Starting phenix.real_space_refine
on Thu May 15 14:59:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hwz_35069/05_2025/8hwz_35069.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hwz_35069/05_2025/8hwz_35069.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hwz_35069/05_2025/8hwz_35069.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hwz_35069/05_2025/8hwz_35069.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hwz_35069/05_2025/8hwz_35069.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hwz_35069/05_2025/8hwz_35069.cif"
  }
  resolution = 3.56
  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=   0.003 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    8453      2.51       5
     N    2432      2.21       5
     O    2728      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13625
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "B"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "C"
      Number of atoms: 1131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1131
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 140}
    Chain: "D"
      Number of atoms: 1130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1130
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "G"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "I"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "K"
      Number of atoms: 1130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1130
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "F"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "H"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "J"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1138
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
    Chain: "L"
      Number of atoms: 1130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1130
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 140}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 8.17, per 1000 atoms: 0.60
  Number of scatterers: 13625
  At special positions: 0
  Unit cell: (103.04, 103.04, 102.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O    2728      8.00
     N    2432      7.00
     C    8453      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: 3.23
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3310

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 0 sheets defined
      83.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 44
    Processing helix  chain 'A' and resid 48 through 77
    Processing helix  chain 'A' and resid 84 through 92
    Processing helix  chain 'A' and resid 103 through 133
      removed outlier: 4.001A  pdb=" N   ASP A 127 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   ALA A 128 " --> pdb=" O   ARG A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 156
    Processing helix  chain 'B' and resid 17 through 44
    Processing helix  chain 'B' and resid 48 through 77
      removed outlier: 3.914A  pdb=" N   LEU B  52 " --> pdb=" O   ASN B  48 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASP B  57 " --> pdb=" O   HIS B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 92
    Processing helix  chain 'B' and resid 103 through 131
      removed outlier: 4.464A  pdb=" N   ASP B 127 " --> pdb=" O   ARG B 123 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   ALA B 128 " --> pdb=" O   ARG B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 156
    Processing helix  chain 'C' and resid 18 through 44
    Processing helix  chain 'C' and resid 48 through 77
    Processing helix  chain 'C' and resid 84 through 92
    Processing helix  chain 'C' and resid 103 through 133
      removed outlier: 4.348A  pdb=" N   ASP C 127 " --> pdb=" O   ARG C 123 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   ALA C 128 " --> pdb=" O   ARG C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 156
    Processing helix  chain 'C' and resid 157 through 159
      No H-bonds generated for 'chain 'C' and resid 157 through 159'
    Processing helix  chain 'D' and resid 17 through 44
      removed outlier: 3.554A  pdb=" N   VAL D  26 " --> pdb=" O   ASN D  22 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 77
      removed outlier: 3.858A  pdb=" N   LEU D  52 " --> pdb=" O   ASN D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 92
    Processing helix  chain 'D' and resid 103 through 133
      removed outlier: 4.064A  pdb=" N   ASP D 127 " --> pdb=" O   ARG D 123 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   ALA D 128 " --> pdb=" O   ARG D 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 133 through 156
    Processing helix  chain 'E' and resid 17 through 44
    Processing helix  chain 'E' and resid 48 through 77
    Processing helix  chain 'E' and resid 84 through 92
    Processing helix  chain 'E' and resid 103 through 133
      removed outlier: 4.058A  pdb=" N   ASP E 127 " --> pdb=" O   ARG E 123 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   ALA E 128 " --> pdb=" O   ARG E 124 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 133 through 156
    Processing helix  chain 'G' and resid 17 through 44
    Processing helix  chain 'G' and resid 48 through 77
      removed outlier: 3.911A  pdb=" N   LEU G  52 " --> pdb=" O   ASN G  48 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASP G  57 " --> pdb=" O   HIS G  53 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 84 through 92
    Processing helix  chain 'G' and resid 103 through 131
      removed outlier: 4.413A  pdb=" N   ASP G 127 " --> pdb=" O   ARG G 123 " (cutoff:3.500A)
      removed outlier: 4.908A  pdb=" N   ALA G 128 " --> pdb=" O   ARG G 124 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 133 through 159
      removed outlier: 4.079A  pdb=" N   GLU G 157 " --> pdb=" O   LEU G 153 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ASN G 158 " --> pdb=" O   ILE G 154 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 17 through 44
    Processing helix  chain 'I' and resid 48 through 77
    Processing helix  chain 'I' and resid 84 through 92
    Processing helix  chain 'I' and resid 103 through 133
      removed outlier: 4.489A  pdb=" N   ASP I 127 " --> pdb=" O   ARG I 123 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   ALA I 128 " --> pdb=" O   ARG I 124 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 133 through 156
    Processing helix  chain 'K' and resid 17 through 43
    Processing helix  chain 'K' and resid 48 through 77
      removed outlier: 3.873A  pdb=" N   LEU K  52 " --> pdb=" O   ASN K  48 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 92
    Processing helix  chain 'K' and resid 103 through 133
      removed outlier: 4.219A  pdb=" N   ASP K 127 " --> pdb=" O   ARG K 123 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   ALA K 128 " --> pdb=" O   ARG K 124 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 133 through 156
    Processing helix  chain 'F' and resid 17 through 44
    Processing helix  chain 'F' and resid 48 through 77
    Processing helix  chain 'F' and resid 84 through 92
    Processing helix  chain 'F' and resid 103 through 133
      removed outlier: 4.040A  pdb=" N   ASP F 127 " --> pdb=" O   ARG F 123 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   ALA F 128 " --> pdb=" O   ARG F 124 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 133 through 156
    Processing helix  chain 'H' and resid 17 through 44
    Processing helix  chain 'H' and resid 48 through 77
      removed outlier: 4.003A  pdb=" N   LEU H  52 " --> pdb=" O   ASN H  48 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP H  57 " --> pdb=" O   HIS H  53 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 84 through 92
    Processing helix  chain 'H' and resid 103 through 131
      removed outlier: 4.615A  pdb=" N   ASP H 127 " --> pdb=" O   ARG H 123 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   ALA H 128 " --> pdb=" O   ARG H 124 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 133 through 156
    Processing helix  chain 'J' and resid 17 through 44
    Processing helix  chain 'J' and resid 48 through 77
    Processing helix  chain 'J' and resid 84 through 92
    Processing helix  chain 'J' and resid 103 through 133
      removed outlier: 4.529A  pdb=" N   ASP J 127 " --> pdb=" O   ARG J 123 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   ALA J 128 " --> pdb=" O   ARG J 124 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 133 through 156
    Processing helix  chain 'J' and resid 157 through 159
      No H-bonds generated for 'chain 'J' and resid 157 through 159'
    Processing helix  chain 'L' and resid 17 through 44
    Processing helix  chain 'L' and resid 48 through 77
      removed outlier: 3.848A  pdb=" N   LEU L  52 " --> pdb=" O   ASN L  48 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 84 through 92
    Processing helix  chain 'L' and resid 103 through 133
      removed outlier: 4.170A  pdb=" N   ASP L 127 " --> pdb=" O   ARG L 123 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   ALA L 128 " --> pdb=" O   ARG L 124 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 133 through 159
      removed outlier: 4.114A  pdb=" N   GLU L 157 " --> pdb=" O   LEU L 153 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ASN L 158 " --> pdb=" O   ILE L 154 " (cutoff:3.500A)

    1185 hydrogen bonds defined for protein.
    3555 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.92

  Time building geometry restraints manager: 3.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4833
        1.34 -     1.45: 1063
        1.45 -     1.57: 7909
        1.57 -     1.68: 0
        1.68 -     1.80: 24
  Bond restraints: 13829
  Sorted by residual:
  bond pdb=" CB  PRO F  98 "
       pdb=" CG  PRO F  98 "
    ideal  model  delta    sigma   weight residual
    1.492  1.544 -0.052 5.00e-02 4.00e+02 1.08e+00
  bond pdb=" CB  MET C  74 "
       pdb=" CG  MET C  74 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.20e-01
  bond pdb=" CB  GLN D  36 "
       pdb=" CG  GLN D  36 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.55e-01
  bond pdb=" C   VAL A 125 "
       pdb=" O   VAL A 125 "
    ideal  model  delta    sigma   weight residual
    1.236  1.249 -0.012 1.35e-02 5.49e+03 8.01e-01
  bond pdb=" CA  THR F  16 "
       pdb=" C   THR F  16 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.10e-02 2.27e+03 7.99e-01
  ... (remaining 13824 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 18464
        1.99 -     3.97: 340
        3.97 -     5.96: 21
        5.96 -     7.94: 0
        7.94 -     9.93: 1
  Bond angle restraints: 18826
  Sorted by residual:
  angle pdb=" N   GLY B  46 "
        pdb=" CA  GLY B  46 "
        pdb=" C   GLY B  46 "
      ideal   model   delta    sigma   weight residual
     110.43  114.48   -4.05 1.35e+00 5.49e-01 9.00e+00
  angle pdb=" N   ARG H 124 "
        pdb=" CA  ARG H 124 "
        pdb=" CB  ARG H 124 "
      ideal   model   delta    sigma   weight residual
     110.01  114.17   -4.16 1.45e+00 4.76e-01 8.24e+00
  angle pdb=" N   HIS B 126 "
        pdb=" CA  HIS B 126 "
        pdb=" C   HIS B 126 "
      ideal   model   delta    sigma   weight residual
     111.07  114.08   -3.01 1.07e+00 8.73e-01 7.91e+00
  angle pdb=" N   HIS G 126 "
        pdb=" CA  HIS G 126 "
        pdb=" C   HIS G 126 "
      ideal   model   delta    sigma   weight residual
     111.28  114.19   -2.91 1.09e+00 8.42e-01 7.11e+00
  angle pdb=" N   VAL I  80 "
        pdb=" CA  VAL I  80 "
        pdb=" C   VAL I  80 "
      ideal   model   delta    sigma   weight residual
     107.89  110.79   -2.90 1.09e+00 8.42e-01 7.08e+00
  ... (remaining 18821 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 7545
       17.92 -    35.83: 663
       35.83 -    53.75: 118
       53.75 -    71.67: 27
       71.67 -    89.58: 22
  Dihedral angle restraints: 8375
    sinusoidal: 3326
      harmonic: 5049
  Sorted by residual:
  dihedral pdb=" CA  TRP I  42 "
           pdb=" C   TRP I  42 "
           pdb=" N   ASN I  43 "
           pdb=" CA  ASN I  43 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.54  -18.46     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  TRP C  42 "
           pdb=" C   TRP C  42 "
           pdb=" N   ASN C  43 "
           pdb=" CA  ASN C  43 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.70  -17.30     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ASP K  86 "
           pdb=" CB  ASP K  86 "
           pdb=" CG  ASP K  86 "
           pdb=" OD1 ASP K  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.46   59.46     1      2.00e+01 2.50e-03 1.18e+01
  ... (remaining 8372 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1316
       0.026 -    0.051: 586
       0.051 -    0.077: 245
       0.077 -    0.102: 67
       0.102 -    0.128: 28
  Chirality restraints: 2242
  Sorted by residual:
  chirality pdb=" CA  VAL F  45 "
            pdb=" N   VAL F  45 "
            pdb=" C   VAL F  45 "
            pdb=" CB  VAL F  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CB  VAL B 125 "
            pdb=" CA  VAL B 125 "
            pdb=" CG1 VAL B 125 "
            pdb=" CG2 VAL B 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ASP A 145 "
            pdb=" N   ASP A 145 "
            pdb=" C   ASP A 145 "
            pdb=" CB  ASP A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 2239 not shown)

  Planarity restraints: 2503
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B  97 "   -0.064 5.00e-02 4.00e+02   9.70e-02 1.51e+01
        pdb=" N   PRO B  98 "    0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO B  98 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B  98 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE F  97 "   -0.053 5.00e-02 4.00e+02   8.04e-02 1.04e+01
        pdb=" N   PRO F  98 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO F  98 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO F  98 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE G  97 "   -0.045 5.00e-02 4.00e+02   6.89e-02 7.60e+00
        pdb=" N   PRO G  98 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO G  98 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO G  98 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 2500 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 167
        2.66 -     3.22: 14222
        3.22 -     3.78: 22863
        3.78 -     4.34: 27347
        4.34 -     4.90: 47587
  Nonbonded interactions: 112186
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN K  39 "
            pdb=" ND2 ASN K  43 "
     model   vdw
     2.103 3.120
  nonbonded pdb=" OD2 ASP H 120 "
            pdb=" NH1 ARG H 124 "
     model   vdw
     2.138 3.120
  nonbonded pdb=" OD2 ASP B 133 "
            pdb=" OG  SER B 135 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" O   GLU A  18 "
            pdb=" ND2 ASN A  22 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OD2 ASP C  68 "
            pdb=" NZ  LYS D  38 "
     model   vdw
     2.241 3.120
  ... (remaining 112181 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'B' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'C' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'D' and resid 17 through 161)
  selection = (chain 'E' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'F' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'G' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'H' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'I' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'J' and (resid 17 through 64 or (resid 65 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 161))
  selection = (chain 'K' and resid 17 through 161)
  selection = (chain 'L' and resid 17 through 161)
}

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:             0.680
  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:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     30.970
  Find NCS groups from input model:        0.660
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
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      :  0.003   0.052  13829  Z= 0.152
  Angle     :  0.620   9.930  18826  Z= 0.365
  Chirality :  0.036   0.128   2242
  Planarity :  0.005   0.097   2503
  Dihedral  : 14.516  89.585   5065
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.07 %
    Favored  : 99.93 %
  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:  4.47 (0.20), residues: 1727
  helix:  3.41 (0.13), residues: 1417
  sheet:  None (None), residues: 0
  loop :  0.52 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 152 
 HIS   0.005   0.001   HIS C  53 
 PHE   0.024   0.002   PHE I  49 
 ARG   0.008   0.001   ARG B 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09094 ( 1185)
  hydrogen bonds       : angle       3.69380 ( 3555)
  covalent geometry    : bond        0.00319 (13829)
  covalent geometry    : angle       0.61970 (18826)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 353
  time to evaluate  : 1.626 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7579 (mp0) cc_final: 0.7375 (tt0)
REVERT: B   24 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8391 (tp40)
REVERT: C   32 GLU cc_start: 0.8494 (tp30) cc_final: 0.8045 (tp30)
REVERT: C   55 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8467 (tp-100)
REVERT: D  157 GLU cc_start: 0.8809 (tp30) cc_final: 0.8474 (tp30)
REVERT: E  157 GLU cc_start: 0.8713 (tp30) cc_final: 0.8436 (tp30)
REVERT: K   22 ASN cc_start: 0.8764 (m110) cc_final: 0.8394 (m110)
REVERT: K  103 SER cc_start: 0.8739 (t) cc_final: 0.8444 (p)
REVERT: K  148 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8270 (mm-30)
REVERT: F   32 GLU cc_start: 0.8313 (tp30) cc_final: 0.8093 (tp30)
REVERT: H   55 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8121 (tp-100)
REVERT: J   32 GLU cc_start: 0.8546 (tp30) cc_final: 0.8178 (tp30)
REVERT: J   43 ASN cc_start: 0.8704 (t0) cc_final: 0.8484 (t0)
REVERT: L  120 ASP cc_start: 0.8126 (t70) cc_final: 0.7909 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 353
  average time/residue: 0.2051
  time to fit residues: 111.7682
Evaluate side-chains
  253 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    1.9990
   chunk 127 optimal weight:    0.8980
   chunk 70 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 131 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9980
   chunk 98 optimal weight:    8.9990
   chunk 152 optimal weight:    5.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  48 ASN
B  41 HIS
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  22 ASN
C  36 GLN
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 158 ASN
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  22 ASN
E  36 GLN
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  41 HIS
I  43 ASN
** I  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 158 ASN
** H  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 158 ASN
** J  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.092058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.080059 restraints weight = 31153.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.083205 restraints weight = 15373.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.085249 restraints weight = 9131.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13829  Z= 0.130
  Angle     :  0.522   8.892  18826  Z= 0.281
  Chirality :  0.036   0.153   2242
  Planarity :  0.005   0.072   2503
  Dihedral  :  4.452  60.933   1883
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  :  8.31 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.50 (0.20), residues: 1727
  helix:  3.44 (0.13), residues: 1417
  sheet:  None (None), residues: 0
  loop :  0.53 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 152 
 HIS   0.006   0.002   HIS K  53 
 PHE   0.021   0.002   PHE A  19 
 ARG   0.007   0.000   ARG J 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04430 ( 1185)
  hydrogen bonds       : angle       3.36149 ( 3555)
  covalent geometry    : bond        0.00285 (13829)
  covalent geometry    : angle       0.52242 (18826)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 292
  time to evaluate  : 1.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7968 (mp0) cc_final: 0.7690 (tt0)
REVERT: A  121 THR cc_start: 0.8098 (m) cc_final: 0.7867 (p)
REVERT: A  157 GLU cc_start: 0.8704 (tp30) cc_final: 0.8208 (tp30)
REVERT: B   24 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8163 (tp40)
REVERT: C   18 GLU cc_start: 0.7536 (mp0) cc_final: 0.7312 (tt0)
REVERT: C   32 GLU cc_start: 0.8304 (tp30) cc_final: 0.7835 (tp30)
REVERT: D   18 GLU cc_start: 0.7876 (pm20) cc_final: 0.7485 (tt0)
REVERT: D  133 ASP cc_start: 0.6848 (t0) cc_final: 0.6617 (t0)
REVERT: E   32 GLU cc_start: 0.8645 (tp30) cc_final: 0.8391 (tp30)
REVERT: E   72 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7662 (mm-30)
REVERT: G  133 ASP cc_start: 0.7433 (t0) cc_final: 0.7036 (t0)
REVERT: I   32 GLU cc_start: 0.8371 (tp30) cc_final: 0.7941 (tp30)
REVERT: K  103 SER cc_start: 0.8374 (t) cc_final: 0.8004 (p)
REVERT: K  133 ASP cc_start: 0.6919 (t0) cc_final: 0.6658 (t0)
REVERT: F   32 GLU cc_start: 0.8346 (tp30) cc_final: 0.8039 (tp30)
REVERT: H   18 GLU cc_start: 0.8023 (mp0) cc_final: 0.7747 (tt0)
REVERT: H   55 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8219 (tp-100)
REVERT: H  125 VAL cc_start: 0.9153 (p) cc_final: 0.8931 (p)
REVERT: J   43 ASN cc_start: 0.8630 (t0) cc_final: 0.8403 (t0)
REVERT: J  133 ASP cc_start: 0.6851 (t0) cc_final: 0.6534 (t0)
REVERT: L   18 GLU cc_start: 0.8025 (pm20) cc_final: 0.7754 (tt0)
REVERT: L  148 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8115 (mm-30)
  outliers start: 52
  outliers final: 35
  residues processed: 319
  average time/residue: 0.1948
  time to fit residues: 97.6874
Evaluate side-chains
  291 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 256
  time to evaluate  : 1.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   48 ASN
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue   74 MET
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  144 ILE
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  154 ILE
Chi-restraints excluded: chain K residue  156 SER
Chi-restraints excluded: chain K residue  158 ASN
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue  154 ILE
Chi-restraints excluded: chain J residue  156 SER
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 8 optimal weight:   20.0000
   chunk 101 optimal weight:    0.9990
   chunk 164 optimal weight:    0.9980
   chunk 158 optimal weight:    4.9990
   chunk 161 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 120 optimal weight:   20.0000
   chunk 103 optimal weight:    6.9990
   chunk 144 optimal weight:    7.9990
   chunk 152 optimal weight:    4.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 158 ASN
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  24 GLN
** I  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  22 ASN
** K  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  48 ASN
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.086249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.074406 restraints weight = 32389.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.077397 restraints weight = 16235.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.079512 restraints weight = 9695.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  13829  Z= 0.187
  Angle     :  0.572  10.141  18826  Z= 0.304
  Chirality :  0.037   0.158   2242
  Planarity :  0.005   0.066   2503
  Dihedral  :  4.598  60.697   1883
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 12.29 %
    Favored  : 83.93 %
  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:  4.21 (0.20), residues: 1727
  helix:  3.25 (0.13), residues: 1416
  sheet:  None (None), residues: 0
  loop :  0.42 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 152 
 HIS   0.006   0.002   HIS K  41 
 PHE   0.027   0.002   PHE I  49 
 ARG   0.005   0.001   ARG A 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04965 ( 1185)
  hydrogen bonds       : angle       3.48640 ( 3555)
  covalent geometry    : bond        0.00433 (13829)
  covalent geometry    : angle       0.57223 (18826)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 264
  time to evaluate  : 1.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.7937 (m-80) cc_final: 0.7573 (m-80)
REVERT: A  157 GLU cc_start: 0.8812 (tp30) cc_final: 0.8317 (tp30)
REVERT: C   18 GLU cc_start: 0.7617 (mp0) cc_final: 0.7379 (tt0)
REVERT: C  135 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8573 (p)
REVERT: D   32 GLU cc_start: 0.8392 (tp30) cc_final: 0.8165 (tp30)
REVERT: E   32 GLU cc_start: 0.8749 (tp30) cc_final: 0.8521 (tp30)
REVERT: E   72 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7777 (mm-30)
REVERT: G   18 GLU cc_start: 0.8404 (tt0) cc_final: 0.8150 (mp0)
REVERT: G  133 ASP cc_start: 0.7492 (t0) cc_final: 0.7179 (t0)
REVERT: I   18 GLU cc_start: 0.8552 (tt0) cc_final: 0.8246 (mp0)
REVERT: I   32 GLU cc_start: 0.8445 (tp30) cc_final: 0.7918 (tp30)
REVERT: I   55 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8532 (tp40)
REVERT: K   18 GLU cc_start: 0.7918 (mp0) cc_final: 0.7616 (tt0)
REVERT: K  103 SER cc_start: 0.8502 (t) cc_final: 0.8139 (p)
REVERT: F   32 GLU cc_start: 0.8396 (tp30) cc_final: 0.7912 (tp30)
REVERT: F   43 ASN cc_start: 0.8730 (t0) cc_final: 0.8513 (t0)
REVERT: H  103 SER cc_start: 0.8720 (t) cc_final: 0.8377 (p)
REVERT: H  124 ARG cc_start: 0.7900 (mpp-170) cc_final: 0.7612 (mtt90)
REVERT: J   18 GLU cc_start: 0.8113 (mp0) cc_final: 0.7765 (tt0)
REVERT: J   43 ASN cc_start: 0.8691 (t0) cc_final: 0.8365 (t0)
REVERT: J  133 ASP cc_start: 0.6861 (t0) cc_final: 0.6624 (t0)
  outliers start: 56
  outliers final: 43
  residues processed: 296
  average time/residue: 0.2166
  time to fit residues: 98.7845
Evaluate side-chains
  292 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 248
  time to evaluate  : 1.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  135 SER
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  144 ILE
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain G residue  144 ILE
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue  154 ILE
Chi-restraints excluded: chain I residue  156 SER
Chi-restraints excluded: chain I residue  161 VAL
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  154 ILE
Chi-restraints excluded: chain K residue  156 SER
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue  154 ILE
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Chi-restraints excluded: chain L residue  103 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 82 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 76 optimal weight:    7.9990
   chunk 56 optimal weight:    8.9990
   chunk 88 optimal weight:    8.9990
   chunk 162 optimal weight:    5.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  48 ASN
** K  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  48 ASN
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.086267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.074762 restraints weight = 32097.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.077637 restraints weight = 16258.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.079612 restraints weight = 9860.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13829  Z= 0.194
  Angle     :  0.580  10.281  18826  Z= 0.306
  Chirality :  0.037   0.157   2242
  Planarity :  0.005   0.060   2503
  Dihedral  :  4.672  60.194   1883
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 13.91 %
    Favored  : 81.50 %
  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:  4.11 (0.20), residues: 1727
  helix:  3.18 (0.13), residues: 1416
  sheet:  None (None), residues: 0
  loop :  0.36 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  42 
 HIS   0.006   0.002   HIS D  41 
 PHE   0.027   0.002   PHE I  49 
 ARG   0.005   0.001   ARG K 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05049 ( 1185)
  hydrogen bonds       : angle       3.52641 ( 3555)
  covalent geometry    : bond        0.00448 (13829)
  covalent geometry    : angle       0.57983 (18826)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 254
  time to evaluate  : 1.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7793 (mp0) cc_final: 0.7486 (tt0)
REVERT: A   55 GLN cc_start: 0.8903 (tp40) cc_final: 0.8653 (tp40)
REVERT: A  100 PHE cc_start: 0.7965 (m-80) cc_final: 0.7603 (m-80)
REVERT: A  157 GLU cc_start: 0.8747 (tp30) cc_final: 0.8460 (tp30)
REVERT: C   32 GLU cc_start: 0.8306 (tp30) cc_final: 0.7866 (tp30)
REVERT: C   55 GLN cc_start: 0.9121 (tp40) cc_final: 0.8745 (tp40)
REVERT: C  133 ASP cc_start: 0.7251 (t0) cc_final: 0.6888 (t0)
REVERT: E   32 GLU cc_start: 0.8776 (tp30) cc_final: 0.8539 (tp30)
REVERT: E   72 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7777 (mm-30)
REVERT: G  133 ASP cc_start: 0.7606 (t0) cc_final: 0.7335 (t0)
REVERT: I   18 GLU cc_start: 0.8482 (tt0) cc_final: 0.8248 (mp0)
REVERT: I   32 GLU cc_start: 0.8468 (tp30) cc_final: 0.7952 (tp30)
REVERT: K  103 SER cc_start: 0.8695 (t) cc_final: 0.8367 (p)
REVERT: K  148 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8396 (mm-30)
REVERT: H  103 SER cc_start: 0.8861 (t) cc_final: 0.8549 (p)
REVERT: J   43 ASN cc_start: 0.8641 (t0) cc_final: 0.8324 (t0)
REVERT: J  133 ASP cc_start: 0.7093 (t0) cc_final: 0.6884 (t0)
REVERT: L   18 GLU cc_start: 0.7732 (mp0) cc_final: 0.7470 (tt0)
REVERT: L   43 ASN cc_start: 0.8922 (t0) cc_final: 0.8678 (t0)
  outliers start: 68
  outliers final: 53
  residues processed: 300
  average time/residue: 0.2102
  time to fit residues: 97.1497
Evaluate side-chains
  296 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 243
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  158 ASN
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  154 ILE
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain G residue  144 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue  154 ILE
Chi-restraints excluded: chain I residue  156 SER
Chi-restraints excluded: chain I residue  161 VAL
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  132 GLU
Chi-restraints excluded: chain K residue  153 LEU
Chi-restraints excluded: chain K residue  154 ILE
Chi-restraints excluded: chain K residue  158 ASN
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   31 ILE
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue  103 SER
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  154 ILE
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue  103 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 113 optimal weight:    0.7980
   chunk 8 optimal weight:    7.9990
   chunk 56 optimal weight:    8.9990
   chunk 127 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 142 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 134 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 147 optimal weight:   10.0000
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  48 ASN
** B  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  39 GLN
K  43 ASN
F  22 ASN
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  22 ASN
L 158 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.091054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.079476 restraints weight = 31462.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.082424 restraints weight = 15552.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.084494 restraints weight = 9336.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13829  Z= 0.120
  Angle     :  0.514  10.091  18826  Z= 0.269
  Chirality :  0.034   0.149   2242
  Planarity :  0.004   0.054   2503
  Dihedral  :  4.495  61.726   1883
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 15.80 %
    Favored  : 80.82 %
  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:  4.39 (0.20), residues: 1727
  helix:  3.35 (0.13), residues: 1416
  sheet:  None (None), residues: 0
  loop :  0.54 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 152 
 HIS   0.006   0.002   HIS K  41 
 PHE   0.015   0.001   PHE I  49 
 ARG   0.004   0.000   ARG K 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04121 ( 1185)
  hydrogen bonds       : angle       3.24203 ( 3555)
  covalent geometry    : bond        0.00259 (13829)
  covalent geometry    : angle       0.51449 (18826)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 294
  time to evaluate  : 1.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7686 (mp0) cc_final: 0.7390 (tt0)
REVERT: A   55 GLN cc_start: 0.8879 (tp40) cc_final: 0.8593 (tp40)
REVERT: A  100 PHE cc_start: 0.7825 (m-80) cc_final: 0.7453 (m-80)
REVERT: A  157 GLU cc_start: 0.8649 (tp30) cc_final: 0.8204 (tp30)
REVERT: B   24 GLN cc_start: 0.8723 (tm-30) cc_final: 0.7992 (tp40)
REVERT: C   32 GLU cc_start: 0.7999 (tp30) cc_final: 0.7776 (tp30)
REVERT: E   24 GLN cc_start: 0.8864 (tm-30) cc_final: 0.7903 (tp40)
REVERT: E   72 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7808 (mm-30)
REVERT: G   24 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8516 (tm-30)
REVERT: G  133 ASP cc_start: 0.7371 (t0) cc_final: 0.7098 (t0)
REVERT: I   32 GLU cc_start: 0.8358 (tp30) cc_final: 0.7930 (tp30)
REVERT: I  153 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8926 (tt)
REVERT: K  103 SER cc_start: 0.8552 (t) cc_final: 0.8204 (p)
REVERT: F   32 GLU cc_start: 0.8400 (tp30) cc_final: 0.8097 (tp30)
REVERT: H  103 SER cc_start: 0.8737 (t) cc_final: 0.8409 (p)
REVERT: L   18 GLU cc_start: 0.7646 (mp0) cc_final: 0.7357 (tt0)
REVERT: L   24 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8281 (tm-30)
REVERT: L  148 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8221 (mm-30)
  outliers start: 50
  outliers final: 44
  residues processed: 326
  average time/residue: 0.2033
  time to fit residues: 103.5968
Evaluate side-chains
  304 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 259
  time to evaluate  : 1.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   48 ASN
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  154 ILE
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain G residue  144 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue  153 LEU
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue   74 MET
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   80 VAL
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain J residue  154 ILE
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 141 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 92 optimal weight:   10.0000
   chunk 71 optimal weight:    0.8980
   chunk 49 optimal weight:    8.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  43 ASN
** F  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.090597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.078830 restraints weight = 31808.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.081836 restraints weight = 15958.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.083759 restraints weight = 9601.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13829  Z= 0.130
  Angle     :  0.527  10.213  18826  Z= 0.275
  Chirality :  0.035   0.154   2242
  Planarity :  0.004   0.056   2503
  Dihedral  :  4.489  63.093   1883
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 17.22 %
    Favored  : 78.87 %
  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:  4.38 (0.20), residues: 1727
  helix:  3.34 (0.13), residues: 1416
  sheet:  None (None), residues: 0
  loop :  0.58 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP I 152 
 HIS   0.006   0.002   HIS L  41 
 PHE   0.016   0.002   PHE I  49 
 ARG   0.004   0.000   ARG E 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04181 ( 1185)
  hydrogen bonds       : angle       3.25020 ( 3555)
  covalent geometry    : bond        0.00293 (13829)
  covalent geometry    : angle       0.52677 (18826)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 273
  time to evaluate  : 1.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7725 (mp0) cc_final: 0.7428 (tt0)
REVERT: A   55 GLN cc_start: 0.8883 (tp40) cc_final: 0.8597 (tp40)
REVERT: A  100 PHE cc_start: 0.7895 (m-80) cc_final: 0.7521 (m-80)
REVERT: A  157 GLU cc_start: 0.8609 (tp30) cc_final: 0.8290 (tp30)
REVERT: B   24 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8013 (tp40)
REVERT: B   65 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8678 (mm-30)
REVERT: C   32 GLU cc_start: 0.7991 (tp30) cc_final: 0.7787 (tp30)
REVERT: E   24 GLN cc_start: 0.8881 (tm-30) cc_final: 0.7890 (tp40)
REVERT: E   72 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7825 (mm-30)
REVERT: G  133 ASP cc_start: 0.7354 (t0) cc_final: 0.7114 (t0)
REVERT: I   32 GLU cc_start: 0.8399 (tp30) cc_final: 0.7959 (tp30)
REVERT: K  103 SER cc_start: 0.8542 (t) cc_final: 0.8194 (p)
REVERT: H  103 SER cc_start: 0.8721 (t) cc_final: 0.8404 (p)
REVERT: J   18 GLU cc_start: 0.7893 (mp0) cc_final: 0.7644 (tt0)
REVERT: L   18 GLU cc_start: 0.7611 (mp0) cc_final: 0.7390 (tt0)
REVERT: L   24 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8237 (tm-30)
REVERT: L  148 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8165 (mm-30)
  outliers start: 58
  outliers final: 50
  residues processed: 310
  average time/residue: 0.2033
  time to fit residues: 97.9077
Evaluate side-chains
  310 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 260
  time to evaluate  : 1.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  156 SER
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  154 ILE
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  103 SER
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain G residue  144 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue  154 ILE
Chi-restraints excluded: chain I residue  161 VAL
Chi-restraints excluded: chain K residue   52 LEU
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue   74 MET
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue   74 MET
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   80 VAL
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 167 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    8.9990
   chunk 71 optimal weight:    4.9990
   chunk 138 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9990
   chunk 144 optimal weight:    7.9990
   chunk 151 optimal weight:    5.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  24 GLN
** K  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 150 GLN
** J  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.088646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.076960 restraints weight = 31886.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.079931 restraints weight = 15905.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.081967 restraints weight = 9561.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13829  Z= 0.153
  Angle     :  0.552  10.544  18826  Z= 0.288
  Chirality :  0.036   0.153   2242
  Planarity :  0.004   0.056   2503
  Dihedral  :  4.545  64.032   1883
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 17.89 %
    Favored  : 77.79 %
  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:  4.21 (0.20), residues: 1727
  helix:  3.26 (0.13), residues: 1427
  sheet:  None (None), residues: 0
  loop :  0.22 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP I 152 
 HIS   0.006   0.001   HIS D  41 
 PHE   0.033   0.002   PHE C  49 
 ARG   0.004   0.000   ARG E 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04460 ( 1185)
  hydrogen bonds       : angle       3.31212 ( 3555)
  covalent geometry    : bond        0.00353 (13829)
  covalent geometry    : angle       0.55181 (18826)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 259
  time to evaluate  : 1.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7782 (mp0) cc_final: 0.7492 (tt0)
REVERT: A   55 GLN cc_start: 0.8947 (tp40) cc_final: 0.8632 (tp40)
REVERT: A  100 PHE cc_start: 0.8060 (m-80) cc_final: 0.7708 (m-80)
REVERT: A  157 GLU cc_start: 0.8709 (tp30) cc_final: 0.8502 (tp30)
REVERT: B   65 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8667 (mm-30)
REVERT: C   32 GLU cc_start: 0.8013 (tp30) cc_final: 0.7796 (tp30)
REVERT: C  133 ASP cc_start: 0.7083 (t0) cc_final: 0.6863 (t0)
REVERT: E   24 GLN cc_start: 0.8895 (tm-30) cc_final: 0.7900 (tp40)
REVERT: E   72 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7987 (mm-30)
REVERT: G   18 GLU cc_start: 0.7820 (mp0) cc_final: 0.7610 (tt0)
REVERT: G  133 ASP cc_start: 0.7442 (t0) cc_final: 0.7176 (t0)
REVERT: I   32 GLU cc_start: 0.8481 (tp30) cc_final: 0.7979 (tp30)
REVERT: K  103 SER cc_start: 0.8580 (t) cc_final: 0.8239 (p)
REVERT: H  103 SER cc_start: 0.8773 (t) cc_final: 0.8472 (p)
REVERT: J   18 GLU cc_start: 0.7937 (mp0) cc_final: 0.7649 (tt0)
REVERT: J   74 MET cc_start: 0.9002 (ttp) cc_final: 0.8793 (ptt)
REVERT: J  133 ASP cc_start: 0.6906 (t0) cc_final: 0.6675 (t0)
REVERT: L   24 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8252 (tm-30)
REVERT: L   55 GLN cc_start: 0.8631 (tp40) cc_final: 0.8402 (tp-100)
  outliers start: 64
  outliers final: 59
  residues processed: 302
  average time/residue: 0.2002
  time to fit residues: 95.0021
Evaluate side-chains
  313 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 254
  time to evaluate  : 2.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  156 SER
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  154 ILE
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  103 SER
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain G residue  144 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue  122 ILE
Chi-restraints excluded: chain I residue  154 ILE
Chi-restraints excluded: chain I residue  161 VAL
Chi-restraints excluded: chain K residue   52 LEU
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  154 ILE
Chi-restraints excluded: chain K residue  158 ASN
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue   74 MET
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   80 VAL
Chi-restraints excluded: chain J residue  103 SER
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Chi-restraints excluded: chain L residue   74 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 64 optimal weight:   20.0000
   chunk 99 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 132 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 76 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.087505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.075474 restraints weight = 32283.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.078494 restraints weight = 16327.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.080465 restraints weight = 9856.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13829  Z= 0.146
  Angle     :  0.555  10.163  18826  Z= 0.289
  Chirality :  0.035   0.168   2242
  Planarity :  0.004   0.055   2503
  Dihedral  :  4.564  64.772   1883
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 17.83 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.19 (0.20), residues: 1727
  helix:  3.25 (0.13), residues: 1427
  sheet:  None (None), residues: 0
  loop :  0.20 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP I 152 
 HIS   0.005   0.002   HIS D  41 
 PHE   0.022   0.002   PHE I  49 
 ARG   0.004   0.000   ARG E 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04440 ( 1185)
  hydrogen bonds       : angle       3.29093 ( 3555)
  covalent geometry    : bond        0.00334 (13829)
  covalent geometry    : angle       0.55507 (18826)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 264
  time to evaluate  : 1.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7945 (mp0) cc_final: 0.7526 (tt0)
REVERT: A   55 GLN cc_start: 0.8917 (tp40) cc_final: 0.8613 (tp40)
REVERT: A  100 PHE cc_start: 0.8089 (m-80) cc_final: 0.7740 (m-80)
REVERT: C   32 GLU cc_start: 0.7984 (tp30) cc_final: 0.7764 (tp30)
REVERT: C  133 ASP cc_start: 0.6994 (t0) cc_final: 0.6743 (t0)
REVERT: E   72 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7956 (mm-30)
REVERT: G  133 ASP cc_start: 0.7416 (t0) cc_final: 0.7083 (t0)
REVERT: I   32 GLU cc_start: 0.8462 (tp30) cc_final: 0.7940 (tp30)
REVERT: K  103 SER cc_start: 0.8449 (t) cc_final: 0.8098 (p)
REVERT: H   96 GLU cc_start: 0.8658 (pm20) cc_final: 0.8428 (pm20)
REVERT: H  103 SER cc_start: 0.8710 (t) cc_final: 0.8394 (p)
REVERT: J   18 GLU cc_start: 0.8041 (mp0) cc_final: 0.7674 (tt0)
REVERT: J   74 MET cc_start: 0.9005 (ttp) cc_final: 0.8802 (ptt)
REVERT: J  133 ASP cc_start: 0.6804 (t0) cc_final: 0.6541 (t0)
REVERT: J  157 GLU cc_start: 0.9007 (tp30) cc_final: 0.8794 (tp30)
REVERT: L   24 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8142 (tm-30)
REVERT: L   55 GLN cc_start: 0.8615 (tp40) cc_final: 0.8391 (tp-100)
REVERT: L  148 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8112 (mm-30)
  outliers start: 66
  outliers final: 61
  residues processed: 309
  average time/residue: 0.1986
  time to fit residues: 95.2601
Evaluate side-chains
  314 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 253
  time to evaluate  : 1.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  154 ILE
Chi-restraints excluded: chain C residue  156 SER
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  154 ILE
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  103 SER
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain G residue  144 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue  103 SER
Chi-restraints excluded: chain I residue  154 ILE
Chi-restraints excluded: chain I residue  161 VAL
Chi-restraints excluded: chain K residue   52 LEU
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  153 LEU
Chi-restraints excluded: chain K residue  154 ILE
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue   74 MET
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  154 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   80 VAL
Chi-restraints excluded: chain J residue  103 SER
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Chi-restraints excluded: chain L residue   74 MET
Chi-restraints excluded: chain L residue  103 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 54 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0980
   chunk 78 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 150 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 145 optimal weight:    4.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.090178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.078101 restraints weight = 31767.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.081205 restraints weight = 16043.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.083383 restraints weight = 9534.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13829  Z= 0.124
  Angle     :  0.532   9.974  18826  Z= 0.277
  Chirality :  0.034   0.169   2242
  Planarity :  0.004   0.053   2503
  Dihedral  :  4.503  67.639   1883
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 18.91 %
    Favored  : 77.58 %
  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:  4.31 (0.20), residues: 1727
  helix:  3.32 (0.13), residues: 1427
  sheet:  None (None), residues: 0
  loop :  0.31 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H 152 
 HIS   0.005   0.002   HIS J  53 
 PHE   0.015   0.001   PHE I  49 
 ARG   0.004   0.000   ARG E 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04043 ( 1185)
  hydrogen bonds       : angle       3.19955 ( 3555)
  covalent geometry    : bond        0.00271 (13829)
  covalent geometry    : angle       0.53217 (18826)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 277
  time to evaluate  : 1.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7797 (mp0) cc_final: 0.7433 (tt0)
REVERT: A   49 PHE cc_start: 0.8597 (t80) cc_final: 0.8257 (t80)
REVERT: A   55 GLN cc_start: 0.8834 (tp40) cc_final: 0.8522 (tp40)
REVERT: A   74 MET cc_start: 0.9049 (ttp) cc_final: 0.8833 (ptt)
REVERT: A  100 PHE cc_start: 0.8184 (m-80) cc_final: 0.7847 (m-80)
REVERT: A  157 GLU cc_start: 0.8773 (tp30) cc_final: 0.8419 (tp30)
REVERT: B   24 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8160 (tp40)
REVERT: C   32 GLU cc_start: 0.7923 (tp30) cc_final: 0.7704 (tp30)
REVERT: D   74 MET cc_start: 0.9241 (ttp) cc_final: 0.9025 (ptt)
REVERT: E   24 GLN cc_start: 0.8772 (tm-30) cc_final: 0.7952 (tp40)
REVERT: E   72 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7952 (mm-30)
REVERT: G  133 ASP cc_start: 0.7295 (t0) cc_final: 0.6969 (t0)
REVERT: I   32 GLU cc_start: 0.8378 (tp30) cc_final: 0.7925 (tp30)
REVERT: K   24 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8288 (tp40)
REVERT: K  103 SER cc_start: 0.8368 (t) cc_final: 0.8005 (p)
REVERT: H   96 GLU cc_start: 0.8665 (pm20) cc_final: 0.8385 (pm20)
REVERT: H  103 SER cc_start: 0.8608 (t) cc_final: 0.8266 (p)
REVERT: J   18 GLU cc_start: 0.7946 (mp0) cc_final: 0.7640 (tt0)
REVERT: L   24 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8112 (tm-30)
REVERT: L   55 GLN cc_start: 0.8554 (tp40) cc_final: 0.8324 (tp-100)
REVERT: L  148 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8216 (mm-30)
  outliers start: 52
  outliers final: 49
  residues processed: 310
  average time/residue: 0.2262
  time to fit residues: 109.5586
Evaluate side-chains
  310 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 261
  time to evaluate  : 1.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  103 SER
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  156 SER
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue   44 VAL
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  154 ILE
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  103 SER
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain G residue  144 ILE
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain K residue   52 LEU
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  153 LEU
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   80 VAL
Chi-restraints excluded: chain J residue  103 SER
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Chi-restraints excluded: chain L residue  103 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 137 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 148 optimal weight:    0.0470
   chunk 71 optimal weight:    3.9990
   chunk 139 optimal weight:    2.9990
   chunk 161 optimal weight:    2.9990
   overall best weight:    2.4086

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 158 ASN
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  55 GLN
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.086515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.074395 restraints weight = 32287.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.077368 restraints weight = 16570.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.079260 restraints weight = 10110.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13829  Z= 0.172
  Angle     :  0.600  10.555  18826  Z= 0.311
  Chirality :  0.036   0.163   2242
  Planarity :  0.004   0.056   2503
  Dihedral  :  4.643  69.038   1883
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 18.97 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.14 (0.20), residues: 1727
  helix:  3.21 (0.13), residues: 1427
  sheet:  None (None), residues: 0
  loop :  0.18 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H  42 
 HIS   0.006   0.001   HIS D  41 
 PHE   0.025   0.002   PHE I  49 
 ARG   0.009   0.000   ARG B 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04615 ( 1185)
  hydrogen bonds       : angle       3.34496 ( 3555)
  covalent geometry    : bond        0.00398 (13829)
  covalent geometry    : angle       0.60010 (18826)

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

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

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3454 Ramachandran restraints generated.
    1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 251
  time to evaluate  : 1.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.7967 (mp0) cc_final: 0.7573 (tt0)
REVERT: A   55 GLN cc_start: 0.8890 (tp40) cc_final: 0.8569 (tp40)
REVERT: A   74 MET cc_start: 0.9140 (ttp) cc_final: 0.8924 (ptt)
REVERT: A  100 PHE cc_start: 0.8232 (m-80) cc_final: 0.7932 (m-80)
REVERT: B   32 GLU cc_start: 0.8983 (tp30) cc_final: 0.8742 (tm-30)
REVERT: C  133 ASP cc_start: 0.7069 (t0) cc_final: 0.6811 (t0)
REVERT: E   24 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8028 (tp40)
REVERT: E   72 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7928 (mm-30)
REVERT: G  133 ASP cc_start: 0.7492 (t0) cc_final: 0.7155 (t0)
REVERT: I   32 GLU cc_start: 0.8474 (tp30) cc_final: 0.7944 (tp30)
REVERT: K  103 SER cc_start: 0.8642 (t) cc_final: 0.8276 (p)
REVERT: H  103 SER cc_start: 0.8723 (t) cc_final: 0.8427 (p)
REVERT: H  157 GLU cc_start: 0.8851 (tp30) cc_final: 0.8624 (tp30)
REVERT: J   18 GLU cc_start: 0.8073 (mp0) cc_final: 0.7750 (tt0)
REVERT: J  133 ASP cc_start: 0.6908 (t0) cc_final: 0.6652 (t0)
REVERT: L   24 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8140 (tm-30)
  outliers start: 57
  outliers final: 56
  residues processed: 286
  average time/residue: 0.1981
  time to fit residues: 88.5528
Evaluate side-chains
  302 residues out of total 1487 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 246
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   80 VAL
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  120 ASP
Chi-restraints excluded: chain C residue  156 SER
Chi-restraints excluded: chain C residue  158 ASN
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain E residue  120 ASP
Chi-restraints excluded: chain E residue  154 ILE
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  103 SER
Chi-restraints excluded: chain G residue  120 ASP
Chi-restraints excluded: chain G residue  136 THR
Chi-restraints excluded: chain G residue  153 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue  103 SER
Chi-restraints excluded: chain I residue  122 ILE
Chi-restraints excluded: chain I residue  161 VAL
Chi-restraints excluded: chain K residue   52 LEU
Chi-restraints excluded: chain K residue   70 ILE
Chi-restraints excluded: chain K residue  120 ASP
Chi-restraints excluded: chain K residue  153 LEU
Chi-restraints excluded: chain F residue   34 SER
Chi-restraints excluded: chain F residue   74 MET
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  154 ILE
Chi-restraints excluded: chain F residue  161 VAL
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue  144 ILE
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain J residue   80 VAL
Chi-restraints excluded: chain J residue  103 SER
Chi-restraints excluded: chain J residue  153 LEU
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue   70 ILE
Chi-restraints excluded: chain L residue   74 MET
Chi-restraints excluded: chain L residue  103 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 135 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 132 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 116 optimal weight:    7.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.086501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.074572 restraints weight = 32654.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.077599 restraints weight = 16476.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.079715 restraints weight = 9827.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  13829  Z= 0.168
  Angle     :  0.812  59.200  18826  Z= 0.466
  Chirality :  0.037   0.445   2242
  Planarity :  0.004   0.056   2503
  Dihedral  :  4.678  69.032   1883
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 18.84 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.06 %
  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:  4.13 (0.20), residues: 1727
  helix:  3.21 (0.13), residues: 1427
  sheet:  None (None), residues: 0
  loop :  0.17 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  42 
 HIS   0.006   0.001   HIS D  41 
 PHE   0.023   0.002   PHE I  49 
 ARG   0.008   0.000   ARG B 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04605 ( 1185)
  hydrogen bonds       : angle       3.33509 ( 3555)
  covalent geometry    : bond        0.00375 (13829)
  covalent geometry    : angle       0.81191 (18826)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3527.43 seconds
wall clock time: 63 minutes 1.54 seconds (3781.54 seconds total)