Starting phenix.real_space_refine
on Thu Mar  6 03:01:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wy0_37914/03_2025/8wy0_37914.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wy0_37914/03_2025/8wy0_37914.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wy0_37914/03_2025/8wy0_37914.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wy0_37914/03_2025/8wy0_37914.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wy0_37914/03_2025/8wy0_37914.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wy0_37914/03_2025/8wy0_37914.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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      37      5.16       5
     C    3021      2.51       5
     N     738      2.21       5
     O     860      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4656
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "a"
      Number of atoms: 234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 234
          Classifications: {'peptide': 29}
          Link IDs: {'PTRANS': 1, 'TRANS': 27}
    Chain: "b"
      Number of atoms: 243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 243
          Classifications: {'peptide': 30}
          Link IDs: {'PTRANS': 1, 'TRANS': 28}
    Chain: "d"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 817
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 3, 'TRANS': 101}
    Chain: "e"
      Number of atoms: 959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 959
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
    Chain: "f"
      Number of atoms: 933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 933
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 5, 'TRANS': 112}
          Chain breaks: 1
    Chain: "g"
      Number of atoms: 890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 890
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 2, 'TRANS': 110}
    Chain: "m"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 250
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "n"
      Number of atoms: 302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 302
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "b"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.32, per 1000 atoms: 0.71
  Number of scatterers: 4656
  At special positions: 0
  Unit cell: (70.0245, 90.4932, 106.653, 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      37     16.00
     O     860      8.00
     N     738      7.00
     C    3021      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS a  32 " - pdb=" SG  CYS b  32 " distance=2.18
    Simple disulfide: pdb=" SG  CYS d  37 " - pdb=" SG  CYS d  73 " distance=2.03
    Simple disulfide: pdb=" SG  CYS d  93 " - pdb=" SG  CYS d  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS e  49 " - pdb=" SG  CYS e  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS e 119 " - pdb=" SG  CYS e 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS f  49 " - pdb=" SG  CYS f  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS f 119 " - pdb=" SG  CYS f 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS g  46 " - pdb=" SG  CYS g  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS g 104 " - pdb=" SG  CYS g 107 " 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: 1.08
  Conformation dependent library (CDL) restraints added in 536.3 milliseconds
  

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1094

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 9 sheets defined
      39.7% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'a' and resid 27 through 52
      removed outlier: 3.961A  pdb=" N   TYR a  33 " --> pdb=" O   PRO a  29 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 30 through 56
    Processing helix  chain 'd' and resid 102 through 126
      removed outlier: 3.620A  pdb=" N   GLY d 106 " --> pdb=" O   ALA d 102 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE d 108 " --> pdb=" O   VAL d 104 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 127 through 152
      removed outlier: 3.754A  pdb=" N   THR e 132 " --> pdb=" O   MET e 128 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   ILE e 133 " --> pdb=" O   SER e 129 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER e 152 " --> pdb=" O   VAL e 148 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 104 through 108
      removed outlier: 3.773A  pdb=" N   ASP f 107 " --> pdb=" O   LYS f 104 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 126 through 154
      removed outlier: 3.552A  pdb=" N   VAL f 130 " --> pdb=" O   ASP f 126 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LEU f 147 " --> pdb=" O   GLY f 143 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL f 148 " --> pdb=" O   LEU f 144 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LYS f 153 " --> pdb=" O   TYR f 149 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASN f 154 " --> pdb=" O   TYR f 150 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 76 through 80
      removed outlier: 3.513A  pdb=" N   LYS g  79 " --> pdb=" O   SER g  76 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 114 through 135
    Processing helix  chain 'm' and resid 260 through 291
      removed outlier: 3.528A  pdb=" N   LEU m 266 " --> pdb=" O   ASN m 262 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU m 269 " --> pdb=" O   SER m 265 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA m 280 " --> pdb=" O   ALA m 276 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ALA m 291 " --> pdb=" O   ALA m 287 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 272 through 307
      removed outlier: 3.927A  pdb=" N   TYR n 283 " --> pdb=" O   THR n 279 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   MET n 284 " --> pdb=" O   SER n 280 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 28
      removed outlier: 7.349A  pdb=" N   VAL d  33 " --> pdb=" O   LEU d  60 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU d  60 " --> pdb=" O   VAL d  33 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46
      removed outlier: 6.817A  pdb=" N   ILE d  70 " --> pdb=" O   VAL d  44 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   TYR d  71 " --> pdb=" O   VAL d  86 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL d  86 " --> pdb=" O   TYR d  71 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   THR d  85 " --> pdb=" O   TYR e 111 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   TYR e 113 " --> pdb=" O   THR d  85 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   GLN d  87 " --> pdb=" O   TYR e 113 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   ARG e 115 " --> pdb=" O   GLN d  87 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   HIS d  89 " --> pdb=" O   ARG e 115 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   PHE e 110 " --> pdb=" O   CYS e  98 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   CYS e  98 " --> pdb=" O   PHE e 110 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL e  97 " --> pdb=" O   GLN e  60 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 97
    Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 41
      removed outlier: 3.506A  pdb=" N   LYS e  37 " --> pdb=" O   THR e  48 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR e  44 " --> pdb=" O   SER e  41 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 41
      removed outlier: 3.985A  pdb=" N   LYS f  37 " --> pdb=" O   THR f  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'f' and resid 113 through 114
      removed outlier: 5.541A  pdb=" N   TYR f 113 " --> pdb=" O   TYR g 100 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'f' and resid 122 through 124
      removed outlier: 3.632A  pdb=" N   ILE g 108 " --> pdb=" O   MET f 123 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'g' and resid 31 through 33
      removed outlier: 3.910A  pdb=" N   GLY g  75 " --> pdb=" O   VAL g  42 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU g  44 " --> pdb=" O   ASN g  73 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   ASN g  73 " --> pdb=" O   LEU g  44 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'g' and resid 55 through 57
      removed outlier: 3.705A  pdb=" N   GLN g  86 " --> pdb=" O   PHE g  56 " (cutoff:3.500A)

    214 hydrogen bonds defined for protein.
    615 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: 1.07

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1440
        1.34 -     1.46: 1109
        1.46 -     1.59: 2143
        1.59 -     1.71: 0
        1.71 -     1.83: 51
  Bond restraints: 4743
  Sorted by residual:
  bond pdb=" CA  THR f  34 "
       pdb=" CB  THR f  34 "
    ideal  model  delta    sigma   weight residual
    1.528  1.553 -0.025 1.68e-02 3.54e+03 2.19e+00
  bond pdb=" CA  LEU g 110 "
       pdb=" CB  LEU g 110 "
    ideal  model  delta    sigma   weight residual
    1.528  1.564 -0.035 2.61e-02 1.47e+03 1.83e+00
  bond pdb=" CA  ASN e 121 "
       pdb=" CB  ASN e 121 "
    ideal  model  delta    sigma   weight residual
    1.533  1.548 -0.015 1.37e-02 5.33e+03 1.18e+00
  bond pdb=" C3  CLR b 201 "
       pdb=" O1  CLR b 201 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.07e+00
  bond pdb=" CB  ASN d  36 "
       pdb=" CG  ASN d  36 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 1.04e+00
  ... (remaining 4738 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 6234
        1.75 -     3.51: 151
        3.51 -     5.26: 33
        5.26 -     7.01: 10
        7.01 -     8.77: 2
  Bond angle restraints: 6430
  Sorted by residual:
  angle pdb=" CA  LYS d  80 "
        pdb=" CB  LYS d  80 "
        pdb=" CG  LYS d  80 "
      ideal   model   delta    sigma   weight residual
     114.10  120.87   -6.77 2.00e+00 2.50e-01 1.15e+01
  angle pdb=" CA  TYR d  79 "
        pdb=" CB  TYR d  79 "
        pdb=" CG  TYR d  79 "
      ideal   model   delta    sigma   weight residual
     113.90  119.74   -5.84 1.80e+00 3.09e-01 1.05e+01
  angle pdb=" N   PRO g  96 "
        pdb=" CA  PRO g  96 "
        pdb=" C   PRO g  96 "
      ideal   model   delta    sigma   weight residual
     110.40  115.33   -4.93 1.61e+00 3.86e-01 9.38e+00
  angle pdb=" CB  LYS f  85 "
        pdb=" CG  LYS f  85 "
        pdb=" CD  LYS f  85 "
      ideal   model   delta    sigma   weight residual
     111.30  118.18   -6.88 2.30e+00 1.89e-01 8.96e+00
  angle pdb=" CB  MET g 103 "
        pdb=" CG  MET g 103 "
        pdb=" SD  MET g 103 "
      ideal   model   delta    sigma   weight residual
     112.70  120.71   -8.01 3.00e+00 1.11e-01 7.12e+00
  ... (remaining 6425 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 2413
       17.75 -    35.50: 374
       35.50 -    53.25: 95
       53.25 -    70.99: 10
       70.99 -    88.74: 5
  Dihedral angle restraints: 2897
    sinusoidal: 1190
      harmonic: 1707
  Sorted by residual:
  dihedral pdb=" CB  CYS e 119 "
           pdb=" SG  CYS e 119 "
           pdb=" SG  CYS e 122 "
           pdb=" CB  CYS e 122 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.92  -52.92     1      1.00e+01 1.00e-02 3.81e+01
  dihedral pdb=" CA  ASN g 106 "
           pdb=" C   ASN g 106 "
           pdb=" N   CYS g 107 "
           pdb=" CA  CYS g 107 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.37  -27.63     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CB  CYS d  37 "
           pdb=" SG  CYS d  37 "
           pdb=" SG  CYS d  73 "
           pdb=" CB  CYS d  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.21   39.79     1      1.00e+01 1.00e-02 2.22e+01
  ... (remaining 2894 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 603
       0.047 -    0.095: 123
       0.095 -    0.142: 32
       0.142 -    0.189: 0
       0.189 -    0.237: 1
  Chirality restraints: 759
  Sorted by residual:
  chirality pdb=" CB  ILE f 133 "
            pdb=" CA  ILE f 133 "
            pdb=" CG1 ILE f 133 "
            pdb=" CG2 ILE f 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  GLU f  91 "
            pdb=" N   GLU f  91 "
            pdb=" C   GLU f  91 "
            pdb=" CB  GLU f  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  ILE d  24 "
            pdb=" N   ILE d  24 "
            pdb=" C   ILE d  24 "
            pdb=" CB  ILE d  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  ... (remaining 756 not shown)

  Planarity restraints: 786
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN e 121 "   -0.013 2.00e-02 2.50e+03   2.68e-02 7.18e+00
        pdb=" C   ASN e 121 "    0.046 2.00e-02 2.50e+03
        pdb=" O   ASN e 121 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   CYS e 122 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU g  97 "   -0.008 2.00e-02 2.50e+03   1.58e-02 2.50e+00
        pdb=" C   LEU g  97 "    0.027 2.00e-02 2.50e+03
        pdb=" O   LEU g  97 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLN g  98 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS g  95 "   -0.025 5.00e-02 4.00e+02   3.76e-02 2.26e+00
        pdb=" N   PRO g  96 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO g  96 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO g  96 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 783 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 152
        2.69 -     3.25: 4671
        3.25 -     3.80: 7081
        3.80 -     4.35: 8584
        4.35 -     4.90: 14176
  Nonbonded interactions: 34664
  Sorted by model distance:
  nonbonded pdb=" O   ILE d  24 "
            pdb=" OH  TYR e  95 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" OG  SER f  88 "
            pdb=" OE1 GLU f  91 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" O   ASN e 121 "
            pdb=" ND2 ASN e 121 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" OD1 ASP e 126 "
            pdb=" OG  SER e 129 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" O   GLN e  92 "
            pdb=" OH  TYR e  96 "
     model   vdw
     2.204 3.040
  ... (remaining 34659 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'a' and resid 27 through 54)
  selection = (chain 'b' and resid 27 through 54)
}
ncs_group {
  reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153))
  selection = (chain 'f' and resid 33 through 153)
}

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:             0.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     14.700
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
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      :  0.003   0.035   4743  Z= 0.201
  Angle     :  0.710   8.769   6430  Z= 0.363
  Chirality :  0.041   0.237    759
  Planarity :  0.004   0.038    786
  Dihedral  : 17.421  88.742   1776
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 36.87 %
    Favored  : 61.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.34), residues: 569
  helix:  1.39 (0.35), residues: 215
  sheet: -2.08 (0.55), residues: 84
  loop : -2.88 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP f  59 
 HIS   0.004   0.001   HIS g  29 
 PHE   0.012   0.001   PHE n 296 
 TYR   0.025   0.002   TYR f  99 
 ARG   0.005   0.001   ARG e 101 

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 190
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: b   47 THR cc_start: 0.8423 (m) cc_final: 0.8167 (p)
REVERT: b   52 ARG cc_start: 0.6619 (tpt170) cc_final: 0.6358 (ttm170)
REVERT: d   27 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8242 (mt-10)
REVERT: d   43 TRP cc_start: 0.7895 (t60) cc_final: 0.7634 (t60)
REVERT: e   72 ASP cc_start: 0.7079 (m-30) cc_final: 0.6803 (m-30)
REVERT: e   74 ASN cc_start: 0.8062 (m-40) cc_final: 0.7771 (m110)
REVERT: f   37 LYS cc_start: 0.7000 (ttpp) cc_final: 0.6564 (tptp)
REVERT: f   60 GLN cc_start: 0.7220 (pm20) cc_final: 0.6861 (mt0)
REVERT: f  117 ARG cc_start: 0.8050 (ttm170) cc_final: 0.7824 (ttp-110)
REVERT: f  123 MET cc_start: 0.6624 (ttt) cc_final: 0.6176 (ttm)
REVERT: g   71 LYS cc_start: 0.6165 (mtmt) cc_final: 0.5918 (mttt)
REVERT: m  288 LYS cc_start: 0.7961 (tptt) cc_final: 0.7590 (tmtt)
REVERT: n  275 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7928 (tm-30)
  outliers start: 6
  outliers final: 3
  residues processed: 193
  average time/residue: 0.1638
  time to fit residues: 39.2565
Evaluate side-chains
  177 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 174
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain d residue   33 VAL
Chi-restraints excluded: chain f residue  148 VAL
Chi-restraints excluded: chain g residue  110 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0670
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.7718

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS
f  61 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.157455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.129357 restraints weight = 7516.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.133411 restraints weight = 4149.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.136117 restraints weight = 2823.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4743  Z= 0.210
  Angle     :  0.672   7.502   6430  Z= 0.338
  Chirality :  0.042   0.170    759
  Planarity :  0.004   0.039    786
  Dihedral  :  5.382  49.213    701
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  7.34 %
    Allowed  : 29.15 %
    Favored  : 63.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.35), residues: 569
  helix:  2.09 (0.35), residues: 218
  sheet: -2.12 (0.52), residues: 93
  loop : -2.73 (0.33), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP f  59 
 HIS   0.005   0.001   HIS f  81 
 PHE   0.015   0.002   PHE n 296 
 TYR   0.028   0.002   TYR f  99 
 ARG   0.003   0.001   ARG e 117 

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 176
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: d   22 PHE cc_start: 0.6681 (m-80) cc_final: 0.6261 (m-80)
REVERT: e   72 ASP cc_start: 0.7237 (m-30) cc_final: 0.6988 (m-30)
REVERT: e   74 ASN cc_start: 0.7514 (m-40) cc_final: 0.7234 (m110)
REVERT: f   79 GLU cc_start: 0.4062 (OUTLIER) cc_final: 0.3029 (mm-30)
REVERT: f   92 GLN cc_start: 0.7655 (mt0) cc_final: 0.7455 (mt0)
REVERT: f  106 GLU cc_start: 0.8954 (pm20) cc_final: 0.8585 (pm20)
REVERT: m  288 LYS cc_start: 0.8753 (tptt) cc_final: 0.8518 (tmtt)
  outliers start: 38
  outliers final: 24
  residues processed: 190
  average time/residue: 0.1702
  time to fit residues: 40.1317
Evaluate side-chains
  186 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   45 ILE
Chi-restraints excluded: chain a residue   47 THR
Chi-restraints excluded: chain a residue   49 LEU
Chi-restraints excluded: chain b residue   36 ASP
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   44 VAL
Chi-restraints excluded: chain b residue   47 THR
Chi-restraints excluded: chain d residue   52 LEU
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue  122 VAL
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  136 VAL
Chi-restraints excluded: chain e residue  146 LEU
Chi-restraints excluded: chain f residue   43 THR
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   79 GLU
Chi-restraints excluded: chain f residue  134 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain g residue   43 LEU
Chi-restraints excluded: chain g residue   54 THR
Chi-restraints excluded: chain g residue  110 LEU
Chi-restraints excluded: chain m residue  266 LEU
Chi-restraints excluded: chain n residue  293 VAL
Chi-restraints excluded: chain n residue  300 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 40 optimal weight:   20.0000
   chunk 51 optimal weight:    0.5980
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.155761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.128625 restraints weight = 7527.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.132462 restraints weight = 4154.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.135040 restraints weight = 2829.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4743  Z= 0.247
  Angle     :  0.678   7.946   6430  Z= 0.343
  Chirality :  0.042   0.134    759
  Planarity :  0.004   0.036    786
  Dihedral  :  5.376  45.033    699
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  7.53 %
    Allowed  : 33.20 %
    Favored  : 59.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.35), residues: 569
  helix:  2.20 (0.34), residues: 219
  sheet: -1.88 (0.55), residues: 88
  loop : -2.83 (0.33), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP d  43 
 HIS   0.004   0.002   HIS f  81 
 PHE   0.012   0.002   PHE n 296 
 TYR   0.023   0.002   TYR e 150 
 ARG   0.004   0.001   ARG e 117 

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 175
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: d   22 PHE cc_start: 0.6767 (m-80) cc_final: 0.6434 (m-80)
REVERT: d   90 TYR cc_start: 0.7869 (m-80) cc_final: 0.7553 (m-80)
REVERT: d   98 GLU cc_start: 0.7890 (tt0) cc_final: 0.7652 (tm-30)
REVERT: e   72 ASP cc_start: 0.7424 (m-30) cc_final: 0.7119 (m-30)
REVERT: e   74 ASN cc_start: 0.7507 (m-40) cc_final: 0.7307 (m-40)
REVERT: f  104 LYS cc_start: 0.8533 (tptt) cc_final: 0.8316 (mmtm)
REVERT: f  106 GLU cc_start: 0.8894 (pm20) cc_final: 0.8686 (pm20)
REVERT: m  288 LYS cc_start: 0.8755 (tptt) cc_final: 0.8503 (tmtt)
  outliers start: 39
  outliers final: 29
  residues processed: 191
  average time/residue: 0.1621
  time to fit residues: 38.7724
Evaluate side-chains
  191 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   45 ILE
Chi-restraints excluded: chain a residue   47 THR
Chi-restraints excluded: chain a residue   49 LEU
Chi-restraints excluded: chain b residue   36 ASP
Chi-restraints excluded: chain b residue   39 LEU
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   44 VAL
Chi-restraints excluded: chain d residue   52 LEU
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue  122 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  136 VAL
Chi-restraints excluded: chain e residue  146 LEU
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   47 LEU
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue  134 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  146 LEU
Chi-restraints excluded: chain f residue  148 VAL
Chi-restraints excluded: chain g residue   43 LEU
Chi-restraints excluded: chain g residue   61 MET
Chi-restraints excluded: chain g residue  131 VAL
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  269 LEU
Chi-restraints excluded: chain n residue  293 VAL
Chi-restraints excluded: chain n residue  300 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 50 optimal weight:    0.5980
   chunk 32 optimal weight:    0.4980
   chunk 22 optimal weight:    0.4980
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
g  28 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.160095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.133232 restraints weight = 7416.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.137110 restraints weight = 4035.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.139686 restraints weight = 2721.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4743  Z= 0.189
  Angle     :  0.646   8.506   6430  Z= 0.322
  Chirality :  0.041   0.131    759
  Planarity :  0.003   0.034    786
  Dihedral  :  4.751  28.374    697
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  7.72 %
    Allowed  : 31.27 %
    Favored  : 61.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.36), residues: 569
  helix:  2.37 (0.34), residues: 218
  sheet: -1.80 (0.54), residues: 82
  loop : -2.69 (0.34), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP g  55 
 HIS   0.004   0.001   HIS f  81 
 PHE   0.010   0.001   PHE d  34 
 TYR   0.016   0.001   TYR e 150 
 ARG   0.004   0.001   ARG f 117 

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 167
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: b   52 ARG cc_start: 0.7664 (tpt170) cc_final: 0.7381 (ttm170)
REVERT: d   22 PHE cc_start: 0.6571 (m-80) cc_final: 0.6342 (m-80)
REVERT: d   90 TYR cc_start: 0.7772 (m-80) cc_final: 0.7494 (m-80)
REVERT: e   72 ASP cc_start: 0.7363 (m-30) cc_final: 0.7054 (m-30)
REVERT: f  104 LYS cc_start: 0.8531 (tptt) cc_final: 0.8242 (mmtm)
REVERT: f  117 ARG cc_start: 0.8211 (ttp-110) cc_final: 0.7989 (ttm-80)
REVERT: m  289 LEU cc_start: 0.8992 (tp) cc_final: 0.8547 (tp)
  outliers start: 40
  outliers final: 29
  residues processed: 186
  average time/residue: 0.1551
  time to fit residues: 36.5366
Evaluate side-chains
  190 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 161
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   32 CYS
Chi-restraints excluded: chain a residue   47 THR
Chi-restraints excluded: chain a residue   49 LEU
Chi-restraints excluded: chain b residue   36 ASP
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   49 LEU
Chi-restraints excluded: chain d residue   52 LEU
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue  104 VAL
Chi-restraints excluded: chain d residue  122 VAL
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   41 SER
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  136 VAL
Chi-restraints excluded: chain e residue  146 LEU
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  134 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  145 LEU
Chi-restraints excluded: chain f residue  148 VAL
Chi-restraints excluded: chain g residue   43 LEU
Chi-restraints excluded: chain g residue  110 LEU
Chi-restraints excluded: chain m residue  266 LEU
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain n residue  300 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 31 optimal weight:    9.9990
   chunk 15 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.159063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.130102 restraints weight = 7553.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.134360 restraints weight = 4086.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.137231 restraints weight = 2752.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4743  Z= 0.203
  Angle     :  0.697   7.993   6430  Z= 0.342
  Chirality :  0.042   0.152    759
  Planarity :  0.003   0.033    786
  Dihedral  :  4.769  28.160    697
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  7.53 %
    Allowed  : 33.20 %
    Favored  : 59.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.35), residues: 569
  helix:  2.47 (0.34), residues: 217
  sheet: -1.61 (0.55), residues: 86
  loop : -2.75 (0.33), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP g  55 
 HIS   0.005   0.001   HIS f  81 
 PHE   0.009   0.001   PHE n 296 
 TYR   0.028   0.001   TYR b  33 
 ARG   0.003   0.000   ARG e 117 

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 168
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: b   52 ARG cc_start: 0.7689 (tpt170) cc_final: 0.7399 (tpp-160)
REVERT: d   90 TYR cc_start: 0.7880 (m-80) cc_final: 0.7525 (m-80)
REVERT: e   72 ASP cc_start: 0.7413 (m-30) cc_final: 0.7034 (m-30)
REVERT: f   59 TRP cc_start: 0.7721 (m100) cc_final: 0.7180 (m100)
REVERT: m  289 LEU cc_start: 0.8971 (tp) cc_final: 0.8509 (tp)
  outliers start: 39
  outliers final: 35
  residues processed: 185
  average time/residue: 0.1514
  time to fit residues: 35.7368
Evaluate side-chains
  194 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 159
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   32 CYS
Chi-restraints excluded: chain a residue   47 THR
Chi-restraints excluded: chain a residue   49 LEU
Chi-restraints excluded: chain b residue   36 ASP
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   49 LEU
Chi-restraints excluded: chain d residue   52 LEU
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue  104 VAL
Chi-restraints excluded: chain d residue  122 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  132 THR
Chi-restraints excluded: chain e residue  136 VAL
Chi-restraints excluded: chain e residue  146 LEU
Chi-restraints excluded: chain f residue   34 THR
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  134 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  145 LEU
Chi-restraints excluded: chain f residue  146 LEU
Chi-restraints excluded: chain f residue  148 VAL
Chi-restraints excluded: chain g residue   43 LEU
Chi-restraints excluded: chain g residue  110 LEU
Chi-restraints excluded: chain g residue  124 VAL
Chi-restraints excluded: chain m residue  266 LEU
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  269 LEU
Chi-restraints excluded: chain n residue  293 VAL
Chi-restraints excluded: chain n residue  300 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0970
   chunk 20 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.154494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.127254 restraints weight = 7523.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.131046 restraints weight = 4187.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.133605 restraints weight = 2865.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.3519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4743  Z= 0.299
  Angle     :  0.750   8.177   6430  Z= 0.367
  Chirality :  0.044   0.136    759
  Planarity :  0.004   0.035    786
  Dihedral  :  5.115  22.991    697
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  9.27 %
    Allowed  : 32.63 %
    Favored  : 58.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.35), residues: 569
  helix:  2.18 (0.34), residues: 217
  sheet: -2.07 (0.54), residues: 87
  loop : -2.58 (0.34), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP g  55 
 HIS   0.005   0.001   HIS f  81 
 PHE   0.016   0.002   PHE e 110 
 TYR   0.016   0.002   TYR e 149 
 ARG   0.004   0.001   ARG e 117 

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 170
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
REVERT: a   32 CYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7986 (t)
REVERT: d   90 TYR cc_start: 0.7891 (m-80) cc_final: 0.7546 (m-80)
REVERT: e   72 ASP cc_start: 0.7545 (m-30) cc_final: 0.7173 (m-30)
REVERT: e  109 ASN cc_start: 0.7953 (m-40) cc_final: 0.7635 (p0)
REVERT: m  289 LEU cc_start: 0.9045 (tp) cc_final: 0.8823 (tt)
  outliers start: 48
  outliers final: 41
  residues processed: 192
  average time/residue: 0.1538
  time to fit residues: 37.4492
Evaluate side-chains
  208 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 166
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   32 CYS
Chi-restraints excluded: chain a residue   47 THR
Chi-restraints excluded: chain a residue   49 LEU
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   36 ASP
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   44 VAL
Chi-restraints excluded: chain b residue   47 THR
Chi-restraints excluded: chain b residue   49 LEU
Chi-restraints excluded: chain d residue   52 LEU
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain d residue  104 VAL
Chi-restraints excluded: chain d residue  122 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   41 SER
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  132 THR
Chi-restraints excluded: chain e residue  136 VAL
Chi-restraints excluded: chain e residue  146 LEU
Chi-restraints excluded: chain f residue   34 THR
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   43 THR
Chi-restraints excluded: chain f residue   47 LEU
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   92 GLN
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  133 ILE
Chi-restraints excluded: chain f residue  134 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  146 LEU
Chi-restraints excluded: chain f residue  148 VAL
Chi-restraints excluded: chain g residue   43 LEU
Chi-restraints excluded: chain g residue   76 SER
Chi-restraints excluded: chain g residue  124 VAL
Chi-restraints excluded: chain g residue  131 VAL
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  269 LEU
Chi-restraints excluded: chain n residue  293 VAL
Chi-restraints excluded: chain n residue  300 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0070
   chunk 44 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.157885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.129422 restraints weight = 7572.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.133574 restraints weight = 4102.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.136391 restraints weight = 2786.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4743  Z= 0.203
  Angle     :  0.731   8.791   6430  Z= 0.357
  Chirality :  0.043   0.157    759
  Planarity :  0.003   0.032    786
  Dihedral  :  4.943  28.874    697
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 33.98 %
    Favored  : 58.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.35), residues: 569
  helix:  2.29 (0.34), residues: 216
  sheet: -1.61 (0.55), residues: 82
  loop : -2.58 (0.34), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP d  43 
 HIS   0.005   0.001   HIS f  81 
 PHE   0.016   0.001   PHE b  40 
 TYR   0.015   0.001   TYR e 150 
 ARG   0.003   0.000   ARG e 117 

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 168
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   32 CYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7828 (t)
REVERT: d   90 TYR cc_start: 0.7852 (m-80) cc_final: 0.7516 (m-80)
REVERT: e   72 ASP cc_start: 0.7497 (m-30) cc_final: 0.7138 (m-30)
REVERT: e  109 ASN cc_start: 0.7989 (m-40) cc_final: 0.7723 (p0)
REVERT: g   85 TYR cc_start: 0.8345 (m-80) cc_final: 0.7974 (m-80)
  outliers start: 37
  outliers final: 34
  residues processed: 185
  average time/residue: 0.1592
  time to fit residues: 37.4513
Evaluate side-chains
  196 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 161
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   32 CYS
Chi-restraints excluded: chain a residue   49 LEU
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   36 ASP
Chi-restraints excluded: chain b residue   47 THR
Chi-restraints excluded: chain b residue   49 LEU
Chi-restraints excluded: chain d residue   52 LEU
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   41 SER
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  132 THR
Chi-restraints excluded: chain e residue  136 VAL
Chi-restraints excluded: chain e residue  146 LEU
Chi-restraints excluded: chain f residue   34 THR
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   47 LEU
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   92 GLN
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  134 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  145 LEU
Chi-restraints excluded: chain f residue  146 LEU
Chi-restraints excluded: chain f residue  148 VAL
Chi-restraints excluded: chain g residue   43 LEU
Chi-restraints excluded: chain g residue  110 LEU
Chi-restraints excluded: chain g residue  124 VAL
Chi-restraints excluded: chain m residue  266 LEU
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  269 LEU
Chi-restraints excluded: chain n residue  300 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.158445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.129900 restraints weight = 7532.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.134108 restraints weight = 4141.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.136953 restraints weight = 2804.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4743  Z= 0.212
  Angle     :  0.740   7.856   6430  Z= 0.358
  Chirality :  0.043   0.139    759
  Planarity :  0.003   0.032    786
  Dihedral  :  4.933  26.671    697
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  7.72 %
    Allowed  : 34.56 %
    Favored  : 57.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.35), residues: 569
  helix:  2.27 (0.34), residues: 215
  sheet: -1.51 (0.53), residues: 87
  loop : -2.56 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP d  43 
 HIS   0.005   0.001   HIS f  81 
 PHE   0.012   0.001   PHE b  40 
 TYR   0.017   0.001   TYR n 283 
 ARG   0.004   0.000   ARG f 117 

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 168
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: d   90 TYR cc_start: 0.7826 (m-80) cc_final: 0.7469 (m-80)
REVERT: e   72 ASP cc_start: 0.7497 (m-30) cc_final: 0.7132 (m-30)
REVERT: e  109 ASN cc_start: 0.8019 (m-40) cc_final: 0.7727 (p0)
  outliers start: 40
  outliers final: 36
  residues processed: 187
  average time/residue: 0.1589
  time to fit residues: 37.6449
Evaluate side-chains
  198 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 162
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 LEU
Chi-restraints excluded: chain b residue   32 CYS
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   49 LEU
Chi-restraints excluded: chain d residue   52 LEU
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   41 SER
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  132 THR
Chi-restraints excluded: chain e residue  146 LEU
Chi-restraints excluded: chain f residue   34 THR
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   43 THR
Chi-restraints excluded: chain f residue   47 LEU
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   92 GLN
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  133 ILE
Chi-restraints excluded: chain f residue  134 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  145 LEU
Chi-restraints excluded: chain f residue  146 LEU
Chi-restraints excluded: chain f residue  148 VAL
Chi-restraints excluded: chain g residue   43 LEU
Chi-restraints excluded: chain g residue   76 SER
Chi-restraints excluded: chain g residue  110 LEU
Chi-restraints excluded: chain g residue  124 VAL
Chi-restraints excluded: chain m residue  266 LEU
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  269 LEU
Chi-restraints excluded: chain n residue  293 VAL
Chi-restraints excluded: chain n residue  300 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 37 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0020
   chunk 6 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.7194

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.153723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.125303 restraints weight = 7609.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.129360 restraints weight = 4142.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.132144 restraints weight = 2826.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.3885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4743  Z= 0.305
  Angle     :  0.839   8.604   6430  Z= 0.407
  Chirality :  0.045   0.145    759
  Planarity :  0.004   0.035    786
  Dihedral  :  5.349  27.573    697
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  8.11 %
    Allowed  : 33.40 %
    Favored  : 58.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.35), residues: 569
  helix:  2.07 (0.34), residues: 217
  sheet: -2.06 (0.53), residues: 87
  loop : -2.62 (0.33), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP d  43 
 HIS   0.005   0.002   HIS f  81 
 PHE   0.011   0.002   PHE b  40 
 TYR   0.028   0.002   TYR n 283 
 ARG   0.016   0.001   ARG b  52 

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 173
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: b   52 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7115 (ttm170)
REVERT: d   90 TYR cc_start: 0.7863 (m-80) cc_final: 0.7484 (m-80)
REVERT: e   72 ASP cc_start: 0.7687 (m-30) cc_final: 0.7298 (m-30)
REVERT: e  109 ASN cc_start: 0.8130 (m-40) cc_final: 0.7844 (p0)
REVERT: m  289 LEU cc_start: 0.8844 (tp) cc_final: 0.8635 (tt)
  outliers start: 42
  outliers final: 38
  residues processed: 191
  average time/residue: 0.1618
  time to fit residues: 39.0849
Evaluate side-chains
  206 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 168
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 LEU
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   32 CYS
Chi-restraints excluded: chain b residue   36 ASP
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   47 THR
Chi-restraints excluded: chain b residue   49 LEU
Chi-restraints excluded: chain d residue   52 LEU
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   41 SER
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  132 THR
Chi-restraints excluded: chain e residue  136 VAL
Chi-restraints excluded: chain e residue  146 LEU
Chi-restraints excluded: chain f residue   34 THR
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   43 THR
Chi-restraints excluded: chain f residue   47 LEU
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   92 GLN
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  133 ILE
Chi-restraints excluded: chain f residue  134 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  145 LEU
Chi-restraints excluded: chain f residue  146 LEU
Chi-restraints excluded: chain f residue  148 VAL
Chi-restraints excluded: chain g residue   43 LEU
Chi-restraints excluded: chain g residue   76 SER
Chi-restraints excluded: chain g residue  124 VAL
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  269 LEU
Chi-restraints excluded: chain n residue  293 VAL
Chi-restraints excluded: chain n residue  300 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS
f  60 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.159221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.131292 restraints weight = 7502.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.135371 restraints weight = 4058.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.138273 restraints weight = 2754.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.4040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4743  Z= 0.218
  Angle     :  0.794  10.461   6430  Z= 0.382
  Chirality :  0.043   0.149    759
  Planarity :  0.003   0.032    786
  Dihedral  :  5.026  25.214    697
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 35.52 %
    Favored  : 57.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.35), residues: 569
  helix:  2.28 (0.34), residues: 216
  sheet: -1.57 (0.55), residues: 82
  loop : -2.58 (0.33), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP d  43 
 HIS   0.004   0.001   HIS f  81 
 PHE   0.010   0.001   PHE n 296 
 TYR   0.021   0.001   TYR n 283 
 ARG   0.012   0.001   ARG b  52 

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

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

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1138 Ramachandran restraints generated.
    569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 169
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: b   52 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7026 (ttm170)
REVERT: d   27 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7269 (mt-10)
REVERT: d   90 TYR cc_start: 0.7790 (m-80) cc_final: 0.7423 (m-80)
REVERT: e   72 ASP cc_start: 0.7571 (m-30) cc_final: 0.7223 (m-30)
REVERT: e  109 ASN cc_start: 0.8058 (m-40) cc_final: 0.7790 (p0)
REVERT: e  117 ARG cc_start: 0.7664 (ttt-90) cc_final: 0.7447 (ttt-90)
REVERT: f  111 TYR cc_start: 0.7528 (m-80) cc_final: 0.6966 (m-80)
REVERT: g   85 TYR cc_start: 0.8318 (m-80) cc_final: 0.7951 (m-80)
REVERT: m  269 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8615 (tp)
REVERT: m  288 LYS cc_start: 0.8765 (tmtt) cc_final: 0.8485 (tmtt)
  outliers start: 37
  outliers final: 30
  residues processed: 183
  average time/residue: 0.1549
  time to fit residues: 35.6308
Evaluate side-chains
  195 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 164
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   49 LEU
Chi-restraints excluded: chain a residue   51 LEU
Chi-restraints excluded: chain b residue   32 CYS
Chi-restraints excluded: chain b residue   49 LEU
Chi-restraints excluded: chain d residue   52 LEU
Chi-restraints excluded: chain d residue   86 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   41 SER
Chi-restraints excluded: chain e residue   48 THR
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  132 THR
Chi-restraints excluded: chain e residue  136 VAL
Chi-restraints excluded: chain e residue  146 LEU
Chi-restraints excluded: chain f residue   34 THR
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   43 THR
Chi-restraints excluded: chain f residue   47 LEU
Chi-restraints excluded: chain f residue   48 THR
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  133 ILE
Chi-restraints excluded: chain f residue  134 VAL
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  146 LEU
Chi-restraints excluded: chain f residue  148 VAL
Chi-restraints excluded: chain g residue   43 LEU
Chi-restraints excluded: chain g residue   76 SER
Chi-restraints excluded: chain g residue  124 VAL
Chi-restraints excluded: chain m residue  268 VAL
Chi-restraints excluded: chain m residue  269 LEU
Chi-restraints excluded: chain n residue  300 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 19 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 24 optimal weight:    0.0030
   chunk 47 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
e  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.160722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.133347 restraints weight = 7480.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.137303 restraints weight = 4131.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.139831 restraints weight = 2819.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4743  Z= 0.211
  Angle     :  0.782   9.741   6430  Z= 0.377
  Chirality :  0.042   0.144    759
  Planarity :  0.003   0.031    786
  Dihedral  :  4.915  25.690    697
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 36.68 %
    Favored  : 57.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.35), residues: 569
  helix:  2.38 (0.34), residues: 215
  sheet: -1.35 (0.55), residues: 82
  loop : -2.60 (0.33), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP d  43 
 HIS   0.005   0.001   HIS f  81 
 PHE   0.012   0.001   PHE f  87 
 TYR   0.029   0.001   TYR f  99 
 ARG   0.013   0.001   ARG f 117 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1778.32 seconds
wall clock time: 31 minutes 42.36 seconds (1902.36 seconds total)