Starting phenix.real_space_refine
on Wed May 14 21:11:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oos_17027/05_2025/8oos_17027.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oos_17027/05_2025/8oos_17027.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oos_17027/05_2025/8oos_17027.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oos_17027/05_2025/8oos_17027.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oos_17027/05_2025/8oos_17027.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oos_17027/05_2025/8oos_17027.cif"
  }
  resolution = 3.29
  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=   0.026
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: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P     219      5.49       5
     Mg      1      5.21       5
     S      36      5.16       5
     C    7085      2.51       5
     N    2272      2.21       5
     O    2689      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12307
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "G"
      Number of atoms: 3622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3622
          Classifications: {'peptide': 439}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 425}
          Chain breaks: 3
    Chain: "K"
      Number of atoms: 2243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 2243
          Classifications: {'DNA': 110}
          Link IDs: {'rna3p': 109}
    Chain: "L"
      Number of atoms: 2201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 2201
          Classifications: {'DNA': 107}
          Link IDs: {'rna3p': 106}
    Chain: "M"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 602
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 2, 'TRANS': 71}
    Chain: "N"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 587
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "O"
      Number of atoms: 842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 842
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "P"
      Number of atoms: 729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 729
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "Q"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "R"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 8.07, per 1000 atoms: 0.66
  Number of scatterers: 12307
  At special positions: 0
  Unit cell: (117.546, 144.672, 108.504, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      36     16.00
     P     219     15.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    2689      8.00
     N    2272      7.00
     C    7085      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.26
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1824

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 8 sheets defined
      64.7% alpha, 5.5% beta
      67 base pairs and 187 stacking pairs defined.
    Time for finding SS restraints: 5.58
  Creating SS restraints...
    Processing helix  chain 'G' and resid 965 through 969
    Processing helix  chain 'G' and resid 973 through 989
    Processing helix  chain 'G' and resid 1002 through 1019
      removed outlier: 3.688A  pdb=" N   ILE G1008 " --> pdb=" O   THR G1004 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   MET G1011 " --> pdb=" O   SER G1007 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1029 through 1031
      No H-bonds generated for 'chain 'G' and resid 1029 through 1031'
    Processing helix  chain 'G' and resid 1032 through 1044
    Processing helix  chain 'G' and resid 1055 through 1063
    Processing helix  chain 'G' and resid 1064 through 1066
      No H-bonds generated for 'chain 'G' and resid 1064 through 1066'
    Processing helix  chain 'G' and resid 1087 through 1092
    Processing helix  chain 'G' and resid 1092 through 1097
    Processing helix  chain 'G' and resid 1108 through 1113
    Processing helix  chain 'G' and resid 1117 through 1124
      removed outlier: 3.684A  pdb=" N   LEU G1123 " --> pdb=" O   ARG G1119 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1143 through 1154
      removed outlier: 4.345A  pdb=" N   LEU G1149 " --> pdb=" O   GLU G1145 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1189 through 1193
    Processing helix  chain 'G' and resid 1223 through 1240
      removed outlier: 4.011A  pdb=" N   GLN G1236 " --> pdb=" O   SER G1232 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ILE G1237 " --> pdb=" O   LEU G1233 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1257 through 1270
      removed outlier: 4.968A  pdb=" N   MET G1262 " --> pdb=" O   MET G1258 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1271 through 1274
    Processing helix  chain 'G' and resid 1544 through 1551
    Processing helix  chain 'G' and resid 1552 through 1569
    Processing helix  chain 'G' and resid 1579 through 1591
    Processing helix  chain 'G' and resid 1604 through 1618
    Processing helix  chain 'G' and resid 1651 through 1663
      removed outlier: 4.062A  pdb=" N   ASP G1655 " --> pdb=" O   ASN G1651 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ALA G1662 " --> pdb=" O   ALA G1658 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1681 through 1701
      removed outlier: 4.264A  pdb=" N   ARG G1685 " --> pdb=" O   THR G1681 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 63 through 76
    Processing helix  chain 'M' and resid 85 through 114
      removed outlier: 3.509A  pdb=" N   MET M  90 " --> pdb=" O   SER M  86 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASP M 106 " --> pdb=" O   GLY M 102 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 120 through 131
      removed outlier: 3.512A  pdb=" N   ILE M 124 " --> pdb=" O   MET M 120 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 24 through 29
      removed outlier: 3.636A  pdb=" N   ILE N  29 " --> pdb=" O   ILE N  26 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 30 through 41
    Processing helix  chain 'N' and resid 49 through 76
      removed outlier: 3.505A  pdb=" N   GLU N  53 " --> pdb=" O   LEU N  49 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG N  55 " --> pdb=" O   TYR N  51 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL N  60 " --> pdb=" O   GLY N  56 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASN N  64 " --> pdb=" O   VAL N  60 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ASP N  68 " --> pdb=" O   ASN N  64 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ALA N  76 " --> pdb=" O   TYR N  72 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 82 through 93
    Processing helix  chain 'O' and resid 16 through 22
    Processing helix  chain 'O' and resid 26 through 37
    Processing helix  chain 'O' and resid 46 through 73
    Processing helix  chain 'O' and resid 79 through 90
    Processing helix  chain 'O' and resid 90 through 97
    Processing helix  chain 'O' and resid 112 through 116
    Processing helix  chain 'P' and resid 34 through 46
      removed outlier: 3.849A  pdb=" N   GLN P  44 " --> pdb=" O   LYS P  40 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 52 through 82
    Processing helix  chain 'P' and resid 87 through 99
    Processing helix  chain 'P' and resid 100 through 119
    Processing helix  chain 'Q' and resid 44 through 55
    Processing helix  chain 'Q' and resid 63 through 77
    Processing helix  chain 'Q' and resid 85 through 114
      removed outlier: 3.695A  pdb=" N   ASP Q 106 " --> pdb=" O   GLY Q 102 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 120 through 131
      removed outlier: 3.555A  pdb=" N   ILE Q 124 " --> pdb=" O   MET Q 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 24 through 29
    Processing helix  chain 'R' and resid 30 through 41
    Processing helix  chain 'R' and resid 49 through 76
      removed outlier: 3.610A  pdb=" N   GLU R  53 " --> pdb=" O   LEU R  49 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASN R  64 " --> pdb=" O   VAL R  60 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   ARG R  67 " --> pdb=" O   GLU R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 82 through 93
      removed outlier: 3.585A  pdb=" N   VAL R  86 " --> pdb=" O   THR R  82 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 1049 through 1051
      removed outlier: 6.336A  pdb=" N   MET G1104 " --> pdb=" O   LEU G1132 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   LEU G1134 " --> pdb=" O   MET G1104 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LEU G1106 " --> pdb=" O   LEU G1134 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLY G 993 " --> pdb=" O   ARG G1131 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ILE G 994 " --> pdb=" O   LEU G1199 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 1214 through 1217
      removed outlier: 6.580A  pdb=" N   ILE G1214 " --> pdb=" O   VAL G1673 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   ARG G1675 " --> pdb=" O   ILE G1214 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ILE G1216 " --> pdb=" O   ARG G1675 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   VAL G1643 " --> pdb=" O   TYR G1674 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   LEU G1573 " --> pdb=" O   ILE G1644 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   VAL G1572 " --> pdb=" O   PHE G1624 " (cutoff:3.500A)
      removed outlier: 7.516A  pdb=" N   LEU G1626 " --> pdb=" O   VAL G1572 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   LEU G1574 " --> pdb=" O   LEU G1626 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   CYS G1597 " --> pdb=" O   LEU G1625 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   SER G1627 " --> pdb=" O   CYS G1597 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   LEU G1599 " --> pdb=" O   SER G1627 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'M' and resid 83 through 84
      removed outlier: 6.699A  pdb=" N   ARG M  83 " --> pdb=" O   VAL N  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'M' and resid 118 through 119
    Processing sheet with id=AA5, first strand: chain 'O' and resid 42 through 43
      removed outlier: 7.062A  pdb=" N   ARG O  42 " --> pdb=" O   ILE P  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'O' and resid 77 through 78
    Processing sheet with id=AA7, first strand: chain 'O' and resid 100 through 102
    Processing sheet with id=AA8, first strand: chain 'Q' and resid 118 through 119

    435 hydrogen bonds defined for protein.
    1260 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      169 hydrogen bonds
      338 hydrogen bond angles
      0 basepair planarities
      67 basepair parallelities
      187 stacking parallelities
  Total time for adding SS restraints: 7.09

  Time building geometry restraints manager: 3.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3106
        1.34 -     1.45: 3293
        1.45 -     1.57: 6077
        1.57 -     1.69: 430
        1.69 -     1.81: 66
  Bond restraints: 12972
  Sorted by residual:
  bond pdb=" F1  ALF G2003 "
       pdb="AL   ALF G2003 "
    ideal  model  delta    sigma   weight residual
    1.684  1.801 -0.117 2.00e-02 2.50e+03 3.44e+01
  bond pdb=" F3  ALF G2003 "
       pdb="AL   ALF G2003 "
    ideal  model  delta    sigma   weight residual
    1.685  1.786 -0.101 2.00e-02 2.50e+03 2.57e+01
  bond pdb=" F4  ALF G2003 "
       pdb="AL   ALF G2003 "
    ideal  model  delta    sigma   weight residual
    1.686  1.785 -0.099 2.00e-02 2.50e+03 2.45e+01
  bond pdb=" F2  ALF G2003 "
       pdb="AL   ALF G2003 "
    ideal  model  delta    sigma   weight residual
    1.685  1.775 -0.090 2.00e-02 2.50e+03 2.02e+01
  bond pdb=" C2'  DG K  25 "
       pdb=" C1'  DG K  25 "
    ideal  model  delta    sigma   weight residual
    1.525  1.479  0.046 2.00e-02 2.50e+03 5.39e+00
  ... (remaining 12967 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.16: 18426
       14.16 -    28.31: 4
       28.31 -    42.47: 0
       42.47 -    56.62: 0
       56.62 -    70.78: 2
  Bond angle restraints: 18432
  Sorted by residual:
  angle pdb=" F1  ALF G2003 "
        pdb="AL   ALF G2003 "
        pdb=" F2  ALF G2003 "
      ideal   model   delta    sigma   weight residual
     108.68  179.46  -70.78 3.00e+00 1.11e-01 5.57e+02
  angle pdb=" F3  ALF G2003 "
        pdb="AL   ALF G2003 "
        pdb=" F4  ALF G2003 "
      ideal   model   delta    sigma   weight residual
     109.63  179.87  -70.24 3.00e+00 1.11e-01 5.48e+02
  angle pdb=" F2  ALF G2003 "
        pdb="AL   ALF G2003 "
        pdb=" F4  ALF G2003 "
      ideal   model   delta    sigma   weight residual
     110.21   89.83   20.38 3.00e+00 1.11e-01 4.62e+01
  angle pdb=" F1  ALF G2003 "
        pdb="AL   ALF G2003 "
        pdb=" F3  ALF G2003 "
      ideal   model   delta    sigma   weight residual
     109.69   89.55   20.14 3.00e+00 1.11e-01 4.51e+01
  angle pdb=" F2  ALF G2003 "
        pdb="AL   ALF G2003 "
        pdb=" F3  ALF G2003 "
      ideal   model   delta    sigma   weight residual
     109.59   90.24   19.35 3.00e+00 1.11e-01 4.16e+01
  ... (remaining 18427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.00: 6155
       33.00 -    66.00: 1045
       66.00 -    98.99: 44
       98.99 -   131.99: 2
      131.99 -   164.99: 1
  Dihedral angle restraints: 7247
    sinusoidal: 4430
      harmonic: 2817
  Sorted by residual:
  dihedral pdb=" O1B ADP G2001 "
           pdb=" O3A ADP G2001 "
           pdb=" PB  ADP G2001 "
           pdb=" PA  ADP G2001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  135.01  164.99     1      2.00e+01 2.50e-03 4.72e+01
  dihedral pdb=" C5' ADP G2001 "
           pdb=" O5' ADP G2001 "
           pdb=" PA  ADP G2001 "
           pdb=" O2A ADP G2001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  177.09  122.92     1      2.00e+01 2.50e-03 3.70e+01
  dihedral pdb=" O2A ADP G2001 "
           pdb=" O3A ADP G2001 "
           pdb=" PA  ADP G2001 "
           pdb=" PB  ADP G2001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   57.31 -117.31     1      2.00e+01 2.50e-03 3.50e+01
  ... (remaining 7244 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1404
       0.050 -    0.100: 553
       0.100 -    0.150: 104
       0.150 -    0.200: 16
       0.200 -    0.250: 1
  Chirality restraints: 2078
  Sorted by residual:
  chirality pdb=" CB  ILE O  79 "
            pdb=" CA  ILE O  79 "
            pdb=" CG1 ILE O  79 "
            pdb=" CG2 ILE O  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CA  ILE O  79 "
            pdb=" N   ILE O  79 "
            pdb=" C   ILE O  79 "
            pdb=" CB  ILE O  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.78e-01
  chirality pdb=" C1'  DG K  25 "
            pdb=" O4'  DG K  25 "
            pdb=" C2'  DG K  25 "
            pdb=" N9   DG K  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.24    0.18 2.00e-01 2.50e+01 7.76e-01
  ... (remaining 2075 not shown)

  Planarity restraints: 1571
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR G1086 "    0.000 2.00e-02 2.50e+03   3.58e-02 2.56e+01
        pdb=" CG  TYR G1086 "    0.004 2.00e-02 2.50e+03
        pdb=" CD1 TYR G1086 "    0.048 2.00e-02 2.50e+03
        pdb=" CD2 TYR G1086 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR G1086 "   -0.051 2.00e-02 2.50e+03
        pdb=" CE2 TYR G1086 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR G1086 "   -0.051 2.00e-02 2.50e+03
        pdb=" OH  TYR G1086 "    0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR Q  41 "    0.006 2.00e-02 2.50e+03   3.01e-02 1.82e+01
        pdb=" CG  TYR Q  41 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD1 TYR Q  41 "    0.041 2.00e-02 2.50e+03
        pdb=" CD2 TYR Q  41 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR Q  41 "   -0.043 2.00e-02 2.50e+03
        pdb=" CE2 TYR Q  41 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR Q  41 "   -0.041 2.00e-02 2.50e+03
        pdb=" OH  TYR Q  41 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G1592 "    0.278 9.50e-02 1.11e+02   1.25e-01 1.20e+01
        pdb=" NE  ARG G1592 "   -0.026 2.00e-02 2.50e+03
        pdb=" CZ  ARG G1592 "    0.024 2.00e-02 2.50e+03
        pdb=" NH1 ARG G1592 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH2 ARG G1592 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1568 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 34
        2.48 -     3.09: 8143
        3.09 -     3.69: 19964
        3.69 -     4.30: 31570
        4.30 -     4.90: 47238
  Nonbonded interactions: 106949
  Sorted by model distance:
  nonbonded pdb="MG    MG G2002 "
            pdb=" F3  ALF G2003 "
     model   vdw
     1.879 2.120
  nonbonded pdb=" O2B ADP G2001 "
            pdb="MG    MG G2002 "
     model   vdw
     2.019 2.170
  nonbonded pdb=" OE2 GLU Q  73 "
            pdb=" ND2 ASN R  25 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" OD1 ASP G1559 "
            pdb=" OH  TYR G1588 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OH  TYR M  99 "
            pdb=" OE1 GLU M 133 "
     model   vdw
     2.228 3.040
  ... (remaining 106944 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 'N' and resid 23 through 93)
  selection = (chain 'R' and resid 23 through 93)
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             4.350
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.990
  Process input model:                     37.010
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
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      :  0.008   0.330  12973  Z= 0.432
  Angle     :  1.289  70.779  18432  Z= 0.612
  Chirality :  0.051   0.250   2078
  Planarity :  0.012   0.125   1571
  Dihedral  : 24.793 164.988   5423
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -2.38 (0.24), residues: 946
  helix: -2.01 (0.17), residues: 578
  sheet:  0.33 (0.85), residues: 45
  loop : -0.58 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP G1650 
 HIS   0.005   0.001   HIS N  75 
 PHE   0.018   0.002   PHE G1096 
 TYR   0.052   0.007   TYR G1086 
 ARG   0.027   0.004   ARG G1592 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22571 (  604)
  hydrogen bonds       : angle       8.28872 ( 1598)
  covalent geometry    : bond        0.00696 (12972)
  covalent geometry    : angle       1.28882 (18432)
  Misc. bond           : bond        0.32952 (    1)

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
REVERT: G 1258 MET cc_start: 0.4246 (mmm) cc_final: 0.3189 (ptm)
REVERT: G 1262 MET cc_start: 0.5481 (tpp) cc_final: 0.5180 (tpt)
REVERT: G 1585 MET cc_start: 0.7331 (tpt) cc_final: 0.7020 (tpp)
REVERT: G 1661 ARG cc_start: 0.4688 (mtp180) cc_final: 0.4473 (mtp85)
REVERT: M  129 ARG cc_start: 0.7293 (tpt-90) cc_final: 0.7036 (tpt90)
REVERT: O   38 ASN cc_start: 0.7476 (t0) cc_final: 0.7146 (t0)
REVERT: O   94 ASN cc_start: 0.7548 (t0) cc_final: 0.7272 (t0)
REVERT: O   99 ARG cc_start: 0.7462 (mmt-90) cc_final: 0.6811 (mtp85)
REVERT: P   40 LYS cc_start: 0.7836 (mttt) cc_final: 0.7421 (mmtp)
REVERT: P   65 ASP cc_start: 0.7485 (t70) cc_final: 0.7089 (t0)
REVERT: R   77 LYS cc_start: 0.7818 (mtmt) cc_final: 0.7379 (mttt)
REVERT: R   95 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7452 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.3822
  time to fit residues: 106.0863
Evaluate side-chains
  153 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0050
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 89 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
G1087 GLN
G1186 GLN
M  85 GLN
P  60 ASN
P  81 ASN
Q 113 HIS
R  64 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.133575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.116746 restraints weight = 17285.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 0.95
r_work: 0.3450 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12973  Z= 0.175
  Angle     :  0.807  30.739  18432  Z= 0.401
  Chirality :  0.039   0.142   2078
  Planarity :  0.005   0.035   1571
  Dihedral  : 29.045 135.115   3441
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  6.44 %
    Favored  : 92.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  0.17 (0.27), residues: 946
  helix:  0.25 (0.20), residues: 587
  sheet:  0.99 (0.87), residues: 42
  loop :  0.03 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP G1650 
 HIS   0.004   0.001   HIS G1663 
 PHE   0.013   0.002   PHE G1096 
 TYR   0.016   0.002   TYR N  88 
 ARG   0.006   0.001   ARG G1201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04858 (  604)
  hydrogen bonds       : angle       4.05905 ( 1598)
  covalent geometry    : bond        0.00377 (12972)
  covalent geometry    : angle       0.80684 (18432)
  Misc. bond           : bond        0.00084 (    1)

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 154
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
REVERT: G 1186 GLN cc_start: 0.3780 (OUTLIER) cc_final: 0.2965 (tt0)
REVERT: G 1240 MET cc_start: 0.1270 (OUTLIER) cc_final: 0.0782 (ppp)
REVERT: N   25 ASN cc_start: 0.7130 (m-40) cc_final: 0.6707 (m110)
REVERT: O   38 ASN cc_start: 0.7599 (t0) cc_final: 0.7356 (t0)
REVERT: R   57 VAL cc_start: 0.8087 (t) cc_final: 0.7771 (m)
REVERT: R   77 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7391 (mttt)
  outliers start: 8
  outliers final: 5
  residues processed: 158
  average time/residue: 0.3514
  time to fit residues: 72.8201
Evaluate side-chains
  138 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 1044 VAL
Chi-restraints excluded: chain G residue 1075 LYS
Chi-restraints excluded: chain G residue 1186 GLN
Chi-restraints excluded: chain G residue 1210 LEU
Chi-restraints excluded: chain G residue 1240 MET
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain Q residue   80 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 112 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
G1263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.133943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.116746 restraints weight = 17472.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 0.99
r_work: 0.3432 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.3219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12973  Z= 0.187
  Angle     :  0.807  31.292  18432  Z= 0.395
  Chirality :  0.039   0.178   2078
  Planarity :  0.005   0.036   1571
  Dihedral  : 28.970 126.074   3441
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 10.61 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.45 (0.27), residues: 946
  helix:  0.61 (0.21), residues: 592
  sheet:  0.18 (0.82), residues: 47
  loop : -0.04 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP G1036 
 HIS   0.006   0.001   HIS G1663 
 PHE   0.020   0.002   PHE G1079 
 TYR   0.019   0.002   TYR O  50 
 ARG   0.007   0.001   ARG O  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04332 (  604)
  hydrogen bonds       : angle       3.87660 ( 1598)
  covalent geometry    : bond        0.00415 (12972)
  covalent geometry    : angle       0.80711 (18432)
  Misc. bond           : bond        0.00054 (    1)

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 1.075 
Fit side-chains
REVERT: G 1264 PHE cc_start: 0.6369 (m-80) cc_final: 0.6147 (m-80)
REVERT: G 1563 ARG cc_start: 0.7094 (mtm-85) cc_final: 0.6772 (mtt90)
REVERT: G 1650 TRP cc_start: 0.5782 (OUTLIER) cc_final: 0.5475 (t60)
REVERT: N   25 ASN cc_start: 0.7219 (m-40) cc_final: 0.6796 (m110)
REVERT: P  117 LYS cc_start: 0.8058 (tttm) cc_final: 0.7826 (tttm)
REVERT: R   57 VAL cc_start: 0.8058 (t) cc_final: 0.7784 (m)
REVERT: R   77 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7459 (mttt)
  outliers start: 11
  outliers final: 7
  residues processed: 143
  average time/residue: 0.3315
  time to fit residues: 62.5516
Evaluate side-chains
  128 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 1044 VAL
Chi-restraints excluded: chain G residue 1268 CYS
Chi-restraints excluded: chain G residue 1650 TRP
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain O residue   19 SER
Chi-restraints excluded: chain Q residue   56 LYS
Chi-restraints excluded: chain Q residue   80 THR
Chi-restraints excluded: chain Q residue  117 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 97 optimal weight:    0.0980
   chunk 0 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 105 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
G1186 GLN
G1263 GLN
G1269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.136215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.119032 restraints weight = 17448.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 1.00
r_work: 0.3473 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12973  Z= 0.146
  Angle     :  0.750  30.525  18432  Z= 0.362
  Chirality :  0.035   0.152   2078
  Planarity :  0.004   0.035   1571
  Dihedral  : 28.498 121.731   3441
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.20 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.00 (0.27), residues: 946
  helix:  1.09 (0.21), residues: 594
  sheet:  0.33 (0.82), residues: 47
  loop :  0.07 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP G1650 
 HIS   0.005   0.001   HIS P  79 
 PHE   0.017   0.001   PHE P  67 
 TYR   0.012   0.001   TYR P  39 
 ARG   0.006   0.000   ARG O  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03649 (  604)
  hydrogen bonds       : angle       3.59289 ( 1598)
  covalent geometry    : bond        0.00314 (12972)
  covalent geometry    : angle       0.75019 (18432)
  Misc. bond           : bond        0.00040 (    1)

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 1.082 
Fit side-chains
REVERT: G 1264 PHE cc_start: 0.6516 (m-80) cc_final: 0.6282 (m-80)
REVERT: G 1563 ARG cc_start: 0.7031 (mtm-85) cc_final: 0.6745 (mtt90)
REVERT: G 1650 TRP cc_start: 0.5675 (OUTLIER) cc_final: 0.5384 (t60)
REVERT: N   25 ASN cc_start: 0.7202 (m-40) cc_final: 0.6807 (m110)
REVERT: P  110 GLU cc_start: 0.7947 (tp30) cc_final: 0.7720 (tp30)
REVERT: R   57 VAL cc_start: 0.8050 (t) cc_final: 0.7810 (m)
REVERT: R   77 LYS cc_start: 0.7710 (mtmt) cc_final: 0.7470 (mttt)
  outliers start: 12
  outliers final: 7
  residues processed: 144
  average time/residue: 0.3283
  time to fit residues: 62.7065
Evaluate side-chains
  128 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 1044 VAL
Chi-restraints excluded: chain G residue 1268 CYS
Chi-restraints excluded: chain G residue 1650 TRP
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain O residue   19 SER
Chi-restraints excluded: chain O residue   79 ILE
Chi-restraints excluded: chain Q residue   56 LYS
Chi-restraints excluded: chain R residue   73 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 70 optimal weight:    0.4980
   chunk 81 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0980
   chunk 22 optimal weight:    5.9990
   chunk 102 optimal weight:    0.6980
   chunk 44 optimal weight:    4.9990
   chunk 96 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
G1141 ASN
G1191 HIS
P  60 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.135860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.118686 restraints weight = 17303.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 0.99
r_work: 0.3470 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12973  Z= 0.150
  Angle     :  0.752  30.952  18432  Z= 0.362
  Chirality :  0.035   0.166   2078
  Planarity :  0.004   0.036   1571
  Dihedral  : 28.413 114.495   3441
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.40 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.14 (0.27), residues: 946
  helix:  1.25 (0.21), residues: 595
  sheet:  0.40 (0.83), residues: 47
  loop :  0.01 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP G1650 
 HIS   0.005   0.001   HIS P  79 
 PHE   0.013   0.001   PHE Q  67 
 TYR   0.030   0.002   TYR N  88 
 ARG   0.006   0.000   ARG O  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03662 (  604)
  hydrogen bonds       : angle       3.58624 ( 1598)
  covalent geometry    : bond        0.00327 (12972)
  covalent geometry    : angle       0.75165 (18432)
  Misc. bond           : bond        0.00008 (    1)

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
REVERT: G 1186 GLN cc_start: 0.4873 (OUTLIER) cc_final: 0.4233 (pt0)
REVERT: G 1264 PHE cc_start: 0.6498 (m-80) cc_final: 0.5922 (m-10)
REVERT: G 1650 TRP cc_start: 0.5706 (OUTLIER) cc_final: 0.5485 (t60)
REVERT: G 1684 GLU cc_start: 0.5498 (pt0) cc_final: 0.5190 (pt0)
REVERT: N   25 ASN cc_start: 0.7226 (m-40) cc_final: 0.6787 (m110)
REVERT: N   57 VAL cc_start: 0.8172 (t) cc_final: 0.7921 (m)
REVERT: P  110 GLU cc_start: 0.7949 (tp30) cc_final: 0.7713 (tp30)
REVERT: R   57 VAL cc_start: 0.8074 (t) cc_final: 0.7836 (m)
REVERT: R   77 LYS cc_start: 0.7683 (mtmt) cc_final: 0.7464 (mttt)
  outliers start: 15
  outliers final: 7
  residues processed: 141
  average time/residue: 0.3023
  time to fit residues: 57.8634
Evaluate side-chains
  130 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 1044 VAL
Chi-restraints excluded: chain G residue 1186 GLN
Chi-restraints excluded: chain G residue 1268 CYS
Chi-restraints excluded: chain G residue 1650 TRP
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain O residue   19 SER
Chi-restraints excluded: chain O residue   79 ILE
Chi-restraints excluded: chain R residue   25 ASN
Chi-restraints excluded: chain R residue   73 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
G1191 HIS
G1207 GLN
G1667 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.134856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.117609 restraints weight = 17789.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 0.99
r_work: 0.3449 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.4033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12973  Z= 0.162
  Angle     :  0.762  31.126  18432  Z= 0.368
  Chirality :  0.036   0.177   2078
  Planarity :  0.004   0.036   1571
  Dihedral  : 28.407 113.737   3441
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.16 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.27), residues: 946
  helix:  1.21 (0.21), residues: 595
  sheet:  0.38 (0.83), residues: 47
  loop : -0.16 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP G1650 
 HIS   0.004   0.001   HIS P  79 
 PHE   0.014   0.002   PHE Q  67 
 TYR   0.050   0.002   TYR N  88 
 ARG   0.005   0.000   ARG G1563 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03842 (  604)
  hydrogen bonds       : angle       3.65460 ( 1598)
  covalent geometry    : bond        0.00357 (12972)
  covalent geometry    : angle       0.76201 (18432)
  Misc. bond           : bond        0.00033 (    1)

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
REVERT: G 1650 TRP cc_start: 0.5773 (OUTLIER) cc_final: 0.5527 (t60)
REVERT: G 1684 GLU cc_start: 0.5479 (pt0) cc_final: 0.5242 (pt0)
REVERT: O   99 ARG cc_start: 0.7810 (mmt-90) cc_final: 0.7397 (mtp85)
REVERT: P  110 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7692 (tp30)
REVERT: Q   56 LYS cc_start: 0.7474 (ptmt) cc_final: 0.7192 (ptmm)
REVERT: R   57 VAL cc_start: 0.8087 (t) cc_final: 0.7841 (m)
REVERT: R   77 LYS cc_start: 0.7670 (mtmt) cc_final: 0.7449 (mttt)
  outliers start: 20
  outliers final: 13
  residues processed: 139
  average time/residue: 0.3130
  time to fit residues: 59.5924
Evaluate side-chains
  132 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 1044 VAL
Chi-restraints excluded: chain G residue 1268 CYS
Chi-restraints excluded: chain G residue 1545 MET
Chi-restraints excluded: chain G residue 1623 ILE
Chi-restraints excluded: chain G residue 1650 TRP
Chi-restraints excluded: chain G residue 1653 THR
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain O residue   19 SER
Chi-restraints excluded: chain O residue   79 ILE
Chi-restraints excluded: chain P residue   80 TYR
Chi-restraints excluded: chain P residue  110 GLU
Chi-restraints excluded: chain Q residue   80 THR
Chi-restraints excluded: chain Q residue  117 VAL
Chi-restraints excluded: chain R residue   25 ASN
Chi-restraints excluded: chain R residue   73 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 21 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
G1151 HIS
G1191 HIS
G1207 GLN
P  60 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.133341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.116184 restraints weight = 17688.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 0.97
r_work: 0.3427 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.4125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12973  Z= 0.180
  Angle     :  0.781  31.396  18432  Z= 0.378
  Chirality :  0.037   0.183   2078
  Planarity :  0.004   0.037   1571
  Dihedral  : 28.563 111.846   3441
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.87 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.84 (0.27), residues: 946
  helix:  1.08 (0.21), residues: 595
  sheet:  0.37 (0.82), residues: 47
  loop : -0.29 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP G1650 
 HIS   0.007   0.001   HIS G1151 
 PHE   0.016   0.002   PHE Q  67 
 TYR   0.044   0.002   TYR N  88 
 ARG   0.004   0.000   ARG O  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  604)
  hydrogen bonds       : angle       3.80128 ( 1598)
  covalent geometry    : bond        0.00405 (12972)
  covalent geometry    : angle       0.78077 (18432)
  Misc. bond           : bond        0.00041 (    1)

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
REVERT: G 1186 GLN cc_start: 0.5358 (OUTLIER) cc_final: 0.4418 (pt0)
REVERT: G 1216 ILE cc_start: 0.8088 (mp) cc_final: 0.7873 (mp)
REVERT: G 1563 ARG cc_start: 0.7237 (mtt90) cc_final: 0.7000 (mtt180)
REVERT: O   99 ARG cc_start: 0.7805 (mmt-90) cc_final: 0.7394 (mtp180)
REVERT: P  110 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7752 (tp30)
REVERT: R   57 VAL cc_start: 0.8057 (t) cc_final: 0.7809 (m)
REVERT: R   77 LYS cc_start: 0.7682 (mtmt) cc_final: 0.7458 (mttt)
  outliers start: 18
  outliers final: 13
  residues processed: 138
  average time/residue: 0.3202
  time to fit residues: 60.7211
Evaluate side-chains
  135 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 1044 VAL
Chi-restraints excluded: chain G residue 1186 GLN
Chi-restraints excluded: chain G residue 1268 CYS
Chi-restraints excluded: chain G residue 1545 MET
Chi-restraints excluded: chain G residue 1623 ILE
Chi-restraints excluded: chain G residue 1653 THR
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain O residue   19 SER
Chi-restraints excluded: chain O residue   79 ILE
Chi-restraints excluded: chain P residue   80 TYR
Chi-restraints excluded: chain P residue  110 GLU
Chi-restraints excluded: chain Q residue   80 THR
Chi-restraints excluded: chain Q residue  117 VAL
Chi-restraints excluded: chain R residue   25 ASN
Chi-restraints excluded: chain R residue   73 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0170
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
G1191 HIS
G1207 GLN
P  79 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.135012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.117896 restraints weight = 17735.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 0.98
r_work: 0.3451 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.4294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12973  Z= 0.154
  Angle     :  0.756  30.759  18432  Z= 0.363
  Chirality :  0.035   0.180   2078
  Planarity :  0.004   0.037   1571
  Dihedral  : 28.370 111.945   3441
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.59 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.27), residues: 946
  helix:  1.23 (0.21), residues: 595
  sheet:  0.48 (0.83), residues: 47
  loop : -0.25 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP G1650 
 HIS   0.008   0.001   HIS P  79 
 PHE   0.014   0.001   PHE Q  67 
 TYR   0.055   0.002   TYR N  88 
 ARG   0.005   0.000   ARG O  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03739 (  604)
  hydrogen bonds       : angle       3.70692 ( 1598)
  covalent geometry    : bond        0.00339 (12972)
  covalent geometry    : angle       0.75576 (18432)
  Misc. bond           : bond        0.00068 (    1)

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
REVERT: O   38 ASN cc_start: 0.7718 (t0) cc_final: 0.7468 (t0)
REVERT: O   99 ARG cc_start: 0.7794 (mmt-90) cc_final: 0.7392 (mtp180)
REVERT: P  110 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7689 (tp30)
REVERT: Q   56 LYS cc_start: 0.7393 (ptmt) cc_final: 0.7132 (ptmm)
REVERT: R   57 VAL cc_start: 0.8049 (t) cc_final: 0.7791 (m)
REVERT: R   77 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7457 (mttt)
  outliers start: 19
  outliers final: 13
  residues processed: 139
  average time/residue: 0.3413
  time to fit residues: 65.1787
Evaluate side-chains
  135 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 1044 VAL
Chi-restraints excluded: chain G residue 1268 CYS
Chi-restraints excluded: chain G residue 1545 MET
Chi-restraints excluded: chain G residue 1623 ILE
Chi-restraints excluded: chain G residue 1653 THR
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain O residue   19 SER
Chi-restraints excluded: chain O residue   79 ILE
Chi-restraints excluded: chain P residue   80 TYR
Chi-restraints excluded: chain P residue   95 VAL
Chi-restraints excluded: chain P residue  110 GLU
Chi-restraints excluded: chain Q residue  117 VAL
Chi-restraints excluded: chain R residue   25 ASN
Chi-restraints excluded: chain R residue   73 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 111 optimal weight:    0.0870
   chunk 16 optimal weight:    1.9990
   chunk 102 optimal weight:    0.0670
   chunk 72 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 73 optimal weight:    0.2980
   chunk 25 optimal weight:    0.0670
   chunk 97 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   overall best weight:    0.2234

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

Flipped N/Q/H residues before XYZ refinement:
G1191 HIS
G1207 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.138175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.121860 restraints weight = 17454.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 0.92
r_work: 0.3508 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.4555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12973  Z= 0.131
  Angle     :  0.739  29.983  18432  Z= 0.352
  Chirality :  0.034   0.149   2078
  Planarity :  0.004   0.038   1571
  Dihedral  : 28.068 112.711   3441
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.14 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.30 (0.28), residues: 946
  helix:  1.44 (0.21), residues: 602
  sheet:  0.65 (0.83), residues: 47
  loop : -0.19 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP G1036 
 HIS   0.002   0.000   HIS G1205 
 PHE   0.011   0.001   PHE Q  67 
 TYR   0.052   0.002   TYR N  88 
 ARG   0.005   0.000   ARG G1679 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03302 (  604)
  hydrogen bonds       : angle       3.58617 ( 1598)
  covalent geometry    : bond        0.00277 (12972)
  covalent geometry    : angle       0.73884 (18432)
  Misc. bond           : bond        0.00050 (    1)

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G 1018 TYR cc_start: 0.7078 (m-10) cc_final: 0.6876 (m-10)
REVERT: G 1186 GLN cc_start: 0.5130 (OUTLIER) cc_final: 0.4532 (pt0)
REVERT: G 1581 MET cc_start: 0.7039 (tpt) cc_final: 0.6786 (tpt)
REVERT: N   57 VAL cc_start: 0.8142 (t) cc_final: 0.7940 (m)
REVERT: O   99 ARG cc_start: 0.7801 (mmt-90) cc_final: 0.7410 (mtp180)
REVERT: P   56 MET cc_start: 0.7103 (tpp) cc_final: 0.6828 (mmm)
REVERT: P  110 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7655 (tp30)
REVERT: R   57 VAL cc_start: 0.8006 (t) cc_final: 0.7799 (m)
  outliers start: 13
  outliers final: 11
  residues processed: 146
  average time/residue: 0.2968
  time to fit residues: 58.6838
Evaluate side-chains
  139 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 1039 GLU
Chi-restraints excluded: chain G residue 1044 VAL
Chi-restraints excluded: chain G residue 1186 GLN
Chi-restraints excluded: chain G residue 1545 MET
Chi-restraints excluded: chain G residue 1623 ILE
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain O residue   19 SER
Chi-restraints excluded: chain O residue   79 ILE
Chi-restraints excluded: chain P residue   80 TYR
Chi-restraints excluded: chain P residue   95 VAL
Chi-restraints excluded: chain P residue  110 GLU
Chi-restraints excluded: chain Q residue  117 VAL
Chi-restraints excluded: chain R residue   25 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0170
   chunk 103 optimal weight:    0.9980
   chunk 111 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0970
   chunk 102 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0170
   chunk 92 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.3254

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

Flipped N/Q/H residues before XYZ refinement:
G1191 HIS
** G1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.137330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.120249 restraints weight = 17638.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 0.99
r_work: 0.3502 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7063
moved from start:          0.4703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12973  Z= 0.134
  Angle     :  0.739  30.278  18432  Z= 0.351
  Chirality :  0.034   0.153   2078
  Planarity :  0.004   0.038   1571
  Dihedral  : 28.071 112.504   3441
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.02 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.38 (0.28), residues: 946
  helix:  1.52 (0.21), residues: 601
  sheet:  0.80 (0.82), residues: 47
  loop : -0.22 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP G1036 
 HIS   0.003   0.001   HIS G1080 
 PHE   0.024   0.001   PHE G1264 
 TYR   0.055   0.002   TYR N  88 
 ARG   0.004   0.000   ARG G1661 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03354 (  604)
  hydrogen bonds       : angle       3.54385 ( 1598)
  covalent geometry    : bond        0.00285 (12972)
  covalent geometry    : angle       0.73889 (18432)
  Misc. bond           : bond        0.00063 (    1)

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

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

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1892 Ramachandran restraints generated.
    946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
REVERT: G 1018 TYR cc_start: 0.7148 (m-10) cc_final: 0.6942 (m-10)
REVERT: G 1240 MET cc_start: 0.1858 (tmm) cc_final: 0.1536 (ppp)
REVERT: N   31 LYS cc_start: 0.7949 (mttm) cc_final: 0.7712 (mttm)
REVERT: N   57 VAL cc_start: 0.8183 (t) cc_final: 0.7947 (m)
REVERT: O   99 ARG cc_start: 0.7757 (mmt-90) cc_final: 0.7383 (mtp180)
REVERT: P  110 GLU cc_start: 0.7806 (tp30) cc_final: 0.7580 (tp30)
  outliers start: 13
  outliers final: 12
  residues processed: 137
  average time/residue: 0.2913
  time to fit residues: 54.6093
Evaluate side-chains
  132 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 1044 VAL
Chi-restraints excluded: chain G residue 1268 CYS
Chi-restraints excluded: chain G residue 1545 MET
Chi-restraints excluded: chain G residue 1623 ILE
Chi-restraints excluded: chain G residue 1665 LEU
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain O residue   19 SER
Chi-restraints excluded: chain O residue   79 ILE
Chi-restraints excluded: chain P residue   80 TYR
Chi-restraints excluded: chain P residue   95 VAL
Chi-restraints excluded: chain Q residue  117 VAL
Chi-restraints excluded: chain R residue   25 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
G1191 HIS
G1663 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.133963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.116699 restraints weight = 17782.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 0.99
r_work: 0.3434 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.4564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12973  Z= 0.180
  Angle     :  0.783  31.386  18432  Z= 0.377
  Chirality :  0.037   0.193   2078
  Planarity :  0.004   0.037   1571
  Dihedral  : 28.416 111.393   3441
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 15.49 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  0.89 (0.27), residues: 946
  helix:  1.16 (0.21), residues: 600
  sheet:  0.68 (0.82), residues: 47
  loop : -0.48 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP G1650 
 HIS   0.003   0.001   HIS N  75 
 PHE   0.016   0.002   PHE Q  67 
 TYR   0.053   0.002   TYR N  88 
 ARG   0.005   0.001   ARG G1661 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  604)
  hydrogen bonds       : angle       3.76517 ( 1598)
  covalent geometry    : bond        0.00406 (12972)
  covalent geometry    : angle       0.78275 (18432)
  Misc. bond           : bond        0.00042 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7189.88 seconds
wall clock time: 124 minutes 41.88 seconds (7481.88 seconds total)