Starting phenix.real_space_refine
on Sun Apr 27 05:00:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yc0_39128/04_2025/8yc0_39128.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yc0_39128/04_2025/8yc0_39128.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yc0_39128/04_2025/8yc0_39128.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yc0_39128/04_2025/8yc0_39128.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yc0_39128/04_2025/8yc0_39128.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yc0_39128/04_2025/8yc0_39128.cif"
  }
  resolution = 4.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.004
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    3009      2.51       5
     N     731      2.21       5
     O     858      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4635
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "a"
      Number of atoms: 203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 203
          Classifications: {'peptide': 26}
          Link IDs: {'PTRANS': 1, 'TRANS': 24}
    Chain: "b"
      Number of atoms: 218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 218
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
    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: 907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 907
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 2, 'TRANS': 112}
    Chain: "m"
      Number of atoms: 268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 268
          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: 3.40, per 1000 atoms: 0.73
  Number of scatterers: 4635
  At special positions: 0
  Unit cell: (100.004, 86.96, 89.134, 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     858      8.00
     N     731      7.00
     C    3009      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=2.03
    Simple disulfide: pdb=" SG  CYS d  37 " - pdb=" SG  CYS d  73 " distance=2.04
    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=2.04
    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=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Conformation dependent library (CDL) restraints added in 508.1 milliseconds
  

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1084

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 8 sheets defined
      40.0% alpha, 15.1% 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 26 through 50
      removed outlier: 4.043A  pdb=" N   LYS a  30 " --> pdb=" O   LEU a  26 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   LEU a  31 " --> pdb=" O   LEU a  27 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   TYR a  33 " --> pdb=" O   PRO a  29 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   LEU a  34 " --> pdb=" O   LYS a  30 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   LEU a  35 " --> pdb=" O   LEU a  31 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 29 through 54
    Processing helix  chain 'd' and resid 100 through 124
      removed outlier: 3.620A  pdb=" N   VAL d 104 " --> pdb=" O   ASP d 100 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ALA d 105 " --> pdb=" O   PRO d 101 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   GLY d 106 " --> pdb=" O   ALA d 102 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 126 through 152
      removed outlier: 3.538A  pdb=" N   VAL e 130 " --> pdb=" O   ASP e 126 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 126 through 154
      removed outlier: 3.517A  pdb=" N   ASN f 154 " --> pdb=" O   TYR f 150 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 76 through 80
      removed outlier: 3.921A  pdb=" N   ASP g  80 " --> pdb=" O   ASN g  77 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 111 through 137
      removed outlier: 3.694A  pdb=" N   SER g 116 " --> pdb=" O   ALA g 112 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   GLY g 117 " --> pdb=" O   ALA g 113 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 257 through 289
      removed outlier: 3.582A  pdb=" N   MET m 261 " --> pdb=" O   GLU m 257 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 253 through 288
    Processing sheet with id=AA1, first strand: chain 'd' and resid 32 through 35
      removed outlier: 7.525A  pdb=" N   VAL d  33 " --> pdb=" O   LEU d  60 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU d  60 " --> pdb=" O   VAL d  33 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'd' and resid 41 through 46
      removed outlier: 3.843A  pdb=" N   VAL d  44 " --> pdb=" O   ILE d  70 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ILE d  70 " --> pdb=" O   VAL d  44 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   GLY d  46 " --> pdb=" O   ARG d  68 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   ARG d  68 " --> pdb=" O   GLY d  46 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   THR d  85 " --> pdb=" O   TYR e 111 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   TYR e 113 " --> pdb=" O   THR d  85 " (cutoff:3.500A)
      removed outlier: 5.635A  pdb=" N   GLN d  87 " --> pdb=" O   TYR e 113 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   ARG e 115 " --> pdb=" O   GLN d  87 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   HIS d  89 " --> pdb=" O   ARG e 115 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   PHE e 110 " --> pdb=" O   CYS e  98 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   CYS e  98 " --> pdb=" O   PHE e 110 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL e  97 " --> pdb=" O   GLN e  60 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   TYR e  99 " --> pdb=" O   LEU e  58 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU e  58 " --> pdb=" O   TYR e  99 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 41
      removed outlier: 3.705A  pdb=" N   LYS e  37 " --> pdb=" O   THR e  48 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLY e  76 " --> pdb=" O   SER e  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 38
      removed outlier: 4.006A  pdb=" N   LYS f  37 " --> pdb=" O   THR f  48 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   THR f  48 " --> pdb=" O   LYS f  37 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU f  82 " --> pdb=" O   LEU f  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'f' and resid 112 through 115
      removed outlier: 5.591A  pdb=" N   TYR f 113 " --> pdb=" O   TYR g 100 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLY g  83 " --> pdb=" O   VAL g  99 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 34
      removed outlier: 3.960A  pdb=" N   LEU g  43 " --> pdb=" O   TYR g  34 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLY g  75 " --> pdb=" O   VAL g  42 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   LEU g  44 " --> pdb=" O   ASN g  73 " (cutoff:3.500A)
      removed outlier: 5.446A  pdb=" N   ASN g  73 " --> pdb=" O   LEU g  44 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'g' and resid 54 through 57
      removed outlier: 6.318A  pdb=" N   TRP g  55 " --> pdb=" O   ILE g  62 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ILE g  62 " --> pdb=" O   TRP g  55 " (cutoff:3.500A)

    223 hydrogen bonds defined for protein.
    648 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: 1.11

  Time building geometry restraints manager: 1.18 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: 1433
        1.34 -     1.47: 1125
        1.47 -     1.59: 2115
        1.59 -     1.71: 0
        1.71 -     1.83: 51
  Bond restraints: 4724
  Sorted by residual:
  bond pdb=" C   ASP a  28 "
       pdb=" N   PRO a  29 "
    ideal  model  delta    sigma   weight residual
    1.333  1.364 -0.031 1.44e-02 4.82e+03 4.62e+00
  bond pdb=" CA  ASP e  63 "
       pdb=" CB  ASP e  63 "
    ideal  model  delta    sigma   weight residual
    1.530  1.551 -0.021 1.69e-02 3.50e+03 1.55e+00
  bond pdb=" CB  PRO f 100 "
       pdb=" CG  PRO f 100 "
    ideal  model  delta    sigma   weight residual
    1.492  1.552 -0.060 5.00e-02 4.00e+02 1.46e+00
  bond pdb=" N   ASN e 121 "
       pdb=" CA  ASN e 121 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.17e+00
  bond pdb=" CB  ASP f 137 "
       pdb=" CG  ASP f 137 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.10e+00
  ... (remaining 4719 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 6304
        2.57 -     5.14: 80
        5.14 -     7.71: 14
        7.71 -    10.28: 4
       10.28 -    12.85: 2
  Bond angle restraints: 6404
  Sorted by residual:
  angle pdb=" C   LEU a  27 "
        pdb=" CA  LEU a  27 "
        pdb=" CB  LEU a  27 "
      ideal   model   delta    sigma   weight residual
     115.89  109.41    6.48 1.32e+00 5.74e-01 2.41e+01
  angle pdb=" CA  CYS f  49 "
        pdb=" CB  CYS f  49 "
        pdb=" SG  CYS f  49 "
      ideal   model   delta    sigma   weight residual
     114.40  123.14   -8.74 2.30e+00 1.89e-01 1.44e+01
  angle pdb=" CA  LEU f 114 "
        pdb=" CB  LEU f 114 "
        pdb=" CG  LEU f 114 "
      ideal   model   delta    sigma   weight residual
     116.30  129.15  -12.85 3.50e+00 8.16e-02 1.35e+01
  angle pdb=" N   GLY d  46 "
        pdb=" CA  GLY d  46 "
        pdb=" C   GLY d  46 "
      ideal   model   delta    sigma   weight residual
     111.56  115.25   -3.69 1.01e+00 9.80e-01 1.33e+01
  angle pdb=" CB  MET m 262 "
        pdb=" CG  MET m 262 "
        pdb=" SD  MET m 262 "
      ideal   model   delta    sigma   weight residual
     112.70  123.09  -10.39 3.00e+00 1.11e-01 1.20e+01
  ... (remaining 6399 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.69: 2343
       16.69 -    33.39: 390
       33.39 -    50.08: 118
       50.08 -    66.78: 20
       66.78 -    83.47: 6
  Dihedral angle restraints: 2877
    sinusoidal: 1184
      harmonic: 1693
  Sorted by residual:
  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  175.13  -82.13     1      1.00e+01 1.00e-02 8.28e+01
  dihedral pdb=" CB  CYS e  49 "
           pdb=" SG  CYS e  49 "
           pdb=" SG  CYS e  98 "
           pdb=" CB  CYS e  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -15.84  -70.16     1      1.00e+01 1.00e-02 6.34e+01
  dihedral pdb=" CB  CYS g 104 "
           pdb=" SG  CYS g 104 "
           pdb=" SG  CYS g 107 "
           pdb=" CB  CYS g 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.55   68.55     1      1.00e+01 1.00e-02 6.09e+01
  ... (remaining 2874 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 504
       0.037 -    0.074: 174
       0.074 -    0.111: 55
       0.111 -    0.148: 16
       0.148 -    0.186: 2
  Chirality restraints: 751
  Sorted by residual:
  chirality pdb=" CA  ASP e  63 "
            pdb=" N   ASP e  63 "
            pdb=" C   ASP e  63 "
            pdb=" CB  ASP e  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.61e-01
  chirality pdb=" CA  ILE d  70 "
            pdb=" N   ILE d  70 "
            pdb=" C   ILE d  70 "
            pdb=" CB  ILE d  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.93e-01
  chirality pdb=" CA  ASN e 121 "
            pdb=" N   ASN e 121 "
            pdb=" C   ASN e 121 "
            pdb=" CB  ASN e 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.43e-01
  ... (remaining 748 not shown)

  Planarity restraints: 785
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR f  99 "    0.057 5.00e-02 4.00e+02   8.59e-02 1.18e+01
        pdb=" N   PRO f 100 "   -0.149 5.00e-02 4.00e+02
        pdb=" CA  PRO f 100 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO f 100 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR e  99 "    0.037 5.00e-02 4.00e+02   5.70e-02 5.19e+00
        pdb=" N   PRO e 100 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO e 100 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO e 100 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS f 104 "    0.020 5.00e-02 4.00e+02   3.10e-02 1.53e+00
        pdb=" N   PRO f 105 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO f 105 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO f 105 "    0.017 5.00e-02 4.00e+02
  ... (remaining 782 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 95
        2.67 -     3.23: 4543
        3.23 -     3.79: 7049
        3.79 -     4.34: 8421
        4.34 -     4.90: 13883
  Nonbonded interactions: 33991
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP e 126 "
            pdb=" N   VAL e 127 "
     model   vdw
     2.114 3.120
  nonbonded pdb=" O   GLN e  92 "
            pdb=" OH  TYR e  96 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" N   GLU f  56 "
            pdb=" OE1 GLU f  56 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" NE2 GLN e  60 "
            pdb=" OD1 ASN e  65 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" O   ILE d  24 "
            pdb=" OH  TYR e  95 "
     model   vdw
     2.279 3.040
  ... (remaining 33986 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 28 through 50)
  selection = (chain 'b' and resid 28 through 50)
}
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:             0.450
  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:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.570
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6349
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   4733  Z= 0.161
  Angle     :  0.781  12.853   6422  Z= 0.392
  Chirality :  0.043   0.186    751
  Planarity :  0.005   0.086    785
  Dihedral  : 17.513  83.473   1766
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 39.73 %
    Favored  : 59.69 %
  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 (0.34), residues: 565
  helix:  2.06 (0.33), residues: 212
  sheet: -1.22 (0.64), residues: 74
  loop : -2.81 (0.30), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP d  43 
 HIS   0.004   0.001   HIS f  61 
 PHE   0.020   0.001   PHE g 118 
 TYR   0.016   0.001   TYR b  42 
 ARG   0.005   0.000   ARG d  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17723 (  223)
  hydrogen bonds       : angle       6.27538 (  648)
  SS BOND              : bond        0.00354 (    9)
  SS BOND              : angle       2.20836 (   18)
  covalent geometry    : bond        0.00354 ( 4724)
  covalent geometry    : angle       0.77359 ( 6404)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 153
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: d   71 TYR cc_start: 0.7273 (m-80) cc_final: 0.6834 (m-10)
REVERT: d   90 TYR cc_start: 0.7388 (m-80) cc_final: 0.6902 (m-80)
REVERT: e   36 TYR cc_start: 0.6981 (m-80) cc_final: 0.5299 (m-10)
REVERT: e   46 ILE cc_start: 0.8085 (mp) cc_final: 0.7838 (mm)
REVERT: e   47 LEU cc_start: 0.8296 (mt) cc_final: 0.8084 (tt)
REVERT: e   49 CYS cc_start: 0.6913 (t) cc_final: 0.5597 (t)
REVERT: e   85 LYS cc_start: 0.7718 (mptt) cc_final: 0.7517 (mptt)
REVERT: e   91 GLU cc_start: 0.8234 (tp30) cc_final: 0.8019 (tm-30)
REVERT: e   92 GLN cc_start: 0.7710 (tt0) cc_final: 0.7193 (tt0)
REVERT: e  117 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7622 (ttt180)
REVERT: e  120 GLU cc_start: 0.8013 (pp20) cc_final: 0.7719 (pp20)
REVERT: e  123 MET cc_start: 0.5173 (mtt) cc_final: 0.4753 (ptp)
REVERT: g   38 GLU cc_start: 0.8295 (pm20) cc_final: 0.8071 (pm20)
REVERT: g   43 LEU cc_start: 0.7667 (mt) cc_final: 0.7448 (mt)
REVERT: g   80 ASP cc_start: 0.8028 (m-30) cc_final: 0.7779 (t0)
REVERT: g  111 ASN cc_start: 0.7321 (m110) cc_final: 0.6954 (p0)
REVERT: m  286 LYS cc_start: 0.7448 (tppt) cc_final: 0.7238 (tptt)
  outliers start: 3
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1871
  time to fit residues: 35.1059
Evaluate side-chains
  136 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
d  38 ASN
** g  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
n 259 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.184885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.159468 restraints weight = 8717.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.159508 restraints weight = 13106.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.160672 restraints weight = 10109.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
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   0.033   4733  Z= 0.170
  Angle     :  0.714   5.993   6422  Z= 0.372
  Chirality :  0.045   0.171    751
  Planarity :  0.005   0.055    785
  Dihedral  :  5.114  50.333    692
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.07 %
    Favored  : 95.74 %
  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: -1.04 (0.34), residues: 565
  helix:  2.03 (0.33), residues: 217
  sheet: -1.30 (0.61), residues: 82
  loop : -3.01 (0.30), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP e  59 
 HIS   0.008   0.002   HIS f  61 
 PHE   0.014   0.001   PHE b  40 
 TYR   0.011   0.002   TYR d  79 
 ARG   0.003   0.001   ARG e 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04944 (  223)
  hydrogen bonds       : angle       4.53383 (  648)
  SS BOND              : bond        0.00371 (    9)
  SS BOND              : angle       2.06632 (   18)
  covalent geometry    : bond        0.00388 ( 4724)
  covalent geometry    : angle       0.70642 ( 6404)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: e   36 TYR cc_start: 0.8125 (m-80) cc_final: 0.6936 (m-10)
REVERT: e  117 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7378 (ttt180)
REVERT: f  110 PHE cc_start: 0.8216 (p90) cc_final: 0.7907 (p90)
REVERT: f  121 ASN cc_start: 0.8333 (m-40) cc_final: 0.7000 (m-40)
REVERT: f  128 MET cc_start: 0.6397 (mpp) cc_final: 0.6174 (mmt)
REVERT: g   39 ASP cc_start: 0.8354 (p0) cc_final: 0.7962 (p0)
REVERT: g   80 ASP cc_start: 0.8348 (m-30) cc_final: 0.8123 (t0)
REVERT: m  286 LYS cc_start: 0.8595 (tppt) cc_final: 0.8362 (tptt)
REVERT: n  259 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7938 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1966
  time to fit residues: 41.3964
Evaluate side-chains
  138 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0070
   chunk 52 optimal weight:    0.6980
   chunk 10 optimal weight:    5.9990
   chunk 2 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
d  89 HIS
e  92 GLN
** g  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
n 259 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.182012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.159916 restraints weight = 7634.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.160757 restraints weight = 6537.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.161569 restraints weight = 5800.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4733  Z= 0.128
  Angle     :  0.650   6.390   6422  Z= 0.335
  Chirality :  0.043   0.188    751
  Planarity :  0.005   0.055    785
  Dihedral  :  5.009  51.354    692
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  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 (0.34), residues: 565
  helix:  2.34 (0.32), residues: 218
  sheet: -1.26 (0.58), residues: 85
  loop : -2.92 (0.30), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP d  43 
 HIS   0.004   0.001   HIS d  89 
 PHE   0.038   0.001   PHE b  40 
 TYR   0.013   0.001   TYR g  34 
 ARG   0.005   0.001   ARG g 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04439 (  223)
  hydrogen bonds       : angle       4.16287 (  648)
  SS BOND              : bond        0.00420 (    9)
  SS BOND              : angle       1.94651 (   18)
  covalent geometry    : bond        0.00274 ( 4724)
  covalent geometry    : angle       0.64261 ( 6404)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
REVERT: e   36 TYR cc_start: 0.7853 (m-80) cc_final: 0.6506 (m-80)
REVERT: e   49 CYS cc_start: 0.6380 (t) cc_final: 0.5972 (t)
REVERT: e  115 ARG cc_start: 0.8040 (tpt170) cc_final: 0.7821 (tpt170)
REVERT: e  117 ARG cc_start: 0.7708 (mtp180) cc_final: 0.7365 (ttt180)
REVERT: f  110 PHE cc_start: 0.8179 (p90) cc_final: 0.7929 (p90)
REVERT: f  115 ARG cc_start: 0.8275 (ttt-90) cc_final: 0.7972 (tpt-90)
REVERT: f  120 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7703 (tm-30)
REVERT: f  121 ASN cc_start: 0.8155 (m-40) cc_final: 0.7474 (m-40)
REVERT: f  125 MET cc_start: 0.8248 (ppp) cc_final: 0.7966 (ppp)
REVERT: f  128 MET cc_start: 0.6157 (mpp) cc_final: 0.5781 (mmt)
REVERT: g   39 ASP cc_start: 0.8053 (p0) cc_final: 0.7711 (p0)
REVERT: g   80 ASP cc_start: 0.8302 (m-30) cc_final: 0.7837 (t0)
REVERT: m  286 LYS cc_start: 0.8542 (tppt) cc_final: 0.8236 (tptt)
REVERT: n  265 MET cc_start: 0.8544 (tpp) cc_final: 0.7826 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1800
  time to fit residues: 34.9557
Evaluate side-chains
  129 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0980
   chunk 10 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
d  38 ASN
** d  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
e  92 GLN
f  81 HIS
** g  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
n 259 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.180680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.158944 restraints weight = 7650.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.159729 restraints weight = 6421.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.159856 restraints weight = 5656.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.3563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4733  Z= 0.133
  Angle     :  0.654   6.565   6422  Z= 0.338
  Chirality :  0.043   0.181    751
  Planarity :  0.004   0.050    785
  Dihedral  :  4.909  49.087    692
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  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: -0.81 (0.34), residues: 565
  helix:  2.11 (0.33), residues: 221
  sheet: -1.20 (0.64), residues: 76
  loop : -2.82 (0.30), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP f  59 
 HIS   0.003   0.001   HIS f  61 
 PHE   0.040   0.001   PHE b  40 
 TYR   0.021   0.001   TYR e  99 
 ARG   0.005   0.001   ARG f 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04365 (  223)
  hydrogen bonds       : angle       4.03192 (  648)
  SS BOND              : bond        0.00589 (    9)
  SS BOND              : angle       1.72069 (   18)
  covalent geometry    : bond        0.00290 ( 4724)
  covalent geometry    : angle       0.64809 ( 6404)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.476 
Fit side-chains
REVERT: d   70 ILE cc_start: 0.8560 (mp) cc_final: 0.8252 (tt)
REVERT: e   36 TYR cc_start: 0.7985 (m-80) cc_final: 0.6851 (m-80)
REVERT: e   98 CYS cc_start: 0.3572 (p) cc_final: 0.3254 (p)
REVERT: e  117 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7413 (ttt180)
REVERT: f   89 GLU cc_start: 0.7398 (tt0) cc_final: 0.6571 (tt0)
REVERT: f  110 PHE cc_start: 0.8139 (p90) cc_final: 0.7907 (p90)
REVERT: f  115 ARG cc_start: 0.8263 (ttt-90) cc_final: 0.8054 (tpt-90)
REVERT: f  120 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7787 (tm-30)
REVERT: f  121 ASN cc_start: 0.8124 (m-40) cc_final: 0.7279 (m-40)
REVERT: f  128 MET cc_start: 0.6408 (mpp) cc_final: 0.5869 (mmt)
REVERT: g   39 ASP cc_start: 0.8262 (p0) cc_final: 0.7842 (p0)
REVERT: g   57 LYS cc_start: 0.7204 (tptm) cc_final: 0.6984 (tptm)
REVERT: m  286 LYS cc_start: 0.8535 (tppt) cc_final: 0.8239 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1730
  time to fit residues: 32.0623
Evaluate side-chains
  126 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
d  38 ASN
e  92 GLN
f  81 HIS
** g  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.179770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.159057 restraints weight = 7801.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.158838 restraints weight = 8921.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.159658 restraints weight = 8637.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.3822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4733  Z= 0.132
  Angle     :  0.660   6.635   6422  Z= 0.339
  Chirality :  0.043   0.172    751
  Planarity :  0.004   0.042    785
  Dihedral  :  5.019  51.731    692
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  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: -0.78 (0.34), residues: 565
  helix:  2.14 (0.33), residues: 220
  sheet: -1.10 (0.61), residues: 83
  loop : -2.84 (0.30), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP f  59 
 HIS   0.003   0.001   HIS f  61 
 PHE   0.013   0.001   PHE g 118 
 TYR   0.015   0.001   TYR g  34 
 ARG   0.006   0.001   ARG f 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04299 (  223)
  hydrogen bonds       : angle       3.98065 (  648)
  SS BOND              : bond        0.00419 (    9)
  SS BOND              : angle       2.21269 (   18)
  covalent geometry    : bond        0.00293 ( 4724)
  covalent geometry    : angle       0.65093 ( 6404)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: d   70 ILE cc_start: 0.8634 (mp) cc_final: 0.8302 (tt)
REVERT: d   87 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7934 (tm-30)
REVERT: e   36 TYR cc_start: 0.8012 (m-80) cc_final: 0.6894 (m-10)
REVERT: e   98 CYS cc_start: 0.3422 (p) cc_final: 0.2986 (p)
REVERT: e  117 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7363 (ttt180)
REVERT: f   46 ILE cc_start: 0.7794 (mm) cc_final: 0.7589 (mm)
REVERT: f  120 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7610 (tm-30)
REVERT: f  121 ASN cc_start: 0.8164 (m-40) cc_final: 0.7182 (m110)
REVERT: f  128 MET cc_start: 0.6085 (mpp) cc_final: 0.5643 (mmt)
REVERT: g   39 ASP cc_start: 0.8185 (p0) cc_final: 0.7677 (p0)
REVERT: g   57 LYS cc_start: 0.7402 (tptm) cc_final: 0.7196 (tptm)
REVERT: g   80 ASP cc_start: 0.8010 (t0) cc_final: 0.7519 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1754
  time to fit residues: 32.2547
Evaluate side-chains
  125 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0770
   chunk 50 optimal weight:    0.5980
   chunk 31 optimal weight:    0.3980
   chunk 53 optimal weight:    0.5980
   chunk 24 optimal weight:    0.3980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
d  38 ASN
d  89 HIS
e  92 GLN
f  81 HIS
** g  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.182660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.161330 restraints weight = 7666.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.162287 restraints weight = 6277.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.162287 restraints weight = 5458.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.4029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4733  Z= 0.125
  Angle     :  0.650   6.589   6422  Z= 0.331
  Chirality :  0.042   0.166    751
  Planarity :  0.004   0.046    785
  Dihedral  :  4.978  51.898    692
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  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: -0.74 (0.34), residues: 565
  helix:  2.15 (0.33), residues: 220
  sheet: -1.12 (0.61), residues: 83
  loop : -2.78 (0.30), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP d  43 
 HIS   0.008   0.001   HIS d  89 
 PHE   0.011   0.001   PHE g 118 
 TYR   0.009   0.001   TYR g 100 
 ARG   0.008   0.001   ARG f 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04026 (  223)
  hydrogen bonds       : angle       3.93546 (  648)
  SS BOND              : bond        0.00486 (    9)
  SS BOND              : angle       2.04892 (   18)
  covalent geometry    : bond        0.00271 ( 4724)
  covalent geometry    : angle       0.64163 ( 6404)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.502 
Fit side-chains
REVERT: d   70 ILE cc_start: 0.8628 (mp) cc_final: 0.8338 (tt)
REVERT: e   36 TYR cc_start: 0.7952 (m-80) cc_final: 0.7079 (m-10)
REVERT: e   98 CYS cc_start: 0.3538 (p) cc_final: 0.2935 (p)
REVERT: e  117 ARG cc_start: 0.7656 (mtp180) cc_final: 0.7362 (ttt180)
REVERT: f  110 PHE cc_start: 0.8063 (p90) cc_final: 0.7856 (p90)
REVERT: f  120 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7778 (tm-30)
REVERT: f  121 ASN cc_start: 0.8237 (m-40) cc_final: 0.7200 (m-40)
REVERT: f  128 MET cc_start: 0.5832 (mpp) cc_final: 0.5521 (mmt)
REVERT: g   39 ASP cc_start: 0.8110 (p0) cc_final: 0.7734 (p0)
REVERT: g   57 LYS cc_start: 0.7323 (tptm) cc_final: 0.7092 (tptm)
REVERT: g   80 ASP cc_start: 0.8048 (t0) cc_final: 0.7625 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1655
  time to fit residues: 29.7147
Evaluate side-chains
  115 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
d  38 ASN
e  92 GLN
f  81 HIS
** g  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.171066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.157380 restraints weight = 7864.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.157657 restraints weight = 9522.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.154713 restraints weight = 8591.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.4194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4733  Z= 0.150
  Angle     :  0.684   6.809   6422  Z= 0.347
  Chirality :  0.044   0.161    751
  Planarity :  0.004   0.041    785
  Dihedral  :  4.974  47.538    692
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  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 (0.34), residues: 565
  helix:  2.07 (0.33), residues: 221
  sheet: -1.21 (0.58), residues: 96
  loop : -2.68 (0.31), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP g  72 
 HIS   0.005   0.001   HIS f  61 
 PHE   0.011   0.001   PHE n 277 
 TYR   0.009   0.001   TYR f 113 
 ARG   0.007   0.001   ARG e 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04417 (  223)
  hydrogen bonds       : angle       3.96271 (  648)
  SS BOND              : bond        0.00377 (    9)
  SS BOND              : angle       2.00459 (   18)
  covalent geometry    : bond        0.00342 ( 4724)
  covalent geometry    : angle       0.67666 ( 6404)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: d   70 ILE cc_start: 0.8730 (mp) cc_final: 0.8434 (tt)
REVERT: e   36 TYR cc_start: 0.7964 (m-80) cc_final: 0.7145 (m-10)
REVERT: e  117 ARG cc_start: 0.7679 (mtp180) cc_final: 0.7355 (ttt180)
REVERT: f  110 PHE cc_start: 0.8123 (p90) cc_final: 0.7872 (p90)
REVERT: f  120 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7766 (tm-30)
REVERT: f  121 ASN cc_start: 0.8168 (m-40) cc_final: 0.7143 (m-40)
REVERT: f  128 MET cc_start: 0.5887 (mpp) cc_final: 0.5567 (mmt)
REVERT: g   39 ASP cc_start: 0.7868 (p0) cc_final: 0.7485 (p0)
REVERT: g   57 LYS cc_start: 0.7531 (tptm) cc_final: 0.7288 (tptm)
REVERT: g   80 ASP cc_start: 0.7813 (t0) cc_final: 0.7566 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1636
  time to fit residues: 29.0522
Evaluate side-chains
  118 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 37 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0470
   chunk 11 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
d  38 ASN
** d  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
e  92 GLN
f  81 HIS
** g  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
n 259 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.172229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.156679 restraints weight = 7861.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.156977 restraints weight = 13134.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.156512 restraints weight = 10723.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.4362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4733  Z= 0.132
  Angle     :  0.688   8.576   6422  Z= 0.346
  Chirality :  0.044   0.256    751
  Planarity :  0.005   0.091    785
  Dihedral  :  5.150  50.779    692
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  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: -0.65 (0.35), residues: 565
  helix:  2.08 (0.33), residues: 221
  sheet: -1.10 (0.60), residues: 94
  loop : -2.65 (0.31), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP f  59 
 HIS   0.003   0.001   HIS f  61 
 PHE   0.010   0.001   PHE n 277 
 TYR   0.008   0.001   TYR g 100 
 ARG   0.006   0.001   ARG f 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04119 (  223)
  hydrogen bonds       : angle       3.92097 (  648)
  SS BOND              : bond        0.00435 (    9)
  SS BOND              : angle       2.44493 (   18)
  covalent geometry    : bond        0.00292 ( 4724)
  covalent geometry    : angle       0.67616 ( 6404)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.521 
Fit side-chains
REVERT: d   70 ILE cc_start: 0.8783 (mp) cc_final: 0.8376 (tt)
REVERT: e   36 TYR cc_start: 0.7606 (m-80) cc_final: 0.5993 (m-80)
REVERT: e   49 CYS cc_start: 0.6284 (t) cc_final: 0.6077 (t)
REVERT: e  117 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7324 (ttt180)
REVERT: f  110 PHE cc_start: 0.8123 (p90) cc_final: 0.7816 (p90)
REVERT: f  120 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7669 (tm-30)
REVERT: f  121 ASN cc_start: 0.8197 (m-40) cc_final: 0.7197 (m-40)
REVERT: f  128 MET cc_start: 0.5821 (mpp) cc_final: 0.5511 (mmt)
REVERT: g   39 ASP cc_start: 0.7761 (p0) cc_final: 0.7364 (p0)
REVERT: g   57 LYS cc_start: 0.7543 (tptm) cc_final: 0.7294 (tptm)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1705
  time to fit residues: 29.3406
Evaluate side-chains
  116 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0870
   chunk 30 optimal weight:    0.3980
   chunk 53 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 39 optimal weight:   20.0000
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
d  38 ASN
** d  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  89 HIS
e  92 GLN
f  81 HIS
** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.172975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.151245 restraints weight = 7832.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.152617 restraints weight = 6196.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.153847 restraints weight = 5232.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.4508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4733  Z= 0.130
  Angle     :  0.675   7.104   6422  Z= 0.343
  Chirality :  0.043   0.200    751
  Planarity :  0.004   0.042    785
  Dihedral  :  5.133  50.300    692
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  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: -0.57 (0.35), residues: 565
  helix:  2.21 (0.33), residues: 221
  sheet: -1.10 (0.59), residues: 94
  loop : -2.63 (0.32), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP d  43 
 HIS   0.002   0.001   HIS f  61 
 PHE   0.009   0.001   PHE n 277 
 TYR   0.012   0.001   TYR g  85 
 ARG   0.008   0.001   ARG d  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03938 (  223)
  hydrogen bonds       : angle       3.83517 (  648)
  SS BOND              : bond        0.00428 (    9)
  SS BOND              : angle       2.28164 (   18)
  covalent geometry    : bond        0.00287 ( 4724)
  covalent geometry    : angle       0.66503 ( 6404)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
REVERT: d   70 ILE cc_start: 0.8834 (mp) cc_final: 0.8414 (tt)
REVERT: e   36 TYR cc_start: 0.7639 (m-80) cc_final: 0.6176 (m-80)
REVERT: e   49 CYS cc_start: 0.6479 (t) cc_final: 0.6267 (t)
REVERT: e  117 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7478 (ttt180)
REVERT: f  120 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7647 (tm-30)
REVERT: f  121 ASN cc_start: 0.8216 (m-40) cc_final: 0.7195 (m-40)
REVERT: f  128 MET cc_start: 0.5656 (mpp) cc_final: 0.5445 (mmt)
REVERT: g   39 ASP cc_start: 0.7957 (p0) cc_final: 0.7564 (p0)
REVERT: g   61 MET cc_start: 0.1831 (tpt) cc_final: 0.1525 (tpt)
REVERT: m  286 LYS cc_start: 0.8448 (tptp) cc_final: 0.8113 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1545
  time to fit residues: 26.8632
Evaluate side-chains
  116 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
d  38 ASN
** d  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
d  89 HIS
e  92 GLN
f  81 HIS
** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.166885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.154453 restraints weight = 7955.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.155105 restraints weight = 9614.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.152457 restraints weight = 8016.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.4634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4733  Z= 0.172
  Angle     :  0.773   8.249   6422  Z= 0.387
  Chirality :  0.045   0.158    751
  Planarity :  0.004   0.040    785
  Dihedral  :  5.267  46.347    692
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  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: -0.94 (0.34), residues: 565
  helix:  1.77 (0.32), residues: 221
  sheet: -1.55 (0.54), residues: 104
  loop : -2.60 (0.32), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP g  72 
 HIS   0.016   0.003   HIS d  89 
 PHE   0.017   0.002   PHE b  40 
 TYR   0.020   0.002   TYR b  42 
 ARG   0.006   0.001   ARG d  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04734 (  223)
  hydrogen bonds       : angle       4.15541 (  648)
  SS BOND              : bond        0.00445 (    9)
  SS BOND              : angle       2.54582 (   18)
  covalent geometry    : bond        0.00399 ( 4724)
  covalent geometry    : angle       0.76229 ( 6404)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.546 
Fit side-chains
REVERT: d   68 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7484 (mtp180)
REVERT: e   36 TYR cc_start: 0.7584 (m-80) cc_final: 0.6200 (m-10)
REVERT: e   49 CYS cc_start: 0.6325 (t) cc_final: 0.5880 (t)
REVERT: f  110 PHE cc_start: 0.8344 (p90) cc_final: 0.8068 (p90)
REVERT: f  120 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7738 (tm-30)
REVERT: f  121 ASN cc_start: 0.8203 (m-40) cc_final: 0.7222 (m-40)
REVERT: f  128 MET cc_start: 0.5774 (mpp) cc_final: 0.5544 (mmt)
REVERT: g   39 ASP cc_start: 0.7826 (p0) cc_final: 0.7403 (p0)
REVERT: g   79 LYS cc_start: 0.8162 (tptt) cc_final: 0.7920 (mtmt)
REVERT: m  267 LEU cc_start: 0.9387 (tp) cc_final: 0.9131 (tt)
REVERT: m  280 ASN cc_start: 0.9089 (t0) cc_final: 0.8885 (t0)
REVERT: m  286 LYS cc_start: 0.8624 (tptp) cc_final: 0.8239 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1714
  time to fit residues: 29.6795
Evaluate side-chains
  119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 38 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
d  38 ASN
** d  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
f  81 HIS
** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.167207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.146943 restraints weight = 7921.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.148105 restraints weight = 6438.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.148545 restraints weight = 5528.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.4760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4733  Z= 0.152
  Angle     :  0.737  11.759   6422  Z= 0.372
  Chirality :  0.044   0.163    751
  Planarity :  0.004   0.044    785
  Dihedral  :  5.314  48.590    692
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  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: -0.82 (0.34), residues: 565
  helix:  1.99 (0.32), residues: 220
  sheet: -1.58 (0.53), residues: 104
  loop : -2.60 (0.32), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP g  72 
 HIS   0.004   0.001   HIS f  61 
 PHE   0.017   0.001   PHE m 281 
 TYR   0.014   0.001   TYR d  90 
 ARG   0.007   0.001   ARG e 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04422 (  223)
  hydrogen bonds       : angle       4.02629 (  648)
  SS BOND              : bond        0.00402 (    9)
  SS BOND              : angle       2.30264 (   18)
  covalent geometry    : bond        0.00346 ( 4724)
  covalent geometry    : angle       0.72828 ( 6404)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1847.67 seconds
wall clock time: 32 minutes 34.45 seconds (1954.45 seconds total)