Starting phenix.real_space_refine
on Thu Mar  6 09:02:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vo9_32049/03_2025/7vo9_32049_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vo9_32049/03_2025/7vo9_32049.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/7vo9_32049/03_2025/7vo9_32049.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vo9_32049/03_2025/7vo9_32049.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vo9_32049/03_2025/7vo9_32049_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vo9_32049/03_2025/7vo9_32049_neut.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=   0.002 sd=   0.043
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: 6
    Type Number    sf(0)   Gaussians
     Zn     12      6.06       5
     P      86      5.49       5
     S      24      5.16       5
     C    3247      2.51       5
     N    1066      2.21       5
     O    1276      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5711
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 881
          Classifications: {'DNA': 43}
          Link IDs: {'rna3p': 42}
    Chain: "B"
      Number of atoms: 882
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 882
          Classifications: {'DNA': 43}
          Link IDs: {'rna3p': 42}
    Chain: "G"
      Number of atoms: 984
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 984
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 2, 'TRANS': 128}
    Chain: "H"
      Number of atoms: 984
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 984
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 2, 'TRANS': 128}
    Chain: "M"
      Number of atoms: 984
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 984
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 2, 'TRANS': 128}
    Chain: "N"
      Number of atoms: 984
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 984
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 2, 'TRANS': 128}
    Chain: "G"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "H"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "M"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "N"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2419  SG  CYS G  90      17.241  31.300  59.728  1.00 71.88           S
  ATOM   2441  SG  CYS G  93      14.793  30.618  62.671  1.00 70.47           S
  ATOM   2714  SG  CYS G 130      14.935  28.682  59.367  1.00 73.41           S
  ATOM   2733  SG  CYS G 133      13.753  32.726  60.427  1.00 76.67           S
  ATOM   2333  SG  CYS G  79      25.843  20.667  68.382  1.00 55.29           S
  ATOM   3403  SG  CYS H  90      50.589  21.848  55.123  1.00 65.50           S
  ATOM   3425  SG  CYS H  93      53.560  23.049  52.848  1.00 67.51           S
  ATOM   3698  SG  CYS H 130      51.610  19.758  52.799  1.00 70.00           S
  ATOM   3717  SG  CYS H 133      54.743  21.183  55.225  1.00 77.21           S
  ATOM   3317  SG  CYS H  79      41.604  31.101  44.386  1.00 60.89           S
  ATOM   4387  SG  CYS M  90      18.888  56.432  98.247  1.00 65.11           S
  ATOM   4409  SG  CYS M  93      16.467  57.794  95.462  1.00 65.03           S
  ATOM   4682  SG  CYS M 130      15.148  58.615  98.647  1.00 66.03           S
  ATOM   4701  SG  CYS M 133      15.423  55.317  97.309  1.00 76.02           S
  ATOM   4301  SG  CYS M  79      28.244  66.312  88.717  1.00 55.78           S
  ATOM   5371  SG  CYS N  90      52.577  62.137 102.734  1.00 63.37           S
  ATOM   5393  SG  CYS N  93      56.120  61.109 103.694  1.00 66.66           S
  ATOM   5666  SG  CYS N 130      54.023  63.902 105.638  1.00 70.51           S
  ATOM   5285  SG  CYS N  79      41.722  54.410 113.951  1.00 42.33           S

  Time building chain proxies: 4.40, per 1000 atoms: 0.77
  Number of scatterers: 5711
  At special positions: 0
  Unit cell: (73.7, 90.2, 144.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn     12     29.99
     S      24     16.00
     P      86     15.00
     O    1276      8.00
     N    1066      7.00
     C    3247      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.32
  Conformation dependent library (CDL) restraints added in 632.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN G 201 "
        pdb="ZN    ZN G 201 " - pdb=" SG  CYS G  93 "
        pdb="ZN    ZN G 201 " - pdb=" SG  CYS G 130 "
        pdb="ZN    ZN G 201 " - pdb=" SG  CYS G  90 "
        pdb="ZN    ZN G 201 " - pdb=" SG  CYS G 133 "
      pdb="  ZN G 202 "
        pdb="ZN    ZN G 202 " - pdb=" NE2 HIS G  85 "
        pdb="ZN    ZN G 202 " - pdb=" NE2 HIS G  87 "
        pdb="ZN    ZN G 202 " - pdb=" SG  CYS G  79 "
      pdb="  ZN G 203 "
        pdb="ZN    ZN G 203 " - pdb=" NE2 HIS G  86 "
        pdb="ZN    ZN G 203 " - pdb=" NE2 HIS G  84 "
        pdb="ZN    ZN G 203 " - pdb=" NE2 HIS G 122 "
      pdb="  ZN H 201 "
        pdb="ZN    ZN H 201 " - pdb=" SG  CYS H  90 "
        pdb="ZN    ZN H 201 " - pdb=" SG  CYS H 130 "
        pdb="ZN    ZN H 201 " - pdb=" SG  CYS H  93 "
        pdb="ZN    ZN H 201 " - pdb=" SG  CYS H 133 "
      pdb="  ZN H 202 "
        pdb="ZN    ZN H 202 " - pdb=" NE2 HIS H  87 "
        pdb="ZN    ZN H 202 " - pdb=" NE2 HIS H  85 "
        pdb="ZN    ZN H 202 " - pdb=" SG  CYS H  79 "
      pdb="  ZN H 203 "
        pdb="ZN    ZN H 203 " - pdb=" NE2 HIS H  86 "
        pdb="ZN    ZN H 203 " - pdb=" NE2 HIS H 122 "
        pdb="ZN    ZN H 203 " - pdb=" NE2 HIS H  84 "
      pdb="  ZN M 201 "
        pdb="ZN    ZN M 201 " - pdb=" SG  CYS M 130 "
        pdb="ZN    ZN M 201 " - pdb=" SG  CYS M 133 "
        pdb="ZN    ZN M 201 " - pdb=" SG  CYS M  90 "
        pdb="ZN    ZN M 201 " - pdb=" SG  CYS M  93 "
      pdb="  ZN M 202 "
        pdb="ZN    ZN M 202 " - pdb=" NE2 HIS M  87 "
        pdb="ZN    ZN M 202 " - pdb=" NE2 HIS M  85 "
        pdb="ZN    ZN M 202 " - pdb=" SG  CYS M  79 "
      pdb="  ZN M 203 "
        pdb="ZN    ZN M 203 " - pdb=" NE2 HIS M  86 "
        pdb="ZN    ZN M 203 " - pdb=" NE2 HIS M  84 "
        pdb="ZN    ZN M 203 " - pdb=" NE2 HIS M 122 "
      pdb="  ZN N 201 "
        pdb="ZN    ZN N 201 " - pdb=" SG  CYS N  93 "
        pdb="ZN    ZN N 201 " - pdb=" SG  CYS N  90 "
        pdb="ZN    ZN N 201 " - pdb=" SG  CYS N 130 "
      pdb="  ZN N 202 "
        pdb="ZN    ZN N 202 " - pdb=" NE2 HIS N  87 "
        pdb="ZN    ZN N 202 " - pdb=" NE2 HIS N  85 "
        pdb="ZN    ZN N 202 " - pdb=" SG  CYS N  79 "
      pdb="  ZN N 203 "
        pdb="ZN    ZN N 203 " - pdb=" NE2 HIS N 122 "
        pdb="ZN    ZN N 203 " - pdb=" NE2 HIS N  84 "
        pdb="ZN    ZN N 203 " - pdb=" NE2 HIS N  86 "
      Number of angles added : 18


  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  960

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 8 sheets defined
      48.9% alpha, 17.9% beta
      31 base pairs and 68 stacking pairs defined.
    Time for finding SS restraints: 2.06
  Creating SS restraints...
    Processing helix  chain 'G' and resid 13 through 26
    Processing helix  chain 'G' and resid 31 through 43
    Processing helix  chain 'G' and resid 47 through 62
    Processing helix  chain 'G' and resid 101 through 116
      removed outlier: 3.724A  pdb=" N   GLU G 105 " --> pdb=" O   GLY G 101 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 131 through 135
    Processing helix  chain 'H' and resid 13 through 26
    Processing helix  chain 'H' and resid 32 through 43
    Processing helix  chain 'H' and resid 47 through 62
    Processing helix  chain 'H' and resid 101 through 116
      removed outlier: 3.882A  pdb=" N   GLU H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 131 through 135
    Processing helix  chain 'M' and resid 13 through 26
    Processing helix  chain 'M' and resid 31 through 43
    Processing helix  chain 'M' and resid 47 through 62
    Processing helix  chain 'M' and resid 101 through 116
    Processing helix  chain 'M' and resid 130 through 135
    Processing helix  chain 'N' and resid 13 through 26
    Processing helix  chain 'N' and resid 32 through 43
    Processing helix  chain 'N' and resid 47 through 62
    Processing helix  chain 'N' and resid 101 through 116
      removed outlier: 3.614A  pdb=" N   GLU N 105 " --> pdb=" O   GLY N 101 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 130 through 135
    Processing sheet with id=AA1, first strand: chain 'G' and resid 65 through 68
    Processing sheet with id=AA2, first strand: chain 'G' and resid 95 through 98
      removed outlier: 3.678A  pdb=" N   LYS G  95 " --> pdb=" O   CYS G  90 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   HIS G  87 " --> pdb=" O   VAL G 124 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ILE G 126 " --> pdb=" O   HIS G  87 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   TYR G 117 " --> pdb=" O   CYS H 130 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   CYS H 130 " --> pdb=" O   TYR G 117 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   ASN G 119 " --> pdb=" O   GLY H 128 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   GLY H 128 " --> pdb=" O   ASN G 119 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ALA G 121 " --> pdb=" O   ILE H 126 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   ILE H 126 " --> pdb=" O   ALA G 121 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   THR G 123 " --> pdb=" O   VAL H 124 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   VAL H 124 " --> pdb=" O   THR G 123 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   GLU G 125 " --> pdb=" O   HIS H 122 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   HIS H 122 " --> pdb=" O   GLU G 125 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   PHE G 127 " --> pdb=" O   VAL H 120 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   VAL H 120 " --> pdb=" O   PHE G 127 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   THR G 129 " --> pdb=" O   VAL H 118 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 30 through 31
    Processing sheet with id=AA4, first strand: chain 'H' and resid 86 through 89
    Processing sheet with id=AA5, first strand: chain 'M' and resid 64 through 68
    Processing sheet with id=AA6, first strand: chain 'M' and resid 96 through 99
      removed outlier: 6.098A  pdb=" N   HIS M  87 " --> pdb=" O   ILE M 126 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   GLY M 128 " --> pdb=" O   HIS M  87 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   VAL M  89 " --> pdb=" O   GLY M 128 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ASN N 119 " --> pdb=" O   THR M 129 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'N' and resid 30 through 31
    Processing sheet with id=AA8, first strand: chain 'N' and resid 95 through 99

    220 hydrogen bonds defined for protein.
    636 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      78 hydrogen bonds
      156 hydrogen bond angles
      0 basepair planarities
      31 basepair parallelities
      68 stacking parallelities
  Total time for adding SS restraints: 1.54

  Time building geometry restraints manager: 1.60 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1007
        1.33 -     1.45: 1909
        1.45 -     1.58: 2866
        1.58 -     1.70: 170
        1.70 -     1.82: 28
  Bond restraints: 5980
  Sorted by residual:
  bond pdb=" N   VAL H  66 "
       pdb=" CA  VAL H  66 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.040 1.11e-02 8.12e+03 1.32e+01
  bond pdb=" N   VAL M  89 "
       pdb=" CA  VAL M  89 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.14e-02 7.69e+03 1.13e+01
  bond pdb=" N   ILE N 126 "
       pdb=" CA  ILE N 126 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.14e-02 7.69e+03 1.11e+01
  bond pdb=" N   VAL M  64 "
       pdb=" CA  VAL M  64 "
    ideal  model  delta    sigma   weight residual
    1.458  1.497 -0.039 1.17e-02 7.31e+03 1.10e+01
  bond pdb=" N   VAL N  64 "
       pdb=" CA  VAL N  64 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.040 1.22e-02 6.72e+03 1.09e+01
  ... (remaining 5975 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 6021
        1.61 -     3.22: 2000
        3.22 -     4.83: 410
        4.83 -     6.44: 28
        6.44 -     8.05: 6
  Bond angle restraints: 8465
  Sorted by residual:
  angle pdb=" C4'  DT A  33 "
        pdb=" C3'  DT A  33 "
        pdb=" O3'  DT A  33 "
      ideal   model   delta    sigma   weight residual
     110.00  118.05   -8.05 1.50e+00 4.44e-01 2.88e+01
  angle pdb=" O3'  DT B  82 "
        pdb=" C3'  DT B  82 "
        pdb=" C2'  DT B  82 "
      ideal   model   delta    sigma   weight residual
     111.50  119.05   -7.55 1.50e+00 4.44e-01 2.53e+01
  angle pdb=" CA  HIS M  86 "
        pdb=" CB  HIS M  86 "
        pdb=" CG  HIS M  86 "
      ideal   model   delta    sigma   weight residual
     113.80  109.06    4.74 1.00e+00 1.00e+00 2.25e+01
  angle pdb=" N   GLY G  94 "
        pdb=" CA  GLY G  94 "
        pdb=" C   GLY G  94 "
      ideal   model   delta    sigma   weight residual
     115.30  108.81    6.49 1.39e+00 5.18e-01 2.18e+01
  angle pdb=" N   GLY M  94 "
        pdb=" CA  GLY M  94 "
        pdb=" C   GLY M  94 "
      ideal   model   delta    sigma   weight residual
     115.36  109.19    6.17 1.33e+00 5.65e-01 2.15e+01
  ... (remaining 8460 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.05: 3015
       35.05 -    70.09: 280
       70.09 -   105.13: 2
      105.13 -   140.18: 7
      140.18 -   175.22: 6
  Dihedral angle restraints: 3310
    sinusoidal: 1818
      harmonic: 1492
  Sorted by residual:
  dihedral pdb=" C   ASP N  60 "
           pdb=" N   ASP N  60 "
           pdb=" CA  ASP N  60 "
           pdb=" CB  ASP N  60 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.02   11.42     0      2.50e+00 1.60e-01 2.09e+01
  dihedral pdb=" C4'  DG A  11 "
           pdb=" C3'  DG A  11 "
           pdb=" O3'  DG A  11 "
           pdb=" P    DA A  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   35.22 -175.22     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DC A   1 "
           pdb=" C3'  DC A   1 "
           pdb=" O3'  DC A   1 "
           pdb=" P    DA A   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   46.22  173.78     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 3307 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 645
       0.083 -    0.165: 255
       0.165 -    0.248: 50
       0.248 -    0.330: 3
       0.330 -    0.412: 3
  Chirality restraints: 956
  Sorted by residual:
  chirality pdb=" C3'  DT B  82 "
            pdb=" C4'  DT B  82 "
            pdb=" O3'  DT B  82 "
            pdb=" C2'  DT B  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.25   -0.41 2.00e-01 2.50e+01 4.25e+00
  chirality pdb=" C3'  DG B  56 "
            pdb=" C4'  DG B  56 "
            pdb=" O3'  DG B  56 "
            pdb=" C2'  DG B  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.31   -0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" CA  ASP N  60 "
            pdb=" N   ASP N  60 "
            pdb=" C   ASP N  60 "
            pdb=" CB  ASP N  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.82e+00
  ... (remaining 953 not shown)

  Planarity restraints: 802
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS G 122 "    0.011 2.00e-02 2.50e+03   2.72e-02 1.11e+01
        pdb=" CG  HIS G 122 "    0.001 2.00e-02 2.50e+03
        pdb=" ND1 HIS G 122 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 HIS G 122 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE1 HIS G 122 "   -0.026 2.00e-02 2.50e+03
        pdb=" NE2 HIS G 122 "    0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS M  86 "   -0.019 2.00e-02 2.50e+03   1.93e-02 5.56e+00
        pdb=" CG  HIS M  86 "    0.031 2.00e-02 2.50e+03
        pdb=" ND1 HIS M  86 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 HIS M  86 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 HIS M  86 "    0.011 2.00e-02 2.50e+03
        pdb=" NE2 HIS M  86 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY M  72 "    0.010 2.00e-02 2.50e+03   2.06e-02 4.26e+00
        pdb=" C   GLY M  72 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   GLY M  72 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLU M  73 "    0.012 2.00e-02 2.50e+03
  ... (remaining 799 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 179
        2.68 -     3.23: 4633
        3.23 -     3.79: 10248
        3.79 -     4.34: 13092
        4.34 -     4.90: 18444
  Nonbonded interactions: 46596
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP H  65 "
            pdb="ZN    ZN H 202 "
     model   vdw
     2.124 2.230
  nonbonded pdb=" OE2 GLU M 105 "
            pdb="ZN    ZN M 203 "
     model   vdw
     2.230 2.230
  nonbonded pdb=" C2'  DG B  42 "
            pdb=" O5'  DT B  43 "
     model   vdw
     2.332 3.440
  nonbonded pdb=" C2'  DT B  71 "
            pdb=" N7   DG B  72 "
     model   vdw
     2.439 3.520
  nonbonded pdb=" O   ILE M 111 "
            pdb=" ND1 HIS M 115 "
     model   vdw
     2.496 3.120
  ... (remaining 46591 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 'G'
  selection = chain 'H'
  selection = chain 'M'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.200
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     19.190
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6173
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      :  0.011   0.044   5980  Z= 0.732
  Angle     :  1.580   8.054   8465  Z= 1.205
  Chirality :  0.088   0.412    956
  Planarity :  0.004   0.027    802
  Dihedral  : 23.203 175.224   2350
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 10.61 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.21 %
  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:  2.89 (0.34), residues: 516
  helix:  3.25 (0.28), residues: 256
  sheet:  0.71 (0.51), residues: 88
  loop :  0.54 (0.42), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP N 107 
 HIS   0.040   0.003   HIS G 122 
 PHE   0.014   0.003   PHE G  29 
 TYR   0.016   0.003   TYR G 117 
 ARG   0.005   0.001   ARG H  77 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 162
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  111 ILE cc_start: 0.7594 (pt) cc_final: 0.6963 (pt)
REVERT: N   52 TYR cc_start: 0.7282 (m-80) cc_final: 0.6971 (m-80)
REVERT: N   99 VAL cc_start: 0.8508 (m) cc_final: 0.8074 (t)
  outliers start: 3
  outliers final: 0
  residues processed: 162
  average time/residue: 0.3189
  time to fit residues: 60.3859
Evaluate side-chains
  72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 15 optimal weight:    0.4980
   chunk 30 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 47 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0060
   chunk 35 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
H 115 HIS
M 119 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.187136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.158249 restraints weight = 11533.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.161548 restraints weight = 18386.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.162850 restraints weight = 10201.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6470
moved from start:          0.3988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5980  Z= 0.247
  Angle     :  0.695   7.689   8465  Z= 0.407
  Chirality :  0.041   0.140    956
  Planarity :  0.004   0.041    802
  Dihedral  : 27.400 178.811   1494
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 19.70 %
    Favored  : 76.77 %
  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:  2.31 (0.34), residues: 516
  helix:  2.75 (0.29), residues: 256
  sheet:  0.61 (0.47), residues: 96
  loop :  0.17 (0.43), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP N 107 
 HIS   0.006   0.001   HIS N  84 
 PHE   0.018   0.003   PHE G 127 
 TYR   0.009   0.001   TYR H 117 
 ARG   0.005   0.001   ARG G  77 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   76 TYR cc_start: 0.7889 (m-80) cc_final: 0.7687 (m-80)
REVERT: M  126 ILE cc_start: 0.8079 (tp) cc_final: 0.7863 (pt)
  outliers start: 14
  outliers final: 5
  residues processed: 89
  average time/residue: 0.2364
  time to fit residues: 25.8202
Evaluate side-chains
  76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue  107 TRP
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain M residue   84 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 9 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** H  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 115 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.177600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.155162 restraints weight = 11175.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.154373 restraints weight = 19722.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.153505 restraints weight = 11603.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.5175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5980  Z= 0.318
  Angle     :  0.735  11.081   8465  Z= 0.417
  Chirality :  0.043   0.141    956
  Planarity :  0.005   0.037    802
  Dihedral  : 28.550 176.163   1494
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 19.44 %
    Favored  : 75.00 %
  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:  1.72 (0.35), residues: 516
  helix:  2.21 (0.31), residues: 256
  sheet: -0.07 (0.46), residues: 104
  loop :  0.34 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.004   TRP M 107 
 HIS   0.013   0.002   HIS N  86 
 PHE   0.016   0.002   PHE G 127 
 TYR   0.010   0.002   TYR N 117 
 ARG   0.005   0.001   ARG M  68 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   87 HIS cc_start: 0.5735 (OUTLIER) cc_final: 0.5375 (m90)
REVERT: H   48 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8536 (tt)
  outliers start: 22
  outliers final: 15
  residues processed: 88
  average time/residue: 0.2631
  time to fit residues: 28.1214
Evaluate side-chains
  80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   19 VAL
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue   87 HIS
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue  107 TRP
Chi-restraints excluded: chain G residue  126 ILE
Chi-restraints excluded: chain H residue   33 GLN
Chi-restraints excluded: chain H residue   48 LEU
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain M residue   66 VAL
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   48 LEU
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   89 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    0.4980
   chunk 45 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** M  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.177958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.155749 restraints weight = 11288.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.152642 restraints weight = 21276.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.152959 restraints weight = 13020.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6641
moved from start:          0.5644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5980  Z= 0.264
  Angle     :  0.675  11.066   8465  Z= 0.385
  Chirality :  0.041   0.184    956
  Planarity :  0.004   0.026    802
  Dihedral  : 28.977 179.023   1494
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 23.48 %
    Favored  : 71.97 %
  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:  1.63 (0.35), residues: 516
  helix:  2.16 (0.31), residues: 256
  sheet: -0.24 (0.45), residues: 104
  loop :  0.37 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.005   TRP M 107 
 HIS   0.005   0.001   HIS N  86 
 PHE   0.017   0.002   PHE G 127 
 TYR   0.012   0.002   TYR N  76 
 ARG   0.011   0.001   ARG H  30 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   24 GLN cc_start: 0.7261 (tm-30) cc_final: 0.6908 (tp-100)
REVERT: G   87 HIS cc_start: 0.5824 (OUTLIER) cc_final: 0.5481 (m90)
REVERT: H   15 GLN cc_start: 0.6815 (mm-40) cc_final: 0.6499 (mt0)
REVERT: M   51 VAL cc_start: 0.7704 (OUTLIER) cc_final: 0.7281 (p)
REVERT: M   65 ASP cc_start: 0.7020 (m-30) cc_final: 0.6579 (m-30)
REVERT: M  104 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8308 (p)
  outliers start: 18
  outliers final: 10
  residues processed: 79
  average time/residue: 0.2291
  time to fit residues: 22.1552
Evaluate side-chains
  73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue   87 HIS
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue  107 TRP
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain M residue   38 MET
Chi-restraints excluded: chain M residue   51 VAL
Chi-restraints excluded: chain M residue   66 VAL
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  132 ASP
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   75 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 18 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 4 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** H  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.179832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.152865 restraints weight = 11151.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.155617 restraints weight = 19967.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.156074 restraints weight = 11231.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6631
moved from start:          0.6180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5980  Z= 0.257
  Angle     :  0.676  11.061   8465  Z= 0.383
  Chirality :  0.040   0.134    956
  Planarity :  0.004   0.031    802
  Dihedral  : 29.251 178.602   1494
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 23.23 %
    Favored  : 70.96 %
  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:  1.54 (0.35), residues: 516
  helix:  2.16 (0.31), residues: 256
  sheet: -0.49 (0.44), residues: 104
  loop :  0.33 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.005   TRP M 107 
 HIS   0.006   0.001   HIS N  86 
 PHE   0.017   0.002   PHE G 127 
 TYR   0.014   0.002   TYR N 117 
 ARG   0.005   0.001   ARG H  30 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 72
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   24 GLN cc_start: 0.7340 (tm-30) cc_final: 0.6998 (tp-100)
REVERT: G   87 HIS cc_start: 0.5836 (OUTLIER) cc_final: 0.5356 (m90)
REVERT: M   51 VAL cc_start: 0.7594 (OUTLIER) cc_final: 0.7075 (p)
REVERT: M   65 ASP cc_start: 0.7218 (m-30) cc_final: 0.6942 (m-30)
REVERT: M  104 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8159 (p)
REVERT: N   95 LYS cc_start: 0.5661 (OUTLIER) cc_final: 0.5366 (pttt)
  outliers start: 23
  outliers final: 13
  residues processed: 86
  average time/residue: 0.2054
  time to fit residues: 22.0737
Evaluate side-chains
  86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue   87 HIS
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue  107 TRP
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain M residue   38 MET
Chi-restraints excluded: chain M residue   51 VAL
Chi-restraints excluded: chain M residue   66 VAL
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  132 ASP
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue   75 VAL
Chi-restraints excluded: chain N residue   89 VAL
Chi-restraints excluded: chain N residue   95 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 50 optimal weight:    0.2980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.178660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.157341 restraints weight = 11233.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.158052 restraints weight = 18241.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.157777 restraints weight = 9002.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.6548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5980  Z= 0.256
  Angle     :  0.686  10.952   8465  Z= 0.384
  Chirality :  0.041   0.261    956
  Planarity :  0.004   0.029    802
  Dihedral  : 29.504 178.680   1494
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 25.25 %
    Favored  : 69.44 %
  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:  1.26 (0.35), residues: 516
  helix:  1.96 (0.31), residues: 256
  sheet: -0.76 (0.43), residues: 104
  loop :  0.29 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP M 107 
 HIS   0.007   0.001   HIS H  86 
 PHE   0.017   0.002   PHE G 127 
 TYR   0.012   0.002   TYR N  76 
 ARG   0.008   0.001   ARG M  11 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   24 GLN cc_start: 0.7333 (tm-30) cc_final: 0.7056 (tp-100)
REVERT: G   87 HIS cc_start: 0.5641 (OUTLIER) cc_final: 0.5103 (m90)
REVERT: M   51 VAL cc_start: 0.7612 (OUTLIER) cc_final: 0.7147 (p)
REVERT: M   65 ASP cc_start: 0.7015 (m-30) cc_final: 0.6713 (m-30)
  outliers start: 21
  outliers final: 15
  residues processed: 83
  average time/residue: 0.2153
  time to fit residues: 22.1623
Evaluate side-chains
  77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue   87 HIS
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue  107 TRP
Chi-restraints excluded: chain G residue  126 ILE
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain M residue   38 MET
Chi-restraints excluded: chain M residue   51 VAL
Chi-restraints excluded: chain M residue   66 VAL
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  132 ASP
Chi-restraints excluded: chain N residue   89 VAL
Chi-restraints excluded: chain N residue   95 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 11 optimal weight:    0.0870
   chunk 13 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0870
   chunk 8 optimal weight:    2.9990
   chunk 52 optimal weight:    0.2980
   chunk 30 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
** M  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.181133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.160052 restraints weight = 11199.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.159304 restraints weight = 18675.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.158728 restraints weight = 10772.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.4227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6545
moved from start:          0.6848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   5980  Z= 0.225
  Angle     :  0.659  11.650   8465  Z= 0.370
  Chirality :  0.038   0.169    956
  Planarity :  0.004   0.048    802
  Dihedral  : 29.471 178.741   1494
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 27.02 %
    Favored  : 68.18 %
  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:  1.22 (0.36), residues: 516
  helix:  1.94 (0.31), residues: 256
  sheet: -0.88 (0.43), residues: 104
  loop :  0.32 (0.48), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.004   TRP H 107 
 HIS   0.005   0.001   HIS N  84 
 PHE   0.017   0.002   PHE G 127 
 TYR   0.009   0.002   TYR N  76 
 ARG   0.005   0.001   ARG N  11 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   24 GLN cc_start: 0.7343 (tm-30) cc_final: 0.7090 (tp-100)
REVERT: G   87 HIS cc_start: 0.5819 (OUTLIER) cc_final: 0.5283 (m90)
REVERT: H   40 LYS cc_start: 0.7644 (ptpp) cc_final: 0.7248 (mtmm)
REVERT: M   65 ASP cc_start: 0.7189 (m-30) cc_final: 0.6917 (m-30)
REVERT: M  104 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8063 (p)
  outliers start: 19
  outliers final: 12
  residues processed: 86
  average time/residue: 0.2323
  time to fit residues: 24.6040
Evaluate side-chains
  83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   87 HIS
Chi-restraints excluded: chain G residue  107 TRP
Chi-restraints excluded: chain G residue  126 ILE
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain M residue   66 VAL
Chi-restraints excluded: chain M residue   88 LEU
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  132 ASP
Chi-restraints excluded: chain N residue   51 VAL
Chi-restraints excluded: chain N residue   75 VAL
Chi-restraints excluded: chain N residue   89 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
N  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.177984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.156519 restraints weight = 11098.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.155880 restraints weight = 20277.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.155799 restraints weight = 10153.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
moved from start:          0.7157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   5980  Z= 0.272
  Angle     :  0.691  11.101   8465  Z= 0.385
  Chirality :  0.040   0.140    956
  Planarity :  0.004   0.038    802
  Dihedral  : 29.691 178.982   1494
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 28.28 %
    Favored  : 66.92 %
  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:  0.99 (0.35), residues: 516
  helix:  1.79 (0.32), residues: 256
  sheet: -1.08 (0.42), residues: 104
  loop :  0.20 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.005   TRP N 107 
 HIS   0.007   0.001   HIS N  86 
 PHE   0.018   0.002   PHE G 127 
 TYR   0.012   0.002   TYR N  76 
 ARG   0.006   0.001   ARG N  11 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: G   24 GLN cc_start: 0.7360 (tm-30) cc_final: 0.7102 (tp-100)
REVERT: M   51 VAL cc_start: 0.7614 (OUTLIER) cc_final: 0.7155 (p)
REVERT: M   65 ASP cc_start: 0.7226 (m-30) cc_final: 0.6961 (m-30)
REVERT: M  104 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7878 (p)
  outliers start: 19
  outliers final: 16
  residues processed: 81
  average time/residue: 0.1941
  time to fit residues: 19.9321
Evaluate side-chains
  80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   41 HIS
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  107 TRP
Chi-restraints excluded: chain G residue  126 ILE
Chi-restraints excluded: chain H residue   30 ARG
Chi-restraints excluded: chain H residue   50 THR
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain M residue   51 VAL
Chi-restraints excluded: chain M residue   66 VAL
Chi-restraints excluded: chain M residue   88 LEU
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  132 ASP
Chi-restraints excluded: chain N residue   51 VAL
Chi-restraints excluded: chain N residue   75 VAL
Chi-restraints excluded: chain N residue   89 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** H  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.176006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.156418 restraints weight = 10970.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.154156 restraints weight = 17417.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.152753 restraints weight = 10084.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6707
moved from start:          0.7499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   5980  Z= 0.367
  Angle     :  0.763  10.951   8465  Z= 0.422
  Chirality :  0.043   0.148    956
  Planarity :  0.005   0.064    802
  Dihedral  : 30.050 178.608   1494
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 19.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 28.03 %
    Favored  : 66.92 %
  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:  0.58 (0.35), residues: 516
  helix:  1.40 (0.31), residues: 256
  sheet: -1.17 (0.43), residues: 104
  loop :  0.03 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.005   TRP N 107 
 HIS   0.011   0.002   HIS N  86 
 PHE   0.020   0.003   PHE N  29 
 TYR   0.016   0.003   TYR N  76 
 ARG   0.005   0.001   ARG M  68 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: M   51 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7299 (p)
REVERT: M   65 ASP cc_start: 0.7189 (m-30) cc_final: 0.6827 (m-30)
REVERT: M  104 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.8042 (p)
  outliers start: 20
  outliers final: 14
  residues processed: 81
  average time/residue: 0.2062
  time to fit residues: 21.0355
Evaluate side-chains
  78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue   67 LEU
Chi-restraints excluded: chain G residue  107 TRP
Chi-restraints excluded: chain H residue   30 ARG
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain M residue   51 VAL
Chi-restraints excluded: chain M residue   66 VAL
Chi-restraints excluded: chain M residue   88 LEU
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  132 ASP
Chi-restraints excluded: chain N residue   51 VAL
Chi-restraints excluded: chain N residue   75 VAL
Chi-restraints excluded: chain N residue   76 TYR
Chi-restraints excluded: chain N residue   89 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0000
   chunk 51 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 14 optimal weight:    0.4980
   chunk 4 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
N  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.178568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.158545 restraints weight = 11423.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.157453 restraints weight = 19042.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.156527 restraints weight = 11647.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6581
moved from start:          0.7576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5980  Z= 0.242
  Angle     :  0.688   9.310   8465  Z= 0.382
  Chirality :  0.039   0.153    956
  Planarity :  0.004   0.033    802
  Dihedral  : 29.770 179.049   1494
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 30.30 %
    Favored  : 65.40 %
  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:  0.90 (0.36), residues: 516
  helix:  1.78 (0.31), residues: 256
  sheet: -1.17 (0.43), residues: 104
  loop :  0.06 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.004   TRP N 107 
 HIS   0.006   0.001   HIS N  86 
 PHE   0.019   0.002   PHE G 127 
 TYR   0.021   0.002   TYR H  76 
 ARG   0.005   0.001   ARG N  14 

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

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

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1032 Ramachandran restraints generated.
    516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   51 VAL cc_start: 0.7815 (OUTLIER) cc_final: 0.7377 (p)
REVERT: M  104 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7439 (p)
  outliers start: 17
  outliers final: 14
  residues processed: 82
  average time/residue: 0.2032
  time to fit residues: 20.8511
Evaluate side-chains
  82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   41 HIS
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue  107 TRP
Chi-restraints excluded: chain H residue   30 ARG
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain M residue   51 VAL
Chi-restraints excluded: chain M residue   66 VAL
Chi-restraints excluded: chain M residue   88 LEU
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  132 ASP
Chi-restraints excluded: chain N residue   51 VAL
Chi-restraints excluded: chain N residue   75 VAL
Chi-restraints excluded: chain N residue   76 TYR
Chi-restraints excluded: chain N residue   89 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0870
   chunk 20 optimal weight:    0.0770
   chunk 57 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.4916

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

Flipped N/Q/H residues before XYZ refinement:
N  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.179965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.153241 restraints weight = 11247.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.155815 restraints weight = 20351.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.156345 restraints weight = 10307.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6609
moved from start:          0.7753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5980  Z= 0.238
  Angle     :  0.687   8.702   8465  Z= 0.382
  Chirality :  0.039   0.155    956
  Planarity :  0.004   0.040    802
  Dihedral  : 29.802 179.732   1494
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 31.06 %
    Favored  : 64.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.35), residues: 516
  helix:  1.78 (0.31), residues: 256
  sheet: -1.11 (0.44), residues: 104
  loop : -0.05 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.004   TRP N 107 
 HIS   0.005   0.001   HIS N  84 
 PHE   0.020   0.002   PHE G 127 
 TYR   0.012   0.002   TYR N  76 
 ARG   0.004   0.001   ARG M  11 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1895.62 seconds
wall clock time: 33 minutes 33.23 seconds (2013.23 seconds total)