Starting phenix.real_space_refine
on Tue Apr 29 05:55:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5u1c_8481/04_2025/5u1c_8481.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5u1c_8481/04_2025/5u1c_8481.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5u1c_8481/04_2025/5u1c_8481.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5u1c_8481/04_2025/5u1c_8481.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5u1c_8481/04_2025/5u1c_8481.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5u1c_8481/04_2025/5u1c_8481.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.012
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: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      92      5.49       5
     Mg      2      5.21       5
     S      28      5.16       5
     C    5188      2.51       5
     N    1534      2.21       5
     O    1750      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8596
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1975
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 10, 'TRANS': 240}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1362
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 6, 'TRANS': 165}
          Chain breaks: 3
    Chain: "G"
      Number of atoms: 162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 162
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
    Chain: "E"
      Number of atoms: 285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 285
          Classifications: {'DNA': 14}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 13}
    Chain: "F"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 512
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "C"
      Number of atoms: 1975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1975
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 10, 'TRANS': 240}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1362
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 6, 'TRANS': 165}
          Chain breaks: 3
    Chain: "H"
      Number of atoms: 162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 162
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
    Chain: "I"
      Number of atoms: 285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 285
          Classifications: {'DNA': 14}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 13}
    Chain: "J"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 512
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    319  SG  CYS A  40      21.270  47.273  39.306  1.00 11.69           S
  ATOM    342  SG  CYS A  43      24.958  47.314  38.194  1.00 10.21           S
  ATOM   4615  SG  CYS C  40      65.198  83.727  39.295  1.00 12.83           S
  ATOM   4638  SG  CYS C  43      61.511  83.683  38.178  1.00 11.35           S

  Time building chain proxies: 6.00, per 1000 atoms: 0.70
  Number of scatterers: 8596
  At special positions: 0
  Unit cell: (87.77, 132.31, 83.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S      28     16.00
     P      92     15.00
     Mg      2     11.99
     O    1750      8.00
     N    1534      7.00
     C    5188      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: 2.54
  Conformation dependent library (CDL) restraints added in 792.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 500 "
        pdb="ZN    ZN A 500 " - pdb=" ND1 HIS A  16 "
        pdb="ZN    ZN A 500 " - pdb=" NE2 HIS A  12 "
        pdb="ZN    ZN A 500 " - pdb=" SG  CYS A  43 "
        pdb="ZN    ZN A 500 " - pdb=" SG  CYS A  40 "
      pdb="  ZN C 500 "
        pdb="ZN    ZN C 500 " - pdb=" ND1 HIS C  16 "
        pdb="ZN    ZN C 500 " - pdb=" NE2 HIS C  12 "
        pdb="ZN    ZN C 500 " - pdb=" SG  CYS C  43 "
        pdb="ZN    ZN C 500 " - pdb=" SG  CYS C  40 "
      Number of angles added : 4


  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 10 sheets defined
      46.8% alpha, 18.7% beta
      42 base pairs and 70 stacking pairs defined.
    Time for finding SS restraints: 3.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 16
      removed outlier: 3.585A  pdb=" N   ASP A   6 " --> pdb=" O   LEU A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 18 through 26
    Processing helix  chain 'A' and resid 29 through 40
    Processing helix  chain 'A' and resid 93 through 106
    Processing helix  chain 'A' and resid 119 through 122
    Processing helix  chain 'A' and resid 123 through 133
      removed outlier: 3.604A  pdb=" N   LYS A 127 " --> pdb=" O   SER A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 147
    Processing helix  chain 'A' and resid 148 through 166
      removed outlier: 3.868A  pdb=" N   GLN A 152 " --> pdb=" O   GLN A 148 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A 156 " --> pdb=" O   GLN A 152 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN A 164 " --> pdb=" O   LYS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 169
      No H-bonds generated for 'chain 'A' and resid 167 through 169'
    Processing helix  chain 'A' and resid 171 through 186
      removed outlier: 3.959A  pdb=" N   ALA A 175 " --> pdb=" O   HIS A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 204
    Processing helix  chain 'B' and resid 67 through 71
    Processing helix  chain 'B' and resid 93 through 108
    Processing helix  chain 'B' and resid 118 through 123
    Processing helix  chain 'B' and resid 123 through 134
      removed outlier: 3.564A  pdb=" N   LYS B 127 " --> pdb=" O   SER B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 166
    Processing helix  chain 'B' and resid 167 through 169
      No H-bonds generated for 'chain 'B' and resid 167 through 169'
    Processing helix  chain 'B' and resid 171 through 186
      removed outlier: 3.593A  pdb=" N   ALA B 175 " --> pdb=" O   HIS B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 204
      removed outlier: 3.506A  pdb=" N   ILE B 204 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 16
      removed outlier: 3.585A  pdb=" N   ASP C   6 " --> pdb=" O   LEU C   2 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 26
    Processing helix  chain 'C' and resid 29 through 40
    Processing helix  chain 'C' and resid 93 through 106
    Processing helix  chain 'C' and resid 119 through 122
    Processing helix  chain 'C' and resid 123 through 133
      removed outlier: 3.604A  pdb=" N   LYS C 127 " --> pdb=" O   SER C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 147
    Processing helix  chain 'C' and resid 148 through 166
      removed outlier: 3.866A  pdb=" N   GLN C 152 " --> pdb=" O   GLN C 148 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS C 156 " --> pdb=" O   GLN C 152 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN C 164 " --> pdb=" O   LYS C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 169
      No H-bonds generated for 'chain 'C' and resid 167 through 169'
    Processing helix  chain 'C' and resid 171 through 186
      removed outlier: 3.959A  pdb=" N   ALA C 175 " --> pdb=" O   HIS C 171 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 204
    Processing helix  chain 'D' and resid 67 through 71
    Processing helix  chain 'D' and resid 93 through 108
    Processing helix  chain 'D' and resid 118 through 123
    Processing helix  chain 'D' and resid 123 through 134
      removed outlier: 3.564A  pdb=" N   LYS D 127 " --> pdb=" O   SER D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 152 through 166
    Processing helix  chain 'D' and resid 167 through 169
      No H-bonds generated for 'chain 'D' and resid 167 through 169'
    Processing helix  chain 'D' and resid 171 through 186
      removed outlier: 3.593A  pdb=" N   ALA D 175 " --> pdb=" O   HIS D 171 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 204
      removed outlier: 3.507A  pdb=" N   ILE D 204 " --> pdb=" O   ILE D 200 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89
      removed outlier: 4.114A  pdb=" N   VAL A  72 " --> pdb=" O   ILE A  89 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   TRP A  61 " --> pdb=" O   HIS A 114 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   VAL A 113 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 227
    Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 244
      removed outlier: 6.427A  pdb=" N   VAL A 250 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   LYS A 244 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   ALA A 248 " --> pdb=" O   LYS A 244 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 88
      removed outlier: 6.722A  pdb=" N   TRP B  61 " --> pdb=" O   HIS B 114 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 257 through 261
      removed outlier: 6.357A  pdb=" N   GLN B 252 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   LEU B 241 " --> pdb=" O   GLN B 252 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 89
      removed outlier: 4.114A  pdb=" N   VAL C  72 " --> pdb=" O   ILE C  89 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   TRP C  61 " --> pdb=" O   HIS C 114 " (cutoff:3.500A)
      removed outlier: 5.793A  pdb=" N   VAL C 113 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 227
    Processing sheet with id=AA8, first strand: chain 'C' and resid 240 through 244
      removed outlier: 6.427A  pdb=" N   VAL C 250 " --> pdb=" O   LEU C 242 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   LYS C 244 " --> pdb=" O   ALA C 248 " (cutoff:3.500A)
      removed outlier: 7.752A  pdb=" N   ALA C 248 " --> pdb=" O   LYS C 244 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 83 through 88
      removed outlier: 6.722A  pdb=" N   TRP D  61 " --> pdb=" O   HIS D 114 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 257 through 261
      removed outlier: 6.357A  pdb=" N   GLN D 252 " --> pdb=" O   LEU D 241 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   LEU D 241 " --> pdb=" O   GLN D 252 " (cutoff:3.500A)

    332 hydrogen bonds defined for protein.
    930 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      104 hydrogen bonds
      208 hydrogen bond angles
      0 basepair planarities
      42 basepair parallelities
      70 stacking parallelities
  Total time for adding SS restraints: 2.88

  Time building geometry restraints manager: 2.98 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: 2023
        1.33 -     1.45: 2224
        1.45 -     1.57: 4499
        1.57 -     1.69: 180
        1.69 -     1.81: 40
  Bond restraints: 8966
  Sorted by residual:
  bond pdb=" C   GLY A 118 "
       pdb=" N   SER A 119 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 1.20e-02 6.94e+03 1.56e+01
  bond pdb=" C   THR A 122 "
       pdb=" N   SER A 123 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.038 1.30e-02 5.92e+03 8.33e+00
  bond pdb=" C1'  DT E  28 "
       pdb=" N1   DT E  28 "
    ideal  model  delta    sigma   weight residual
    1.490  1.548 -0.058 3.00e-02 1.11e+03 3.69e+00
  bond pdb=" C1'  DT I  28 "
       pdb=" N1   DT I  28 "
    ideal  model  delta    sigma   weight residual
    1.490  1.547 -0.057 3.00e-02 1.11e+03 3.63e+00
  bond pdb=" C4'  DC H   6 "
       pdb=" C3'  DC H   6 "
    ideal  model  delta    sigma   weight residual
    1.523  1.560 -0.037 2.00e-02 2.50e+03 3.47e+00
  ... (remaining 8961 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 12133
        2.28 -     4.57: 353
        4.57 -     6.85: 25
        6.85 -     9.13: 1
        9.13 -    11.41: 4
  Bond angle restraints: 12516
  Sorted by residual:
  angle pdb=" O   GLY C 118 "
        pdb=" C   GLY C 118 "
        pdb=" N   SER C 119 "
      ideal   model   delta    sigma   weight residual
     122.70  111.29   11.41 1.30e+00 5.92e-01 7.71e+01
  angle pdb=" O   GLY A 118 "
        pdb=" C   GLY A 118 "
        pdb=" N   SER A 119 "
      ideal   model   delta    sigma   weight residual
     122.70  111.62   11.08 1.30e+00 5.92e-01 7.26e+01
  angle pdb=" CA  GLY C 118 "
        pdb=" C   GLY C 118 "
        pdb=" N   SER C 119 "
      ideal   model   delta    sigma   weight residual
     116.69  127.81  -11.12 2.04e+00 2.40e-01 2.97e+01
  angle pdb=" CA  GLY A 118 "
        pdb=" C   GLY A 118 "
        pdb=" N   SER A 119 "
      ideal   model   delta    sigma   weight residual
     116.69  127.67  -10.98 2.04e+00 2.40e-01 2.90e+01
  angle pdb=" C   GLY C 118 "
        pdb=" N   SER C 119 "
        pdb=" CA  SER C 119 "
      ideal   model   delta    sigma   weight residual
     120.79  127.08   -6.29 1.39e+00 5.18e-01 2.05e+01
  ... (remaining 12511 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.72: 4642
       33.72 -    67.44: 418
       67.44 -   101.15: 10
      101.15 -   134.87: 0
      134.87 -   168.59: 2
  Dihedral angle restraints: 5072
    sinusoidal: 2656
      harmonic: 2416
  Sorted by residual:
  dihedral pdb=" CA  GLN A 148 "
           pdb=" C   GLN A 148 "
           pdb=" N   GLY A 149 "
           pdb=" CA  GLY A 149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.75  -22.25     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  GLN C 148 "
           pdb=" C   GLN C 148 "
           pdb=" N   GLY C 149 "
           pdb=" CA  GLY C 149 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.75  -22.25     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  SER C 195 "
           pdb=" C   SER C 195 "
           pdb=" N   ALA C 196 "
           pdb=" CA  ALA C 196 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.85  -21.15     0      5.00e+00 4.00e-02 1.79e+01
  ... (remaining 5069 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 861
       0.045 -    0.091: 394
       0.091 -    0.136: 110
       0.136 -    0.182: 21
       0.182 -    0.227: 2
  Chirality restraints: 1388
  Sorted by residual:
  chirality pdb=" CA  LYS C  46 "
            pdb=" N   LYS C  46 "
            pdb=" C   LYS C  46 "
            pdb=" CB  LYS C  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  LYS A  46 "
            pdb=" N   LYS A  46 "
            pdb=" C   LYS A  46 "
            pdb=" CB  LYS A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  ILE A  89 "
            pdb=" N   ILE A  89 "
            pdb=" C   ILE A  89 "
            pdb=" CB  ILE A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.99e-01
  ... (remaining 1385 not shown)

  Planarity restraints: 1258
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC F  20 "   -0.014 2.00e-02 2.50e+03   1.47e-02 4.87e+00
        pdb=" N1   DC F  20 "    0.013 2.00e-02 2.50e+03
        pdb=" C2   DC F  20 "   -0.031 2.00e-02 2.50e+03
        pdb=" O2   DC F  20 "    0.022 2.00e-02 2.50e+03
        pdb=" N3   DC F  20 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DC F  20 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4   DC F  20 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DC F  20 "    0.008 2.00e-02 2.50e+03
        pdb=" C6   DC F  20 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  20 "    0.014 2.00e-02 2.50e+03   1.45e-02 4.73e+00
        pdb=" N1   DC J  20 "   -0.013 2.00e-02 2.50e+03
        pdb=" C2   DC J  20 "    0.030 2.00e-02 2.50e+03
        pdb=" O2   DC J  20 "   -0.021 2.00e-02 2.50e+03
        pdb=" N3   DC J  20 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DC J  20 "    0.005 2.00e-02 2.50e+03
        pdb=" N4   DC J  20 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DC J  20 "   -0.008 2.00e-02 2.50e+03
        pdb=" C6   DC J  20 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  19 "   -0.026 2.00e-02 2.50e+03   1.43e-02 4.62e+00
        pdb=" N1   DC I  19 "    0.033 2.00e-02 2.50e+03
        pdb=" C2   DC I  19 "    0.001 2.00e-02 2.50e+03
        pdb=" O2   DC I  19 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DC I  19 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DC I  19 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4   DC I  19 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DC I  19 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DC I  19 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1255 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 64
        2.55 -     3.14: 6733
        3.14 -     3.73: 13641
        3.73 -     4.31: 19417
        4.31 -     4.90: 30282
  Nonbonded interactions: 70137
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 228 "
            pdb=" OD1 ASP A 229 "
     model   vdw
     1.964 3.040
  nonbonded pdb=" O   ARG C 228 "
            pdb=" OD1 ASP C 229 "
     model   vdw
     1.965 3.040
  nonbonded pdb=" OD2 ASP A  64 "
            pdb="MG    MG A 501 "
     model   vdw
     1.976 2.170
  nonbonded pdb=" OD2 ASP C  64 "
            pdb="MG    MG C 501 "
     model   vdw
     1.977 2.170
  nonbonded pdb=" OG1 THR A  93 "
            pdb=" OP1  DC F  30 "
     model   vdw
     2.051 3.040
  ... (remaining 70132 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'F'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.880
  Find NCS groups from input model:        0.160
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
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      :  0.013   0.689   8974  Z= 0.499
  Angle     :  1.066  34.856  12520  Z= 0.555
  Chirality :  0.054   0.227   1388
  Planarity :  0.005   0.035   1258
  Dihedral  : 20.206 168.589   3512
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.28 %
    Favored  : 99.43 %
  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: -4.03 (0.24), residues: 822
  helix: -2.67 (0.22), residues: 320
  sheet: -2.02 (0.34), residues: 194
  loop : -2.86 (0.30), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP D 235 
 HIS   0.014   0.002   HIS B 183 
 PHE   0.024   0.003   PHE C 121 
 TYR   0.020   0.003   TYR B  99 
 ARG   0.007   0.001   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14310 (  436)
  hydrogen bonds       : angle       8.53030 ( 1138)
  metal coordination   : bond        0.36142 (    8)
  metal coordination   : angle      30.91728 (    4)
  covalent geometry    : bond        0.00775 ( 8966)
  covalent geometry    : angle       0.91224 (12516)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 271
  time to evaluate  : 0.821 
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: A   60 ILE cc_start: 0.8554 (mt) cc_final: 0.8226 (tp)
REVERT: A   85 GLU cc_start: 0.7344 (tp30) cc_final: 0.7080 (tp30)
REVERT: C   22 MET cc_start: 0.7141 (mtm) cc_final: 0.6867 (mtp)
REVERT: C   60 ILE cc_start: 0.8428 (mt) cc_final: 0.8197 (tp)
REVERT: C   85 GLU cc_start: 0.7345 (tp30) cc_final: 0.6977 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 273
  average time/residue: 0.2718
  time to fit residues: 94.3925
Evaluate side-chains
  134 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 68 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 27 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 HIS
B 114 HIS
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 GLN
** C  78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 144 ASN
C 183 HIS
C 252 GLN
** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.114804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.096534 restraints weight = 21374.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.098620 restraints weight = 12979.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.099969 restraints weight = 9536.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.4119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   8974  Z= 0.254
  Angle     :  0.717  13.052  12520  Z= 0.394
  Chirality :  0.046   0.155   1388
  Planarity :  0.006   0.056   1258
  Dihedral  : 26.466 179.872   1916
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 12.93 %
    Favored  : 83.52 %
  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: -2.01 (0.26), residues: 822
  helix: -0.89 (0.24), residues: 340
  sheet: -0.81 (0.34), residues: 210
  loop : -2.10 (0.34), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  61 
 HIS   0.009   0.001   HIS B 183 
 PHE   0.019   0.002   PHE C 181 
 TYR   0.018   0.002   TYR A  99 
 ARG   0.006   0.001   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04723 (  436)
  hydrogen bonds       : angle       5.29712 ( 1138)
  metal coordination   : bond        0.01807 (    8)
  metal coordination   : angle       9.61379 (    4)
  covalent geometry    : bond        0.00560 ( 8966)
  covalent geometry    : angle       0.69621 (12516)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.816 
Fit side-chains
REVERT: A   69 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7324 (tt0)
REVERT: A  103 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8263 (mtpt)
REVERT: A  178 MET cc_start: 0.8794 (mtt) cc_final: 0.6833 (mtt)
REVERT: A  230 SER cc_start: 0.7439 (m) cc_final: 0.6977 (t)
REVERT: B   65 CYS cc_start: 0.7429 (p) cc_final: 0.7157 (t)
REVERT: B  132 TRP cc_start: 0.8795 (t60) cc_final: 0.7915 (t60)
REVERT: C   15 TYR cc_start: 0.8729 (m-10) cc_final: 0.8515 (m-10)
REVERT: C   20 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8265 (ttm-80)
REVERT: C  107 ARG cc_start: 0.7102 (mpp80) cc_final: 0.6850 (mpp80)
REVERT: C  178 MET cc_start: 0.8798 (mtt) cc_final: 0.6778 (mtt)
REVERT: C  230 SER cc_start: 0.7403 (m) cc_final: 0.6946 (t)
REVERT: D   65 CYS cc_start: 0.7442 (p) cc_final: 0.7117 (t)
REVERT: D  132 TRP cc_start: 0.8828 (t60) cc_final: 0.7980 (t60)
  outliers start: 25
  outliers final: 14
  residues processed: 177
  average time/residue: 0.2202
  time to fit residues: 52.2726
Evaluate side-chains
  132 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  103 LYS
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 86 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 4 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 171 HIS
A 184 ASN
B 114 HIS
C 171 HIS
C 184 ASN
C 252 GLN
D 114 HIS
** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.117370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.098219 restraints weight = 21744.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.100592 restraints weight = 12543.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.102121 restraints weight = 8908.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.4761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8974  Z= 0.148
  Angle     :  0.608   9.441  12520  Z= 0.335
  Chirality :  0.043   0.166   1388
  Planarity :  0.004   0.054   1258
  Dihedral  : 26.410 178.846   1916
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.34 %
    Favored  : 82.10 %
  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: -0.83 (0.28), residues: 822
  helix:  0.25 (0.26), residues: 352
  sheet: -0.16 (0.35), residues: 210
  loop : -1.86 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 132 
 HIS   0.006   0.001   HIS D 183 
 PHE   0.012   0.001   PHE C 100 
 TYR   0.018   0.002   TYR A  99 
 ARG   0.005   0.001   ARG D 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  436)
  hydrogen bonds       : angle       4.87432 ( 1138)
  metal coordination   : bond        0.00647 (    8)
  metal coordination   : angle       6.79613 (    4)
  covalent geometry    : bond        0.00323 ( 8966)
  covalent geometry    : angle       0.59612 (12516)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.891 
Fit side-chains
REVERT: A   69 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7210 (tt0)
REVERT: A  144 ASN cc_start: 0.9036 (t0) cc_final: 0.8827 (t0)
REVERT: A  178 MET cc_start: 0.8953 (mtt) cc_final: 0.7057 (mtt)
REVERT: A  181 PHE cc_start: 0.8801 (t80) cc_final: 0.8594 (t80)
REVERT: A  184 ASN cc_start: 0.8346 (m-40) cc_final: 0.8065 (m110)
REVERT: A  230 SER cc_start: 0.7520 (m) cc_final: 0.7012 (t)
REVERT: A  269 ARG cc_start: 0.4757 (tmt170) cc_final: 0.4484 (tpt90)
REVERT: B   65 CYS cc_start: 0.7364 (p) cc_final: 0.7004 (t)
REVERT: B  132 TRP cc_start: 0.8804 (t60) cc_final: 0.8127 (t60)
REVERT: C   15 TYR cc_start: 0.8681 (m-10) cc_final: 0.8331 (m-10)
REVERT: C   20 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.7982 (ttm-80)
REVERT: C  144 ASN cc_start: 0.9075 (t0) cc_final: 0.8861 (t0)
REVERT: C  178 MET cc_start: 0.8933 (mtt) cc_final: 0.7143 (mtt)
REVERT: C  184 ASN cc_start: 0.8476 (m-40) cc_final: 0.8252 (m110)
REVERT: C  230 SER cc_start: 0.7487 (m) cc_final: 0.6979 (t)
REVERT: D   65 CYS cc_start: 0.7391 (p) cc_final: 0.7065 (t)
REVERT: D  132 TRP cc_start: 0.8810 (t60) cc_final: 0.7911 (t60)
  outliers start: 18
  outliers final: 12
  residues processed: 151
  average time/residue: 0.2033
  time to fit residues: 42.4922
Evaluate side-chains
  130 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  162 ILE
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 114 HIS
** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 168 GLN
D 222 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.114193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.095344 restraints weight = 21418.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.097505 restraints weight = 12777.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.098989 restraints weight = 9261.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.5240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8974  Z= 0.186
  Angle     :  0.607   6.552  12520  Z= 0.341
  Chirality :  0.043   0.148   1388
  Planarity :  0.004   0.040   1258
  Dihedral  : 26.680 179.502   1916
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.19 %
    Favored  : 80.26 %
  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: -0.47 (0.28), residues: 822
  helix:  0.57 (0.26), residues: 352
  sheet:  0.02 (0.36), residues: 214
  loop : -1.74 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  61 
 HIS   0.008   0.001   HIS B 183 
 PHE   0.024   0.002   PHE D 100 
 TYR   0.015   0.002   TYR A 143 
 ARG   0.004   0.001   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03941 (  436)
  hydrogen bonds       : angle       4.81017 ( 1138)
  metal coordination   : bond        0.01114 (    8)
  metal coordination   : angle       4.65750 (    4)
  covalent geometry    : bond        0.00416 ( 8966)
  covalent geometry    : angle       0.60140 (12516)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A   69 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7549 (tt0)
REVERT: A  103 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8352 (ttmt)
REVERT: A  144 ASN cc_start: 0.9034 (t0) cc_final: 0.8682 (t0)
REVERT: A  178 MET cc_start: 0.9054 (mtt) cc_final: 0.7503 (mtt)
REVERT: B   83 TYR cc_start: 0.7862 (t80) cc_final: 0.7164 (t80)
REVERT: B  132 TRP cc_start: 0.8852 (t60) cc_final: 0.8008 (t60)
REVERT: C   15 TYR cc_start: 0.8742 (m-10) cc_final: 0.8397 (m-10)
REVERT: C  178 MET cc_start: 0.8996 (mtt) cc_final: 0.7287 (mtt)
REVERT: C  184 ASN cc_start: 0.8599 (m-40) cc_final: 0.8347 (m110)
REVERT: D  132 TRP cc_start: 0.8887 (t60) cc_final: 0.7945 (t60)
  outliers start: 25
  outliers final: 16
  residues processed: 151
  average time/residue: 0.1935
  time to fit residues: 40.7530
Evaluate side-chains
  136 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    0.3980
   chunk 4 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A  51 HIS
** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 ASN
C  51 HIS
D 114 HIS
** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 177 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.115571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.096982 restraints weight = 21686.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.099105 restraints weight = 13279.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.100507 restraints weight = 9737.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.5566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8974  Z= 0.152
  Angle     :  0.581   7.558  12520  Z= 0.327
  Chirality :  0.042   0.195   1388
  Planarity :  0.004   0.033   1258
  Dihedral  : 26.648 179.672   1916
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 20.31 %
    Favored  : 76.85 %
  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: -0.18 (0.29), residues: 822
  helix:  0.83 (0.26), residues: 350
  sheet:  0.12 (0.36), residues: 214
  loop : -1.58 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 132 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.025   0.002   PHE B 100 
 TYR   0.014   0.002   TYR A 143 
 ARG   0.005   0.001   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03698 (  436)
  hydrogen bonds       : angle       4.68096 ( 1138)
  metal coordination   : bond        0.00531 (    8)
  metal coordination   : angle       4.47132 (    4)
  covalent geometry    : bond        0.00338 ( 8966)
  covalent geometry    : angle       0.57603 (12516)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8038 (mtmt)
REVERT: A  144 ASN cc_start: 0.9037 (t0) cc_final: 0.8667 (t0)
REVERT: A  178 MET cc_start: 0.8908 (mtt) cc_final: 0.8233 (mtt)
REVERT: B   83 TYR cc_start: 0.7835 (t80) cc_final: 0.7269 (t80)
REVERT: B   85 GLU cc_start: 0.7823 (tt0) cc_final: 0.7607 (tt0)
REVERT: B  229 ASP cc_start: 0.7506 (m-30) cc_final: 0.7291 (m-30)
REVERT: C   99 TYR cc_start: 0.7601 (t80) cc_final: 0.7367 (t80)
REVERT: C  178 MET cc_start: 0.8873 (mtt) cc_final: 0.8276 (mtt)
REVERT: C  184 ASN cc_start: 0.8597 (m-40) cc_final: 0.8330 (m110)
REVERT: C  191 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7704 (mm)
REVERT: D  178 MET cc_start: 0.7811 (tpp) cc_final: 0.7562 (tpp)
  outliers start: 20
  outliers final: 14
  residues processed: 137
  average time/residue: 0.2160
  time to fit residues: 40.7417
Evaluate side-chains
  129 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 17 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 36 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
D 114 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.114672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.095937 restraints weight = 21566.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.098204 restraints weight = 12726.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.099696 restraints weight = 9107.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.5815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8974  Z= 0.164
  Angle     :  0.585   6.373  12520  Z= 0.331
  Chirality :  0.043   0.232   1388
  Planarity :  0.004   0.033   1258
  Dihedral  : 26.741 179.783   1916
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.45 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.29), residues: 822
  helix:  0.84 (0.26), residues: 352
  sheet:  0.15 (0.37), residues: 214
  loop : -1.55 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 132 
 HIS   0.004   0.001   HIS A  51 
 PHE   0.017   0.001   PHE B 100 
 TYR   0.014   0.002   TYR D  83 
 ARG   0.004   0.000   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03729 (  436)
  hydrogen bonds       : angle       4.66292 ( 1138)
  metal coordination   : bond        0.00898 (    8)
  metal coordination   : angle       3.78971 (    4)
  covalent geometry    : bond        0.00369 ( 8966)
  covalent geometry    : angle       0.58160 (12516)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 ASN cc_start: 0.9106 (t0) cc_final: 0.8653 (t0)
REVERT: A  178 MET cc_start: 0.9041 (mtt) cc_final: 0.8810 (mtm)
REVERT: B   74 LEU cc_start: 0.8726 (mp) cc_final: 0.7914 (tp)
REVERT: B   83 TYR cc_start: 0.8038 (t80) cc_final: 0.7324 (t80)
REVERT: B   85 GLU cc_start: 0.7916 (tt0) cc_final: 0.7569 (tt0)
REVERT: B  229 ASP cc_start: 0.7779 (m-30) cc_final: 0.7557 (m-30)
REVERT: B  232 ASP cc_start: 0.8425 (t0) cc_final: 0.8083 (m-30)
REVERT: C  178 MET cc_start: 0.8964 (mtt) cc_final: 0.8281 (mtt)
REVERT: C  184 ASN cc_start: 0.8604 (m-40) cc_final: 0.8222 (m110)
REVERT: C  191 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7735 (mm)
  outliers start: 24
  outliers final: 16
  residues processed: 140
  average time/residue: 0.2284
  time to fit residues: 42.7821
Evaluate side-chains
  128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 ASN
** C  78 HIS ** 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 = 0.3713 r_free = 0.3713 target = 0.112720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.094281 restraints weight = 21803.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.096340 restraints weight = 13346.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.097786 restraints weight = 9819.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.6044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8974  Z= 0.201
  Angle     :  0.613   5.341  12520  Z= 0.347
  Chirality :  0.044   0.196   1388
  Planarity :  0.004   0.042   1258
  Dihedral  : 26.910 179.781   1916
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 19.89 %
    Favored  : 75.99 %
  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: -0.27 (0.29), residues: 822
  helix:  0.74 (0.26), residues: 350
  sheet:  0.10 (0.37), residues: 210
  loop : -1.58 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 132 
 HIS   0.004   0.001   HIS A  12 
 PHE   0.021   0.002   PHE B 100 
 TYR   0.017   0.002   TYR A 143 
 ARG   0.004   0.001   ARG D 199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04057 (  436)
  hydrogen bonds       : angle       4.81934 ( 1138)
  metal coordination   : bond        0.01510 (    8)
  metal coordination   : angle       3.19304 (    4)
  covalent geometry    : bond        0.00451 ( 8966)
  covalent geometry    : angle       0.61028 (12516)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A  144 ASN cc_start: 0.9030 (t0) cc_final: 0.8628 (t0)
REVERT: A  178 MET cc_start: 0.8984 (mtt) cc_final: 0.8341 (mtm)
REVERT: B   83 TYR cc_start: 0.8072 (t80) cc_final: 0.7845 (t80)
REVERT: B  232 ASP cc_start: 0.8401 (t0) cc_final: 0.8121 (m-30)
REVERT: C  178 MET cc_start: 0.8909 (mtt) cc_final: 0.8700 (mtm)
REVERT: C  184 ASN cc_start: 0.8614 (m-40) cc_final: 0.8288 (m110)
REVERT: C  191 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7880 (mm)
REVERT: D  178 MET cc_start: 0.7865 (tpp) cc_final: 0.7413 (tpp)
REVERT: D  232 ASP cc_start: 0.8468 (t0) cc_final: 0.8237 (m-30)
  outliers start: 29
  outliers final: 22
  residues processed: 132
  average time/residue: 0.2141
  time to fit residues: 39.0942
Evaluate side-chains
  126 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.113851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.095786 restraints weight = 21904.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.097959 restraints weight = 12711.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.099421 restraints weight = 8999.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.6180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8974  Z= 0.166
  Angle     :  0.616  10.677  12520  Z= 0.341
  Chirality :  0.043   0.231   1388
  Planarity :  0.004   0.037   1258
  Dihedral  : 26.710 179.501   1916
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 21.02 %
    Favored  : 75.28 %
  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: -0.27 (0.29), residues: 822
  helix:  0.81 (0.27), residues: 350
  sheet:  0.05 (0.36), residues: 220
  loop : -1.71 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  61 
 HIS   0.004   0.001   HIS A  12 
 PHE   0.012   0.001   PHE C 181 
 TYR   0.014   0.002   TYR A 143 
 ARG   0.008   0.001   ARG C 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03854 (  436)
  hydrogen bonds       : angle       4.80770 ( 1138)
  metal coordination   : bond        0.00792 (    8)
  metal coordination   : angle       3.53381 (    4)
  covalent geometry    : bond        0.00372 ( 8966)
  covalent geometry    : angle       0.61292 (12516)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A  178 MET cc_start: 0.9010 (mtt) cc_final: 0.8397 (mtm)
REVERT: C  178 MET cc_start: 0.8899 (mtt) cc_final: 0.8315 (mtm)
REVERT: C  184 ASN cc_start: 0.8525 (m-40) cc_final: 0.8151 (m110)
REVERT: C  191 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7949 (mm)
REVERT: D  178 MET cc_start: 0.7922 (tpp) cc_final: 0.7705 (tpp)
  outliers start: 26
  outliers final: 20
  residues processed: 128
  average time/residue: 0.1689
  time to fit residues: 31.7892
Evaluate side-chains
  122 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 ASN ** 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 = 0.3721 r_free = 0.3721 target = 0.113193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.094933 restraints weight = 21540.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.097135 restraints weight = 12316.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.098662 restraints weight = 8672.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.6300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8974  Z= 0.171
  Angle     :  0.620   9.428  12520  Z= 0.345
  Chirality :  0.043   0.149   1388
  Planarity :  0.004   0.036   1258
  Dihedral  : 26.552 179.453   1916
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.59 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.29), residues: 822
  helix:  0.78 (0.27), residues: 352
  sheet:  0.03 (0.36), residues: 220
  loop : -1.73 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  61 
 HIS   0.005   0.001   HIS A  51 
 PHE   0.018   0.001   PHE D 100 
 TYR   0.016   0.002   TYR D  83 
 ARG   0.009   0.001   ARG C 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03835 (  436)
  hydrogen bonds       : angle       4.84617 ( 1138)
  metal coordination   : bond        0.00900 (    8)
  metal coordination   : angle       3.19950 (    4)
  covalent geometry    : bond        0.00385 ( 8966)
  covalent geometry    : angle       0.61717 (12516)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.954 
Fit side-chains
REVERT: A  178 MET cc_start: 0.9055 (mtt) cc_final: 0.8379 (mtm)
REVERT: C  178 MET cc_start: 0.8983 (mtt) cc_final: 0.8369 (mtm)
REVERT: C  184 ASN cc_start: 0.8543 (m-40) cc_final: 0.8212 (m-40)
REVERT: C  191 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7965 (mm)
REVERT: D  178 MET cc_start: 0.8071 (tpp) cc_final: 0.7823 (tpp)
  outliers start: 23
  outliers final: 22
  residues processed: 120
  average time/residue: 0.1684
  time to fit residues: 29.9643
Evaluate side-chains
  123 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 11 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0170
   chunk 48 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    1.2026

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.113150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.094324 restraints weight = 21454.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.096455 restraints weight = 12276.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.098024 restraints weight = 8737.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.6442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8974  Z= 0.152
  Angle     :  0.620   9.263  12520  Z= 0.343
  Chirality :  0.043   0.239   1388
  Planarity :  0.004   0.036   1258
  Dihedral  : 26.439 179.453   1916
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.88 %
    Favored  : 74.86 %
  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: -0.15 (0.29), residues: 822
  helix:  0.88 (0.27), residues: 354
  sheet:  0.23 (0.38), residues: 206
  loop : -1.68 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 132 
 HIS   0.005   0.001   HIS A  51 
 PHE   0.009   0.001   PHE A 121 
 TYR   0.016   0.002   TYR D  83 
 ARG   0.012   0.001   ARG C 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03636 (  436)
  hydrogen bonds       : angle       4.79674 ( 1138)
  metal coordination   : bond        0.00527 (    8)
  metal coordination   : angle       3.45461 (    4)
  covalent geometry    : bond        0.00340 ( 8966)
  covalent geometry    : angle       0.61708 (12516)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A  178 MET cc_start: 0.9025 (mtt) cc_final: 0.8394 (mtm)
REVERT: A  181 PHE cc_start: 0.9016 (t80) cc_final: 0.8759 (t80)
REVERT: A  194 TYR cc_start: 0.7743 (m-80) cc_final: 0.7217 (m-80)
REVERT: C  178 MET cc_start: 0.8961 (mtt) cc_final: 0.8355 (mtm)
REVERT: C  184 ASN cc_start: 0.8508 (m-40) cc_final: 0.8125 (m110)
REVERT: C  191 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8000 (mm)
REVERT: D   85 GLU cc_start: 0.7909 (tt0) cc_final: 0.7706 (tt0)
  outliers start: 23
  outliers final: 20
  residues processed: 120
  average time/residue: 0.1671
  time to fit residues: 29.7315
Evaluate side-chains
  123 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain C residue   13 GLU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  259 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 82 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 55 optimal weight:    0.2980
   chunk 73 optimal weight:    0.0870
   chunk 20 optimal weight:    1.9990
   chunk 68 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.8764

-------------------------------------------------------------------------------
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 = 0.3736 r_free = 0.3736 target = 0.114475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.096199 restraints weight = 21450.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.098275 restraints weight = 12577.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.099740 restraints weight = 9054.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.6543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8974  Z= 0.140
  Angle     :  0.614   8.928  12520  Z= 0.339
  Chirality :  0.043   0.253   1388
  Planarity :  0.004   0.036   1258
  Dihedral  : 26.312 178.893   1916
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.02 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.29), residues: 822
  helix:  1.00 (0.27), residues: 354
  sheet:  0.33 (0.38), residues: 206
  loop : -1.63 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 132 
 HIS   0.005   0.001   HIS A  51 
 PHE   0.017   0.001   PHE D 100 
 TYR   0.017   0.001   TYR B  83 
 ARG   0.006   0.001   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03462 (  436)
  hydrogen bonds       : angle       4.75088 ( 1138)
  metal coordination   : bond        0.00343 (    8)
  metal coordination   : angle       3.22335 (    4)
  covalent geometry    : bond        0.00311 ( 8966)
  covalent geometry    : angle       0.61188 (12516)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2616.88 seconds
wall clock time: 46 minutes 25.16 seconds (2785.16 seconds total)