Starting phenix.real_space_refine
on Sat Jul 26 14:04:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fxs_50853/07_2025/9fxs_50853.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fxs_50853/07_2025/9fxs_50853.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fxs_50853/07_2025/9fxs_50853.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fxs_50853/07_2025/9fxs_50853.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fxs_50853/07_2025/9fxs_50853.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fxs_50853/07_2025/9fxs_50853.cif"
  }
  resolution = 4.2
  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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    5369      2.51       5
     N    1511      2.21       5
     O    1628      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8535
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1037
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1037
          Classifications: {'peptide': 137}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 129}
    Chain: "C"
      Number of atoms: 1549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1549
          Classifications: {'peptide': 199}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 5084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 656, 5084
          Classifications: {'peptide': 656}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 24, 'TRANS': 631}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "I"
      Number of atoms: 865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 865
          Classifications: {'peptide': 114}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 107}
          Chain breaks: 4
  Time building chain proxies: 5.81, per 1000 atoms: 0.68
  Number of scatterers: 8535
  At special positions: 0
  Unit cell: (93.84, 80.58, 129.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1628      8.00
     N    1511      7.00
     C    5369      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  64 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 810 " - pdb=" SG  CYS D 832 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  24 " - pdb=" SG  CYS I  64 " 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=0, symmetry=0
  Time building additional restraints: 2.32
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2010

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 15 sheets defined
      4.4% alpha, 40.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 43 through 45
      No H-bonds generated for 'chain 'B' and resid 43 through 45'
    Processing helix  chain 'C' and resid 125 through 131
      removed outlier: 3.613A  pdb=" N   GLU C 129 " --> pdb=" O   GLN C 126 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS C 130 " --> pdb=" O   ALA C 127 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU C 131 " --> pdb=" O   ALA C 128 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 242 through 245
    Processing helix  chain 'D' and resid 360 through 362
      No H-bonds generated for 'chain 'D' and resid 360 through 362'
    Processing helix  chain 'D' and resid 443 through 448
      removed outlier: 3.612A  pdb=" N   THR D 448 " --> pdb=" O   ALA D 445 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 558 through 560
      No H-bonds generated for 'chain 'D' and resid 558 through 560'
    Processing helix  chain 'D' and resid 567 through 571
      removed outlier: 3.522A  pdb=" N   ARG D 570 " --> pdb=" O   SER D 567 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   HIS D 571 " --> pdb=" O   GLN D 568 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 567 through 571'
    Processing helix  chain 'D' and resid 782 through 784
      No H-bonds generated for 'chain 'D' and resid 782 through 784'
    Processing helix  chain 'I' and resid 30 through 32
      No H-bonds generated for 'chain 'I' and resid 30 through 32'
    Processing helix  chain 'I' and resid 65 through 71
    Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 41
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 33 through 41
    current: chain 'B' and resid 121 through 123
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 121 through 123
    current: chain 'I' and resid 9 through 20
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 55 through 64
      removed outlier: 5.970A  pdb=" N   GLY B 127 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 4
    Processing sheet with id=AA4, first strand: chain 'C' and resid 8 through 12
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 8 through 12
    current: chain 'C' and resid 54 through 58
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 54 through 58
    current: chain 'C' and resid 102 through 116
  WARNING: can't find start of bonding for strands!
    previous: chain 'I' and resid 34 through 36
    current: chain 'I' and resid 151 through 159
    Processing sheet with id=AA5, first strand: chain 'C' and resid 132 through 135
    Processing sheet with id=AA6, first strand: chain 'C' and resid 165 through 167
      removed outlier: 3.858A  pdb=" N   ALA C 165 " --> pdb=" O   VAL C 152 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU C 150 " --> pdb=" O   VAL C 167 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   LEU C 155 " --> pdb=" O   THR C 186 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   THR C 186 " --> pdb=" O   LEU C 155 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   TYR C 187 " --> pdb=" O   MET C 200 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   MET C 200 " --> pdb=" O   TYR C 187 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 139 through 152
      removed outlier: 4.430A  pdb=" N   SER D 147 " --> pdb=" O   TYR D 163 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   THR D 182 " --> pdb=" O   HIS D 200 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   HIS D 200 " --> pdb=" O   THR D 182 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   SER D 184 " --> pdb=" O   TRP D 198 " (cutoff:3.500A)
      removed outlier: 5.622A  pdb=" N   TRP D 198 " --> pdb=" O   SER D 184 " (cutoff:3.500A)
      removed outlier: 16.627A  pdb=" N   ILE D 201 " --> pdb=" O   TYR D 222 " (cutoff:3.500A)
      removed outlier: 10.899A  pdb=" N   TYR D 222 " --> pdb=" O   ILE D 201 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   THR D 203 " --> pdb=" O   ASP D 220 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLY D 219 " --> pdb=" O   GLY D 235 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 232 through 235
    current: chain 'D' and resid 329 through 338
      removed outlier: 4.441A  pdb=" N   THR D 354 " --> pdb=" O   SER D 332 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ALA D 377 " --> pdb=" O   GLN D 370 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   TYR D 375 " --> pdb=" O   ALA D 372 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   ARG D 481 " --> pdb=" O   SER D 437 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   THR D 506 " --> pdb=" O   ARG D 481 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   LYS D 483 " --> pdb=" O   HIS D 504 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   HIS D 504 " --> pdb=" O   LYS D 483 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   GLN D 485 " --> pdb=" O   GLY D 502 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   GLY D 502 " --> pdb=" O   GLN D 485 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   THR D 487 " --> pdb=" O   LEU D 500 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   LEU D 500 " --> pdb=" O   THR D 487 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   THR D 489 " --> pdb=" O   LEU D 498 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   LEU D 498 " --> pdb=" O   THR D 489 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   GLN D 491 " --> pdb=" O   SER D 496 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   SER D 496 " --> pdb=" O   GLN D 491 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLN D 505 " --> pdb=" O   ASP D 514 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ASP D 514 " --> pdb=" O   GLN D 505 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN D 539 " --> pdb=" O   GLY D 544 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLY D 544 " --> pdb=" O   ASN D 539 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   THR D 625 " --> pdb=" O   SER D 605 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ILE D 637 " --> pdb=" O   LEU D 626 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 259 through 260
    Processing sheet with id=AA9, first strand: chain 'D' and resid 274 through 280
      removed outlier: 3.969A  pdb=" N   TYR D 276 " --> pdb=" O   ILE D 268 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   PHE D 313 " --> pdb=" O   VAL D 301 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 700 through 702
      removed outlier: 3.960A  pdb=" N   VAL D 674 " --> pdb=" O   LEU D 702 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL D 673 " --> pdb=" O   VAL D 741 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   ALA D 743 " --> pdb=" O   VAL D 673 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   LEU D 675 " --> pdb=" O   ALA D 743 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 713 through 714
    Processing sheet with id=AB3, first strand: chain 'D' and resid 724 through 726
    Processing sheet with id=AB4, first strand: chain 'D' and resid 786 through 792
      removed outlier: 5.322A  pdb=" N   ILE D 751 " --> pdb=" O   GLY D 791 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LEU D 828 " --> pdb=" O   LEU D 754 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 778 through 780
      removed outlier: 3.612A  pdb=" N   GLY D 796 " --> pdb=" O   TYR D 814 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL D 798 " --> pdb=" O   ALA D 812 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ALA D 812 " --> pdb=" O   VAL D 798 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'I' and resid 25 through 28

    292 hydrogen bonds defined for protein.
    780 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: 2.90

  Time building geometry restraints manager: 2.76 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2858
        1.34 -     1.46: 1904
        1.46 -     1.58: 3901
        1.58 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 8711
  Sorted by residual:
  bond pdb=" CA  GLY D 387 "
       pdb=" C   GLY D 387 "
    ideal  model  delta    sigma   weight residual
    1.514  1.530 -0.016 1.41e-02 5.03e+03 1.30e+00
  bond pdb=" N   GLY D 387 "
       pdb=" CA  GLY D 387 "
    ideal  model  delta    sigma   weight residual
    1.449  1.464 -0.015 1.45e-02 4.76e+03 1.01e+00
  bond pdb=" C   LEU D 403 "
       pdb=" N   PRO D 404 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.19e-02 7.06e+03 7.22e-01
  bond pdb=" N   GLY D 148 "
       pdb=" CA  GLY D 148 "
    ideal  model  delta    sigma   weight residual
    1.456  1.446  0.009 1.16e-02 7.43e+03 6.19e-01
  bond pdb=" C   VAL D 432 "
       pdb=" N   GLY D 433 "
    ideal  model  delta    sigma   weight residual
    1.331  1.320  0.010 1.46e-02 4.69e+03 4.70e-01
  ... (remaining 8706 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 11498
        1.02 -     2.05: 256
        2.05 -     3.07: 66
        3.07 -     4.09: 11
        4.09 -     5.12: 3
  Bond angle restraints: 11834
  Sorted by residual:
  angle pdb=" C   ILE D 209 "
        pdb=" N   ILE D 210 "
        pdb=" CA  ILE D 210 "
      ideal   model   delta    sigma   weight residual
     120.33  123.82   -3.49 8.00e-01 1.56e+00 1.90e+01
  angle pdb=" N   GLY D 591 "
        pdb=" CA  GLY D 591 "
        pdb=" C   GLY D 591 "
      ideal   model   delta    sigma   weight residual
     110.80  115.41   -4.61 1.71e+00 3.42e-01 7.28e+00
  angle pdb=" C   ILE D 210 "
        pdb=" CA  ILE D 210 "
        pdb=" CB  ILE D 210 "
      ideal   model   delta    sigma   weight residual
     114.00  110.90    3.10 1.31e+00 5.83e-01 5.62e+00
  angle pdb=" C   ARG B  62 "
        pdb=" N   GLU B  63 "
        pdb=" CA  GLU B  63 "
      ideal   model   delta    sigma   weight residual
     121.54  125.63   -4.09 1.91e+00 2.74e-01 4.58e+00
  angle pdb=" C   VAL D 394 "
        pdb=" N   ASP D 395 "
        pdb=" CA  ASP D 395 "
      ideal   model   delta    sigma   weight residual
     121.75  118.11    3.64 1.73e+00 3.34e-01 4.43e+00
  ... (remaining 11829 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.26: 4725
       16.26 -    32.52: 335
       32.52 -    48.78: 62
       48.78 -    65.03: 23
       65.03 -    81.29: 2
  Dihedral angle restraints: 5147
    sinusoidal: 1997
      harmonic: 3150
  Sorted by residual:
  dihedral pdb=" CB  CYS D 810 "
           pdb=" SG  CYS D 810 "
           pdb=" SG  CYS D 832 "
           pdb=" CB  CYS D 832 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  142.96  -49.96     1      1.00e+01 1.00e-02 3.42e+01
  dihedral pdb=" CA  ASP C  26 "
           pdb=" CB  ASP C  26 "
           pdb=" CG  ASP C  26 "
           pdb=" OD1 ASP C  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.88   57.88     1      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" CA  ARG D 250 "
           pdb=" CB  ARG D 250 "
           pdb=" CG  ARG D 250 "
           pdb=" CD  ARG D 250 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.80  -58.20     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 5144 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 801
       0.027 -    0.053: 319
       0.053 -    0.080: 86
       0.080 -    0.106: 67
       0.106 -    0.133: 39
  Chirality restraints: 1312
  Sorted by residual:
  chirality pdb=" CA  ILE C  67 "
            pdb=" N   ILE C  67 "
            pdb=" C   ILE C  67 "
            pdb=" CB  ILE C  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CA  VAL D 394 "
            pdb=" N   VAL D 394 "
            pdb=" C   VAL D 394 "
            pdb=" CB  VAL D 394 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.85e-01
  chirality pdb=" CA  ILE D 128 "
            pdb=" N   ILE D 128 "
            pdb=" C   ILE D 128 "
            pdb=" CB  ILE D 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.84e-01
  ... (remaining 1309 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 146 "    0.021 5.00e-02 4.00e+02   3.16e-02 1.59e+00
        pdb=" N   PRO C 147 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO C 147 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 147 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 320 "    0.019 5.00e-02 4.00e+02   2.87e-02 1.31e+00
        pdb=" N   PRO D 321 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO D 321 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO D 321 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 197 "    0.017 5.00e-02 4.00e+02   2.61e-02 1.09e+00
        pdb=" N   PRO C 198 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO C 198 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C 198 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1118
        2.76 -     3.30: 7578
        3.30 -     3.83: 13892
        3.83 -     4.37: 15527
        4.37 -     4.90: 27654
  Nonbonded interactions: 65769
  Sorted by model distance:
  nonbonded pdb=" O   LEU I  61 "
            pdb=" OG1 THR I 129 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   LEU D 389 "
            pdb=" OH  TYR D 418 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   PHE D 252 "
            pdb=" OH  TYR D 317 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OE1 GLN D 647 "
            pdb=" OH  TYR D 649 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG  SER C 136 "
            pdb=" OG  SER C 139 "
     model   vdw
     2.283 3.040
  ... (remaining 65764 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.690
  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:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     24.910
  Find NCS groups from input model:        0.120
  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:             0.010
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
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      :  0.002   0.025   8714  Z= 0.088
  Angle     :  0.425   5.118  11840  Z= 0.235
  Chirality :  0.040   0.133   1312
  Planarity :  0.003   0.032   1548
  Dihedral  : 12.013  81.293   3128
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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:  0.42 (0.24), residues: 1072
  helix: -0.86 (1.64), residues: 13
  sheet:  0.66 (0.22), residues: 521
  loop :  0.03 (0.25), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 530 
 HIS   0.002   0.000   HIS B  46 
 PHE   0.008   0.001   PHE I 155 
 TYR   0.007   0.001   TYR D 650 
 ARG   0.002   0.000   ARG D 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12486 (  292)
  hydrogen bonds       : angle       6.24824 (  780)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       0.52691 (    6)
  covalent geometry    : bond        0.00171 ( 8711)
  covalent geometry    : angle       0.42458 (11834)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   33 MET cc_start: 0.8442 (ptt) cc_final: 0.8093 (ptt)
REVERT: B   43 ASN cc_start: 0.8859 (p0) cc_final: 0.8558 (p0)
REVERT: B   99 ASN cc_start: 0.9365 (m110) cc_final: 0.9120 (m110)
REVERT: B  136 LYS cc_start: 0.8826 (mttt) cc_final: 0.8568 (mtpt)
REVERT: C   17 GLN cc_start: 0.8885 (pm20) cc_final: 0.8670 (pm20)
REVERT: C   78 ASP cc_start: 0.7896 (p0) cc_final: 0.7543 (p0)
REVERT: C  154 GLU cc_start: 0.8670 (tt0) cc_final: 0.8364 (tt0)
REVERT: C  193 TYR cc_start: 0.8701 (m-10) cc_final: 0.8429 (m-10)
REVERT: D  209 ILE cc_start: 0.9170 (mt) cc_final: 0.8784 (mm)
REVERT: D  217 THR cc_start: 0.9187 (m) cc_final: 0.8951 (p)
REVERT: D  252 PHE cc_start: 0.9098 (t80) cc_final: 0.8637 (t80)
REVERT: D  273 TYR cc_start: 0.7505 (m-80) cc_final: 0.6813 (m-80)
REVERT: D  323 LEU cc_start: 0.9429 (mt) cc_final: 0.9209 (mt)
REVERT: D  350 PHE cc_start: 0.8865 (p90) cc_final: 0.8575 (p90)
REVERT: D  364 THR cc_start: 0.9523 (m) cc_final: 0.8866 (p)
REVERT: D  578 MET cc_start: 0.7686 (tpt) cc_final: 0.7388 (tpt)
REVERT: D  646 LYS cc_start: 0.8895 (mttt) cc_final: 0.8620 (mmtt)
REVERT: D  672 THR cc_start: 0.8091 (p) cc_final: 0.7731 (p)
REVERT: D  726 LEU cc_start: 0.9445 (mt) cc_final: 0.9157 (mp)
REVERT: D  790 SER cc_start: 0.8393 (t) cc_final: 0.7899 (p)
REVERT: D  816 LEU cc_start: 0.7382 (mt) cc_final: 0.6970 (mt)
REVERT: I   27 GLU cc_start: 0.8844 (pm20) cc_final: 0.8462 (pm20)
REVERT: I  130 SER cc_start: 0.8408 (p) cc_final: 0.8049 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.2200
  time to fit residues: 86.3411
Evaluate side-chains
  182 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
B  46 HIS
D 385 ASN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 516 GLN
D 554 ASN
** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  14 GLN
I  32 GLN
I  77 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.087202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.071996 restraints weight = 29015.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.074110 restraints weight = 15931.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.075502 restraints weight = 10535.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   8714  Z= 0.261
  Angle     :  0.614   7.061  11840  Z= 0.321
  Chirality :  0.042   0.146   1312
  Planarity :  0.005   0.048   1548
  Dihedral  :  3.811  15.271   1200
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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:  0.26 (0.25), residues: 1072
  helix: -1.83 (1.50), residues: 13
  sheet:  0.54 (0.22), residues: 520
  loop : -0.04 (0.26), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 530 
 HIS   0.005   0.001   HIS D 580 
 PHE   0.012   0.002   PHE I  76 
 TYR   0.020   0.002   TYR C 149 
 ARG   0.005   0.001   ARG D 481 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03630 (  292)
  hydrogen bonds       : angle       5.72765 (  780)
  SS BOND              : bond        0.00935 (    3)
  SS BOND              : angle       1.30729 (    6)
  covalent geometry    : bond        0.00563 ( 8711)
  covalent geometry    : angle       0.61371 (11834)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 GLN cc_start: 0.8818 (mm-40) cc_final: 0.7734 (mm-40)
REVERT: B   33 MET cc_start: 0.8211 (ptt) cc_final: 0.7755 (ptp)
REVERT: B   50 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7257 (mt-10)
REVERT: B   51 ASP cc_start: 0.8430 (p0) cc_final: 0.8095 (p0)
REVERT: B   62 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7661 (mmm160)
REVERT: B   99 ASN cc_start: 0.9409 (m110) cc_final: 0.9078 (m110)
REVERT: B  106 ASP cc_start: 0.9148 (p0) cc_final: 0.8736 (p0)
REVERT: B  120 ASN cc_start: 0.8820 (m-40) cc_final: 0.8484 (t0)
REVERT: B  123 ARG cc_start: 0.7571 (mpt90) cc_final: 0.7260 (mmt180)
REVERT: B  128 SER cc_start: 0.8749 (p) cc_final: 0.8294 (m)
REVERT: B  133 PHE cc_start: 0.9195 (m-80) cc_final: 0.8988 (m-80)
REVERT: B  136 LYS cc_start: 0.8737 (mttt) cc_final: 0.8476 (mtpt)
REVERT: C   78 ASP cc_start: 0.8002 (p0) cc_final: 0.7616 (p0)
REVERT: C  154 GLU cc_start: 0.8703 (tt0) cc_final: 0.8481 (tt0)
REVERT: C  193 TYR cc_start: 0.8750 (m-10) cc_final: 0.8514 (m-10)
REVERT: D  244 MET cc_start: 0.8600 (mmm) cc_final: 0.8383 (mmm)
REVERT: D  273 TYR cc_start: 0.7990 (m-80) cc_final: 0.7307 (m-80)
REVERT: D  323 LEU cc_start: 0.9410 (mt) cc_final: 0.8787 (tp)
REVERT: D  548 MET cc_start: 0.8457 (tpt) cc_final: 0.8105 (tpp)
REVERT: D  578 MET cc_start: 0.8008 (tpt) cc_final: 0.7626 (tpt)
REVERT: D  646 LYS cc_start: 0.8976 (mttt) cc_final: 0.8736 (mmtt)
REVERT: D  695 ASP cc_start: 0.8207 (p0) cc_final: 0.7921 (p0)
REVERT: D  716 ASP cc_start: 0.9142 (t0) cc_final: 0.8650 (t0)
REVERT: D  790 SER cc_start: 0.8367 (t) cc_final: 0.8101 (p)
REVERT: I   27 GLU cc_start: 0.8849 (pm20) cc_final: 0.8510 (pm20)
REVERT: I   76 PHE cc_start: 0.8089 (m-80) cc_final: 0.6700 (m-80)
REVERT: I  130 SER cc_start: 0.8539 (p) cc_final: 0.8100 (t)
REVERT: I  136 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7890 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.2069
  time to fit residues: 55.1074
Evaluate side-chains
  148 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 76 optimal weight:    0.0570
   chunk 95 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 96 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   chunk 46 optimal weight:   10.0000
   chunk 92 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0270
   chunk 30 optimal weight:    0.0040
   overall best weight:    0.4170

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

Flipped N/Q/H residues before XYZ refinement:
B 115 ASN
D 385 ASN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.089469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.074072 restraints weight = 28810.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.076329 restraints weight = 15596.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.077829 restraints weight = 10158.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.067   8714  Z= 0.105
  Angle     :  0.538   8.288  11840  Z= 0.278
  Chirality :  0.043   0.142   1312
  Planarity :  0.004   0.041   1548
  Dihedral  :  3.545  23.746   1200
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.32 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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:  0.25 (0.25), residues: 1072
  helix: -2.03 (1.23), residues: 13
  sheet:  0.57 (0.23), residues: 524
  loop : -0.09 (0.25), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 530 
 HIS   0.003   0.001   HIS D 200 
 PHE   0.012   0.001   PHE D 416 
 TYR   0.012   0.001   TYR D 366 
 ARG   0.003   0.000   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02950 (  292)
  hydrogen bonds       : angle       5.44644 (  780)
  SS BOND              : bond        0.00395 (    3)
  SS BOND              : angle       3.46392 (    6)
  covalent geometry    : bond        0.00239 ( 8711)
  covalent geometry    : angle       0.53265 (11834)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9293 (ptpt) cc_final: 0.9062 (pttt)
REVERT: B   33 MET cc_start: 0.8150 (ptt) cc_final: 0.7809 (ptp)
REVERT: B   42 SER cc_start: 0.9340 (p) cc_final: 0.9081 (p)
REVERT: B  106 ASP cc_start: 0.8961 (p0) cc_final: 0.8588 (p0)
REVERT: B  123 ARG cc_start: 0.7685 (mpt90) cc_final: 0.7389 (mpt90)
REVERT: B  133 PHE cc_start: 0.9202 (m-80) cc_final: 0.8953 (m-80)
REVERT: B  136 LYS cc_start: 0.8707 (mttt) cc_final: 0.8444 (mtpt)
REVERT: C   34 GLN cc_start: 0.8801 (tt0) cc_final: 0.8491 (tt0)
REVERT: C   78 ASP cc_start: 0.8037 (p0) cc_final: 0.7685 (p0)
REVERT: C   81 SER cc_start: 0.9026 (m) cc_final: 0.8405 (t)
REVERT: C  154 GLU cc_start: 0.8777 (tt0) cc_final: 0.8518 (tt0)
REVERT: C  193 TYR cc_start: 0.8721 (m-10) cc_final: 0.8447 (m-10)
REVERT: D  273 TYR cc_start: 0.7882 (m-80) cc_final: 0.7357 (m-80)
REVERT: D  350 PHE cc_start: 0.8816 (p90) cc_final: 0.8585 (p90)
REVERT: D  483 LYS cc_start: 0.9501 (ttmt) cc_final: 0.9285 (tptm)
REVERT: D  578 MET cc_start: 0.7831 (tpt) cc_final: 0.7433 (tpt)
REVERT: D  646 LYS cc_start: 0.8963 (mttt) cc_final: 0.8688 (mmtt)
REVERT: D  695 ASP cc_start: 0.8142 (p0) cc_final: 0.7879 (p0)
REVERT: D  716 ASP cc_start: 0.8812 (t0) cc_final: 0.8499 (t0)
REVERT: D  719 THR cc_start: 0.8901 (p) cc_final: 0.8127 (p)
REVERT: D  726 LEU cc_start: 0.9459 (mt) cc_final: 0.9137 (mp)
REVERT: I   76 PHE cc_start: 0.8416 (m-80) cc_final: 0.7913 (m-80)
REVERT: I  130 SER cc_start: 0.8504 (p) cc_final: 0.8004 (t)
REVERT: I  136 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7872 (mmmt)
  outliers start: 1
  outliers final: 1
  residues processed: 209
  average time/residue: 0.2091
  time to fit residues: 59.8357
Evaluate side-chains
  153 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0050
   chunk 24 optimal weight:    0.0040
   chunk 25 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 104 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    1.4010

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

Flipped N/Q/H residues before XYZ refinement:
B  99 ASN
B 120 ASN
D 385 ASN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 600 ASN
** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  77 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.087686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.072404 restraints weight = 29311.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.074585 restraints weight = 15812.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.076039 restraints weight = 10332.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8714  Z= 0.149
  Angle     :  0.518   6.289  11840  Z= 0.272
  Chirality :  0.042   0.191   1312
  Planarity :  0.003   0.037   1548
  Dihedral  :  3.561  15.094   1200
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.88 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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:  0.22 (0.25), residues: 1072
  helix: -2.33 (1.19), residues: 14
  sheet:  0.53 (0.23), residues: 528
  loop : -0.07 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 530 
 HIS   0.002   0.001   HIS I 132 
 PHE   0.017   0.001   PHE I 155 
 TYR   0.011   0.001   TYR D 276 
 ARG   0.002   0.000   ARG D 451 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03007 (  292)
  hydrogen bonds       : angle       5.43944 (  780)
  SS BOND              : bond        0.01251 (    3)
  SS BOND              : angle       0.93296 (    6)
  covalent geometry    : bond        0.00326 ( 8711)
  covalent geometry    : angle       0.51793 (11834)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9300 (ptpt) cc_final: 0.9047 (pttt)
REVERT: B   33 MET cc_start: 0.7982 (ptt) cc_final: 0.7695 (ptp)
REVERT: B   99 ASN cc_start: 0.9327 (m-40) cc_final: 0.9058 (m110)
REVERT: B  106 ASP cc_start: 0.8990 (p0) cc_final: 0.8049 (p0)
REVERT: B  108 GLU cc_start: 0.9137 (pt0) cc_final: 0.8562 (pm20)
REVERT: B  123 ARG cc_start: 0.7726 (mpt90) cc_final: 0.7380 (mpt90)
REVERT: B  128 SER cc_start: 0.8725 (p) cc_final: 0.8492 (m)
REVERT: B  133 PHE cc_start: 0.9256 (m-80) cc_final: 0.8933 (m-80)
REVERT: B  136 LYS cc_start: 0.8747 (mttt) cc_final: 0.8508 (mtpt)
REVERT: C   26 ASP cc_start: 0.8111 (t0) cc_final: 0.7905 (t0)
REVERT: C   34 GLN cc_start: 0.8850 (tt0) cc_final: 0.8534 (tt0)
REVERT: C   78 ASP cc_start: 0.8061 (p0) cc_final: 0.7678 (p0)
REVERT: C  154 GLU cc_start: 0.8805 (tt0) cc_final: 0.8535 (tt0)
REVERT: D  273 TYR cc_start: 0.8175 (m-80) cc_final: 0.7355 (m-80)
REVERT: D  350 PHE cc_start: 0.8842 (p90) cc_final: 0.8573 (p90)
REVERT: D  483 LYS cc_start: 0.9518 (ttmt) cc_final: 0.9289 (tptm)
REVERT: D  578 MET cc_start: 0.7676 (tpt) cc_final: 0.7240 (tpt)
REVERT: D  646 LYS cc_start: 0.9007 (mttt) cc_final: 0.8743 (mmtt)
REVERT: D  695 ASP cc_start: 0.8236 (p0) cc_final: 0.7949 (p0)
REVERT: D  716 ASP cc_start: 0.8924 (t0) cc_final: 0.8470 (t0)
REVERT: I   13 MET cc_start: 0.8191 (mmm) cc_final: 0.7938 (mmt)
REVERT: I  130 SER cc_start: 0.8570 (p) cc_final: 0.8096 (t)
REVERT: I  136 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7781 (mmmt)
  outliers start: 1
  outliers final: 1
  residues processed: 193
  average time/residue: 0.2011
  time to fit residues: 53.3081
Evaluate side-chains
  151 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 66 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0060
   chunk 56 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    2.8004

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

Flipped N/Q/H residues before XYZ refinement:
D 385 ASN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 491 GLN
** D 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  32 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.084055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.069267 restraints weight = 30041.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.071190 restraints weight = 17175.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.072516 restraints weight = 11642.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   8714  Z= 0.263
  Angle     :  0.646   8.618  11840  Z= 0.336
  Chirality :  0.043   0.149   1312
  Planarity :  0.005   0.081   1548
  Dihedral  :  4.140  19.062   1200
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -0.08 (0.25), residues: 1072
  helix: -2.34 (1.26), residues: 14
  sheet:  0.32 (0.22), residues: 515
  loop : -0.26 (0.25), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 530 
 HIS   0.004   0.001   HIS I  60 
 PHE   0.014   0.002   PHE D 228 
 TYR   0.014   0.002   TYR D 418 
 ARG   0.005   0.001   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03555 (  292)
  hydrogen bonds       : angle       5.85611 (  780)
  SS BOND              : bond        0.00762 (    3)
  SS BOND              : angle       0.82643 (    6)
  covalent geometry    : bond        0.00575 ( 8711)
  covalent geometry    : angle       0.64564 (11834)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9343 (ptpt) cc_final: 0.9075 (pttt)
REVERT: B   41 SER cc_start: 0.7655 (t) cc_final: 0.7361 (t)
REVERT: B   99 ASN cc_start: 0.9363 (m-40) cc_final: 0.8998 (m110)
REVERT: B  106 ASP cc_start: 0.8955 (p0) cc_final: 0.8707 (p0)
REVERT: B  128 SER cc_start: 0.8711 (p) cc_final: 0.8363 (m)
REVERT: B  133 PHE cc_start: 0.9370 (m-80) cc_final: 0.9115 (m-80)
REVERT: B  143 ARG cc_start: 0.8386 (mpt180) cc_final: 0.8173 (mmt180)
REVERT: C   19 GLN cc_start: 0.8866 (pm20) cc_final: 0.8663 (pm20)
REVERT: C   26 ASP cc_start: 0.8059 (t0) cc_final: 0.7845 (t70)
REVERT: C   34 GLN cc_start: 0.8927 (tt0) cc_final: 0.8404 (tt0)
REVERT: C   69 ASP cc_start: 0.8180 (p0) cc_final: 0.7967 (p0)
REVERT: C   78 ASP cc_start: 0.8105 (p0) cc_final: 0.7760 (p0)
REVERT: C  154 GLU cc_start: 0.8791 (tt0) cc_final: 0.8530 (tt0)
REVERT: D  273 TYR cc_start: 0.8228 (m-80) cc_final: 0.7691 (m-80)
REVERT: D  578 MET cc_start: 0.7838 (tpt) cc_final: 0.7203 (tpp)
REVERT: D  626 LEU cc_start: 0.9190 (mm) cc_final: 0.8947 (pp)
REVERT: D  646 LYS cc_start: 0.9087 (mttt) cc_final: 0.8809 (mmtt)
REVERT: D  695 ASP cc_start: 0.8290 (p0) cc_final: 0.8014 (p0)
REVERT: D  716 ASP cc_start: 0.9153 (t0) cc_final: 0.8728 (t0)
REVERT: D  717 THR cc_start: 0.8499 (p) cc_final: 0.7975 (t)
REVERT: I   40 ILE cc_start: 0.7625 (pt) cc_final: 0.7415 (pt)
REVERT: I  130 SER cc_start: 0.8707 (p) cc_final: 0.8306 (t)
REVERT: I  160 GLN cc_start: 0.8188 (mt0) cc_final: 0.7694 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.2181
  time to fit residues: 55.1645
Evaluate side-chains
  138 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 57 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 120 ASN
D 342 ASN
D 385 ASN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 670 ASN
I  77 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.085359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.070400 restraints weight = 29573.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.072489 restraints weight = 16133.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.073892 restraints weight = 10603.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8714  Z= 0.160
  Angle     :  0.557   6.569  11840  Z= 0.292
  Chirality :  0.042   0.140   1312
  Planarity :  0.004   0.061   1548
  Dihedral  :  3.897  15.856   1200
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.55 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -0.10 (0.25), residues: 1072
  helix: -2.66 (1.12), residues: 14
  sheet:  0.37 (0.22), residues: 511
  loop : -0.34 (0.25), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 530 
 HIS   0.002   0.001   HIS I  60 
 PHE   0.017   0.001   PHE B  57 
 TYR   0.017   0.001   TYR D 441 
 ARG   0.006   0.000   ARG D 215 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03088 (  292)
  hydrogen bonds       : angle       5.71362 (  780)
  SS BOND              : bond        0.00343 (    3)
  SS BOND              : angle       1.26033 (    6)
  covalent geometry    : bond        0.00355 ( 8711)
  covalent geometry    : angle       0.55660 (11834)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9340 (ptpt) cc_final: 0.9058 (pttt)
REVERT: B   33 MET cc_start: 0.8387 (ptp) cc_final: 0.7585 (ptp)
REVERT: B   37 MET cc_start: 0.8368 (mpp) cc_final: 0.8156 (mpp)
REVERT: B   42 SER cc_start: 0.9220 (p) cc_final: 0.9006 (t)
REVERT: B   99 ASN cc_start: 0.9361 (m-40) cc_final: 0.9032 (m110)
REVERT: B  106 ASP cc_start: 0.9045 (p0) cc_final: 0.8176 (p0)
REVERT: B  107 ASP cc_start: 0.9207 (p0) cc_final: 0.8976 (p0)
REVERT: B  108 GLU cc_start: 0.9108 (pt0) cc_final: 0.8583 (pm20)
REVERT: B  128 SER cc_start: 0.8786 (p) cc_final: 0.8482 (m)
REVERT: B  133 PHE cc_start: 0.9391 (m-80) cc_final: 0.9020 (m-80)
REVERT: C   19 GLN cc_start: 0.8828 (pm20) cc_final: 0.8578 (pm20)
REVERT: C   34 GLN cc_start: 0.8801 (tt0) cc_final: 0.8383 (tt0)
REVERT: C   78 ASP cc_start: 0.8029 (p0) cc_final: 0.7620 (p0)
REVERT: C   81 SER cc_start: 0.9117 (m) cc_final: 0.8331 (t)
REVERT: C  154 GLU cc_start: 0.8882 (tt0) cc_final: 0.8537 (tt0)
REVERT: D  273 TYR cc_start: 0.8285 (m-80) cc_final: 0.7702 (m-80)
REVERT: D  578 MET cc_start: 0.7778 (tpt) cc_final: 0.7139 (tpp)
REVERT: D  637 ILE cc_start: 0.9437 (mm) cc_final: 0.9229 (mm)
REVERT: D  646 LYS cc_start: 0.9149 (mttt) cc_final: 0.8916 (mmtt)
REVERT: D  695 ASP cc_start: 0.8320 (p0) cc_final: 0.7997 (p0)
REVERT: D  716 ASP cc_start: 0.9165 (t0) cc_final: 0.8687 (t0)
REVERT: D  717 THR cc_start: 0.8483 (p) cc_final: 0.7972 (t)
REVERT: I  130 SER cc_start: 0.8686 (p) cc_final: 0.8312 (t)
REVERT: I  136 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8039 (mmmt)
  outliers start: 1
  outliers final: 1
  residues processed: 184
  average time/residue: 0.2079
  time to fit residues: 52.7281
Evaluate side-chains
  147 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 80 optimal weight:    6.9990
   chunk 79 optimal weight:    8.9990
   chunk 61 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 107 optimal weight:   10.0000
   chunk 58 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0060
   chunk 11 optimal weight:    0.0570
   chunk 42 optimal weight:    2.9990
   chunk 73 optimal weight:   20.0000
   overall best weight:    1.7518

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

Flipped N/Q/H residues before XYZ refinement:
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 385 ASN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 516 GLN
** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 670 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.084858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.069911 restraints weight = 29801.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.071872 restraints weight = 16610.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.073231 restraints weight = 11134.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.3621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8714  Z= 0.174
  Angle     :  0.568   8.568  11840  Z= 0.295
  Chirality :  0.042   0.148   1312
  Planarity :  0.004   0.039   1548
  Dihedral  :  3.932  17.028   1200
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -0.16 (0.25), residues: 1072
  helix: -2.51 (1.17), residues: 14
  sheet:  0.30 (0.23), residues: 512
  loop : -0.35 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 530 
 HIS   0.003   0.001   HIS I  60 
 PHE   0.016   0.002   PHE B  57 
 TYR   0.013   0.001   TYR D 276 
 ARG   0.005   0.000   ARG D 215 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03099 (  292)
  hydrogen bonds       : angle       5.73038 (  780)
  SS BOND              : bond        0.00416 (    3)
  SS BOND              : angle       0.93910 (    6)
  covalent geometry    : bond        0.00385 ( 8711)
  covalent geometry    : angle       0.56780 (11834)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9268 (ptpt) cc_final: 0.8996 (pttt)
REVERT: B   33 MET cc_start: 0.8346 (ptp) cc_final: 0.7911 (ptp)
REVERT: B   37 MET cc_start: 0.8434 (mpp) cc_final: 0.8218 (mpp)
REVERT: B   41 SER cc_start: 0.7721 (t) cc_final: 0.7300 (t)
REVERT: B   99 ASN cc_start: 0.9332 (m-40) cc_final: 0.9052 (m110)
REVERT: B  106 ASP cc_start: 0.8990 (p0) cc_final: 0.8173 (p0)
REVERT: B  107 ASP cc_start: 0.9206 (p0) cc_final: 0.8993 (p0)
REVERT: B  108 GLU cc_start: 0.9122 (pt0) cc_final: 0.8596 (pm20)
REVERT: B  128 SER cc_start: 0.8752 (p) cc_final: 0.8430 (m)
REVERT: B  133 PHE cc_start: 0.9403 (m-80) cc_final: 0.9004 (m-80)
REVERT: C   19 GLN cc_start: 0.8862 (pm20) cc_final: 0.8638 (pm20)
REVERT: C   26 ASP cc_start: 0.7927 (t0) cc_final: 0.7720 (t70)
REVERT: C   34 GLN cc_start: 0.8697 (tt0) cc_final: 0.8306 (tt0)
REVERT: C   69 ASP cc_start: 0.8079 (p0) cc_final: 0.7831 (p0)
REVERT: C   78 ASP cc_start: 0.8019 (p0) cc_final: 0.7615 (p0)
REVERT: C   81 SER cc_start: 0.9094 (m) cc_final: 0.8275 (t)
REVERT: C  154 GLU cc_start: 0.8809 (tt0) cc_final: 0.8506 (tt0)
REVERT: D  244 MET cc_start: 0.8745 (mmm) cc_final: 0.8525 (mmm)
REVERT: D  578 MET cc_start: 0.7815 (tpt) cc_final: 0.7160 (tpp)
REVERT: D  626 LEU cc_start: 0.8962 (pp) cc_final: 0.8671 (pp)
REVERT: D  695 ASP cc_start: 0.8244 (p0) cc_final: 0.7920 (p0)
REVERT: D  716 ASP cc_start: 0.9120 (t0) cc_final: 0.8711 (t0)
REVERT: D  717 THR cc_start: 0.8573 (p) cc_final: 0.8061 (t)
REVERT: I  130 SER cc_start: 0.8735 (p) cc_final: 0.8384 (t)
REVERT: I  136 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8074 (mmmt)
REVERT: I  160 GLN cc_start: 0.8079 (mt0) cc_final: 0.7401 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.2168
  time to fit residues: 54.2300
Evaluate side-chains
  143 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 105 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
D 385 ASN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 670 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.083845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.068882 restraints weight = 30439.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.070852 restraints weight = 16764.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.072220 restraints weight = 11174.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.3881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   8714  Z= 0.242
  Angle     :  0.629   7.052  11840  Z= 0.327
  Chirality :  0.043   0.143   1312
  Planarity :  0.004   0.038   1548
  Dihedral  :  4.243  20.986   1200
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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 (0.25), residues: 1072
  helix: -2.94 (1.09), residues: 14
  sheet:  0.11 (0.22), residues: 522
  loop : -0.34 (0.25), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 530 
 HIS   0.003   0.001   HIS D 580 
 PHE   0.017   0.002   PHE B  57 
 TYR   0.015   0.002   TYR D 418 
 ARG   0.007   0.001   ARG D 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03297 (  292)
  hydrogen bonds       : angle       5.97335 (  780)
  SS BOND              : bond        0.00389 (    3)
  SS BOND              : angle       1.22203 (    6)
  covalent geometry    : bond        0.00532 ( 8711)
  covalent geometry    : angle       0.62840 (11834)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9279 (ptpt) cc_final: 0.9017 (pttt)
REVERT: B   37 MET cc_start: 0.8485 (mpp) cc_final: 0.8225 (mpp)
REVERT: B   83 LYS cc_start: 0.7842 (ttmt) cc_final: 0.7624 (ttmt)
REVERT: B   99 ASN cc_start: 0.9314 (m-40) cc_final: 0.9045 (m-40)
REVERT: B  106 ASP cc_start: 0.9003 (p0) cc_final: 0.8183 (p0)
REVERT: B  107 ASP cc_start: 0.9233 (p0) cc_final: 0.9008 (p0)
REVERT: B  108 GLU cc_start: 0.9142 (pt0) cc_final: 0.8582 (pm20)
REVERT: B  128 SER cc_start: 0.8764 (p) cc_final: 0.8470 (m)
REVERT: B  133 PHE cc_start: 0.9470 (m-80) cc_final: 0.9078 (m-80)
REVERT: C   19 GLN cc_start: 0.8959 (pm20) cc_final: 0.8704 (pm20)
REVERT: C   34 GLN cc_start: 0.8691 (tt0) cc_final: 0.8312 (tt0)
REVERT: C   69 ASP cc_start: 0.8080 (p0) cc_final: 0.7852 (p0)
REVERT: C   78 ASP cc_start: 0.8095 (p0) cc_final: 0.7753 (p0)
REVERT: C   81 SER cc_start: 0.9197 (m) cc_final: 0.8404 (t)
REVERT: C  154 GLU cc_start: 0.8863 (tt0) cc_final: 0.8603 (tt0)
REVERT: D  244 MET cc_start: 0.8753 (mmm) cc_final: 0.8543 (mmm)
REVERT: D  578 MET cc_start: 0.7839 (tpt) cc_final: 0.7223 (tpp)
REVERT: D  626 LEU cc_start: 0.8962 (pp) cc_final: 0.8639 (pp)
REVERT: D  695 ASP cc_start: 0.8352 (p0) cc_final: 0.8026 (p0)
REVERT: D  716 ASP cc_start: 0.9154 (t0) cc_final: 0.8785 (t0)
REVERT: I   27 GLU cc_start: 0.8473 (pm20) cc_final: 0.8203 (pm20)
REVERT: I   31 LYS cc_start: 0.8629 (tmtt) cc_final: 0.8394 (tmtt)
REVERT: I  130 SER cc_start: 0.8785 (p) cc_final: 0.8432 (t)
REVERT: I  136 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8031 (mmmt)
REVERT: I  160 GLN cc_start: 0.8220 (mt0) cc_final: 0.7753 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.2135
  time to fit residues: 50.3655
Evaluate side-chains
  131 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 96 optimal weight:    0.0470
   chunk 48 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 76 optimal weight:    9.9990
   chunk 9 optimal weight:    6.9990
   chunk 103 optimal weight:    9.9990
   overall best weight:    3.0084

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

Flipped N/Q/H residues before XYZ refinement:
D 342 ASN
D 385 ASN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 670 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.082760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.067811 restraints weight = 31529.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.069793 restraints weight = 17628.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.071130 restraints weight = 11783.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.4095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064   8714  Z= 0.272
  Angle     :  0.650   6.992  11840  Z= 0.338
  Chirality :  0.043   0.157   1312
  Planarity :  0.004   0.038   1548
  Dihedral  :  4.436  24.879   1200
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -0.48 (0.25), residues: 1072
  helix: -2.76 (1.14), residues: 14
  sheet: -0.05 (0.23), residues: 522
  loop : -0.40 (0.25), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 204 
 HIS   0.003   0.001   HIS D 200 
 PHE   0.023   0.002   PHE D 525 
 TYR   0.019   0.002   TYR D 441 
 ARG   0.004   0.001   ARG D 481 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03426 (  292)
  hydrogen bonds       : angle       6.13297 (  780)
  SS BOND              : bond        0.00402 (    3)
  SS BOND              : angle       1.01956 (    6)
  covalent geometry    : bond        0.00597 ( 8711)
  covalent geometry    : angle       0.64956 (11834)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9273 (ptpt) cc_final: 0.9000 (pttt)
REVERT: B   37 MET cc_start: 0.8450 (mpp) cc_final: 0.8237 (mpp)
REVERT: B   41 SER cc_start: 0.7665 (t) cc_final: 0.7149 (t)
REVERT: B   83 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7625 (ttmt)
REVERT: B   99 ASN cc_start: 0.9362 (m-40) cc_final: 0.9086 (m-40)
REVERT: B  106 ASP cc_start: 0.9022 (p0) cc_final: 0.8726 (p0)
REVERT: B  108 GLU cc_start: 0.9154 (pt0) cc_final: 0.8743 (pt0)
REVERT: B  128 SER cc_start: 0.8795 (p) cc_final: 0.8466 (m)
REVERT: C   19 GLN cc_start: 0.9027 (pm20) cc_final: 0.8789 (pm20)
REVERT: C   34 GLN cc_start: 0.8724 (tt0) cc_final: 0.8298 (tt0)
REVERT: C   69 ASP cc_start: 0.8043 (p0) cc_final: 0.7834 (p0)
REVERT: C   78 ASP cc_start: 0.8141 (p0) cc_final: 0.7837 (p0)
REVERT: C  154 GLU cc_start: 0.8863 (tt0) cc_final: 0.8560 (tt0)
REVERT: D  448 THR cc_start: 0.9462 (p) cc_final: 0.8636 (p)
REVERT: D  578 MET cc_start: 0.7916 (tpt) cc_final: 0.7232 (tpp)
REVERT: D  626 LEU cc_start: 0.8997 (pp) cc_final: 0.8671 (pp)
REVERT: D  695 ASP cc_start: 0.8402 (p0) cc_final: 0.8072 (p0)
REVERT: D  716 ASP cc_start: 0.9173 (t0) cc_final: 0.8823 (t0)
REVERT: I   31 LYS cc_start: 0.8562 (tmtt) cc_final: 0.8344 (tmtt)
REVERT: I  136 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8014 (mmmt)
REVERT: I  155 PHE cc_start: 0.8997 (m-80) cc_final: 0.8794 (m-80)
REVERT: I  160 GLN cc_start: 0.8306 (mt0) cc_final: 0.7831 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.2334
  time to fit residues: 52.6087
Evaluate side-chains
  128 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 28 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 73 optimal weight:   20.0000
   chunk 58 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 143 ASN
D 385 ASN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 670 ASN
I 150 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.084474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.069637 restraints weight = 30698.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.071671 restraints weight = 16914.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.073020 restraints weight = 11247.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8714  Z= 0.152
  Angle     :  0.581   7.228  11840  Z= 0.303
  Chirality :  0.043   0.164   1312
  Planarity :  0.004   0.041   1548
  Dihedral  :  4.195  26.658   1200
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.33 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -0.34 (0.25), residues: 1072
  helix: -2.46 (1.19), residues: 14
  sheet:  0.14 (0.23), residues: 512
  loop : -0.42 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 204 
 HIS   0.003   0.001   HIS D 328 
 PHE   0.022   0.002   PHE D 525 
 TYR   0.010   0.001   TYR D 418 
 ARG   0.005   0.000   ARG I  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02955 (  292)
  hydrogen bonds       : angle       6.00398 (  780)
  SS BOND              : bond        0.00263 (    3)
  SS BOND              : angle       1.22432 (    6)
  covalent geometry    : bond        0.00341 ( 8711)
  covalent geometry    : angle       0.58035 (11834)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9211 (ptpt) cc_final: 0.8949 (pttt)
REVERT: B   37 MET cc_start: 0.8428 (mpp) cc_final: 0.8178 (mpp)
REVERT: B   41 SER cc_start: 0.7788 (t) cc_final: 0.7441 (t)
REVERT: B   99 ASN cc_start: 0.9292 (m-40) cc_final: 0.9068 (m110)
REVERT: B  106 ASP cc_start: 0.9083 (p0) cc_final: 0.8726 (p0)
REVERT: B  123 ARG cc_start: 0.8076 (mpt90) cc_final: 0.7781 (mmt180)
REVERT: B  128 SER cc_start: 0.8731 (p) cc_final: 0.8420 (m)
REVERT: C   19 GLN cc_start: 0.9012 (pm20) cc_final: 0.8789 (pm20)
REVERT: C   34 GLN cc_start: 0.8601 (tt0) cc_final: 0.8194 (tt0)
REVERT: C   78 ASP cc_start: 0.8057 (p0) cc_final: 0.7733 (p0)
REVERT: C   81 SER cc_start: 0.9161 (m) cc_final: 0.8278 (t)
REVERT: D  143 ASN cc_start: 0.9378 (OUTLIER) cc_final: 0.9062 (t0)
REVERT: D  578 MET cc_start: 0.7885 (tpt) cc_final: 0.7224 (tpp)
REVERT: D  626 LEU cc_start: 0.8939 (pp) cc_final: 0.8621 (pp)
REVERT: D  695 ASP cc_start: 0.8351 (p0) cc_final: 0.8030 (p0)
REVERT: D  716 ASP cc_start: 0.9180 (t0) cc_final: 0.8793 (t0)
REVERT: D  792 MET cc_start: 0.7506 (mmp) cc_final: 0.7279 (mmm)
REVERT: I   31 LYS cc_start: 0.8487 (tmtt) cc_final: 0.8259 (tmtt)
REVERT: I   60 HIS cc_start: 0.7854 (m-70) cc_final: 0.7620 (m90)
REVERT: I  136 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8013 (mmmt)
REVERT: I  160 GLN cc_start: 0.8101 (mt0) cc_final: 0.7467 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 170
  average time/residue: 0.2261
  time to fit residues: 52.8781
Evaluate side-chains
  137 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 55 optimal weight:    0.5980
   chunk 7 optimal weight:    0.4980
   chunk 103 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 156 ASN
D 385 ASN
** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 670 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.085575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.070902 restraints weight = 30664.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.072925 restraints weight = 16806.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.074362 restraints weight = 11138.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.4161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8714  Z= 0.126
  Angle     :  0.587   9.827  11840  Z= 0.301
  Chirality :  0.044   0.208   1312
  Planarity :  0.004   0.058   1548
  Dihedral  :  4.076  25.817   1200
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    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: -0.37 (0.25), residues: 1072
  helix: -2.57 (1.00), residues: 20
  sheet:  0.14 (0.23), residues: 514
  loop : -0.45 (0.25), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 530 
 HIS   0.002   0.001   HIS D 200 
 PHE   0.021   0.001   PHE D 525 
 TYR   0.016   0.001   TYR D 276 
 ARG   0.007   0.000   ARG C 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02814 (  292)
  hydrogen bonds       : angle       5.84310 (  780)
  SS BOND              : bond        0.00261 (    3)
  SS BOND              : angle       1.20331 (    6)
  covalent geometry    : bond        0.00286 ( 8711)
  covalent geometry    : angle       0.58640 (11834)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2989.00 seconds
wall clock time: 52 minutes 23.44 seconds (3143.44 seconds total)