Starting phenix.real_space_refine
on Sun May 18 16:03:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dow_47094/05_2025/9dow_47094.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dow_47094/05_2025/9dow_47094.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dow_47094/05_2025/9dow_47094.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dow_47094/05_2025/9dow_47094.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dow_47094/05_2025/9dow_47094.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dow_47094/05_2025/9dow_47094.cif"
  }
  resolution = 3.1
  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=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9143 atoms to isotropic.
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
     P      75      5.49       5
     S      56      5.16       5
     Na      1      4.78       5
     C    5968      2.51       5
     N    1680      2.21       5
     O    2036      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9816
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 4100
          Classifications: {'peptide': 506}
          Link IDs: {'PTRANS': 29, 'TRANS': 476}
    Chain: "B"
      Number of atoms: 4092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 4092
          Classifications: {'peptide': 505}
          Link IDs: {'PTRANS': 29, 'TRANS': 475}
    Chain: "C"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1557
          Classifications: {'RNA': 73}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 30, 'rna3p_pyr': 30}
          Link IDs: {'rna2p': 13, 'rna3p': 59}
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Classifications: {'RNA': 1}
          Modifications used: {'rna2p': 1}
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Classifications: {'RNA': 1}
          Modifications used: {'rna2p': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.26, per 1000 atoms: 0.64
  Number of scatterers: 9816
  At special positions: 0
  Unit cell: (81.32, 104.86, 136.96, 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)
     S      56     16.00
     P      75     15.00
     Na      1     11.00
     O    2036      8.00
     N    1680      7.00
     C    5968      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.53
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1898

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      40.0% alpha, 20.4% beta
      27 base pairs and 30 stacking pairs defined.
    Time for finding SS restraints: 3.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 90
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 161 through 163
      No H-bonds generated for 'chain 'A' and resid 161 through 163'
    Processing helix  chain 'A' and resid 165 through 176
      removed outlier: 3.702A  pdb=" N   LYS A 175 " --> pdb=" O   HIS A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 229 through 237
    Processing helix  chain 'A' and resid 238 through 261
      removed outlier: 3.826A  pdb=" N   GLN A 242 " --> pdb=" O   ASP A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 311
    Processing helix  chain 'A' and resid 346 through 366
      removed outlier: 4.219A  pdb=" N   GLU A 352 " --> pdb=" O   HIS A 348 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ILE A 353 " --> pdb=" O   ASP A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 405
    Processing helix  chain 'A' and resid 410 through 414
    Processing helix  chain 'A' and resid 416 through 430
    Processing helix  chain 'A' and resid 439 through 452
    Processing helix  chain 'A' and resid 453 through 456
    Processing helix  chain 'A' and resid 504 through 519
      removed outlier: 3.630A  pdb=" N   LYS A 519 " --> pdb=" O   GLN A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 539
    Processing helix  chain 'A' and resid 551 through 559
    Processing helix  chain 'A' and resid 563 through 567
    Processing helix  chain 'B' and resid 73 through 90
    Processing helix  chain 'B' and resid 104 through 113
    Processing helix  chain 'B' and resid 165 through 176
    Processing helix  chain 'B' and resid 222 through 229
    Processing helix  chain 'B' and resid 229 through 237
    Processing helix  chain 'B' and resid 238 through 261
      removed outlier: 3.905A  pdb=" N   GLN B 242 " --> pdb=" O   ASP B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 311
    Processing helix  chain 'B' and resid 346 through 366
      removed outlier: 4.077A  pdb=" N   GLU B 352 " --> pdb=" O   HIS B 348 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE B 353 " --> pdb=" O   ASP B 349 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLU B 355 " --> pdb=" O   MET B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 405
    Processing helix  chain 'B' and resid 418 through 430
    Processing helix  chain 'B' and resid 439 through 452
      removed outlier: 3.805A  pdb=" N   LEU B 443 " --> pdb=" O   THR B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 456
    Processing helix  chain 'B' and resid 468 through 470
      No H-bonds generated for 'chain 'B' and resid 468 through 470'
    Processing helix  chain 'B' and resid 504 through 521
    Processing helix  chain 'B' and resid 530 through 539
    Processing helix  chain 'B' and resid 551 through 559
    Processing helix  chain 'B' and resid 563 through 568
      removed outlier: 4.152A  pdb=" N   VAL B 567 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 207
      removed outlier: 6.834A  pdb=" N   ILE A 181 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
      removed outlier: 8.828A  pdb=" N   LYS A 153 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 9.248A  pdb=" N   ILE A 198 " --> pdb=" O   LYS A 153 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   GLN A 155 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 7.720A  pdb=" N   MET A 157 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ALA A 134 " --> pdb=" O   ASP A 146 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ARG A 148 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   ILE A 132 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 265
      removed outlier: 5.776A  pdb=" N   LEU A 264 " --> pdb=" O   TYR A 316 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   ILE A 318 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ILE A 495 " --> pdb=" O   GLY A 550 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   GLU A 494 " --> pdb=" O   VAL A 490 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   VAL A 490 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   CYS A 496 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272
    Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 373
    Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 466
    Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 158
      removed outlier: 4.285A  pdb=" N   LEU B 142 " --> pdb=" O   SER B 138 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ALA B 134 " --> pdb=" O   ASP B 146 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ARG B 148 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   ILE B 132 " --> pdb=" O   ARG B 148 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   ILE B 181 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   GLY B 183 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   ILE B 203 " --> pdb=" O   GLY B 183 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   GLN B 185 " --> pdb=" O   TYR B 201 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 271 through 272
      removed outlier: 4.007A  pdb=" N   MET B 292 " --> pdb=" O   HIS B 287 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 314 through 322
      removed outlier: 6.626A  pdb=" N   ILE B 495 " --> pdb=" O   GLY B 550 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   GLU B 494 " --> pdb=" O   VAL B 490 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   VAL B 490 " --> pdb=" O   GLU B 494 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   CYS B 496 " --> pdb=" O   LEU B 488 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   GLU B 484 " --> pdb=" O   THR B 500 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   HIS B 465 " --> pdb=" O   THR B 483 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ARG B 485 " --> pdb=" O   CYS B 463 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   CYS B 463 " --> pdb=" O   ARG B 485 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   GLU B 487 " --> pdb=" O   PHE B 461 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   PHE B 461 " --> pdb=" O   GLU B 487 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 370 through 373

    376 hydrogen bonds defined for protein.
    1080 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      69 hydrogen bonds
      114 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      30 stacking parallelities
  Total time for adding SS restraints: 3.33

  Time building geometry restraints manager: 2.90 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2870
        1.34 -     1.46: 2102
        1.46 -     1.58: 4978
        1.58 -     1.70: 147
        1.70 -     1.82: 96
  Bond restraints: 10193
  Sorted by residual:
  bond pdb=" C4  AMP B 602 "
       pdb=" C5  AMP B 602 "
    ideal  model  delta    sigma   weight residual
    1.490  1.380  0.110 2.00e-02 2.50e+03 3.04e+01
  bond pdb=" C4  AMP A 602 "
       pdb=" C5  AMP A 602 "
    ideal  model  delta    sigma   weight residual
    1.490  1.382  0.108 2.00e-02 2.50e+03 2.91e+01
  bond pdb=" C5  AMP B 602 "
       pdb=" C6  AMP B 602 "
    ideal  model  delta    sigma   weight residual
    1.490  1.405  0.085 2.00e-02 2.50e+03 1.79e+01
  bond pdb=" C5  AMP A 602 "
       pdb=" C6  AMP A 602 "
    ideal  model  delta    sigma   weight residual
    1.490  1.407  0.083 2.00e-02 2.50e+03 1.73e+01
  bond pdb=" C   ARG A 392 "
       pdb=" N   ARG A 393 "
    ideal  model  delta    sigma   weight residual
    1.330  1.373 -0.043 1.40e-02 5.10e+03 9.58e+00
  ... (remaining 10188 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 13763
        1.99 -     3.98: 316
        3.98 -     5.98: 34
        5.98 -     7.97: 14
        7.97 -     9.96: 5
  Bond angle restraints: 14132
  Sorted by residual:
  angle pdb=" CA  ASP A 445 "
        pdb=" CB  ASP A 445 "
        pdb=" CG  ASP A 445 "
      ideal   model   delta    sigma   weight residual
     112.60  116.99   -4.39 1.00e+00 1.00e+00 1.93e+01
  angle pdb=" CA  LYS B 407 "
        pdb=" CB  LYS B 407 "
        pdb=" CG  LYS B 407 "
      ideal   model   delta    sigma   weight residual
     114.10  121.42   -7.32 2.00e+00 2.50e-01 1.34e+01
  angle pdb=" N   ASP A 445 "
        pdb=" CA  ASP A 445 "
        pdb=" C   ASP A 445 "
      ideal   model   delta    sigma   weight residual
     111.71  107.98    3.73 1.15e+00 7.56e-01 1.05e+01
  angle pdb=" CA  THR B 336 "
        pdb=" CB  THR B 336 "
        pdb=" OG1 THR B 336 "
      ideal   model   delta    sigma   weight residual
     109.60  104.75    4.85 1.50e+00 4.44e-01 1.05e+01
  angle pdb=" CA  VAL B 397 "
        pdb=" C   VAL B 397 "
        pdb=" O   VAL B 397 "
      ideal   model   delta    sigma   weight residual
     121.17  117.81    3.36 1.06e+00 8.90e-01 1.01e+01
  ... (remaining 14127 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.95: 5607
       25.95 -    51.91: 488
       51.91 -    77.86: 180
       77.86 -   103.81: 12
      103.81 -   129.77: 3
  Dihedral angle restraints: 6290
    sinusoidal: 3339
      harmonic: 2951
  Sorted by residual:
  dihedral pdb=" CA  PRO B 409 "
           pdb=" C   PRO B 409 "
           pdb=" N   GLU B 410 "
           pdb=" CA  GLU B 410 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.53  -17.47     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" C2' AMP B 602 "
           pdb=" C1' AMP B 602 "
           pdb=" N9  AMP B 602 "
           pdb=" C4  AMP B 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
      91.55  151.75  -60.19     1      2.00e+01 2.50e-03 1.21e+01
  dihedral pdb=" CA  THR B 388 "
           pdb=" C   THR B 388 "
           pdb=" N   PRO B 389 "
           pdb=" CA  PRO B 389 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.32  -16.68     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 6287 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1255
       0.043 -    0.085: 245
       0.085 -    0.128: 76
       0.128 -    0.170: 17
       0.170 -    0.213: 5
  Chirality restraints: 1598
  Sorted by residual:
  chirality pdb=" CA  HIS B 465 "
            pdb=" N   HIS B 465 "
            pdb=" C   HIS B 465 "
            pdb=" CB  HIS B 465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  HIS A 465 "
            pdb=" N   HIS A 465 "
            pdb=" C   HIS A 465 "
            pdb=" CB  HIS A 465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.72e-01
  chirality pdb=" CA  MET B 271 "
            pdb=" N   MET B 271 "
            pdb=" C   MET B 271 "
            pdb=" CB  MET B 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.67e-01
  ... (remaining 1595 not shown)

  Planarity restraints: 1549
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 393 "   -0.237 9.50e-02 1.11e+02   1.06e-01 6.91e+00
        pdb=" NE  ARG A 393 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 393 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 393 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 393 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 241 "    0.219 9.50e-02 1.11e+02   9.80e-02 5.89e+00
        pdb=" NE  ARG B 241 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 241 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 241 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 241 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 507 "   -0.208 9.50e-02 1.11e+02   9.31e-02 5.33e+00
        pdb=" NE  ARG B 507 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 507 "    0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 507 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 507 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1546 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1697
        2.77 -     3.30: 9443
        3.30 -     3.83: 17905
        3.83 -     4.37: 20643
        4.37 -     4.90: 33515
  Nonbonded interactions: 83203
  Sorted by model distance:
  nonbonded pdb=" O   GLN A  86 "
            pdb=" ND2 ASN A  90 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" O   ALA A 137 "
            pdb=" N6    A C  38 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" OD1 ASP A 386 "
            pdb=" OG1 THR A 388 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" N   GLU B 168 "
            pdb=" OE1 GLU B 168 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" O2'   A C  38 "
            pdb=" O5'   U C  39 "
     model   vdw
     2.294 3.040
  ... (remaining 83198 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 72 through 576 or resid 601 or resid 602))
  selection = chain 'B'
}

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:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.610
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.110  10193  Z= 0.259
  Angle     :  0.698   9.960  14132  Z= 0.394
  Chirality :  0.041   0.213   1598
  Planarity :  0.007   0.106   1549
  Dihedral  : 20.023 129.766   4392
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 25.86 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.26), residues: 1007
  helix:  1.24 (0.27), residues: 356
  sheet: -0.37 (0.36), residues: 228
  loop : -1.35 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 547 
 HIS   0.003   0.000   HIS A 465 
 PHE   0.038   0.001   PHE B 414 
 TYR   0.007   0.001   TYR A 316 
 ARG   0.003   0.000   ARG B 420 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13089 (  445)
  hydrogen bonds       : angle       5.90210 ( 1194)
  covalent geometry    : bond        0.00431 (10193)
  covalent geometry    : angle       0.69816 (14132)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: B  107 ASP cc_start: 0.8559 (t70) cc_final: 0.8353 (t0)
REVERT: B  157 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6994 (ptp)
  outliers start: 14
  outliers final: 10
  residues processed: 97
  average time/residue: 0.2107
  time to fit residues: 29.1570
Evaluate side-chains
  86 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  463 CYS
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  601 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0770
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.8940

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
B  82 GLN
B 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.131714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.081559 restraints weight = 16359.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 2.96
r_work: 0.2941 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.0942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10193  Z= 0.137
  Angle     :  0.561   6.143  14132  Z= 0.281
  Chirality :  0.037   0.151   1598
  Planarity :  0.005   0.055   1549
  Dihedral  : 18.778 114.450   2301
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 22.74 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.27), residues: 1007
  helix:  1.43 (0.27), residues: 370
  sheet: -0.26 (0.36), residues: 227
  loop : -1.24 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 547 
 HIS   0.003   0.001   HIS A 287 
 PHE   0.028   0.001   PHE A 340 
 TYR   0.008   0.001   TYR B 163 
 ARG   0.004   0.000   ARG B 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04140 (  445)
  hydrogen bonds       : angle       4.76982 ( 1194)
  covalent geometry    : bond        0.00312 (10193)
  covalent geometry    : angle       0.56063 (14132)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 81
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A  494 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7452 (tp30)
REVERT: B  107 ASP cc_start: 0.8698 (t70) cc_final: 0.8388 (t0)
REVERT: B  119 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.6828 (m-30)
REVERT: B  123 ASP cc_start: 0.8558 (p0) cc_final: 0.8313 (p0)
REVERT: B  407 LYS cc_start: 0.9108 (mptt) cc_final: 0.8657 (tptt)
  outliers start: 28
  outliers final: 15
  residues processed: 103
  average time/residue: 0.1949
  time to fit residues: 30.0121
Evaluate side-chains
  90 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  494 GLU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  490 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 19 optimal weight:    0.0370
   chunk 50 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0770
   chunk 71 optimal weight:    0.8980
   chunk 86 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 104 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 101 optimal weight:   20.0000
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.132611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.082397 restraints weight = 16538.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 2.98
r_work: 0.2982 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10193  Z= 0.110
  Angle     :  0.531   6.952  14132  Z= 0.263
  Chirality :  0.036   0.144   1598
  Planarity :  0.004   0.055   1549
  Dihedral  : 18.629 118.785   2290
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 22.30 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.27), residues: 1007
  helix:  1.53 (0.27), residues: 370
  sheet: -0.24 (0.36), residues: 228
  loop : -1.21 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 547 
 HIS   0.002   0.000   HIS A 476 
 PHE   0.026   0.001   PHE A 340 
 TYR   0.007   0.001   TYR A 316 
 ARG   0.002   0.000   ARG B 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03765 (  445)
  hydrogen bonds       : angle       4.52223 ( 1194)
  covalent geometry    : bond        0.00247 (10193)
  covalent geometry    : angle       0.53112 (14132)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 77
  time to evaluate  : 0.968 
Fit side-chains
REVERT: B  107 ASP cc_start: 0.8558 (t70) cc_final: 0.8302 (t0)
REVERT: B  123 ASP cc_start: 0.8564 (p0) cc_final: 0.8208 (p0)
REVERT: B  124 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.7022 (pp)
  outliers start: 28
  outliers final: 12
  residues processed: 99
  average time/residue: 0.1777
  time to fit residues: 26.7346
Evaluate side-chains
  87 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  124 ILE
Chi-restraints excluded: chain B residue  195 GLU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  490 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 100 optimal weight:   30.0000
   chunk 87 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   chunk 83 optimal weight:    7.9990
   chunk 103 optimal weight:    5.9990
   chunk 36 optimal weight:   30.0000
   chunk 57 optimal weight:    0.8980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3932 r_free = 0.3932 target = 0.130787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.080562 restraints weight = 16585.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 2.98
r_work: 0.2903 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10193  Z= 0.167
  Angle     :  0.551   5.934  14132  Z= 0.275
  Chirality :  0.037   0.147   1598
  Planarity :  0.005   0.056   1549
  Dihedral  : 18.631 124.422   2286
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 22.41 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.27), residues: 1007
  helix:  1.47 (0.27), residues: 371
  sheet: -0.32 (0.36), residues: 227
  loop : -1.19 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 547 
 HIS   0.002   0.001   HIS A 215 
 PHE   0.031   0.002   PHE A 340 
 TYR   0.008   0.001   TYR B 316 
 ARG   0.002   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04032 (  445)
  hydrogen bonds       : angle       4.55067 ( 1194)
  covalent geometry    : bond        0.00394 (10193)
  covalent geometry    : angle       0.55147 (14132)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.986 
Fit side-chains
REVERT: B  107 ASP cc_start: 0.8603 (t70) cc_final: 0.8295 (t0)
REVERT: B  123 ASP cc_start: 0.8663 (p0) cc_final: 0.8256 (p0)
REVERT: B  407 LYS cc_start: 0.9074 (mptt) cc_final: 0.8659 (tptt)
  outliers start: 25
  outliers final: 19
  residues processed: 97
  average time/residue: 0.1792
  time to fit residues: 26.4452
Evaluate side-chains
  94 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  512 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 105 optimal weight:   30.0000
   chunk 95 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 89 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.4020 r_free = 0.4020 target = 0.134617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.083985 restraints weight = 17353.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.91
r_work: 0.3068 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10193  Z= 0.124
  Angle     :  0.531   6.005  14132  Z= 0.263
  Chirality :  0.036   0.144   1598
  Planarity :  0.004   0.055   1549
  Dihedral  : 18.558 122.615   2286
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 22.63 %
    Favored  : 74.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.27), residues: 1007
  helix:  1.49 (0.27), residues: 372
  sheet: -0.31 (0.36), residues: 227
  loop : -1.15 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 547 
 HIS   0.002   0.000   HIS A 476 
 PHE   0.027   0.001   PHE A 340 
 TYR   0.008   0.001   TYR A 316 
 ARG   0.002   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (  445)
  hydrogen bonds       : angle       4.44920 ( 1194)
  covalent geometry    : bond        0.00287 (10193)
  covalent geometry    : angle       0.53148 (14132)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A  285 THR cc_start: 0.8883 (m) cc_final: 0.8582 (p)
REVERT: A  445 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8762 (p0)
REVERT: B  107 ASP cc_start: 0.8609 (t70) cc_final: 0.8286 (t0)
REVERT: B  123 ASP cc_start: 0.8398 (p0) cc_final: 0.7880 (p0)
REVERT: B  195 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7430 (mp0)
  outliers start: 28
  outliers final: 18
  residues processed: 99
  average time/residue: 0.1860
  time to fit residues: 28.6919
Evaluate side-chains
  93 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  445 ASP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  195 GLU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  336 THR
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  512 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 87 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.4000 r_free = 0.4000 target = 0.133333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.083611 restraints weight = 17198.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.81
r_work: 0.3050 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10193  Z= 0.152
  Angle     :  0.545   5.928  14132  Z= 0.270
  Chirality :  0.036   0.148   1598
  Planarity :  0.005   0.056   1549
  Dihedral  : 18.520 126.045   2286
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 22.52 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.27), residues: 1007
  helix:  1.46 (0.27), residues: 371
  sheet: -0.38 (0.35), residues: 232
  loop : -1.18 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 547 
 HIS   0.002   0.000   HIS A 215 
 PHE   0.030   0.002   PHE A 340 
 TYR   0.010   0.001   TYR A 499 
 ARG   0.002   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  445)
  hydrogen bonds       : angle       4.49385 ( 1194)
  covalent geometry    : bond        0.00356 (10193)
  covalent geometry    : angle       0.54494 (14132)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 1.007 
Fit side-chains
REVERT: A  285 THR cc_start: 0.8906 (m) cc_final: 0.8587 (p)
REVERT: A  445 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8751 (p0)
REVERT: A  477 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7865 (mtm-85)
REVERT: B  107 ASP cc_start: 0.8614 (t70) cc_final: 0.8264 (t0)
REVERT: B  123 ASP cc_start: 0.8301 (p0) cc_final: 0.7720 (p0)
REVERT: B  195 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7302 (mp0)
REVERT: B  407 LYS cc_start: 0.9070 (mptt) cc_final: 0.8727 (tptt)
  outliers start: 30
  outliers final: 20
  residues processed: 102
  average time/residue: 0.1760
  time to fit residues: 27.3312
Evaluate side-chains
  99 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  445 ASP
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  195 GLU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  336 THR
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  512 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 101 optimal weight:   20.0000
   chunk 55 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.131482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.081417 restraints weight = 17591.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.80
r_work: 0.3015 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10193  Z= 0.226
  Angle     :  0.590   5.901  14132  Z= 0.295
  Chirality :  0.038   0.153   1598
  Planarity :  0.005   0.056   1549
  Dihedral  : 18.560 128.068   2286
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 22.74 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.27), residues: 1007
  helix:  1.32 (0.27), residues: 371
  sheet: -0.43 (0.35), residues: 232
  loop : -1.19 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 547 
 HIS   0.003   0.001   HIS A 215 
 PHE   0.035   0.002   PHE A 340 
 TYR   0.010   0.001   TYR A 347 
 ARG   0.003   0.000   ARG B 485 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04370 (  445)
  hydrogen bonds       : angle       4.68429 ( 1194)
  covalent geometry    : bond        0.00532 (10193)
  covalent geometry    : angle       0.59027 (14132)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 1.065 
Fit side-chains
REVERT: A  285 THR cc_start: 0.8927 (m) cc_final: 0.8602 (p)
REVERT: A  477 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7914 (mtm-85)
REVERT: B  107 ASP cc_start: 0.8637 (t70) cc_final: 0.8312 (t0)
REVERT: B  123 ASP cc_start: 0.8277 (p0) cc_final: 0.7788 (p0)
REVERT: B  168 GLU cc_start: 0.8528 (pm20) cc_final: 0.8248 (pm20)
REVERT: B  195 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7288 (mp0)
REVERT: B  392 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7688 (mtp85)
REVERT: B  407 LYS cc_start: 0.9061 (mptt) cc_final: 0.8773 (tptt)
REVERT: B  566 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8801 (mm-30)
  outliers start: 31
  outliers final: 21
  residues processed: 106
  average time/residue: 0.1873
  time to fit residues: 29.7398
Evaluate side-chains
  101 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  195 GLU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  336 THR
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  392 ARG
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  512 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 69 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0870
   chunk 22 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.3927 r_free = 0.3927 target = 0.130915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.080914 restraints weight = 16665.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.97
r_work: 0.2959 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10193  Z= 0.109
  Angle     :  0.543   6.933  14132  Z= 0.268
  Chirality :  0.036   0.151   1598
  Planarity :  0.005   0.055   1549
  Dihedral  : 18.415 120.751   2286
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 23.86 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.27), residues: 1007
  helix:  1.46 (0.27), residues: 372
  sheet: -0.31 (0.36), residues: 227
  loop : -1.11 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 547 
 HIS   0.002   0.000   HIS A 476 
 PHE   0.026   0.001   PHE A 340 
 TYR   0.009   0.001   TYR A 316 
 ARG   0.004   0.000   ARG B 161 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03703 (  445)
  hydrogen bonds       : angle       4.41630 ( 1194)
  covalent geometry    : bond        0.00246 (10193)
  covalent geometry    : angle       0.54262 (14132)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.983 
Fit side-chains
REVERT: A  285 THR cc_start: 0.8749 (m) cc_final: 0.8512 (p)
REVERT: A  451 PHE cc_start: 0.8926 (m-80) cc_final: 0.8632 (m-80)
REVERT: A  477 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7650 (mtm-85)
REVERT: B  123 ASP cc_start: 0.8456 (p0) cc_final: 0.8004 (p0)
REVERT: B  168 GLU cc_start: 0.8516 (pm20) cc_final: 0.8198 (pm20)
REVERT: B  407 LYS cc_start: 0.8988 (mptt) cc_final: 0.8625 (tptt)
REVERT: B  566 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8759 (mm-30)
  outliers start: 21
  outliers final: 17
  residues processed: 98
  average time/residue: 0.1983
  time to fit residues: 29.6616
Evaluate side-chains
  93 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  336 THR
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  512 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 106 optimal weight:   30.0000
   chunk 93 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   chunk 19 optimal weight:    0.2980
   chunk 69 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.3944 r_free = 0.3944 target = 0.131518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.081611 restraints weight = 16701.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 2.93
r_work: 0.2932 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10193  Z= 0.121
  Angle     :  0.550   8.257  14132  Z= 0.270
  Chirality :  0.036   0.142   1598
  Planarity :  0.005   0.056   1549
  Dihedral  : 18.371 124.163   2286
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 23.97 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.27), residues: 1007
  helix:  1.51 (0.27), residues: 372
  sheet: -0.31 (0.36), residues: 227
  loop : -1.10 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 547 
 HIS   0.002   0.000   HIS A 476 
 PHE   0.026   0.001   PHE A 340 
 TYR   0.009   0.001   TYR A 499 
 ARG   0.002   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03732 (  445)
  hydrogen bonds       : angle       4.41418 ( 1194)
  covalent geometry    : bond        0.00279 (10193)
  covalent geometry    : angle       0.55043 (14132)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A  285 THR cc_start: 0.8759 (m) cc_final: 0.8468 (p)
REVERT: A  451 PHE cc_start: 0.8907 (m-80) cc_final: 0.8599 (m-80)
REVERT: A  477 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7646 (mtm-85)
REVERT: B  123 ASP cc_start: 0.8413 (p0) cc_final: 0.7974 (p0)
REVERT: B  168 GLU cc_start: 0.8531 (pm20) cc_final: 0.8205 (pm20)
REVERT: B  407 LYS cc_start: 0.9008 (mptt) cc_final: 0.8586 (tptt)
REVERT: B  434 CYS cc_start: 0.7383 (p) cc_final: 0.7110 (p)
  outliers start: 20
  outliers final: 18
  residues processed: 98
  average time/residue: 0.1806
  time to fit residues: 26.8481
Evaluate side-chains
  96 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  336 THR
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  512 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0870
   chunk 96 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 102 optimal weight:   10.0000
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.6360

-------------------------------------------------------------------------------
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 = 0.3951 r_free = 0.3951 target = 0.132075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.082320 restraints weight = 16593.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.94
r_work: 0.2968 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10193  Z= 0.113
  Angle     :  0.548   9.454  14132  Z= 0.268
  Chirality :  0.036   0.172   1598
  Planarity :  0.005   0.055   1549
  Dihedral  : 18.314 123.155   2286
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 23.86 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.27), residues: 1007
  helix:  1.50 (0.27), residues: 373
  sheet: -0.34 (0.36), residues: 227
  loop : -1.08 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 547 
 HIS   0.002   0.000   HIS A 476 
 PHE   0.026   0.001   PHE A 340 
 TYR   0.009   0.001   TYR A 499 
 ARG   0.005   0.000   ARG B 161 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03651 (  445)
  hydrogen bonds       : angle       4.36450 ( 1194)
  covalent geometry    : bond        0.00259 (10193)
  covalent geometry    : angle       0.54843 (14132)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 1.094 
Fit side-chains
REVERT: A  285 THR cc_start: 0.8788 (m) cc_final: 0.8493 (p)
REVERT: A  451 PHE cc_start: 0.8917 (m-80) cc_final: 0.8607 (m-80)
REVERT: A  477 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7659 (mtm-85)
REVERT: B  123 ASP cc_start: 0.8385 (p0) cc_final: 0.7937 (p0)
REVERT: B  168 GLU cc_start: 0.8552 (pm20) cc_final: 0.8226 (pm20)
REVERT: B  195 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7147 (mp0)
REVERT: B  407 LYS cc_start: 0.8976 (mptt) cc_final: 0.8554 (tptt)
REVERT: B  434 CYS cc_start: 0.7380 (p) cc_final: 0.7103 (p)
  outliers start: 20
  outliers final: 18
  residues processed: 98
  average time/residue: 0.1921
  time to fit residues: 28.6061
Evaluate side-chains
  97 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  195 GLU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  336 THR
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  512 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 99 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3920 r_free = 0.3920 target = 0.130405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.080488 restraints weight = 16625.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.95
r_work: 0.2948 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10193  Z= 0.136
  Angle     :  0.555   9.535  14132  Z= 0.273
  Chirality :  0.037   0.173   1598
  Planarity :  0.005   0.056   1549
  Dihedral  : 18.303 124.999   2286
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 23.75 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.27), residues: 1007
  helix:  1.50 (0.27), residues: 372
  sheet: -0.35 (0.36), residues: 227
  loop : -1.06 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 547 
 HIS   0.002   0.000   HIS A 133 
 PHE   0.028   0.001   PHE A 340 
 TYR   0.010   0.001   TYR A 499 
 ARG   0.002   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03780 (  445)
  hydrogen bonds       : angle       4.40400 ( 1194)
  covalent geometry    : bond        0.00319 (10193)
  covalent geometry    : angle       0.55464 (14132)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5155.36 seconds
wall clock time: 89 minutes 51.44 seconds (5391.44 seconds total)