Starting phenix.real_space_refine
on Thu Feb 13 21:13:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d6v_30594/02_2025/7d6v_30594.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d6v_30594/02_2025/7d6v_30594.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d6v_30594/02_2025/7d6v_30594.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d6v_30594/02_2025/7d6v_30594.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d6v_30594/02_2025/7d6v_30594.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d6v_30594/02_2025/7d6v_30594.cif"
  }
  resolution = 2.53
  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=  -0.001 sd=   0.085
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    5561      2.51       5
     N    1541      2.21       5
     O    1614      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 79 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: 8793
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 601, 4601
          Classifications: {'peptide': 601}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "B"
      Number of atoms: 1910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1910
          Classifications: {'peptide': 239}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 13, 'TRANS': 225}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 2139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2139
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 249}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    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: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 71
          Unusual residues: {'FES': 1, 'PEV': 1, 'UQ1': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5025  SG  CYS B  54      43.083  50.586  44.645  1.00 17.96           S
  ATOM   5054  SG  CYS B  59      46.564  51.189  45.166  1.00 16.18           S
  ATOM   5070  SG  CYS B  62      43.079  56.301  48.844  1.00 14.75           S
  ATOM   5161  SG  CYS B  74      40.401  53.492  48.121  1.00 17.98           S
  ATOM   5790  SG  CYS B 151      52.563  51.713  59.294  1.00 11.26           S
  ATOM   6290  SG  CYS B 213      46.003  47.869  59.192  1.00 12.06           S
  ATOM   5742  SG  CYS B 145      51.917  46.652  54.909  1.00 12.48           S
  ATOM   5765  SG  CYS B 148      48.381  52.961  54.895  1.00 11.97           S
  ATOM   6261  SG  CYS B 209      50.606  50.711  65.541  1.00 14.99           S
  ATOM   6217  SG  CYS B 203      56.391  50.847  69.558  1.00 11.63           S
  ATOM   7358  SG  CYS C 114      48.947  46.333  81.743  1.00 10.87           S
  ATOM   8103  SG  CYS C 206      51.468  39.576  81.272  1.00 11.05           S

  Time building chain proxies: 6.24, per 1000 atoms: 0.71
  Number of scatterers: 8793
  At special positions: 0
  Unit cell: (86.92, 87.74, 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    1614      8.00
     N    1541      7.00
     C    5561      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 208 " - pdb=" SG  CYS C 132 " distance=2.03

  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: 2.30
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" F3S B 303 "
        pdb="FE4  F3S B 303 " - pdb=" SG  CYS B 203 "
        pdb="FE3  F3S B 303 " - pdb=" SG  CYS B 209 "
        pdb="FE1  F3S B 303 " - pdb=" SG  CYS B 155 "
      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 303 "
        pdb="FE2  FES C 303 " - pdb=" SG  CYS C 206 "
        pdb="FE1  FES C 303 " - pdb=" SG  CYS C 114 "
        pdb="FE2  FES C 303 " - pdb=" NE2 HIS C 155 "
        pdb="FE1  FES C 303 " - pdb=" NE2 HIS C 240 "
      pdb=" SF4 B 302 "
        pdb="FE3  SF4 B 302 " - pdb=" SG  CYS B 145 "
        pdb="FE4  SF4 B 302 " - pdb=" SG  CYS B 148 "
        pdb="FE1  SF4 B 302 " - pdb=" SG  CYS B 151 "
        pdb="FE2  SF4 B 302 " - pdb=" SG  CYS B 213 "
      Number of angles added : 29


  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2024

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 11 sheets defined
      46.0% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 31
    Processing helix  chain 'A' and resid 45 through 50
    Processing helix  chain 'A' and resid 66 through 77
    Processing helix  chain 'A' and resid 83 through 103
      Proline residue:  A  95  - end of helix
      removed outlier: 3.666A  pdb=" N   GLU A 102 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   THR A 103 " --> pdb=" O   TRP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 160
    Processing helix  chain 'A' and resid 212 through 216
    Processing helix  chain 'A' and resid 229 through 237
    Processing helix  chain 'A' and resid 321 through 335
      removed outlier: 3.801A  pdb=" N   VAL A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 361
    Processing helix  chain 'A' and resid 361 through 373
    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: 3.717A  pdb=" N   SER A 430 " --> pdb=" O   GLY A 426 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 470
      removed outlier: 3.532A  pdb=" N   VAL A 461 " --> pdb=" O   SER A 457 " (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 519
    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: 4.206A  pdb=" N   ARG A 541 " --> pdb=" O   ALA A 537 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ASN A 542 " --> pdb=" O   ILE A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 619
    Processing helix  chain 'B' and resid 32 through 44
    Processing helix  chain 'B' and resid 74 through 76
      No H-bonds generated for 'chain 'B' and resid 74 through 76'
    Processing helix  chain 'B' and resid 106 through 113
      removed outlier: 3.879A  pdb=" N   ARG B 113 " --> pdb=" O   TYR B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 129
      removed outlier: 4.133A  pdb=" N   TYR B 129 " --> pdb=" O   PRO B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 143
      removed outlier: 5.127A  pdb=" N   ARG B 138 " --> pdb=" O   GLU B 134 " (cutoff:3.500A)
      removed outlier: 5.604A  pdb=" N   SER B 139 " --> pdb=" O   ASP B 135 " (cutoff:3.500A)
      removed outlier: 3.640A  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
    Processing helix  chain 'B' and resid 170 through 182
    Processing helix  chain 'B' and resid 190 through 197
      removed outlier: 3.655A  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
    Processing helix  chain 'C' and resid 32 through 56
      removed outlier: 3.509A  pdb=" N   LEU C  36 " --> pdb=" O   TRP C  32 " (cutoff:3.500A)
      removed outlier: 4.408A  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
    Processing helix  chain 'C' and resid 146 through 151
      removed outlier: 3.963A  pdb=" N   LEU C 151 " --> pdb=" O   PHE C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 176
      removed outlier: 3.731A  pdb=" N   PHE C 158 " --> pdb=" O   ILE C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 205
    Processing helix  chain 'C' and resid 206 through 214
      removed outlier: 3.523A  pdb=" N   GLY C 214 " --> pdb=" O   ARG C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 219 through 222
      removed outlier: 3.580A  pdb=" N   LYS C 222 " --> pdb=" O   HIS C 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 219 through 222'
    Processing helix  chain 'C' and resid 223 through 238
    Processing helix  chain 'C' and resid 239 through 265
      removed outlier: 3.722A  pdb=" N   TRP C 245 " --> pdb=" O   MET C 241 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   THR C 265 " --> pdb=" O   VAL C 261 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7
      removed outlier: 6.326A  pdb=" N   GLU A   5 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ILE A 178 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   ALA A 187 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   GLU A 176 " --> pdb=" O   ALA A 187 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   GLY A 189 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ILE A 174 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   TYR A 191 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   THR A 172 " --> pdb=" O   TYR A 191 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 169
      removed outlier: 6.517A  pdb=" N   VAL A  34 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   PHE A 169 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   VAL A  36 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 6.165A  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: 5.620A  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 253
      removed outlier: 6.250A  pdb=" N   HIS A 249 " --> pdb=" O   CYS A 387 " (cutoff:3.500A)
      removed outlier: 5.540A  pdb=" N   CYS A 387 " --> pdb=" O   HIS A 249 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   THR A 251 " --> pdb=" O   PRO A 385 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   MET A 253 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   VAL A 383 " --> pdb=" O   MET A 253 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 500
    Processing sheet with id=AA7, first strand: chain 'A' and resid 582 through 585
    Processing sheet with id=AA8, first strand: chain 'B' and resid 17 through 27
      removed outlier: 9.474A  pdb=" N   VAL B  87 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   LYS B   7 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 65
    Processing sheet with id=AB1, first strand: chain 'B' and resid 97 through 99
      removed outlier: 6.802A  pdb=" N   VAL B 102 " --> pdb=" O   MET B  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 60 through 61

    363 hydrogen bonds defined for protein.
    1035 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: 2.53

  Time building geometry restraints manager: 2.60 seconds

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

  Histogram of bond lengths:
        1.14 -     1.71: 8905
        1.71 -     2.29: 101
        2.29 -     2.87: 3
        2.87 -     3.45: 0
        3.45 -     4.03: 3
  Bond restraints: 9012
  Sorted by residual:
  bond pdb=" S4  F3S B 303 "
       pdb="FE1  F3S B 303 "
    ideal  model  delta    sigma   weight residual
    2.233  4.027 -1.794 2.00e-02 2.50e+03 8.05e+03
  bond pdb=" S2  F3S B 303 "
       pdb="FE3  F3S B 303 "
    ideal  model  delta    sigma   weight residual
    2.300  3.879 -1.579 2.00e-02 2.50e+03 6.24e+03
  bond pdb=" S1  F3S B 303 "
       pdb="FE4  F3S B 303 "
    ideal  model  delta    sigma   weight residual
    2.258  3.771 -1.513 2.00e-02 2.50e+03 5.72e+03
  bond pdb=" C   CYS B  59 "
       pdb=" N   GLY B  60 "
    ideal  model  delta    sigma   weight residual
    1.329  1.569 -0.240 1.36e-02 5.41e+03 3.12e+02
  bond pdb=" C   LYS B  58 "
       pdb=" N   CYS B  59 "
    ideal  model  delta    sigma   weight residual
    1.332  1.203  0.129 1.29e-02 6.01e+03 1.00e+02
  ... (remaining 9007 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.17: 12197
       10.17 -    20.34: 33
       20.34 -    30.51: 4
       30.51 -    40.67: 5
       40.67 -    50.84: 2
  Bond angle restraints: 12241
  Sorted by residual:
  angle pdb=" N   CYS B  59 "
        pdb=" CA  CYS B  59 "
        pdb=" C   CYS B  59 "
      ideal   model   delta    sigma   weight residual
     112.93  138.97  -26.04 1.33e+00 5.65e-01 3.83e+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   61.75   50.84 3.00e+00 1.11e-01 2.87e+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   67.94   46.81 3.00e+00 1.11e-01 2.43e+02
  angle pdb=" S1  F3S B 303 "
        pdb="FE3  F3S B 303 "
        pdb=" S2  F3S B 303 "
      ideal   model   delta    sigma   weight residual
     103.25   65.38   37.87 3.00e+00 1.11e-01 1.59e+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   90.00   14.33 1.14e+00 7.69e-01 1.58e+02
  ... (remaining 12236 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.95: 5138
       28.95 -    57.89: 189
       57.89 -    86.83: 24
       86.83 -   115.78: 1
      115.78 -   144.72: 1
  Dihedral angle restraints: 5353
    sinusoidal: 2190
      harmonic: 3163
  Sorted by residual:
  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  157.98  -35.18     0      2.50e+00 1.60e-01 1.98e+02
  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 -156.75   34.15     0      2.50e+00 1.60e-01 1.87e+02
  dihedral pdb=" CA  SER C 128 "
           pdb=" C   SER C 128 "
           pdb=" N   PRO C 129 "
           pdb=" CA  PRO C 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  138.70   41.30     0      5.00e+00 4.00e-02 6.82e+01
  ... (remaining 5350 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    3.621: 1323
       3.621 -    7.241: 0
       7.241 -   10.862: 0
      10.862 -   14.482: 0
      14.482 -   18.103: 1
  Chirality restraints: 1324
  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   -7.33   18.10 2.00e-01 2.50e+01 8.19e+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    0.81    1.70 2.00e-01 2.50e+01 7.24e+01
  chirality pdb="FE1  SF4 B 302 "
            pdb=" S2  SF4 B 302 "
            pdb=" S3  SF4 B 302 "
            pdb=" S4  SF4 B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False    -10.55   -9.73   -0.82 2.00e-01 2.50e+01 1.69e+01
  ... (remaining 1321 not shown)

  Planarity restraints: 1575
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 208 "   -0.022 2.00e-02 2.50e+03   4.40e-02 1.93e+01
        pdb=" C   CYS B 208 "    0.076 2.00e-02 2.50e+03
        pdb=" O   CYS B 208 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   CYS B 209 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 606 "   -0.066 5.00e-02 4.00e+02   9.78e-02 1.53e+01
        pdb=" N   PRO A 607 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO A 607 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 607 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 128 "   -0.051 5.00e-02 4.00e+02   7.71e-02 9.51e+00
        pdb=" N   PRO C 129 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO C 129 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO C 129 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 1572 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 531
        2.73 -     3.27: 8610
        3.27 -     3.81: 15072
        3.81 -     4.36: 19248
        4.36 -     4.90: 31856
  Nonbonded interactions: 75317
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 575 "
            pdb=" N   TRP A 576 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" OD1 ASP B 237 "
            pdb=" OH  TYR C 157 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OD2 ASP A  73 "
            pdb=" NH2 ARG A 128 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" S1  F3S B 303 "
            pdb="FE1  F3S B 303 "
     model   vdw
     2.219 2.688
  nonbonded pdb=" NE2 HIS B 161 "
            pdb=" OE1 GLU C 136 "
     model   vdw
     2.242 3.120
  ... (remaining 75312 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:             3.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.720
  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:12.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
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      :  0.031   1.794   9012  Z= 2.241
  Angle     :  1.559  50.842  12241  Z= 0.789
  Chirality :  0.504  18.103   1324
  Planarity :  0.006   0.098   1575
  Dihedral  : 14.912 144.725   3326
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.58 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -0.92 (0.25), residues: 1096
  helix:  1.04 (0.26), residues: 445
  sheet: -0.30 (0.56), residues: 88
  loop : -2.15 (0.24), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  60 
 HIS   0.004   0.001   HIS A 131 
 PHE   0.023   0.002   PHE B 173 
 TYR   0.018   0.002   TYR C 116 
 ARG   0.010   0.001   ARG A 448 

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.088 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 1.6301
  time to fit residues: 211.7223
Evaluate side-chains
  102 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 44 optimal weight:    0.2980
   chunk 85 optimal weight:    0.0970
   chunk 33 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
A 170 HIS
A 247 GLN
B 195 GLN
C  33 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.127872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.111486 restraints weight = 9990.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.19
r_work: 0.3290 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.0972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.093   9012  Z= 0.220
  Angle     :  1.077  86.961  12241  Z= 0.445
  Chirality :  0.056   1.255   1324
  Planarity :  0.006   0.092   1575
  Dihedral  :  9.985 140.268   1323
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  7.73 %
    Favored  : 91.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -0.53 (0.26), residues: 1096
  helix:  1.56 (0.26), residues: 448
  sheet: -0.18 (0.58), residues: 86
  loop : -2.11 (0.24), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  95 
 HIS   0.004   0.001   HIS A 131 
 PHE   0.018   0.002   PHE B 173 
 TYR   0.025   0.001   TYR C 121 
 ARG   0.005   0.000   ARG C 216 

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A  418 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8206 (ttp)
REVERT: B  197 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7532 (mp0)
REVERT: B  218 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8745 (mmtp)
  outliers start: 11
  outliers final: 5
  residues processed: 110
  average time/residue: 1.5138
  time to fit residues: 175.9545
Evaluate side-chains
  109 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  418 MET
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain C residue  259 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0010
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 170 HIS
A 602 GLN
C  33 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.128224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.111679 restraints weight = 10274.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.22
r_work: 0.3293 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.104   9012  Z= 0.225
  Angle     :  1.039  82.740  12241  Z= 0.425
  Chirality :  0.059   1.446   1324
  Planarity :  0.005   0.079   1575
  Dihedral  :  9.351 140.281   1323
  Min Nonbonded Distance : 1.787

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  9.93 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -0.43 (0.26), residues: 1096
  helix:  1.75 (0.26), residues: 448
  sheet: -0.19 (0.55), residues: 96
  loop : -2.18 (0.24), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 131 
 PHE   0.019   0.002   PHE B 173 
 TYR   0.024   0.001   TYR C 121 
 ARG   0.006   0.000   ARG C 216 

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
REVERT: B  218 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8702 (mmtp)
  outliers start: 18
  outliers final: 6
  residues processed: 110
  average time/residue: 1.5336
  time to fit residues: 178.2063
Evaluate side-chains
  104 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  259 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0870
   chunk 26 optimal weight:    8.9990
   chunk 88 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0970
   chunk 39 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.0362

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

Flipped N/Q/H residues before XYZ refinement:
A 170 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.126504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.110388 restraints weight = 10488.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 1.19
r_work: 0.3250 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   9012  Z= 0.280
  Angle     :  1.059  82.996  12241  Z= 0.441
  Chirality :  0.060   1.432   1324
  Planarity :  0.006   0.080   1575
  Dihedral  :  9.462 140.676   1323
  Min Nonbonded Distance : 1.798

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.26 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -0.41 (0.26), residues: 1096
  helix:  1.71 (0.26), residues: 448
  sheet: -0.41 (0.56), residues: 90
  loop : -2.05 (0.24), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  95 
 HIS   0.003   0.001   HIS B 161 
 PHE   0.024   0.002   PHE B 173 
 TYR   0.023   0.002   TYR C 116 
 ARG   0.005   0.000   ARG C 216 

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 1.015 
Fit side-chains
REVERT: A  610 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5391 (pp)
REVERT: B  141 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8220 (tt0)
REVERT: B  197 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7666 (mt-10)
  outliers start: 23
  outliers final: 8
  residues processed: 110
  average time/residue: 1.4106
  time to fit residues: 164.8796
Evaluate side-chains
  105 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  455 LYS
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  259 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 92 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 44 optimal weight:    0.1980
   chunk 49 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0040
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A 170 HIS
C  33 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.128604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.112277 restraints weight = 10112.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 1.21
r_work: 0.3307 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.103   9012  Z= 0.212
  Angle     :  1.027  83.337  12241  Z= 0.417
  Chirality :  0.058   1.426   1324
  Planarity :  0.005   0.078   1575
  Dihedral  :  9.053 138.510   1323
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 12.03 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -0.27 (0.26), residues: 1096
  helix:  1.86 (0.26), residues: 448
  sheet: -0.33 (0.56), residues: 90
  loop : -2.00 (0.24), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 131 
 PHE   0.019   0.001   PHE B 173 
 TYR   0.022   0.001   TYR C 121 
 ARG   0.006   0.000   ARG C 216 

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.8165 (m-30) cc_final: 0.7949 (m-30)
REVERT: A  418 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.7844 (ttt)
REVERT: A  610 LEU cc_start: 0.5631 (OUTLIER) cc_final: 0.5024 (pp)
REVERT: B  141 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8133 (tt0)
  outliers start: 26
  outliers final: 10
  residues processed: 113
  average time/residue: 1.3906
  time to fit residues: 167.1224
Evaluate side-chains
  110 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  418 MET
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  496 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  141 GLU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  259 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 53 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0770
   chunk 85 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 170 HIS
C  33 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.127973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.111590 restraints weight = 10064.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.21
r_work: 0.3295 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.104   9012  Z= 0.225
  Angle     :  1.030  83.256  12241  Z= 0.419
  Chirality :  0.059   1.424   1324
  Planarity :  0.005   0.078   1575
  Dihedral  :  8.937 138.183   1323
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 12.69 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -0.22 (0.26), residues: 1096
  helix:  1.88 (0.26), residues: 448
  sheet: -0.31 (0.56), residues: 90
  loop : -1.95 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 131 
 PHE   0.021   0.002   PHE B 173 
 TYR   0.021   0.001   TYR C 121 
 ARG   0.006   0.000   ARG C 216 

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.8127 (m-30) cc_final: 0.7897 (m-30)
REVERT: A  158 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6597 (mp0)
REVERT: A  418 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.7826 (ttt)
REVERT: A  610 LEU cc_start: 0.5323 (OUTLIER) cc_final: 0.4778 (pp)
REVERT: B  141 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8130 (tt0)
REVERT: B  197 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7684 (mp0)
REVERT: C  140 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8151 (mmtt)
  outliers start: 25
  outliers final: 12
  residues processed: 116
  average time/residue: 1.4853
  time to fit residues: 182.7744
Evaluate side-chains
  115 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  158 GLU
Chi-restraints excluded: chain A residue  418 MET
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  496 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  141 GLU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain C residue  140 LYS
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  259 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 170 HIS
C  33 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.123005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.106885 restraints weight = 10505.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.20
r_work: 0.3203 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.110   9012  Z= 0.437
  Angle     :  1.117  82.404  12241  Z= 0.480
  Chirality :  0.064   1.450   1324
  Planarity :  0.007   0.078   1575
  Dihedral  :  9.546 142.197   1323
  Min Nonbonded Distance : 1.789

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.49 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 12.91 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -0.53 (0.26), residues: 1096
  helix:  1.51 (0.26), residues: 448
  sheet: -0.36 (0.55), residues: 90
  loop : -2.03 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  95 
 HIS   0.006   0.001   HIS C 211 
 PHE   0.028   0.003   PHE B 173 
 TYR   0.029   0.002   TYR C 116 
 ARG   0.008   0.001   ARG C  18 

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A  606 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.4768 (ptt90)
REVERT: A  610 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.5408 (pp)
REVERT: C  140 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8344 (mmtt)
  outliers start: 27
  outliers final: 13
  residues processed: 112
  average time/residue: 1.4760
  time to fit residues: 175.2136
Evaluate side-chains
  109 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  514 GLU
Chi-restraints excluded: chain A residue  559 GLU
Chi-restraints excluded: chain A residue  592 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 B residue  205 ILE
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  140 LYS
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  259 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 22 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0870
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 170 HIS
A 602 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.127019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.110560 restraints weight = 10283.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.22
r_work: 0.3274 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.104   9012  Z= 0.226
  Angle     :  1.039  83.265  12241  Z= 0.425
  Chirality :  0.059   1.431   1324
  Planarity :  0.005   0.075   1575
  Dihedral  :  8.866 138.859   1323
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.36 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -0.32 (0.26), residues: 1096
  helix:  1.76 (0.26), residues: 448
  sheet: -0.31 (0.56), residues: 90
  loop : -1.99 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  52 
 HIS   0.004   0.001   HIS B 161 
 PHE   0.020   0.001   PHE B 173 
 TYR   0.021   0.001   TYR C 121 
 ARG   0.007   0.000   ARG C 216 

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A  418 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.7864 (ttt)
REVERT: A  610 LEU cc_start: 0.5467 (OUTLIER) cc_final: 0.4836 (pp)
REVERT: C  140 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8099 (mmtt)
  outliers start: 20
  outliers final: 11
  residues processed: 108
  average time/residue: 1.4324
  time to fit residues: 164.3193
Evaluate side-chains
  108 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  418 MET
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  496 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  205 ILE
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  140 LYS
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  259 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 170 HIS
C  33 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.126204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.109744 restraints weight = 10218.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.21
r_work: 0.3265 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   9012  Z= 0.251
  Angle     :  1.047  83.198  12241  Z= 0.431
  Chirality :  0.059   1.429   1324
  Planarity :  0.006   0.077   1575
  Dihedral  :  8.591 139.212   1323
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.85 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.02 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -0.29 (0.26), residues: 1096
  helix:  1.76 (0.26), residues: 448
  sheet: -0.27 (0.56), residues: 90
  loop : -1.94 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  95 
 HIS   0.004   0.001   HIS B 161 
 PHE   0.022   0.002   PHE B 173 
 TYR   0.021   0.001   TYR C 116 
 ARG   0.007   0.000   ARG C 216 

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 1.011 
Fit side-chains
REVERT: A  418 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.7865 (ttt)
REVERT: A  610 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.4853 (pp)
REVERT: B  197 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7645 (mt-10)
REVERT: C  140 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8124 (mmtt)
  outliers start: 20
  outliers final: 11
  residues processed: 106
  average time/residue: 1.5373
  time to fit residues: 172.3459
Evaluate side-chains
  108 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  418 MET
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  559 GLU
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  197 GLU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain C residue  140 LYS
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  259 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 102 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0020
   chunk 98 optimal weight:    0.7980
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A 170 HIS
A 602 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.125415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.108451 restraints weight = 10477.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.26
r_work: 0.3209 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   9012  Z= 0.233
  Angle     :  1.039  83.345  12241  Z= 0.425
  Chirality :  0.059   1.422   1324
  Planarity :  0.005   0.075   1575
  Dihedral  :  8.319 137.864   1323
  Min Nonbonded Distance : 1.801

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 13.91 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -0.24 (0.26), residues: 1096
  helix:  1.80 (0.26), residues: 448
  sheet: -0.25 (0.56), residues: 90
  loop : -1.91 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  95 
 HIS   0.004   0.001   HIS B 161 
 PHE   0.021   0.002   PHE B 173 
 TYR   0.020   0.001   TYR C 121 
 ARG   0.007   0.000   ARG C 216 

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
REVERT: A  418 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.7827 (ttt)
REVERT: A  610 LEU cc_start: 0.5073 (OUTLIER) cc_final: 0.4618 (pp)
REVERT: B  197 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7660 (mt-10)
  outliers start: 19
  outliers final: 11
  residues processed: 106
  average time/residue: 1.5143
  time to fit residues: 170.0789
Evaluate side-chains
  109 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  418 MET
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  559 GLU
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  197 GLU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  259 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 86 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0050
   chunk 57 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
A 170 HIS
C  33 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.125460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.108503 restraints weight = 10461.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.26
r_work: 0.3221 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   9012  Z= 0.234
  Angle     :  1.042  83.307  12241  Z= 0.427
  Chirality :  0.059   1.423   1324
  Planarity :  0.005   0.087   1575
  Dihedral  :  8.241 137.287   1323
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.35 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    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: -0.20 (0.26), residues: 1096
  helix:  1.82 (0.26), residues: 448
  sheet: -0.21 (0.56), residues: 90
  loop : -1.88 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  95 
 HIS   0.004   0.001   HIS B 161 
 PHE   0.021   0.002   PHE B 173 
 TYR   0.020   0.001   TYR C 121 
 ARG   0.007   0.000   ARG C 216 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6127.80 seconds
wall clock time: 109 minutes 8.00 seconds (6548.00 seconds total)