50 optimal weight:    0.2980
   chunk 83 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0570
   chunk 39 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 80 optimal weight:    0.0050
   overall best weight:    0.3712

-------------------------------------------------------------------------------
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 = 0.3408 r_free = 0.3408 target = 0.114833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.099061 restraints weight = 11985.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.78
r_work: 0.3118 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.106   8930  Z= 0.195
  Angle     :  1.023  81.534  12132  Z= 0.411
  Chirality :  0.060   1.537   1317
  Planarity :  0.005   0.103   1560
  Dihedral  :  7.574  92.901   1310
  Min Nonbonded Distance : 1.784

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.56 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.64 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.26), residues: 1089
  helix:  1.08 (0.27), residues: 441
  sheet: -1.19 (0.56), residues: 81
  loop : -2.30 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  95 
 HIS   0.003   0.000   HIS A 170 
 PHE   0.012   0.001   PHE C  96 
 TYR   0.021   0.001   TYR C 121 
 ARG   0.003   0.000   ARG A 606 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 GLU cc_start: 0.5306 (tt0) cc_final: 0.4862 (mp0)
REVERT: A  324 GLU cc_start: 0.6502 (tm-30) cc_final: 0.6203 (tm-30)
REVERT: A  441 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7667 (tt)
REVERT: A  445 ASP cc_start: 0.8220 (m-30) cc_final: 0.7776 (m-30)
REVERT: A  462 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7034 (pt0)
REVERT: A  502 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7837 (tm-30)
REVERT: A  559 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8433 (pt0)
REVERT: A  572 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.5958 (ppp)
REVERT: A  603 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8228 (p)
REVERT: A  606 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.4847 (ppt170)
REVERT: A  612 CYS cc_start: 0.1491 (OUTLIER) cc_final: 0.0074 (m)
REVERT: C   63 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7264 (p0)
REVERT: C  185 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7724 (t80)
REVERT: C  235 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8408 (mtmp)
REVERT: C  259 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7951 (ttm)
REVERT: C  269 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5276 (mp)
  outliers start: 28
  outliers final: 12
  residues processed: 106
  average time/residue: 1.2747
  time to fit residues: 144.5568
Evaluate side-chains
  101 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  559 GLU
Chi-restraints excluded: chain A residue  572 MET
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  606 ARG
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  612 CYS
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  185 PHE
Chi-restraints excluded: chain C residue  235 LYS
Chi-restraints excluded: chain C residue  259 MET
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain C residue  269 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 97 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3371 r_free = 0.3371 target = 0.112023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.096061 restraints weight = 12261.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 1.81
r_work: 0.3070 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   8930  Z= 0.257
  Angle     :  1.041  81.238  12132  Z= 0.423
  Chirality :  0.062   1.546   1317
  Planarity :  0.005   0.103   1560
  Dihedral  :  7.678  91.977   1310
  Min Nonbonded Distance : 1.779

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.83 %
    Favored  : 90.17 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 16.78 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.26), residues: 1089
  helix:  1.04 (0.27), residues: 441
  sheet: -0.81 (0.56), residues: 92
  loop : -2.33 (0.25), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  95 
 HIS   0.005   0.001   HIS A 170 
 PHE   0.014   0.001   PHE B 173 
 TYR   0.021   0.001   TYR C 121 
 ARG   0.003   0.000   ARG C 239 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 77
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 GLU cc_start: 0.5372 (tt0) cc_final: 0.4931 (mp0)
REVERT: A  324 GLU cc_start: 0.6481 (tm-30) cc_final: 0.6172 (tm-30)
REVERT: A  441 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7828 (tt)
REVERT: A  445 ASP cc_start: 0.8277 (m-30) cc_final: 0.7859 (m-30)
REVERT: A  502 GLU cc_start: 0.8502 (tm-30) cc_final: 0.7870 (tm-30)
REVERT: A  559 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.7776 (pp20)
REVERT: A  572 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6121 (ppp)
REVERT: A  603 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8239 (p)
REVERT: A  606 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.4876 (ppt170)
REVERT: A  612 CYS cc_start: 0.1798 (OUTLIER) cc_final: 0.0273 (m)
REVERT: B   69 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8278 (mmm-85)
REVERT: C   63 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7302 (p0)
REVERT: C  259 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7962 (ttm)
REVERT: C  269 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5377 (mp)
  outliers start: 27
  outliers final: 13
  residues processed: 100
  average time/residue: 1.4017
  time to fit residues: 149.3708
Evaluate side-chains
  98 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  559 GLU
Chi-restraints excluded: chain A residue  572 MET
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  606 ARG
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  612 CYS
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain B residue   69 ARG
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  208 CYS
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  259 MET
Chi-restraints excluded: chain C residue  269 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 104 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 89 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.111916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.096041 restraints weight = 12345.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 1.80
r_work: 0.3070 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   8930  Z= 0.252
  Angle     :  1.041  81.212  12132  Z= 0.423
  Chirality :  0.062   1.552   1317
  Planarity :  0.005   0.106   1560
  Dihedral  :  7.622  89.650   1310
  Min Nonbonded Distance : 1.781

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.44 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.26), residues: 1089
  helix:  1.04 (0.27), residues: 441
  sheet: -1.06 (0.57), residues: 81
  loop : -2.32 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  95 
 HIS   0.004   0.001   HIS A 170 
 PHE   0.014   0.001   PHE B 173 
 TYR   0.020   0.001   TYR C 121 
 ARG   0.003   0.000   ARG C 239 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 76
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 GLU cc_start: 0.5374 (tt0) cc_final: 0.4930 (mp0)
REVERT: A  324 GLU cc_start: 0.6513 (tm-30) cc_final: 0.6195 (tm-30)
REVERT: A  441 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7820 (tt)
REVERT: A  445 ASP cc_start: 0.8257 (m-30) cc_final: 0.7836 (m-30)
REVERT: A  502 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7910 (tm-30)
REVERT: A  559 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.7710 (pp20)
REVERT: A  572 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.6079 (ppp)
REVERT: A  603 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8241 (p)
REVERT: A  612 CYS cc_start: 0.1601 (OUTLIER) cc_final: 0.0074 (m)
REVERT: B   69 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8277 (mmm-85)
REVERT: C   63 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7294 (p0)
REVERT: C  185 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7687 (t80)
REVERT: C  259 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7957 (ttm)
REVERT: C  269 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5339 (mp)
  outliers start: 31
  outliers final: 16
  residues processed: 99
  average time/residue: 1.3207
  time to fit residues: 139.4312
Evaluate side-chains
  99 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  559 GLU
Chi-restraints excluded: chain A residue  572 MET
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  612 CYS
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain B residue    9 ARG
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain B residue   69 ARG
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  185 PHE
Chi-restraints excluded: chain C residue  259 MET
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain C residue  269 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3374 r_free = 0.3374 target = 0.112220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.096289 restraints weight = 12308.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.81
r_work: 0.3064 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   8930  Z= 0.243
  Angle     :  1.039  81.259  12132  Z= 0.421
  Chirality :  0.062   1.552   1317
  Planarity :  0.005   0.109   1560
  Dihedral  :  7.535  87.603   1310
  Min Nonbonded Distance : 1.782

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.92 %
    Favored  : 90.08 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.00 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.64 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.26), residues: 1089
  helix:  1.05 (0.27), residues: 441
  sheet: -1.03 (0.57), residues: 81
  loop : -2.32 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  95 
 HIS   0.004   0.001   HIS A 170 
 PHE   0.013   0.001   PHE B 173 
 TYR   0.020   0.001   TYR C 121 
 ARG   0.004   0.000   ARG C 239 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 78
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 GLU cc_start: 0.5350 (tt0) cc_final: 0.4898 (mp0)
REVERT: A  324 GLU cc_start: 0.6500 (tm-30) cc_final: 0.6184 (tm-30)
REVERT: A  441 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7816 (tt)
REVERT: A  445 ASP cc_start: 0.8228 (m-30) cc_final: 0.7805 (m-30)
REVERT: A  502 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7924 (tm-30)
REVERT: A  559 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.7694 (pp20)
REVERT: A  572 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.6071 (ppp)
REVERT: A  603 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8204 (p)
REVERT: A  612 CYS cc_start: 0.1579 (OUTLIER) cc_final: 0.0069 (m)
REVERT: B   69 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8277 (mmm-85)
REVERT: C   63 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7285 (p0)
REVERT: C  259 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7943 (ttm)
REVERT: C  269 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5325 (mp)
  outliers start: 27
  outliers final: 17
  residues processed: 98
  average time/residue: 1.2797
  time to fit residues: 134.1528
Evaluate side-chains
  100 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  559 GLU
Chi-restraints excluded: chain A residue  572 MET
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  612 CYS
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain B residue    9 ARG
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain B residue   69 ARG
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  208 CYS
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  259 MET
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain C residue  269 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3373 r_free = 0.3373 target = 0.112186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.096279 restraints weight = 12271.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 1.80
r_work: 0.3074 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   8930  Z= 0.248
  Angle     :  1.043  81.231  12132  Z= 0.423
  Chirality :  0.062   1.553   1317
  Planarity :  0.005   0.107   1560
  Dihedral  :  7.502  86.043   1310
  Min Nonbonded Distance : 1.781

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.78 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.26), residues: 1089
  helix:  1.05 (0.27), residues: 441
  sheet: -1.03 (0.58), residues: 81
  loop : -2.31 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  95 
 HIS   0.004   0.001   HIS A 170 
 PHE   0.013   0.001   PHE B 173 
 TYR   0.021   0.001   TYR C 121 
 ARG   0.004   0.000   ARG C 239 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 76
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 GLU cc_start: 0.5380 (tt0) cc_final: 0.4941 (mp0)
REVERT: A  324 GLU cc_start: 0.6514 (tm-30) cc_final: 0.6197 (tm-30)
REVERT: A  441 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7811 (tt)
REVERT: A  445 ASP cc_start: 0.8237 (m-30) cc_final: 0.7812 (m-30)
REVERT: A  502 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7923 (tm-30)
REVERT: A  559 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.7696 (pp20)
REVERT: A  572 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6087 (ppp)
REVERT: A  603 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8207 (p)
REVERT: A  612 CYS cc_start: 0.1688 (OUTLIER) cc_final: 0.0248 (m)
REVERT: B   69 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8280 (mmm-85)
REVERT: C   63 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7293 (p0)
REVERT: C  259 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7955 (ttm)
REVERT: C  269 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5319 (mp)
  outliers start: 26
  outliers final: 15
  residues processed: 95
  average time/residue: 1.3421
  time to fit residues: 136.4420
Evaluate side-chains
  99 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  559 GLU
Chi-restraints excluded: chain A residue  572 MET
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  612 CYS
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain B residue    9 ARG
Chi-restraints excluded: chain B residue   16 THR
Chi-restraints excluded: chain B residue   69 ARG
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  208 CYS
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  259 MET
Chi-restraints excluded: chain C residue  269 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 95 optimal weight:    0.2980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.8588

-------------------------------------------------------------------------------
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 = 0.3363 r_free = 0.3363 target = 0.111493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.095646 restraints weight = 12243.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.79
r_work: 0.3067 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   8930  Z= 0.265
  Angle     :  1.048  81.123  12132  Z= 0.427
  Chirality :  0.062   1.557   1317
  Planarity :  0.005   0.111   1560
  Dihedral  :  7.543  84.888   1310
  Min Nonbonded Distance : 1.780

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.92 %
    Favored  : 90.08 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.89 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.26), residues: 1089
  helix:  1.03 (0.27), residues: 441
  sheet: -1.00 (0.58), residues: 81
  loop : -2.34 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  95 
 HIS   0.005   0.001   HIS A 170 
 PHE   0.014   0.001   PHE B 173 
 TYR   0.021   0.001   TYR C 121 
 ARG   0.004   0.000   ARG C 239 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5398.39 seconds
wall clock time: 96 minutes 12.65 seconds (5772.65 seconds total)