Starting phenix.real_space_refine
on Wed Sep 17 12:21:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fxs_50853/09_2025/9fxs_50853.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fxs_50853/09_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_50853/09_2025/9fxs_50853.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fxs_50853/09_2025/9fxs_50853.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fxs_50853/09_2025/9fxs_50853.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fxs_50853/09_2025/9fxs_50853.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 1, 'GLN:plan1': 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: 1.77, per 1000 atoms: 0.21
  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: 0.65
  Conformation dependent library (CDL) restraints added in 426.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.34
  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: 1.61

  Time building geometry restraints manager: 0.90 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:             1.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.260
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.550
-------------------------------------------------------------------------------
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 : 6.47
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG D 234 
 TYR   0.007   0.001   TYR D 650 
 PHE   0.008   0.001   PHE I 155 
 TRP   0.009   0.001   TRP D 530 
 HIS   0.002   0.000   HIS B  46 

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

*********************** 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  : 0.201 
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: symmetry clash
   revert: symmetry clash
REVERT: B   33 MET cc_start: 0.8442 (ptt) cc_final: 0.8091 (ptt)
REVERT: B   43 ASN cc_start: 0.8859 (p0) cc_final: 0.8547 (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: 0.8569 (mtpt)
REVERT: C   17 GLN cc_start: 0.8885 (pm20) cc_final: 0.8672 (pm20)
REVERT: C   78 ASP cc_start: 0.7896 (p0) cc_final: 0.7542 (p0)
REVERT: C  154 GLU cc_start: 0.8670 (tt0) cc_final: 0.8397 (tt0)
REVERT: C  193 TYR cc_start: 0.8701 (m-10) cc_final: 0.8428 (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: 0.8950 (p)
REVERT: D  252 PHE cc_start: 0.9098 (t80) cc_final: 0.8643 (t80)
REVERT: D  273 TYR cc_start: 0.7505 (m-80) cc_final: 0.6810 (m-80)
REVERT: D  323 LEU cc_start: 0.9429 (mt) cc_final: 0.9205 (mt)
REVERT: D  350 PHE cc_start: 0.8865 (p90) cc_final: 0.8576 (p90)
REVERT: D  364 THR cc_start: 0.9523 (m) cc_final: 0.8859 (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: 0.8621 (mmtt)
REVERT: D  672 THR cc_start: 0.8091 (p) cc_final: 0.7730 (p)
REVERT: D  726 LEU cc_start: 0.9445 (mt) cc_final: 0.9156 (mp)
REVERT: D  790 SER cc_start: 0.8393 (t) cc_final: 0.7900 (p)
REVERT: D  816 LEU cc_start: 0.7382 (mt) cc_final: 0.6968 (mt)
REVERT: I   27 GLU cc_start: 0.8844 (pm20) cc_final: 0.8465 (pm20)
REVERT: I  130 SER cc_start: 0.8408 (p) cc_final: 0.8055 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.0991
  time to fit residues: 39.2458
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  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
B  46 HIS
** C  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 412 GLN
D 505 GLN
D 516 GLN
D 554 ASN
** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  14 GLN
I  32 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.089505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.074283 restraints weight = 28935.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.076480 restraints weight = 15610.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.078076 restraints weight = 10210.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.078987 restraints weight = 7523.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.079857 restraints weight = 6149.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8714  Z= 0.181
  Angle     :  0.534   6.408  11840  Z= 0.280
  Chirality :  0.042   0.140   1312
  Planarity :  0.004   0.050   1548
  Dihedral  :  3.453  17.388   1200
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.21 %
    Favored  : 96.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.25), residues: 1072
  helix: -1.54 (1.49), residues: 13
  sheet:  0.64 (0.22), residues: 521
  loop :  0.04 (0.26), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 207 
 TYR   0.014   0.001   TYR C 149 
 PHE   0.009   0.001   PHE D 416 
 TRP   0.009   0.001   TRP D 530 
 HIS   0.004   0.001   HIS B  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 8711)
  covalent geometry    : angle       0.53352 (11834)
  SS BOND              : bond        0.00672 (    3)
  SS BOND              : angle       1.24130 (    6)
  hydrogen bonds       : bond        0.03360 (  292)
  hydrogen bonds       : angle       5.56327 (  780)

*********************** 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
  209 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.312 
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   33 MET cc_start: 0.8263 (ptt) cc_final: 0.7776 (ptp)
REVERT: B   51 ASP cc_start: 0.8370 (p0) cc_final: 0.8130 (p0)
REVERT: B   62 ARG cc_start: 0.8201 (mmm-85) cc_final: 0.7507 (mmm160)
REVERT: B  106 ASP cc_start: 0.8899 (p0) cc_final: 0.8590 (p0)
REVERT: B  123 ARG cc_start: 0.7492 (mpt90) cc_final: 0.7271 (mpt90)
REVERT: B  128 SER cc_start: 0.8694 (p) cc_final: 0.8187 (m)
REVERT: B  136 LYS cc_start: 0.8765 (mttt) cc_final: 0.8514 (mtpt)
REVERT: C   34 GLN cc_start: 0.8747 (tt0) cc_final: 0.8429 (tt0)
REVERT: C   78 ASP cc_start: 0.8011 (p0) cc_final: 0.7649 (p0)
REVERT: C  154 GLU cc_start: 0.8692 (tt0) cc_final: 0.8468 (tt0)
REVERT: C  193 TYR cc_start: 0.8798 (m-10) cc_final: 0.8549 (m-10)
REVERT: D  273 TYR cc_start: 0.7734 (m-80) cc_final: 0.7105 (m-80)
REVERT: D  350 PHE cc_start: 0.8821 (p90) cc_final: 0.8555 (p90)
REVERT: D  548 MET cc_start: 0.8598 (tpt) cc_final: 0.8326 (tpp)
REVERT: D  578 MET cc_start: 0.7986 (tpt) cc_final: 0.7599 (tpt)
REVERT: D  646 LYS cc_start: 0.8919 (mttt) cc_final: 0.8672 (mmtt)
REVERT: D  695 ASP cc_start: 0.8224 (p0) cc_final: 0.7947 (p0)
REVERT: D  716 ASP cc_start: 0.9154 (t0) cc_final: 0.8675 (t0)
REVERT: D  790 SER cc_start: 0.8245 (t) cc_final: 0.8035 (p)
REVERT: I   27 GLU cc_start: 0.8733 (pm20) cc_final: 0.8397 (pm20)
REVERT: I   76 PHE cc_start: 0.8182 (m-80) cc_final: 0.6685 (m-80)
REVERT: I  130 SER cc_start: 0.8481 (p) cc_final: 0.8045 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0904
  time to fit residues: 26.1881
Evaluate side-chains
  156 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 24 optimal weight:    0.5980
   chunk 31 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
B  99 ASN
C  25 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**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.086327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.071202 restraints weight = 29405.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.073309 restraints weight = 16069.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.074697 restraints weight = 10583.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.075739 restraints weight = 7901.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.076377 restraints weight = 6411.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8714  Z= 0.223
  Angle     :  0.599   7.665  11840  Z= 0.312
  Chirality :  0.042   0.146   1312
  Planarity :  0.004   0.042   1548
  Dihedral  :  3.864  26.067   1200
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.76 %
    Favored  : 96.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.25), residues: 1072
  helix: -2.39 (1.22), residues: 14
  sheet:  0.51 (0.22), residues: 521
  loop : -0.14 (0.26), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 207 
 TYR   0.014   0.002   TYR C 149 
 PHE   0.015   0.002   PHE I  76 
 TRP   0.011   0.001   TRP D 530 
 HIS   0.003   0.001   HIS I 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 8711)
  covalent geometry    : angle       0.59537 (11834)
  SS BOND              : bond        0.00634 (    3)
  SS BOND              : angle       2.84889 (    6)
  hydrogen bonds       : bond        0.03380 (  292)
  hydrogen bonds       : angle       5.71751 (  780)

*********************** 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
  190 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 189
  time to evaluate  : 0.362 
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: 0.9316 (ptpt) cc_final: 0.9083 (pttt)
REVERT: B   33 MET cc_start: 0.8235 (ptt) cc_final: 0.7941 (ptp)
REVERT: B   50 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7111 (mt-10)
REVERT: B   51 ASP cc_start: 0.8506 (p0) cc_final: 0.8111 (p0)
REVERT: B   99 ASN cc_start: 0.9329 (m-40) cc_final: 0.9032 (m110)
REVERT: B  106 ASP cc_start: 0.8985 (p0) cc_final: 0.8278 (p0)
REVERT: B  108 GLU cc_start: 0.9017 (pt0) cc_final: 0.8712 (pm20)
REVERT: B  123 ARG cc_start: 0.7588 (mpt90) cc_final: 0.7356 (mpt90)
REVERT: B  133 PHE cc_start: 0.9425 (m-80) cc_final: 0.8903 (m-80)
REVERT: B  136 LYS cc_start: 0.8723 (mttt) cc_final: 0.8417 (mtpt)
REVERT: C   34 GLN cc_start: 0.8919 (tt0) cc_final: 0.8560 (tt0)
REVERT: C   78 ASP cc_start: 0.8010 (p0) cc_final: 0.7593 (p0)
REVERT: C   81 SER cc_start: 0.9156 (m) cc_final: 0.8417 (t)
REVERT: C  154 GLU cc_start: 0.8740 (tt0) cc_final: 0.8481 (tt0)
REVERT: D  273 TYR cc_start: 0.8099 (m-80) cc_final: 0.7335 (m-80)
REVERT: D  350 PHE cc_start: 0.8835 (p90) cc_final: 0.8540 (p90)
REVERT: D  578 MET cc_start: 0.7989 (tpt) cc_final: 0.7536 (tpt)
REVERT: D  695 ASP cc_start: 0.8150 (p0) cc_final: 0.7914 (p0)
REVERT: D  716 ASP cc_start: 0.8923 (t0) cc_final: 0.8488 (t0)
REVERT: D  719 THR cc_start: 0.8912 (p) cc_final: 0.8268 (p)
REVERT: I   27 GLU cc_start: 0.8621 (pm20) cc_final: 0.8302 (pm20)
REVERT: I   31 LYS cc_start: 0.8667 (tmtt) cc_final: 0.8390 (tmtt)
REVERT: I   76 PHE cc_start: 0.8449 (m-80) cc_final: 0.7909 (m-80)
REVERT: I  130 SER cc_start: 0.8555 (p) cc_final: 0.8095 (t)
REVERT: I  136 LYS cc_start: 0.8153 (mmpt) cc_final: 0.7806 (mmmt)
  outliers start: 1
  outliers final: 1
  residues processed: 190
  average time/residue: 0.1022
  time to fit residues: 26.5742
Evaluate side-chains
  148 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 102 optimal weight:    0.2980
   chunk 105 optimal weight:    7.9990
   chunk 9 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
B 115 ASN
** C  25 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**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.087601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.072348 restraints weight = 29824.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.074512 restraints weight = 16150.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.075974 restraints weight = 10577.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.076981 restraints weight = 7875.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.077669 restraints weight = 6402.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   8714  Z= 0.122
  Angle     :  0.536   7.298  11840  Z= 0.281
  Chirality :  0.043   0.165   1312
  Planarity :  0.004   0.040   1548
  Dihedral  :  3.695  22.383   1200
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  2.88 %
    Favored  : 96.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.25), residues: 1072
  helix: -2.66 (1.11), residues: 14
  sheet:  0.48 (0.22), residues: 528
  loop : -0.12 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  25 
 TYR   0.011   0.001   TYR D 434 
 PHE   0.014   0.001   PHE I 155 
 TRP   0.014   0.001   TRP D 530 
 HIS   0.003   0.001   HIS B  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8711)
  covalent geometry    : angle       0.53439 (11834)
  SS BOND              : bond        0.00343 (    3)
  SS BOND              : angle       2.05758 (    6)
  hydrogen bonds       : bond        0.03004 (  292)
  hydrogen bonds       : angle       5.54456 (  780)

*********************** 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
  192 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 190
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9285 (ptpt) cc_final: 0.9062 (pttt)
REVERT: B   33 MET cc_start: 0.8247 (ptt) cc_final: 0.7823 (ptt)
REVERT: B   42 SER cc_start: 0.9391 (p) cc_final: 0.9184 (p)
REVERT: B   46 HIS cc_start: 0.7415 (m90) cc_final: 0.6832 (m90)
REVERT: B   99 ASN cc_start: 0.9363 (m-40) cc_final: 0.9054 (m110)
REVERT: B  106 ASP cc_start: 0.9041 (p0) cc_final: 0.8310 (p0)
REVERT: B  108 GLU cc_start: 0.9187 (pt0) cc_final: 0.8926 (pm20)
REVERT: B  120 ASN cc_start: 0.8447 (t0) cc_final: 0.7920 (t0)
REVERT: B  133 PHE cc_start: 0.9407 (m-80) cc_final: 0.8809 (m-80)
REVERT: B  136 LYS cc_start: 0.8758 (mttt) cc_final: 0.8470 (mtpt)
REVERT: C   34 GLN cc_start: 0.8846 (tt0) cc_final: 0.8458 (tt0)
REVERT: C   78 ASP cc_start: 0.7959 (p0) cc_final: 0.7555 (p0)
REVERT: C   81 SER cc_start: 0.8996 (m) cc_final: 0.8389 (t)
REVERT: C  154 GLU cc_start: 0.8764 (tt0) cc_final: 0.8474 (tt0)
REVERT: D  143 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8936 (t0)
REVERT: D  273 TYR cc_start: 0.8016 (m-80) cc_final: 0.7380 (m-80)
REVERT: D  350 PHE cc_start: 0.8862 (p90) cc_final: 0.8530 (p90)
REVERT: D  548 MET cc_start: 0.8546 (tpt) cc_final: 0.8257 (tpp)
REVERT: D  578 MET cc_start: 0.7689 (tpt) cc_final: 0.7266 (tpt)
REVERT: D  695 ASP cc_start: 0.8178 (p0) cc_final: 0.7891 (p0)
REVERT: D  716 ASP cc_start: 0.8971 (t0) cc_final: 0.8700 (t0)
REVERT: D  726 LEU cc_start: 0.9444 (mt) cc_final: 0.9098 (mp)
REVERT: I   27 GLU cc_start: 0.8604 (pm20) cc_final: 0.8332 (pm20)
REVERT: I   31 LYS cc_start: 0.8526 (tmtt) cc_final: 0.8277 (tmtt)
REVERT: I   76 PHE cc_start: 0.8447 (m-80) cc_final: 0.7923 (m-80)
REVERT: I  130 SER cc_start: 0.8593 (p) cc_final: 0.8103 (t)
REVERT: I  136 LYS cc_start: 0.8099 (mmpt) cc_final: 0.7663 (mmmt)
  outliers start: 2
  outliers final: 0
  residues processed: 191
  average time/residue: 0.0967
  time to fit residues: 25.5659
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  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0000
   chunk 30 optimal weight:    8.9990
   chunk 77 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0570
   chunk 40 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.7704

-------------------------------------------------------------------------------
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 505 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 = 0.3363 r_free = 0.3363 target = 0.087671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.072535 restraints weight = 29507.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.074685 restraints weight = 15913.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.076179 restraints weight = 10396.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.077164 restraints weight = 7694.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.077855 restraints weight = 6247.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8714  Z= 0.109
  Angle     :  0.525   7.802  11840  Z= 0.273
  Chirality :  0.042   0.143   1312
  Planarity :  0.003   0.039   1548
  Dihedral  :  3.585  17.390   1200
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.99 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.25), residues: 1072
  helix: -2.64 (1.12), residues: 14
  sheet:  0.60 (0.23), residues: 524
  loop : -0.12 (0.25), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 143 
 TYR   0.009   0.001   TYR D 650 
 PHE   0.012   0.001   PHE D 416 
 TRP   0.014   0.001   TRP D 530 
 HIS   0.002   0.001   HIS I 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8711)
  covalent geometry    : angle       0.52420 (11834)
  SS BOND              : bond        0.00331 (    3)
  SS BOND              : angle       1.08816 (    6)
  hydrogen bonds       : bond        0.02881 (  292)
  hydrogen bonds       : angle       5.41066 (  780)

*********************** 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
  193 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9262 (ptpt) cc_final: 0.9025 (pttt)
REVERT: B   41 SER cc_start: 0.8525 (t) cc_final: 0.7929 (t)
REVERT: B   42 SER cc_start: 0.9464 (p) cc_final: 0.8995 (t)
REVERT: B   43 ASN cc_start: 0.8346 (p0) cc_final: 0.8108 (p0)
REVERT: B   46 HIS cc_start: 0.7407 (m90) cc_final: 0.7186 (m90)
REVERT: B  106 ASP cc_start: 0.9057 (p0) cc_final: 0.8312 (p0)
REVERT: B  108 GLU cc_start: 0.9179 (pt0) cc_final: 0.8931 (pm20)
REVERT: B  120 ASN cc_start: 0.8463 (t0) cc_final: 0.7935 (t0)
REVERT: B  133 PHE cc_start: 0.9395 (m-80) cc_final: 0.8761 (m-80)
REVERT: B  136 LYS cc_start: 0.8636 (mttt) cc_final: 0.8391 (mtpt)
REVERT: C   34 GLN cc_start: 0.8819 (tt0) cc_final: 0.8446 (tt0)
REVERT: C   69 ASP cc_start: 0.8157 (p0) cc_final: 0.7909 (p0)
REVERT: C   78 ASP cc_start: 0.7988 (p0) cc_final: 0.7584 (p0)
REVERT: C  154 GLU cc_start: 0.8773 (tt0) cc_final: 0.8508 (tt0)
REVERT: D  273 TYR cc_start: 0.7997 (m-80) cc_final: 0.7541 (m-80)
REVERT: D  350 PHE cc_start: 0.8829 (p90) cc_final: 0.8469 (p90)
REVERT: D  578 MET cc_start: 0.7716 (tpt) cc_final: 0.7281 (tpt)
REVERT: D  695 ASP cc_start: 0.8152 (p0) cc_final: 0.7871 (p0)
REVERT: D  716 ASP cc_start: 0.8996 (t0) cc_final: 0.8596 (t0)
REVERT: I   31 LYS cc_start: 0.8538 (tmtt) cc_final: 0.8331 (tmtt)
REVERT: I   76 PHE cc_start: 0.8511 (m-80) cc_final: 0.7837 (m-80)
REVERT: I  130 SER cc_start: 0.8600 (p) cc_final: 0.8199 (t)
REVERT: I  136 LYS cc_start: 0.8069 (mmpt) cc_final: 0.7798 (mmtm)
  outliers start: 1
  outliers final: 0
  residues processed: 192
  average time/residue: 0.0931
  time to fit residues: 25.0215
Evaluate side-chains
  151 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 63 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 74 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0570
   chunk 24 optimal weight:    0.5980
   chunk 72 optimal weight:    5.9990
   overall best weight:    1.5300

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

Flipped N/Q/H residues before XYZ refinement:
B  99 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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.086530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.071559 restraints weight = 30344.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.073653 restraints weight = 16598.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.075096 restraints weight = 10950.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.076033 restraints weight = 8201.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.076771 restraints weight = 6720.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.3289

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= 0.156
  Angle     :  0.540   5.724  11840  Z= 0.282
  Chirality :  0.042   0.140   1312
  Planarity :  0.004   0.042   1548
  Dihedral  :  3.737  18.518   1200
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.25), residues: 1072
  helix: -2.67 (1.12), residues: 14
  sheet:  0.46 (0.22), residues: 525
  loop : -0.13 (0.25), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 215 
 TYR   0.013   0.001   TYR I 159 
 PHE   0.018   0.002   PHE D 228 
 TRP   0.014   0.001   TRP D 530 
 HIS   0.003   0.001   HIS I 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8711)
  covalent geometry    : angle       0.53925 (11834)
  SS BOND              : bond        0.00305 (    3)
  SS BOND              : angle       0.91604 (    6)
  hydrogen bonds       : bond        0.03041 (  292)
  hydrogen bonds       : angle       5.45575 (  780)

*********************** 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
  189 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9317 (ptpt) cc_final: 0.9083 (pttt)
REVERT: B   33 MET cc_start: 0.8482 (ptp) cc_final: 0.7734 (ptp)
REVERT: B   42 SER cc_start: 0.9412 (p) cc_final: 0.9205 (p)
REVERT: B   46 HIS cc_start: 0.7484 (m90) cc_final: 0.7241 (m90)
REVERT: B   51 ASP cc_start: 0.8474 (p0) cc_final: 0.8241 (p0)
REVERT: B   99 ASN cc_start: 0.9330 (m-40) cc_final: 0.8994 (m110)
REVERT: B  106 ASP cc_start: 0.9064 (p0) cc_final: 0.8668 (p0)
REVERT: B  133 PHE cc_start: 0.9402 (m-80) cc_final: 0.8902 (m-80)
REVERT: B  136 LYS cc_start: 0.8661 (mttt) cc_final: 0.8439 (mtpt)
REVERT: C   34 GLN cc_start: 0.8752 (tt0) cc_final: 0.8325 (tt0)
REVERT: C   78 ASP cc_start: 0.7928 (p0) cc_final: 0.7510 (p0)
REVERT: C   81 SER cc_start: 0.9028 (m) cc_final: 0.8223 (t)
REVERT: C  154 GLU cc_start: 0.8805 (tt0) cc_final: 0.8525 (tt0)
REVERT: D  146 PHE cc_start: 0.8949 (t80) cc_final: 0.8747 (t80)
REVERT: D  273 TYR cc_start: 0.8230 (m-80) cc_final: 0.7563 (m-80)
REVERT: D  350 PHE cc_start: 0.8865 (p90) cc_final: 0.8544 (p90)
REVERT: D  578 MET cc_start: 0.7732 (tpt) cc_final: 0.7134 (tpp)
REVERT: D  695 ASP cc_start: 0.8176 (p0) cc_final: 0.7874 (p0)
REVERT: D  716 ASP cc_start: 0.9071 (t0) cc_final: 0.8705 (t0)
REVERT: D  717 THR cc_start: 0.8364 (p) cc_final: 0.7856 (t)
REVERT: D  719 THR cc_start: 0.8969 (p) cc_final: 0.8375 (p)
REVERT: I   31 LYS cc_start: 0.8549 (tmtt) cc_final: 0.8296 (tmtt)
REVERT: I   76 PHE cc_start: 0.8529 (m-80) cc_final: 0.7998 (m-80)
REVERT: I  130 SER cc_start: 0.8666 (p) cc_final: 0.8226 (t)
REVERT: I  136 LYS cc_start: 0.8059 (mmpt) cc_final: 0.7834 (mmtm)
REVERT: I  159 TYR cc_start: 0.8951 (m-80) cc_final: 0.8545 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.0917
  time to fit residues: 24.2508
Evaluate side-chains
  149 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 72 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 88 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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**
D 670 ASN
I  77 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.084513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.069434 restraints weight = 30560.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.071497 restraints weight = 16728.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.072918 restraints weight = 11075.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.073856 restraints weight = 8305.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.074570 restraints weight = 6813.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8714  Z= 0.187
  Angle     :  0.585   8.102  11840  Z= 0.302
  Chirality :  0.042   0.141   1312
  Planarity :  0.004   0.037   1548
  Dihedral  :  3.871  18.091   1200
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.25), residues: 1072
  helix: -2.75 (1.10), residues: 14
  sheet:  0.40 (0.22), residues: 520
  loop : -0.22 (0.25), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  62 
 TYR   0.011   0.001   TYR D 418 
 PHE   0.016   0.002   PHE D 228 
 TRP   0.014   0.001   TRP D 530 
 HIS   0.004   0.001   HIS B 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 8711)
  covalent geometry    : angle       0.58479 (11834)
  SS BOND              : bond        0.00467 (    3)
  SS BOND              : angle       1.11919 (    6)
  hydrogen bonds       : bond        0.03101 (  292)
  hydrogen bonds       : angle       5.57905 (  780)

*********************** 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
  187 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9330 (ptpt) cc_final: 0.9001 (pttt)
REVERT: B   33 MET cc_start: 0.8575 (ptp) cc_final: 0.7855 (ptp)
REVERT: B   41 SER cc_start: 0.8421 (t) cc_final: 0.7999 (p)
REVERT: B   42 SER cc_start: 0.9518 (p) cc_final: 0.8940 (t)
REVERT: B   43 ASN cc_start: 0.8420 (p0) cc_final: 0.7212 (p0)
REVERT: B   51 ASP cc_start: 0.8574 (p0) cc_final: 0.8214 (p0)
REVERT: B   61 LEU cc_start: 0.9439 (mm) cc_final: 0.8710 (mm)
REVERT: B   66 THR cc_start: 0.8982 (p) cc_final: 0.8658 (m)
REVERT: B   71 ARG cc_start: 0.7836 (ttp-110) cc_final: 0.7471 (ttp-110)
REVERT: B   99 ASN cc_start: 0.9341 (m-40) cc_final: 0.8995 (m110)
REVERT: B  106 ASP cc_start: 0.8950 (p0) cc_final: 0.8255 (p0)
REVERT: B  108 GLU cc_start: 0.9248 (pt0) cc_final: 0.8938 (pm20)
REVERT: B  133 PHE cc_start: 0.9542 (m-80) cc_final: 0.8934 (m-80)
REVERT: B  136 LYS cc_start: 0.8652 (mttt) cc_final: 0.8359 (mtpt)
REVERT: C   19 GLN cc_start: 0.8822 (pm20) cc_final: 0.8578 (pm20)
REVERT: C   34 GLN cc_start: 0.8734 (tt0) cc_final: 0.8317 (tt0)
REVERT: C   69 ASP cc_start: 0.8048 (p0) cc_final: 0.7789 (p0)
REVERT: C   78 ASP cc_start: 0.8006 (p0) cc_final: 0.7607 (p0)
REVERT: C   81 SER cc_start: 0.9140 (m) cc_final: 0.8409 (t)
REVERT: C  154 GLU cc_start: 0.8810 (tt0) cc_final: 0.8514 (tt0)
REVERT: D  273 TYR cc_start: 0.8225 (m-80) cc_final: 0.7697 (m-80)
REVERT: D  578 MET cc_start: 0.7773 (tpt) cc_final: 0.7204 (tpp)
REVERT: D  626 LEU cc_start: 0.8938 (pp) cc_final: 0.8670 (pp)
REVERT: D  695 ASP cc_start: 0.8270 (p0) cc_final: 0.7957 (p0)
REVERT: D  716 ASP cc_start: 0.9127 (t0) cc_final: 0.8713 (t0)
REVERT: D  717 THR cc_start: 0.8405 (p) cc_final: 0.7884 (t)
REVERT: I   31 LYS cc_start: 0.8615 (tmtt) cc_final: 0.8294 (tmtt)
REVERT: I   76 PHE cc_start: 0.8468 (m-80) cc_final: 0.8204 (m-80)
REVERT: I  130 SER cc_start: 0.8684 (p) cc_final: 0.8271 (t)
REVERT: I  160 GLN cc_start: 0.8155 (mt0) cc_final: 0.7639 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0919
  time to fit residues: 23.9958
Evaluate side-chains
  144 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 107 optimal weight:    8.9990
   chunk 49 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 101 optimal weight:   10.0000
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.086805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.071691 restraints weight = 30246.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.073764 restraints weight = 16673.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.075178 restraints weight = 11064.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.076214 restraints weight = 8303.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.076901 restraints weight = 6771.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
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      :  0.003   0.030   8714  Z= 0.117
  Angle     :  0.558   7.427  11840  Z= 0.287
  Chirality :  0.042   0.136   1312
  Planarity :  0.004   0.040   1548
  Dihedral  :  3.845  22.187   1200
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.25), residues: 1072
  helix: -3.08 (0.86), residues: 20
  sheet:  0.37 (0.23), residues: 526
  loop : -0.24 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  25 
 TYR   0.015   0.001   TYR D 276 
 PHE   0.035   0.002   PHE I 105 
 TRP   0.013   0.001   TRP D 530 
 HIS   0.004   0.001   HIS B  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8711)
  covalent geometry    : angle       0.55717 (11834)
  SS BOND              : bond        0.00401 (    3)
  SS BOND              : angle       1.68774 (    6)
  hydrogen bonds       : bond        0.02745 (  292)
  hydrogen bonds       : angle       5.43250 (  780)

*********************** 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
  186 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9278 (ptpt) cc_final: 0.9004 (pttt)
REVERT: B   33 MET cc_start: 0.8200 (ptp) cc_final: 0.7910 (ptp)
REVERT: B   41 SER cc_start: 0.8637 (t) cc_final: 0.8143 (t)
REVERT: B   43 ASN cc_start: 0.8235 (p0) cc_final: 0.7463 (p0)
REVERT: B   51 ASP cc_start: 0.8557 (p0) cc_final: 0.8163 (p0)
REVERT: B   66 THR cc_start: 0.9035 (p) cc_final: 0.8730 (m)
REVERT: B   99 ASN cc_start: 0.9350 (m-40) cc_final: 0.9013 (m110)
REVERT: B  106 ASP cc_start: 0.9006 (p0) cc_final: 0.8235 (p0)
REVERT: B  108 GLU cc_start: 0.9181 (pt0) cc_final: 0.8909 (pm20)
REVERT: B  120 ASN cc_start: 0.8352 (t0) cc_final: 0.8135 (t0)
REVERT: B  133 PHE cc_start: 0.9511 (m-80) cc_final: 0.8848 (m-80)
REVERT: B  136 LYS cc_start: 0.8642 (mttt) cc_final: 0.8285 (mtpt)
REVERT: C   34 GLN cc_start: 0.8633 (tt0) cc_final: 0.8213 (tt0)
REVERT: C   69 ASP cc_start: 0.8022 (p0) cc_final: 0.7803 (p0)
REVERT: C   78 ASP cc_start: 0.7913 (p0) cc_final: 0.7500 (p0)
REVERT: C   81 SER cc_start: 0.9029 (m) cc_final: 0.8203 (t)
REVERT: C  154 GLU cc_start: 0.8779 (tt0) cc_final: 0.8476 (tt0)
REVERT: D  273 TYR cc_start: 0.8210 (m-80) cc_final: 0.7669 (m-80)
REVERT: D  350 PHE cc_start: 0.8863 (p90) cc_final: 0.8615 (p90)
REVERT: D  578 MET cc_start: 0.7771 (tpt) cc_final: 0.7173 (tpp)
REVERT: D  626 LEU cc_start: 0.8906 (pp) cc_final: 0.8574 (pp)
REVERT: D  695 ASP cc_start: 0.8163 (p0) cc_final: 0.7837 (p0)
REVERT: D  716 ASP cc_start: 0.9080 (t0) cc_final: 0.8662 (t0)
REVERT: D  717 THR cc_start: 0.8354 (p) cc_final: 0.7824 (t)
REVERT: I   76 PHE cc_start: 0.8560 (m-80) cc_final: 0.8029 (m-80)
REVERT: I  130 SER cc_start: 0.8694 (p) cc_final: 0.8273 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0918
  time to fit residues: 23.7803
Evaluate side-chains
  146 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 42 optimal weight:    0.1980
   chunk 39 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   chunk 61 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    1.8388

-------------------------------------------------------------------------------
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 516 GLN
** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 670 ASN
I  77 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.085577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.070621 restraints weight = 29588.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.072655 restraints weight = 16117.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.074109 restraints weight = 10667.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.075148 restraints weight = 7949.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.075862 restraints weight = 6413.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8714  Z= 0.181
  Angle     :  0.591   8.420  11840  Z= 0.305
  Chirality :  0.042   0.140   1312
  Planarity :  0.004   0.045   1548
  Dihedral  :  4.025  25.554   1200
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.25), residues: 1072
  helix: -2.76 (1.15), residues: 14
  sheet:  0.30 (0.23), residues: 529
  loop : -0.23 (0.25), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG I  71 
 TYR   0.011   0.001   TYR D 418 
 PHE   0.018   0.002   PHE D 525 
 TRP   0.013   0.001   TRP D 530 
 HIS   0.005   0.001   HIS D 580 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 8711)
  covalent geometry    : angle       0.59044 (11834)
  SS BOND              : bond        0.00313 (    3)
  SS BOND              : angle       1.56632 (    6)
  hydrogen bonds       : bond        0.03115 (  292)
  hydrogen bonds       : angle       5.52741 (  780)

*********************** 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
  176 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.340 
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: 0.9261 (ptpt) cc_final: 0.8975 (pttt)
REVERT: B   33 MET cc_start: 0.8207 (ptp) cc_final: 0.7832 (ptp)
REVERT: B   37 MET cc_start: 0.8489 (mpp) cc_final: 0.8261 (mpp)
REVERT: B   51 ASP cc_start: 0.8601 (p0) cc_final: 0.8118 (p0)
REVERT: B   66 THR cc_start: 0.8971 (p) cc_final: 0.8647 (m)
REVERT: B   99 ASN cc_start: 0.9324 (m-40) cc_final: 0.9024 (m110)
REVERT: B  106 ASP cc_start: 0.8926 (p0) cc_final: 0.8208 (p0)
REVERT: B  108 GLU cc_start: 0.9253 (pt0) cc_final: 0.8904 (pm20)
REVERT: B  133 PHE cc_start: 0.9556 (m-80) cc_final: 0.8933 (m-80)
REVERT: B  136 LYS cc_start: 0.8624 (mttt) cc_final: 0.8230 (mtpt)
REVERT: C   34 GLN cc_start: 0.8697 (tt0) cc_final: 0.8235 (tt0)
REVERT: C   69 ASP cc_start: 0.7983 (p0) cc_final: 0.7754 (p0)
REVERT: C   78 ASP cc_start: 0.7927 (p0) cc_final: 0.7564 (p0)
REVERT: C   81 SER cc_start: 0.9142 (m) cc_final: 0.8270 (t)
REVERT: C  154 GLU cc_start: 0.8847 (tt0) cc_final: 0.8464 (tt0)
REVERT: D  578 MET cc_start: 0.7784 (tpt) cc_final: 0.7145 (tpp)
REVERT: D  626 LEU cc_start: 0.8965 (pp) cc_final: 0.8646 (pp)
REVERT: D  695 ASP cc_start: 0.8270 (p0) cc_final: 0.7953 (p0)
REVERT: D  716 ASP cc_start: 0.9129 (t0) cc_final: 0.8758 (t0)
REVERT: D  717 THR cc_start: 0.8400 (p) cc_final: 0.7855 (t)
REVERT: D  792 MET cc_start: 0.7423 (mmp) cc_final: 0.7196 (mmm)
REVERT: I   27 GLU cc_start: 0.8362 (pm20) cc_final: 0.7848 (pm20)
REVERT: I   76 PHE cc_start: 0.8471 (m-80) cc_final: 0.8204 (m-80)
REVERT: I  130 SER cc_start: 0.8679 (p) cc_final: 0.8288 (t)
REVERT: I  155 PHE cc_start: 0.8884 (m-80) cc_final: 0.8642 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.0985
  time to fit residues: 23.8221
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  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:    0.0170
   chunk 27 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 100 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 92 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   chunk 24 optimal weight:    0.0060
   overall best weight:    1.2040

-------------------------------------------------------------------------------
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 104 GLN
D 385 ASN
** D 412 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 = 0.086153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.071249 restraints weight = 29877.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.073279 restraints weight = 16268.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.074711 restraints weight = 10755.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.075675 restraints weight = 8008.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.076326 restraints weight = 6541.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.3832

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= 0.135
  Angle     :  0.578   7.446  11840  Z= 0.297
  Chirality :  0.043   0.150   1312
  Planarity :  0.004   0.042   1548
  Dihedral  :  3.908  25.200   1200
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.25), residues: 1072
  helix: -2.78 (0.95), residues: 19
  sheet:  0.32 (0.23), residues: 520
  loop : -0.27 (0.25), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  62 
 TYR   0.016   0.001   TYR D 276 
 PHE   0.018   0.001   PHE D 525 
 TRP   0.013   0.001   TRP D 204 
 HIS   0.002   0.001   HIS D 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8711)
  covalent geometry    : angle       0.57763 (11834)
  SS BOND              : bond        0.00318 (    3)
  SS BOND              : angle       1.38462 (    6)
  hydrogen bonds       : bond        0.02873 (  292)
  hydrogen bonds       : angle       5.47911 (  780)

********************** 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
  176 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LYS cc_start: 0.9244 (ptpt) cc_final: 0.8995 (pttt)
REVERT: B   33 MET cc_start: 0.8238 (ptp) cc_final: 0.7502 (ptp)
REVERT: B   51 ASP cc_start: 0.8616 (p0) cc_final: 0.8116 (p0)
REVERT: B   61 LEU cc_start: 0.9446 (mm) cc_final: 0.9145 (mm)
REVERT: B   66 THR cc_start: 0.8911 (p) cc_final: 0.8587 (m)
REVERT: B   99 ASN cc_start: 0.9331 (m-40) cc_final: 0.9071 (m110)
REVERT: B  106 ASP cc_start: 0.8980 (p0) cc_final: 0.8345 (p0)
REVERT: B  133 PHE cc_start: 0.9515 (m-80) cc_final: 0.8855 (m-80)
REVERT: B  136 LYS cc_start: 0.8633 (mttt) cc_final: 0.8237 (mtpt)
REVERT: C   34 GLN cc_start: 0.8616 (tt0) cc_final: 0.8260 (tt0)
REVERT: C   69 ASP cc_start: 0.7903 (p0) cc_final: 0.7677 (p0)
REVERT: C   78 ASP cc_start: 0.7903 (p0) cc_final: 0.7487 (p0)
REVERT: C   81 SER cc_start: 0.9132 (m) cc_final: 0.8288 (t)
REVERT: D  350 PHE cc_start: 0.8841 (p90) cc_final: 0.8538 (p90)
REVERT: D  578 MET cc_start: 0.7889 (tpt) cc_final: 0.7264 (tpp)
REVERT: D  626 LEU cc_start: 0.8939 (pp) cc_final: 0.8617 (pp)
REVERT: D  695 ASP cc_start: 0.8199 (p0) cc_final: 0.7878 (p0)
REVERT: D  716 ASP cc_start: 0.9123 (t0) cc_final: 0.8732 (t0)
REVERT: D  717 THR cc_start: 0.8427 (p) cc_final: 0.7878 (t)
REVERT: D  792 MET cc_start: 0.7327 (mmp) cc_final: 0.7079 (mmm)
REVERT: I   16 GLN cc_start: 0.8227 (tp40) cc_final: 0.7543 (pm20)
REVERT: I   22 GLU cc_start: 0.8010 (pp20) cc_final: 0.7580 (pp20)
REVERT: I   23 THR cc_start: 0.8790 (m) cc_final: 0.8277 (m)
REVERT: I   62 ARG cc_start: 0.6094 (ptp-170) cc_final: 0.5875 (ptp-170)
REVERT: I   76 PHE cc_start: 0.8478 (m-80) cc_final: 0.8125 (m-80)
REVERT: I  130 SER cc_start: 0.8701 (p) cc_final: 0.8301 (t)
REVERT: I  155 PHE cc_start: 0.8952 (m-80) cc_final: 0.8669 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.0959
  time to fit residues: 23.4001
Evaluate side-chains
  136 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 79 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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**
C 156 ASN
D 385 ASN
** D 412 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.086811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.072029 restraints weight = 29531.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.074115 restraints weight = 16076.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.075548 restraints weight = 10543.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.076580 restraints weight = 7824.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.077249 restraints weight = 6332.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3897

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= 0.123
  Angle     :  0.595   9.931  11840  Z= 0.302
  Chirality :  0.043   0.207   1312
  Planarity :  0.004   0.040   1548
  Dihedral  :  3.862  24.379   1200
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.25), residues: 1072
  helix: -2.70 (0.96), residues: 19
  sheet:  0.36 (0.23), residues: 520
  loop : -0.30 (0.25), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 188 
 TYR   0.014   0.001   TYR D 273 
 PHE   0.029   0.001   PHE D 525 
 TRP   0.014   0.001   TRP D 530 
 HIS   0.002   0.000   HIS D 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8711)
  covalent geometry    : angle       0.59427 (11834)
  SS BOND              : bond        0.00339 (    3)
  SS BOND              : angle       1.34716 (    6)
  hydrogen bonds       : bond        0.02851 (  292)
  hydrogen bonds       : angle       5.43583 (  780)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1505.43 seconds
wall clock time: 26 minutes 49.80 seconds (1609.80 seconds total)