Starting phenix.real_space_refine
on Tue Feb 11 12:20:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vo9_32049/02_2025/7vo9_32049_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vo9_32049/02_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_32049/02_2025/7vo9_32049.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vo9_32049/02_2025/7vo9_32049.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vo9_32049/02_2025/7vo9_32049_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vo9_32049/02_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-5592/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: 4.18, per 1000 atoms: 0.73
  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: 1.40
  Conformation dependent library (CDL) restraints added in 631.1 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: 2.24
  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: 1.86

  Time building geometry restraints manager: 1.63 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:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.840
  Find NCS groups from input model:        0.190
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.410
-------------------------------------------------------------------------------
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  : 0.503 
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: 0.3402
  time to fit residues: 63.6126
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  : 0.450 
-------------------------------------------------------------------------------
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 = 0.158241 restraints weight = 11533.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.161484 restraints weight = 18431.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.162874 restraints weight = 10199.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.4268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6469
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  : 0.518 
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: 0.7887 (m-80) cc_final: 0.7687 (m-80)
REVERT: M  126 ILE cc_start: 0.8079 (tp) cc_final: 0.7861 (pt)
  outliers start: 14
  outliers final: 5
  residues processed: 89
  average time/residue: 0.2376
  time to fit residues: 25.9597
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  : 0.476 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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**
N 115 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.178942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.154449 restraints weight = 11237.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.156346 restraints weight = 19755.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.155692 restraints weight = 9973.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.4227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6577
moved from start:          0.4970

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= 0.285
  Angle     :  0.704  10.756   8465  Z= 0.402
  Chirality :  0.042   0.134    956
  Planarity :  0.004   0.030    802
  Dihedral  : 28.282 175.885   1494
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 19.70 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.35), residues: 516
  helix:  2.41 (0.31), residues: 256
  sheet:  0.03 (0.46), residues: 104
  loop :  0.39 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.004   TRP M 107 
 HIS   0.011   0.002   HIS N  86 
 PHE   0.015   0.002   PHE G 127 
 TYR   0.010   0.002   TYR N 117 
 ARG   0.004   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
  92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.531 
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: G   87 HIS cc_start: 0.5761 (OUTLIER) cc_final: 0.5439 (m90)
REVERT: H   56 GLN cc_start: 0.7100 (mt0) cc_final: 0.6874 (mm-40)
  outliers start: 19
  outliers final: 12
  residues processed: 86
  average time/residue: 0.2692
  time to fit residues: 28.4694
Evaluate side-chains
  77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   31 SER
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 M residue   66 VAL
Chi-restraints excluded: chain M residue   99 VAL
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:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0980
   chunk 45 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4508 r_free = 0.4508 target = 0.178962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.153227 restraints weight = 11366.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.155588 restraints weight = 21280.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.155307 restraints weight = 9764.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6585
moved from start:          0.5595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5980  Z= 0.243
  Angle     :  0.667  11.066   8465  Z= 0.379
  Chirality :  0.040   0.149    956
  Planarity :  0.004   0.022    802
  Dihedral  : 28.941 179.366   1494
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 22.73 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.35), residues: 516
  helix:  2.12 (0.31), residues: 256
  sheet: -0.11 (0.47), residues: 104
  loop :  0.46 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.004   TRP M 107 
 HIS   0.004   0.001   HIS N  84 
 PHE   0.016   0.002   PHE G 127 
 TYR   0.011   0.002   TYR N  76 
 ARG   0.006   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
  95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   24 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6989 (tp-100)
REVERT: G   87 HIS cc_start: 0.5755 (OUTLIER) cc_final: 0.5381 (m90)
REVERT: H   15 GLN cc_start: 0.6808 (mm-40) cc_final: 0.6428 (mt0)
REVERT: M   51 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7019 (p)
REVERT: M  104 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8271 (p)
REVERT: N   95 LYS cc_start: 0.5655 (mtmt) cc_final: 0.5335 (pttt)
  outliers start: 22
  outliers final: 13
  residues processed: 87
  average time/residue: 0.2464
  time to fit residues: 26.1875
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  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   19 VAL
Chi-restraints excluded: chain G residue   49 THR
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 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   99 VAL
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  132 ASP
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   75 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.4507 r_free = 0.4507 target = 0.178411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.150726 restraints weight = 11223.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.152739 restraints weight = 21167.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.153512 restraints weight = 11318.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
moved from start:          0.6093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5980  Z= 0.268
  Angle     :  0.689  10.582   8465  Z= 0.387
  Chirality :  0.040   0.147    956
  Planarity :  0.004   0.033    802
  Dihedral  : 29.244 179.490   1494
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 22.22 %
    Favored  : 71.46 %
  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:  1.56 (0.35), residues: 516
  helix:  2.11 (0.31), residues: 256
  sheet: -0.32 (0.46), residues: 104
  loop :  0.34 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP M 107 
 HIS   0.008   0.001   HIS N  86 
 PHE   0.017   0.002   PHE G 127 
 TYR   0.016   0.002   TYR N 117 
 ARG   0.006   0.001   ARG N  11 

*********************** 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
  97 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 72
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   24 GLN cc_start: 0.7355 (tm-30) cc_final: 0.7005 (tp-100)
REVERT: G   87 HIS cc_start: 0.5762 (OUTLIER) cc_final: 0.5247 (m90)
REVERT: H   15 GLN cc_start: 0.6782 (mm-40) cc_final: 0.6571 (mt0)
REVERT: M   51 VAL cc_start: 0.7710 (OUTLIER) cc_final: 0.7123 (p)
REVERT: M   65 ASP cc_start: 0.7248 (m-30) cc_final: 0.6805 (m-30)
REVERT: M  104 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8360 (p)
  outliers start: 25
  outliers final: 16
  residues processed: 88
  average time/residue: 0.2349
  time to fit residues: 25.3333
Evaluate side-chains
  86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   19 VAL
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   88 LEU
Chi-restraints excluded: chain M residue   51 VAL
Chi-restraints excluded: chain M residue   66 VAL
Chi-restraints excluded: chain M residue   99 VAL
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  132 ASP
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue   75 VAL
Chi-restraints excluded: chain N residue   89 VAL
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:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.4520 r_free = 0.4520 target = 0.179306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.152722 restraints weight = 11191.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.153365 restraints weight = 19399.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.154935 restraints weight = 12875.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6658
moved from start:          0.6406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   5980  Z= 0.280
  Angle     :  0.694  10.886   8465  Z= 0.387
  Chirality :  0.040   0.139    956
  Planarity :  0.004   0.033    802
  Dihedral  : 29.490 177.325   1494
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 25.00 %
    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:  1.25 (0.35), residues: 516
  helix:  1.90 (0.31), residues: 256
  sheet: -0.62 (0.44), residues: 104
  loop :  0.24 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.005   TRP M 107 
 HIS   0.007   0.001   HIS N  86 
 PHE   0.018   0.002   PHE G 127 
 TYR   0.013   0.002   TYR N  76 
 ARG   0.006   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
  92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   24 GLN cc_start: 0.7362 (tm-30) cc_final: 0.7071 (tp-100)
REVERT: G   87 HIS cc_start: 0.5702 (OUTLIER) cc_final: 0.5159 (m90)
REVERT: M   51 VAL cc_start: 0.7735 (OUTLIER) cc_final: 0.7106 (p)
REVERT: M   65 ASP cc_start: 0.7267 (m-30) cc_final: 0.6877 (m-30)
  outliers start: 22
  outliers final: 16
  residues processed: 82
  average time/residue: 0.2873
  time to fit residues: 28.7577
Evaluate side-chains
  82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   19 VAL
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   88 LEU
Chi-restraints excluded: chain H residue  126 ILE
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   99 VAL
Chi-restraints excluded: chain M residue  132 ASP
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue   75 VAL
Chi-restraints excluded: chain N residue   89 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0000
   chunk 42 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 8 optimal weight:    0.1980
   chunk 52 optimal weight:    0.4980
   chunk 30 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.4384

-------------------------------------------------------------------------------
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 = 0.4530 r_free = 0.4530 target = 0.180634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.153261 restraints weight = 11469.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.155517 restraints weight = 19581.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.156509 restraints weight = 10431.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
moved from start:          0.6785

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= 0.221
  Angle     :  0.670  11.605   8465  Z= 0.377
  Chirality :  0.039   0.229    956
  Planarity :  0.003   0.022    802
  Dihedral  : 29.428 178.350   1494
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 24.49 %
    Favored  : 68.43 %
  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 (0.35), residues: 516
  helix:  1.85 (0.31), residues: 256
  sheet: -0.68 (0.44), residues: 104
  loop :  0.32 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.004   TRP H 107 
 HIS   0.007   0.001   HIS M 115 
 PHE   0.018   0.002   PHE G 127 
 TYR   0.009   0.002   TYR N 117 
 ARG   0.007   0.001   ARG H  30 

*********************** 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
  109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 81
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   24 GLN cc_start: 0.7283 (tm-30) cc_final: 0.7066 (tp-100)
REVERT: G   87 HIS cc_start: 0.5751 (OUTLIER) cc_final: 0.5214 (m90)
REVERT: M   51 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7189 (p)
REVERT: M   65 ASP cc_start: 0.7140 (m-30) cc_final: 0.6832 (m-30)
  outliers start: 28
  outliers final: 17
  residues processed: 94
  average time/residue: 0.2563
  time to fit residues: 29.0902
Evaluate side-chains
  91 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
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   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   88 LEU
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain H residue  126 ILE
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   99 VAL
Chi-restraints excluded: chain M residue  132 ASP
Chi-restraints excluded: chain N residue   38 MET
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   51 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:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 19 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  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.176702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.154584 restraints weight = 11076.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.154367 restraints weight = 20805.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.154245 restraints weight = 9865.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.7121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   5980  Z= 0.318
  Angle     :  0.730  11.050   8465  Z= 0.406
  Chirality :  0.042   0.224    956
  Planarity :  0.004   0.049    802
  Dihedral  : 29.746 178.894   1494
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 17.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 26.52 %
    Favored  : 67.42 %
  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:  0.86 (0.35), residues: 516
  helix:  1.56 (0.31), residues: 256
  sheet: -0.90 (0.43), residues: 104
  loop :  0.17 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.005   TRP H 107 
 HIS   0.009   0.002   HIS N  86 
 PHE   0.017   0.002   PHE G 127 
 TYR   0.016   0.002   TYR N  76 
 ARG   0.006   0.001   ARG H  30 

*********************** 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
  96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   24 GLN cc_start: 0.7373 (tm-30) cc_final: 0.7135 (tp-100)
REVERT: G   87 HIS cc_start: 0.5741 (OUTLIER) cc_final: 0.5091 (m90)
REVERT: M   51 VAL cc_start: 0.7744 (OUTLIER) cc_final: 0.7288 (p)
REVERT: M   65 ASP cc_start: 0.7116 (m-30) cc_final: 0.6842 (m-30)
REVERT: N   14 ARG cc_start: 0.5446 (tmm160) cc_final: 0.5243 (tmm160)
  outliers start: 24
  outliers final: 19
  residues processed: 89
  average time/residue: 0.2025
  time to fit residues: 22.6286
Evaluate side-chains
  85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
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   87 HIS
Chi-restraints excluded: chain G residue   88 LEU
Chi-restraints excluded: chain G residue  107 TRP
Chi-restraints excluded: chain H residue   30 ARG
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain H residue  126 ILE
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  132 ASP
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue   51 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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  56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  87 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.176945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.153109 restraints weight = 11227.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.154602 restraints weight = 21530.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.154160 restraints weight = 10052.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6655
moved from start:          0.7401

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= 0.310
  Angle     :  0.737  11.007   8465  Z= 0.411
  Chirality :  0.042   0.202    956
  Planarity :  0.004   0.046    802
  Dihedral  : 29.766 179.908   1494
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 17.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 26.52 %
    Favored  : 67.17 %
  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:  0.63 (0.35), residues: 516
  helix:  1.39 (0.31), residues: 256
  sheet: -1.00 (0.43), residues: 104
  loop :  0.05 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.006   TRP N 107 
 HIS   0.008   0.001   HIS N  86 
 PHE   0.018   0.002   PHE G 127 
 TYR   0.017   0.002   TYR N  76 
 ARG   0.005   0.001   ARG H  16 

*********************** 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
  93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   87 HIS cc_start: 0.5849 (OUTLIER) cc_final: 0.5159 (m90)
REVERT: M   51 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7121 (p)
REVERT: M   65 ASP cc_start: 0.7296 (m-30) cc_final: 0.6994 (m-30)
  outliers start: 25
  outliers final: 19
  residues processed: 85
  average time/residue: 0.2378
  time to fit residues: 24.9168
Evaluate side-chains
  82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   19 VAL
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   87 HIS
Chi-restraints excluded: chain G residue  107 TRP
Chi-restraints excluded: chain H residue   88 LEU
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  132 ASP
Chi-restraints excluded: chain N residue   39 LEU
Chi-restraints excluded: chain N residue   50 THR
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
Chi-restraints excluded: chain N residue   95 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    0.1980
   chunk 26 optimal weight:    0.8980
   chunk 51 optimal weight:    0.1980
   chunk 52 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 4 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4514 r_free = 0.4514 target = 0.178740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.149453 restraints weight = 11414.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.153376 restraints weight = 20172.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.153840 restraints weight = 9528.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.7574

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     :  0.732  11.454   8465  Z= 0.402
  Chirality :  0.040   0.199    956
  Planarity :  0.004   0.036    802
  Dihedral  : 29.596 179.334   1494
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 27.78 %
    Favored  : 67.42 %
  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:  0.73 (0.35), residues: 516
  helix:  1.53 (0.31), residues: 256
  sheet: -1.03 (0.43), residues: 104
  loop :  0.02 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.005   TRP N 107 
 HIS   0.005   0.001   HIS N  84 
 PHE   0.018   0.002   PHE G 127 
 TYR   0.014   0.002   TYR N  76 
 ARG   0.009   0.001   ARG H  53 

********************** 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
  83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   87 HIS cc_start: 0.5843 (OUTLIER) cc_final: 0.5152 (m90)
REVERT: M   51 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7179 (p)
REVERT: M   65 ASP cc_start: 0.7152 (m-30) cc_final: 0.6863 (m-30)
  outliers start: 19
  outliers final: 16
  residues processed: 78
  average time/residue: 0.2058
  time to fit residues: 20.3478
Evaluate side-chains
  81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   19 VAL
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   87 HIS
Chi-restraints excluded: chain G residue  107 TRP
Chi-restraints excluded: chain H residue   88 LEU
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  132 ASP
Chi-restraints excluded: chain N residue   50 THR
Chi-restraints excluded: chain N residue   51 VAL
Chi-restraints excluded: chain N residue   76 TYR
Chi-restraints excluded: chain N residue   89 VAL
Chi-restraints excluded: chain N residue   95 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.178474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.151491 restraints weight = 11158.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.154452 restraints weight = 21479.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.154694 restraints weight = 9656.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.4188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
moved from start:          0.7665

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= 0.289
  Angle     :  0.757  10.989   8465  Z= 0.416
  Chirality :  0.042   0.217    956
  Planarity :  0.004   0.043    802
  Dihedral  : 29.767 179.478   1494
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 27.53 %
    Favored  : 67.17 %
  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:  0.67 (0.35), residues: 516
  helix:  1.50 (0.31), residues: 256
  sheet: -1.08 (0.43), residues: 104
  loop : -0.02 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.005   TRP N 107 
 HIS   0.008   0.001   HIS N  86 
 PHE   0.018   0.002   PHE G 127 
 TYR   0.015   0.002   TYR N  76 
 ARG   0.007   0.001   ARG H  53 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1901.80 seconds
wall clock time: 34 minutes 45.13 seconds (2085.13 seconds total)