Starting phenix.real_space_refine
on Tue Jul 29 06:51:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j6s_36013/07_2025/8j6s_36013.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j6s_36013/07_2025/8j6s_36013.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j6s_36013/07_2025/8j6s_36013.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j6s_36013/07_2025/8j6s_36013.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j6s_36013/07_2025/8j6s_36013.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j6s_36013/07_2025/8j6s_36013.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1568 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P     197      5.49       5
     S      15      5.16       5
     C    5640      2.51       5
     N    1918      2.21       5
     O    2260      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10030
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "G"
      Number of atoms: 484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 484
          Classifications: {'peptide': 75}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 83
    Chain: "H"
      Number of atoms: 468
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 468
          Classifications: {'peptide': 71}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 69}
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 122
          Unresolved non-hydrogen dihedrals: 78
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 55
    Chain: "E"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 663
          Classifications: {'peptide': 90}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 98
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 50
    Chain: "F"
      Number of atoms: 482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 482
          Classifications: {'peptide': 74}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 111
          Unresolved non-hydrogen angles: 139
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 55
    Chain: "I"
      Number of atoms: 2009
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 2009
          Classifications: {'DNA': 99}
          Link IDs: {'rna3p': 98}
    Chain: "C"
      Number of atoms: 676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 676
          Classifications: {'peptide': 88}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 85}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "D"
      Number of atoms: 571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 571
          Classifications: {'peptide': 73}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 568
          Classifications: {'peptide': 76}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "B"
      Number of atoms: 510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 510
          Classifications: {'peptide': 69}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "J"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2031
          Classifications: {'DNA': 98}
          Link IDs: {'rna3p': 97}
    Chain: "L"
      Number of atoms: 1494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 1494
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 264}
          Link IDs: {'PTRANS': 9, 'TRANS': 292}
          Chain breaks: 7
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 962
          Unresolved non-hydrogen angles: 1252
          Unresolved non-hydrogen dihedrals: 822
          Unresolved non-hydrogen chiralities: 92
          Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 15, 'TYR:plan': 11, 'ASN:plan1': 12, 'TRP:plan': 8, 'ASP:plan': 20, 'PHE:plan': 16, 'GLU:plan': 11, 'HIS:plan': 10}
          Unresolved non-hydrogen planarities: 534
    Chain: "K"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 74
          Classifications: {'peptide': 15}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'TRANS': 14}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 20
  Time building chain proxies: 6.54, per 1000 atoms: 0.65
  Number of scatterers: 10030
  At special positions: 0
  Unit cell: (103, 114, 113, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     P     197     15.00
     O    2260      8.00
     N    1918      7.00
     C    5640      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.92
  Conformation dependent library (CDL) restraints added in 956.6 milliseconds
  

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1768

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      53.2% alpha, 12.3% beta
      90 base pairs and 149 stacking pairs defined.
    Time for finding SS restraints: 4.90
  Creating SS restraints...
    Processing helix  chain 'G' and resid 63 through 79
      removed outlier: 3.716A  pdb=" N   PHE G  67 " --> pdb=" O   ARG G  63 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 85 through 114
      removed outlier: 3.570A  pdb=" N   ALA G 114 " --> pdb=" O   CYS G 110 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 120 through 132
      removed outlier: 3.800A  pdb=" N   ILE G 124 " --> pdb=" O   MET G 120 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 25 through 29
      removed outlier: 3.556A  pdb=" N   ILE H  29 " --> pdb=" O   ILE H  26 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 30 through 42
    Processing helix  chain 'H' and resid 49 through 76
      removed outlier: 4.098A  pdb=" N   ARG H  55 " --> pdb=" O   TYR H  51 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASN H  64 " --> pdb=" O   VAL H  60 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL H  65 " --> pdb=" O   PHE H  61 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 82 through 94
    Processing helix  chain 'E' and resid 46 through 57
      removed outlier: 4.225A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.392A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.942A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL F  87 " --> pdb=" O   ALA F  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 57
      removed outlier: 3.684A  pdb=" N   SER C  57 " --> pdb=" O   ARG C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 79
      removed outlier: 3.564A  pdb=" N   PHE C  67 " --> pdb=" O   ARG C  63 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE C  78 " --> pdb=" O   ILE C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 114
    Processing helix  chain 'C' and resid 120 through 131
    Processing helix  chain 'D' and resid 25 through 29
    Processing helix  chain 'D' and resid 30 through 42
    Processing helix  chain 'D' and resid 49 through 76
      removed outlier: 3.514A  pdb=" N   ARG D  55 " --> pdb=" O   TYR D  51 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   GLY D  56 " --> pdb=" O   GLU D  52 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL D  57 " --> pdb=" O   GLU D  53 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ARG D  67 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 94
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.864A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.829A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLN A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 77
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.557A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 704 through 708
    Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.940A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84
      removed outlier: 7.016A  pdb=" N   ARG C  83 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119
    Processing sheet with id=AA4, first strand: chain 'L' and resid 2 through 6
      removed outlier: 3.949A  pdb=" N   CYS L 370 " --> pdb=" O   CYS L   6 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 18 through 21
      removed outlier: 3.658A  pdb=" N   SER L  18 " --> pdb=" O   ALA L  35 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ALA L  35 " --> pdb=" O   SER L  18 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   LYS L  45 " --> pdb=" O   PHE L  58 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   PHE L  58 " --> pdb=" O   LYS L  45 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 74
      removed outlier: 5.850A  pdb=" N   LYS L  94 " --> pdb=" O   VAL L 121 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   VAL L 121 " --> pdb=" O   LYS L  94 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 132 through 137
      removed outlier: 6.409A  pdb=" N   ALA L 153 " --> pdb=" O   ILE L 166 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   ILE L 166 " --> pdb=" O   ALA L 153 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ILE L 155 " --> pdb=" O   ILE L 164 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLN L 162 " --> pdb=" O   ASP L 157 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 174 through 179
      removed outlier: 6.438A  pdb=" N   LEU L 195 " --> pdb=" O   ASN L 208 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   ASN L 208 " --> pdb=" O   LEU L 195 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   VAL L 197 " --> pdb=" O   ALA L 206 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 241 through 242
      removed outlier: 4.223A  pdb=" N   ALA L 279 " --> pdb=" O   VAL L 268 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 290 through 293
      removed outlier: 3.751A  pdb=" N   SER L 342 " --> pdb=" O   VAL K 684 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   VAL K 684 " --> pdb=" O   SER L 342 " (cutoff:3.500A)

    426 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      225 hydrogen bonds
      434 hydrogen bond angles
      0 basepair planarities
      90 basepair parallelities
      149 stacking parallelities
  Total time for adding SS restraints: 4.69

  Time building geometry restraints manager: 3.42 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: 2473
        1.34 -     1.46: 2881
        1.46 -     1.58: 4782
        1.58 -     1.70: 392
        1.70 -     1.82: 23
  Bond restraints: 10551
  Sorted by residual:
  bond pdb=" CB  MET E 120 "
       pdb=" CG  MET E 120 "
    ideal  model  delta    sigma   weight residual
    1.520  1.575 -0.055 3.00e-02 1.11e+03 3.39e+00
  bond pdb=" CB  PRO B  32 "
       pdb=" CG  PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.492  1.560 -0.068 5.00e-02 4.00e+02 1.87e+00
  bond pdb=" C3'  DC J  75 "
       pdb=" O3'  DC J  75 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.62e+00
  bond pdb=" CB  GLN E  68 "
       pdb=" CG  GLN E  68 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.62e+00
  bond pdb=" CB  PRO C  66 "
       pdb=" CG  PRO C  66 "
    ideal  model  delta    sigma   weight residual
    1.492  1.553 -0.061 5.00e-02 4.00e+02 1.49e+00
  ... (remaining 10546 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 14969
        2.52 -     5.05: 176
        5.05 -     7.57: 28
        7.57 -    10.10: 6
       10.10 -    12.62: 2
  Bond angle restraints: 15181
  Sorted by residual:
  angle pdb=" CA  PRO C  66 "
        pdb=" N   PRO C  66 "
        pdb=" CD  PRO C  66 "
      ideal   model   delta    sigma   weight residual
     112.00  103.82    8.18 1.40e+00 5.10e-01 3.42e+01
  angle pdb=" CA  PRO G 121 "
        pdb=" N   PRO G 121 "
        pdb=" CD  PRO G 121 "
      ideal   model   delta    sigma   weight residual
     112.00  104.18    7.82 1.40e+00 5.10e-01 3.12e+01
  angle pdb=" CA  ARG B  36 "
        pdb=" CB  ARG B  36 "
        pdb=" CG  ARG B  36 "
      ideal   model   delta    sigma   weight residual
     114.10  123.36   -9.26 2.00e+00 2.50e-01 2.14e+01
  angle pdb=" CB  MET E 120 "
        pdb=" CG  MET E 120 "
        pdb=" SD  MET E 120 "
      ideal   model   delta    sigma   weight residual
     112.70  125.32  -12.62 3.00e+00 1.11e-01 1.77e+01
  angle pdb=" CA  ARG B  92 "
        pdb=" CB  ARG B  92 "
        pdb=" CG  ARG B  92 "
      ideal   model   delta    sigma   weight residual
     114.10  121.86   -7.76 2.00e+00 2.50e-01 1.51e+01
  ... (remaining 15176 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.83: 4721
       34.83 -    69.65: 1009
       69.65 -   104.48: 49
      104.48 -   139.31: 0
      139.31 -   174.13: 4
  Dihedral angle restraints: 5783
    sinusoidal: 3085
      harmonic: 2698
  Sorted by residual:
  dihedral pdb=" CA  MET G 120 "
           pdb=" C   MET G 120 "
           pdb=" N   PRO G 121 "
           pdb=" CA  PRO G 121 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.91  -24.09     0      5.00e+00 4.00e-02 2.32e+01
  dihedral pdb=" CA  ARG A  63 "
           pdb=" C   ARG A  63 "
           pdb=" N   LYS A  64 "
           pdb=" CA  LYS A  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.25  -21.75     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  ARG G  63 "
           pdb=" C   ARG G  63 "
           pdb=" N   LYS G  64 "
           pdb=" CA  LYS G  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.80  -21.20     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 5780 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1486
       0.050 -    0.099: 270
       0.099 -    0.149: 67
       0.149 -    0.199: 7
       0.199 -    0.249: 3
  Chirality restraints: 1833
  Sorted by residual:
  chirality pdb=" CA  PRO C  66 "
            pdb=" N   PRO C  66 "
            pdb=" C   PRO C  66 "
            pdb=" CB  PRO C  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  LEU E  65 "
            pdb=" N   LEU E  65 "
            pdb=" C   LEU E  65 "
            pdb=" CB  LEU E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  PRO G 121 "
            pdb=" N   PRO G 121 "
            pdb=" C   PRO G 121 "
            pdb=" CB  PRO G 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1830 not shown)

  Planarity restraints: 1279
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET G 120 "   -0.087 5.00e-02 4.00e+02   1.26e-01 2.56e+01
        pdb=" N   PRO G 121 "    0.218 5.00e-02 4.00e+02
        pdb=" CA  PRO G 121 "   -0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO G 121 "   -0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C  65 "   -0.074 5.00e-02 4.00e+02   1.07e-01 1.85e+01
        pdb=" N   PRO C  66 "    0.186 5.00e-02 4.00e+02
        pdb=" CA  PRO C  66 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO C  66 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  31 "   -0.057 5.00e-02 4.00e+02   8.33e-02 1.11e+01
        pdb=" N   PRO B  32 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "   -0.047 5.00e-02 4.00e+02
  ... (remaining 1276 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 55
        2.51 -     3.10: 7159
        3.10 -     3.70: 18366
        3.70 -     4.30: 23082
        4.30 -     4.90: 33522
  Nonbonded interactions: 82184
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  63 "
            pdb=" C5'  DA J  33 "
     model   vdw
     1.907 3.520
  nonbonded pdb=" O2   DC I  56 "
            pdb=" N2   DG J  92 "
     model   vdw
     2.068 2.496
  nonbonded pdb=" OG1 THR H  30 "
            pdb=" OP1  DC I  36 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" O2   DC I  66 "
            pdb=" N2   DG J  82 "
     model   vdw
     2.104 2.496
  nonbonded pdb=" OG1 THR D  80 "
            pdb=" OP1  DC J  75 "
     model   vdw
     2.110 3.040
  ... (remaining 82179 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 59 through 60 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 61 through 63 or (resid 64 through 65 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 66 or (resid 67 through 98 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 99 through 104 or (r \ 
esid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 t \ 
hrough 124 or (resid 125 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 126 through 133))
  selection = (chain 'C' and ((resid 59 through 60 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 61 through 63 or (resid 64 through 65 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 66 or (resid 67 through 98 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 99 through 124 or (r \ 
esid 125 and (name N or name CA or name C or name O or name CB )) or resid 126 t \ 
hrough 132 or (resid 133 and (name N or name CA or name C or name O or name CB ) \ 
)))
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'B' and ((resid 26 through 27 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 28 or (resid 29 through 30 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 31 through 34 or (resid 35 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 36 through 38 or (resid 39 thro \ 
ugh 40 and (name N or name CA or name C or name O or name CB )) or resid 41 thro \ 
ugh 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 45 through 48 or (resid 49 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 50 through 51 or (resid 52 through 55 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 56 through 63 or (resid 64 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 65 or (resid 66 through  \ 
85 and (name N or name CA or name C or name O or name CB )) or resid 86 through  \ 
90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 92 through 94))
  selection = (chain 'D' and ((resid 26 through 27 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 28 or (resid 29 through 30 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 31 through 34 or (resid 35 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 36 through 38 or (resid 39 thro \ 
ugh 40 and (name N or name CA or name C or name O or name CB )) or resid 41 thro \ 
ugh 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 45 through 48 or (resid 49 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 50 through 52 or (resid 53 through 55 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 56 through 58 or (resid 59 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 60 through 62 or (resid  \ 
63 through 64 and (name N or name CA or name C or name O or name CB )) or resid  \ 
65 or (resid 66 through 85 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 86 through 90 or (resid 91 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 92 through 94))
  selection = (chain 'F' and (resid 26 through 34 or (resid 35 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 36 through 38 or (resid 39 through 40 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 41 through 52 or (res \ 
id 53 through 55 and (name N or name CA or name C or name O or name CB )) or res \ 
id 56 through 63 or (resid 64 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 65 or (resid 66 through 85 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 86 through 94))
  selection = (chain 'H' and ((resid 26 through 30 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 31 through 43 or (resid 44 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 45 through 48 or (resid 49 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 50 through 71 or (resid 72 thro \ 
ugh 85 and (name N or name CA or name C or name O or name CB )) or resid 86 thro \ 
ugh 94))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     31.460
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
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      :  0.004   0.068  10551  Z= 0.189
  Angle     :  0.795  12.621  15181  Z= 0.456
  Chirality :  0.044   0.249   1833
  Planarity :  0.007   0.126   1279
  Dihedral  : 29.579 174.135   4015
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 22.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 38.36 %
    Favored  : 60.58 %
  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: -0.40 (0.27), residues: 897
  helix:  0.23 (0.23), residues: 457
  sheet:  1.13 (0.47), residues: 126
  loop : -1.51 (0.32), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP L  10 
 HIS   0.013   0.004   HIS D  75 
 PHE   0.022   0.002   PHE E  84 
 TYR   0.044   0.002   TYR H  72 
 ARG   0.015   0.001   ARG B  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16855 (  651)
  hydrogen bonds       : angle       6.28185 ( 1667)
  covalent geometry    : bond        0.00416 (10551)
  covalent geometry    : angle       0.79481 (15181)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 199
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   92 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8508 (ttp80)
REVERT: E   97 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8020 (mm-30)
REVERT: E  130 ILE cc_start: 0.8796 (tp) cc_final: 0.8119 (tp)
REVERT: E  131 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7980 (mtp180)
REVERT: C   51 ILE cc_start: 0.8959 (mp) cc_final: 0.8346 (mp)
REVERT: C   93 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7623 (tm-30)
REVERT: D   59 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8582 (tppp)
REVERT: D   60 VAL cc_start: 0.9102 (t) cc_final: 0.8865 (p)
REVERT: A   90 MET cc_start: 0.8099 (tmt) cc_final: 0.7265 (tmm)
  outliers start: 4
  outliers final: 1
  residues processed: 200
  average time/residue: 0.2848
  time to fit residues: 73.5742
Evaluate side-chains
  151 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   84 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:   10.0000
   chunk 54 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 32 optimal weight:    8.9990
   chunk 50 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 97 optimal weight:    0.3980
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 GLN
C 108 ASN
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  64 ASN
D  75 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.054148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.038158 restraints weight = 71339.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.039233 restraints weight = 42012.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.039971 restraints weight = 30149.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  10551  Z= 0.218
  Angle     :  0.713   8.596  15181  Z= 0.403
  Chirality :  0.041   0.236   1833
  Planarity :  0.005   0.069   1279
  Dihedral  : 31.489 179.352   3123
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 19.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 34.13 %
    Favored  : 59.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.27), residues: 897
  helix:  0.55 (0.22), residues: 469
  sheet:  0.92 (0.47), residues: 129
  loop : -1.34 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP L  10 
 HIS   0.008   0.003   HIS C 113 
 PHE   0.015   0.002   PHE C 104 
 TYR   0.030   0.002   TYR H  72 
 ARG   0.021   0.001   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06361 (  651)
  hydrogen bonds       : angle       4.33061 ( 1667)
  covalent geometry    : bond        0.00476 (10551)
  covalent geometry    : angle       0.71260 (15181)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  104 PHE cc_start: 0.9775 (m-10) cc_final: 0.9573 (m-10)
REVERT: G  128 ARG cc_start: 0.9546 (tpp80) cc_final: 0.9292 (mmm160)
REVERT: G  129 ARG cc_start: 0.9696 (ttt-90) cc_final: 0.9375 (mmm160)
REVERT: H   90 LEU cc_start: 0.9563 (mt) cc_final: 0.9334 (pp)
REVERT: H   92 ARG cc_start: 0.9206 (mtp-110) cc_final: 0.8831 (ttp80)
REVERT: H   93 GLN cc_start: 0.9515 (tp40) cc_final: 0.9051 (tm-30)
REVERT: E   97 GLU cc_start: 0.9347 (mm-30) cc_final: 0.8937 (mm-30)
REVERT: E  131 ARG cc_start: 0.9440 (tpp80) cc_final: 0.9076 (mtp180)
REVERT: F   88 TYR cc_start: 0.8857 (m-80) cc_final: 0.8518 (m-80)
REVERT: D   59 LYS cc_start: 0.9643 (mmmm) cc_final: 0.9344 (tppp)
REVERT: D   63 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8775 (mm-30)
REVERT: A   90 MET cc_start: 0.8482 (tmt) cc_final: 0.7653 (tmm)
REVERT: A   94 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8451 (mm-30)
REVERT: A  106 ASP cc_start: 0.9411 (t70) cc_final: 0.9115 (t70)
REVERT: A  129 ARG cc_start: 0.9266 (ttp-170) cc_final: 0.9059 (ttm110)
  outliers start: 24
  outliers final: 11
  residues processed: 178
  average time/residue: 0.2422
  time to fit residues: 58.1814
Evaluate side-chains
  151 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  118 THR
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  113 HIS
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  108 ASN
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  107 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 108 ASN
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 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 = 0.3480 r_free = 0.3480 target = 0.052559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.036710 restraints weight = 74341.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.037794 restraints weight = 42717.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.038489 restraints weight = 30168.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  10551  Z= 0.226
  Angle     :  0.702  11.719  15181  Z= 0.394
  Chirality :  0.041   0.297   1833
  Planarity :  0.005   0.056   1279
  Dihedral  : 31.608 178.979   3121
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 19.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 37.83 %
    Favored  : 56.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.27), residues: 897
  helix:  0.75 (0.23), residues: 468
  sheet:  0.83 (0.48), residues: 129
  loop : -1.24 (0.32), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP L  10 
 HIS   0.006   0.002   HIS C 113 
 PHE   0.018   0.001   PHE C  84 
 TYR   0.025   0.002   TYR H  72 
 ARG   0.010   0.001   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06260 (  651)
  hydrogen bonds       : angle       4.11441 ( 1667)
  covalent geometry    : bond        0.00501 (10551)
  covalent geometry    : angle       0.70212 (15181)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  119 ILE cc_start: 0.9258 (pt) cc_final: 0.9003 (mp)
REVERT: G  128 ARG cc_start: 0.9540 (tpp80) cc_final: 0.9303 (mmm160)
REVERT: G  129 ARG cc_start: 0.9714 (ttt-90) cc_final: 0.9370 (mmm160)
REVERT: H   92 ARG cc_start: 0.9191 (mtp-110) cc_final: 0.8801 (ttp80)
REVERT: E   97 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8628 (mm-30)
REVERT: E  131 ARG cc_start: 0.9467 (tpp80) cc_final: 0.9226 (mtp180)
REVERT: F   88 TYR cc_start: 0.8910 (m-80) cc_final: 0.8419 (m-80)
REVERT: C  120 MET cc_start: 0.7539 (mpp) cc_final: 0.7333 (mpp)
REVERT: D   59 LYS cc_start: 0.9620 (mmmm) cc_final: 0.9258 (tppp)
REVERT: D   63 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8468 (mm-30)
REVERT: D   67 ARG cc_start: 0.9190 (ttp80) cc_final: 0.8681 (ttm-80)
REVERT: D   85 ASP cc_start: 0.8955 (m-30) cc_final: 0.8707 (t0)
REVERT: A   90 MET cc_start: 0.8402 (tmt) cc_final: 0.7515 (tmm)
REVERT: A   94 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8453 (mm-30)
REVERT: A   97 GLU cc_start: 0.8920 (pp20) cc_final: 0.8691 (pp20)
REVERT: A  129 ARG cc_start: 0.9297 (ttp-170) cc_final: 0.9015 (ttm110)
REVERT: B   40 ARG cc_start: 0.9354 (tpp80) cc_final: 0.9118 (tpp80)
REVERT: B   66 ILE cc_start: 0.9631 (pt) cc_final: 0.8403 (pt)
REVERT: B   67 ARG cc_start: 0.9695 (tpp-160) cc_final: 0.9378 (mmp80)
  outliers start: 20
  outliers final: 17
  residues processed: 160
  average time/residue: 0.2695
  time to fit residues: 57.2887
Evaluate side-chains
  153 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   45 ARG
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  108 ASN
Chi-restraints excluded: chain F residue   39 ARG
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain D residue   96 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   86 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 12 optimal weight:   30.0000
   chunk 3 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 56 optimal weight:   30.0000
   chunk 50 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.053739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.037748 restraints weight = 74419.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.038869 restraints weight = 42056.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.039613 restraints weight = 29496.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10551  Z= 0.170
  Angle     :  0.691  13.099  15181  Z= 0.377
  Chirality :  0.041   0.307   1833
  Planarity :  0.004   0.049   1279
  Dihedral  : 31.446 179.239   3121
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 33.60 %
    Favored  : 58.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.27), residues: 897
  helix:  0.96 (0.23), residues: 469
  sheet:  0.84 (0.49), residues: 129
  loop : -1.19 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP L  10 
 HIS   0.005   0.002   HIS H  75 
 PHE   0.026   0.002   PHE A  67 
 TYR   0.022   0.001   TYR H  72 
 ARG   0.007   0.001   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05178 (  651)
  hydrogen bonds       : angle       3.77362 ( 1667)
  covalent geometry    : bond        0.00376 (10551)
  covalent geometry    : angle       0.69051 (15181)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  128 ARG cc_start: 0.9507 (tpp80) cc_final: 0.9140 (mmm160)
REVERT: G  129 ARG cc_start: 0.9700 (ttt-90) cc_final: 0.9335 (mmm160)
REVERT: H   92 ARG cc_start: 0.9199 (mtp-110) cc_final: 0.8788 (ttp80)
REVERT: E   97 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8701 (mm-30)
REVERT: E  125 GLN cc_start: 0.9555 (mm-40) cc_final: 0.9219 (mm-40)
REVERT: F   39 ARG cc_start: 0.9604 (OUTLIER) cc_final: 0.9232 (tpp80)
REVERT: F   88 TYR cc_start: 0.8922 (m-80) cc_final: 0.8337 (m-80)
REVERT: C   55 GLN cc_start: 0.8553 (mt0) cc_final: 0.8266 (mp10)
REVERT: C   90 MET cc_start: 0.8984 (tpp) cc_final: 0.8633 (tpp)
REVERT: C  120 MET cc_start: 0.7553 (mpp) cc_final: 0.7334 (mpp)
REVERT: D   59 LYS cc_start: 0.9615 (mmmm) cc_final: 0.9208 (tppp)
REVERT: D   63 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8454 (mm-30)
REVERT: D   64 ASN cc_start: 0.9278 (m110) cc_final: 0.8955 (m-40)
REVERT: D   67 ARG cc_start: 0.9190 (ttp80) cc_final: 0.8684 (ttm-80)
REVERT: D   85 ASP cc_start: 0.8964 (m-30) cc_final: 0.8696 (t0)
REVERT: A   90 MET cc_start: 0.8510 (tmt) cc_final: 0.7543 (tmm)
REVERT: A   94 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8596 (mm-30)
REVERT: B   40 ARG cc_start: 0.9372 (tpp80) cc_final: 0.9168 (tpp80)
REVERT: B   62 LEU cc_start: 0.9698 (mm) cc_final: 0.9440 (mm)
REVERT: B   66 ILE cc_start: 0.9620 (pt) cc_final: 0.8351 (pt)
REVERT: B   67 ARG cc_start: 0.9697 (tpp-160) cc_final: 0.9367 (mmp80)
  outliers start: 28
  outliers final: 17
  residues processed: 171
  average time/residue: 0.2657
  time to fit residues: 59.5029
Evaluate side-chains
  153 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   63 ARG
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   39 ARG
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   86 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 36 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 31 optimal weight:   10.0000
   chunk 78 optimal weight:   50.0000
   chunk 86 optimal weight:    6.9990
   chunk 75 optimal weight:    8.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
E 108 ASN
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 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 = 0.3458 r_free = 0.3458 target = 0.051243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.035569 restraints weight = 76818.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.036614 restraints weight = 43793.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.037325 restraints weight = 30901.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  10551  Z= 0.256
  Angle     :  0.716  10.581  15181  Z= 0.398
  Chirality :  0.041   0.188   1833
  Planarity :  0.005   0.053   1279
  Dihedral  : 31.693 178.821   3121
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 20.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  8.47 %
    Allowed  : 36.77 %
    Favored  : 54.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.27), residues: 897
  helix:  0.91 (0.23), residues: 470
  sheet:  0.69 (0.48), residues: 129
  loop : -1.17 (0.33), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP L  10 
 HIS   0.005   0.002   HIS G 113 
 PHE   0.023   0.002   PHE C  84 
 TYR   0.018   0.001   TYR H  72 
 ARG   0.008   0.001   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06994 (  651)
  hydrogen bonds       : angle       3.93159 ( 1667)
  covalent geometry    : bond        0.00564 (10551)
  covalent geometry    : angle       0.71592 (15181)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 145
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  128 ARG cc_start: 0.9511 (tpp80) cc_final: 0.9072 (mmm160)
REVERT: G  129 ARG cc_start: 0.9740 (ttt-90) cc_final: 0.9369 (mmm160)
REVERT: H   92 ARG cc_start: 0.9145 (mtp-110) cc_final: 0.8751 (ttp80)
REVERT: H   93 GLN cc_start: 0.9543 (tp40) cc_final: 0.9085 (tm-30)
REVERT: E  125 GLN cc_start: 0.9556 (mm-40) cc_final: 0.9244 (mm-40)
REVERT: F   39 ARG cc_start: 0.9635 (OUTLIER) cc_final: 0.9345 (tpp80)
REVERT: F   88 TYR cc_start: 0.9031 (m-80) cc_final: 0.8492 (m-80)
REVERT: C   90 MET cc_start: 0.9090 (tpp) cc_final: 0.8777 (tpp)
REVERT: C  120 MET cc_start: 0.7686 (mpp) cc_final: 0.7350 (mpp)
REVERT: D   59 LYS cc_start: 0.9680 (mmmm) cc_final: 0.9223 (tppp)
REVERT: D   63 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8444 (mm-30)
REVERT: D   64 ASN cc_start: 0.9367 (m110) cc_final: 0.8958 (m110)
REVERT: D   67 ARG cc_start: 0.9232 (ttp80) cc_final: 0.8662 (ttm-80)
REVERT: D   85 ASP cc_start: 0.8950 (m-30) cc_final: 0.8637 (t0)
REVERT: A   90 MET cc_start: 0.8586 (tmt) cc_final: 0.7715 (tmm)
REVERT: A   94 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8591 (mm-30)
REVERT: A  120 MET cc_start: 0.8892 (mtt) cc_final: 0.8295 (mpp)
REVERT: A  129 ARG cc_start: 0.9262 (ttm110) cc_final: 0.8786 (ptm160)
REVERT: B   40 ARG cc_start: 0.9418 (tpp80) cc_final: 0.9175 (tpp80)
REVERT: B   55 ARG cc_start: 0.9484 (OUTLIER) cc_final: 0.9109 (mmt90)
REVERT: B   66 ILE cc_start: 0.9645 (pt) cc_final: 0.8436 (pt)
REVERT: B   67 ARG cc_start: 0.9688 (tpp-160) cc_final: 0.9388 (mmp80)
REVERT: B   85 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8062 (m-30)
  outliers start: 32
  outliers final: 20
  residues processed: 165
  average time/residue: 0.2561
  time to fit residues: 56.0743
Evaluate side-chains
  157 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   63 ARG
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   39 ARG
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  124 ILE
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue   96 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   85 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    6.9990
   chunk 100 optimal weight:   50.0000
   chunk 29 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 32 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.051313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.035408 restraints weight = 77043.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.036465 restraints weight = 43656.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.037153 restraints weight = 30680.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.4102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  10551  Z= 0.223
  Angle     :  0.730  12.477  15181  Z= 0.396
  Chirality :  0.041   0.291   1833
  Planarity :  0.004   0.049   1279
  Dihedral  : 31.712 179.783   3121
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 18.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  8.73 %
    Allowed  : 37.83 %
    Favored  : 53.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.27), residues: 897
  helix:  0.91 (0.23), residues: 469
  sheet:  0.73 (0.47), residues: 128
  loop : -1.12 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP L  10 
 HIS   0.004   0.002   HIS C 113 
 PHE   0.021   0.002   PHE C  84 
 TYR   0.017   0.001   TYR H  72 
 ARG   0.011   0.001   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06008 (  651)
  hydrogen bonds       : angle       3.88215 ( 1667)
  covalent geometry    : bond        0.00493 (10551)
  covalent geometry    : angle       0.72972 (15181)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  104 PHE cc_start: 0.9801 (m-10) cc_final: 0.9528 (m-80)
REVERT: G  128 ARG cc_start: 0.9473 (tpp80) cc_final: 0.9045 (mmm160)
REVERT: G  129 ARG cc_start: 0.9726 (ttt-90) cc_final: 0.9349 (mmm160)
REVERT: H   92 ARG cc_start: 0.9119 (mtp-110) cc_final: 0.8861 (ttp80)
REVERT: H   93 GLN cc_start: 0.9541 (tp40) cc_final: 0.9156 (tm-30)
REVERT: E   97 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8690 (mm-30)
REVERT: F   39 ARG cc_start: 0.9656 (OUTLIER) cc_final: 0.9375 (tpp80)
REVERT: F   88 TYR cc_start: 0.9042 (m-80) cc_final: 0.8472 (m-80)
REVERT: C   90 MET cc_start: 0.9062 (tpp) cc_final: 0.8696 (tpp)
REVERT: C  120 MET cc_start: 0.7766 (mpp) cc_final: 0.7397 (mpp)
REVERT: D   59 LYS cc_start: 0.9679 (mmmm) cc_final: 0.8783 (tppp)
REVERT: D   63 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8503 (mm-30)
REVERT: D   64 ASN cc_start: 0.9373 (m110) cc_final: 0.8845 (m110)
REVERT: D   67 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8648 (ttm-80)
REVERT: D   75 HIS cc_start: 0.9342 (t-90) cc_final: 0.9039 (m-70)
REVERT: D   85 ASP cc_start: 0.9008 (m-30) cc_final: 0.8679 (t0)
REVERT: A   90 MET cc_start: 0.8605 (tmt) cc_final: 0.7701 (tmm)
REVERT: A   94 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8680 (mm-30)
REVERT: B   40 ARG cc_start: 0.9384 (tpp80) cc_final: 0.9129 (tpp80)
REVERT: B   55 ARG cc_start: 0.9417 (OUTLIER) cc_final: 0.8877 (mmt90)
REVERT: B   66 ILE cc_start: 0.9668 (pt) cc_final: 0.8529 (pt)
REVERT: B   67 ARG cc_start: 0.9684 (tpp-160) cc_final: 0.9395 (mmp80)
  outliers start: 33
  outliers final: 27
  residues processed: 165
  average time/residue: 0.2617
  time to fit residues: 58.2600
Evaluate side-chains
  162 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   63 ARG
Chi-restraints excluded: chain G residue   99 TYR
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  108 ASN
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   39 ARG
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain D residue   96 THR
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   92 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 77 optimal weight:    0.2980
   chunk 43 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 85 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.060166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.044651 restraints weight = 91857.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.045908 restraints weight = 48873.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.046709 restraints weight = 33007.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.4344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10551  Z= 0.162
  Angle     :  0.729  13.308  15181  Z= 0.389
  Chirality :  0.041   0.355   1833
  Planarity :  0.004   0.052   1279
  Dihedral  : 31.382 178.528   3121
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 15.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 43.65 %
    Favored  : 50.79 %
  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:  0.50 (0.27), residues: 897
  helix:  1.03 (0.23), residues: 469
  sheet:  0.98 (0.47), residues: 123
  loop : -0.98 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP L  10 
 HIS   0.005   0.002   HIS G 113 
 PHE   0.014   0.001   PHE C  84 
 TYR   0.017   0.001   TYR H  72 
 ARG   0.012   0.001   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04934 (  651)
  hydrogen bonds       : angle       3.66800 ( 1667)
  covalent geometry    : bond        0.00357 (10551)
  covalent geometry    : angle       0.72891 (15181)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   63 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8664 (ttt-90)
REVERT: G  128 ARG cc_start: 0.9470 (tpp80) cc_final: 0.9105 (mmm160)
REVERT: G  129 ARG cc_start: 0.9771 (ttt-90) cc_final: 0.9363 (mmm160)
REVERT: H   92 ARG cc_start: 0.9152 (mtp-110) cc_final: 0.8915 (ttp80)
REVERT: H   93 GLN cc_start: 0.9400 (tp40) cc_final: 0.9120 (tm-30)
REVERT: E   97 GLU cc_start: 0.9337 (mm-30) cc_final: 0.8740 (mm-30)
REVERT: E  131 ARG cc_start: 0.9284 (mtt180) cc_final: 0.9039 (mtp180)
REVERT: F   39 ARG cc_start: 0.9670 (OUTLIER) cc_final: 0.9387 (tpp80)
REVERT: F   53 GLU cc_start: 0.9244 (tt0) cc_final: 0.8869 (tt0)
REVERT: F   88 TYR cc_start: 0.9023 (m-80) cc_final: 0.8330 (m-80)
REVERT: C   86 SER cc_start: 0.9695 (t) cc_final: 0.9457 (p)
REVERT: C   90 MET cc_start: 0.9079 (tpp) cc_final: 0.8616 (tpp)
REVERT: D   39 ARG cc_start: 0.9576 (tpp-160) cc_final: 0.9312 (tpp80)
REVERT: D   59 LYS cc_start: 0.9604 (mmmm) cc_final: 0.9012 (tppp)
REVERT: D   63 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8537 (mm-30)
REVERT: D   64 ASN cc_start: 0.9351 (m110) cc_final: 0.8966 (m110)
REVERT: D   67 ARG cc_start: 0.9160 (ttp80) cc_final: 0.8665 (ttm-80)
REVERT: D   75 HIS cc_start: 0.9334 (t-90) cc_final: 0.9013 (m-70)
REVERT: D   85 ASP cc_start: 0.8942 (m-30) cc_final: 0.8651 (t0)
REVERT: A   94 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8766 (mm-30)
REVERT: A  129 ARG cc_start: 0.9264 (ttm110) cc_final: 0.8811 (ptm160)
REVERT: B   40 ARG cc_start: 0.9386 (tpp80) cc_final: 0.9182 (tpp80)
REVERT: B   55 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.8797 (ttm-80)
REVERT: B   85 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8202 (m-30)
  outliers start: 21
  outliers final: 13
  residues processed: 169
  average time/residue: 0.3226
  time to fit residues: 73.2380
Evaluate side-chains
  159 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 1.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   63 ARG
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   39 ARG
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   92 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 2 optimal weight:   50.0000
   chunk 83 optimal weight:   50.0000
   chunk 49 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 7 optimal weight:    6.9990
   chunk 95 optimal weight:   50.0000
   chunk 66 optimal weight:    0.7980
   chunk 97 optimal weight:   40.0000
   chunk 82 optimal weight:   20.0000
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
C  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.052227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.036621 restraints weight = 75289.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.037692 restraints weight = 42935.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.038398 restraints weight = 30197.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.4503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  10551  Z= 0.195
  Angle     :  0.751  16.151  15181  Z= 0.402
  Chirality :  0.042   0.432   1833
  Planarity :  0.004   0.045   1279
  Dihedral  : 31.403 175.871   3121
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 19.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 44.44 %
    Favored  : 50.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.27), residues: 897
  helix:  0.99 (0.23), residues: 474
  sheet:  1.05 (0.47), residues: 122
  loop : -0.97 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP L  10 
 HIS   0.005   0.002   HIS G 113 
 PHE   0.042   0.002   PHE A  67 
 TYR   0.016   0.001   TYR H  72 
 ARG   0.011   0.001   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05564 (  651)
  hydrogen bonds       : angle       3.83635 ( 1667)
  covalent geometry    : bond        0.00440 (10551)
  covalent geometry    : angle       0.75110 (15181)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   63 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8646 (ttt-90)
REVERT: G  104 PHE cc_start: 0.9724 (m-10) cc_final: 0.9413 (m-80)
REVERT: G  129 ARG cc_start: 0.9757 (ttt-90) cc_final: 0.9477 (mmm-85)
REVERT: H   93 GLN cc_start: 0.9503 (tp40) cc_final: 0.8793 (tm-30)
REVERT: E   97 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8672 (mm-30)
REVERT: E  120 MET cc_start: 0.9294 (mmm) cc_final: 0.8371 (mmt)
REVERT: F   39 ARG cc_start: 0.9669 (tpp80) cc_final: 0.9391 (tpp80)
REVERT: F   88 TYR cc_start: 0.9025 (m-80) cc_final: 0.8412 (m-80)
REVERT: C   55 GLN cc_start: 0.8518 (mt0) cc_final: 0.8239 (mp10)
REVERT: C   86 SER cc_start: 0.9692 (t) cc_final: 0.9454 (p)
REVERT: C   90 MET cc_start: 0.9082 (tpp) cc_final: 0.8688 (tpp)
REVERT: C  120 MET cc_start: 0.7769 (mpp) cc_final: 0.7417 (mpp)
REVERT: D   59 LYS cc_start: 0.9662 (mmmm) cc_final: 0.8735 (tppp)
REVERT: D   63 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8530 (mm-30)
REVERT: D   64 ASN cc_start: 0.9395 (m110) cc_final: 0.8857 (m110)
REVERT: D   67 ARG cc_start: 0.9117 (ttp80) cc_final: 0.8555 (ttm-80)
REVERT: D   75 HIS cc_start: 0.9342 (t-90) cc_final: 0.9046 (m-70)
REVERT: D   85 ASP cc_start: 0.8981 (m-30) cc_final: 0.8629 (t0)
REVERT: A   90 MET cc_start: 0.8535 (tmt) cc_final: 0.7568 (tmm)
REVERT: A   94 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8636 (mm-30)
  outliers start: 21
  outliers final: 19
  residues processed: 159
  average time/residue: 0.2555
  time to fit residues: 54.0431
Evaluate side-chains
  155 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   63 ARG
Chi-restraints excluded: chain G residue   99 TYR
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  108 ASN
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   92 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    7.9990
   chunk 65 optimal weight:    6.9990
   chunk 32 optimal weight:    7.9990
   chunk 10 optimal weight:    0.1980
   chunk 2 optimal weight:   50.0000
   chunk 48 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
G 113 HIS
E 108 ASN
C 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.052688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.036903 restraints weight = 77221.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.038015 restraints weight = 43434.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.038736 restraints weight = 30285.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.4717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  10551  Z= 0.179
  Angle     :  0.770  15.439  15181  Z= 0.408
  Chirality :  0.042   0.442   1833
  Planarity :  0.004   0.051   1279
  Dihedral  : 31.427 176.520   3121
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 18.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 43.65 %
    Favored  : 50.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.28), residues: 897
  helix:  0.96 (0.23), residues: 473
  sheet:  1.08 (0.47), residues: 122
  loop : -0.86 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP L  10 
 HIS   0.005   0.002   HIS G 113 
 PHE   0.027   0.001   PHE A  67 
 TYR   0.016   0.001   TYR H  72 
 ARG   0.014   0.001   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05257 (  651)
  hydrogen bonds       : angle       3.85229 ( 1667)
  covalent geometry    : bond        0.00405 (10551)
  covalent geometry    : angle       0.77037 (15181)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 145
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   63 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8662 (ttt-90)
REVERT: G  129 ARG cc_start: 0.9743 (ttt-90) cc_final: 0.9440 (mmm-85)
REVERT: H   93 GLN cc_start: 0.9504 (tp40) cc_final: 0.9002 (tp40)
REVERT: E   97 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8663 (mm-30)
REVERT: E  120 MET cc_start: 0.9203 (mmm) cc_final: 0.8257 (mmt)
REVERT: F   39 ARG cc_start: 0.9683 (OUTLIER) cc_final: 0.9400 (tpp80)
REVERT: F   88 TYR cc_start: 0.8998 (m-80) cc_final: 0.8396 (m-80)
REVERT: C   86 SER cc_start: 0.9673 (t) cc_final: 0.9435 (p)
REVERT: C   90 MET cc_start: 0.9074 (tpp) cc_final: 0.8679 (tpp)
REVERT: D   39 ARG cc_start: 0.9581 (tpp-160) cc_final: 0.9345 (tpp80)
REVERT: D   59 LYS cc_start: 0.9663 (mmmm) cc_final: 0.9078 (tppp)
REVERT: D   63 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8434 (mm-30)
REVERT: D   64 ASN cc_start: 0.9389 (m110) cc_final: 0.8831 (m110)
REVERT: D   67 ARG cc_start: 0.9135 (ttp80) cc_final: 0.8562 (ttm-80)
REVERT: D   75 HIS cc_start: 0.9317 (t-90) cc_final: 0.9022 (m-70)
REVERT: D   85 ASP cc_start: 0.8983 (m-30) cc_final: 0.8625 (t0)
REVERT: A  120 MET cc_start: 0.8829 (mtt) cc_final: 0.8394 (mpp)
REVERT: B   55 ARG cc_start: 0.9371 (OUTLIER) cc_final: 0.8705 (mtp85)
REVERT: B   67 ARG cc_start: 0.9650 (tpp-160) cc_final: 0.9155 (mmm160)
  outliers start: 23
  outliers final: 17
  residues processed: 161
  average time/residue: 0.2747
  time to fit residues: 58.5004
Evaluate side-chains
  161 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   63 ARG
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  108 ASN
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   39 ARG
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   92 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 73 optimal weight:    7.9990
   chunk 82 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 3 optimal weight:    6.9990
   chunk 30 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.050441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.034859 restraints weight = 78445.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.035922 restraints weight = 44177.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.036607 restraints weight = 30839.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.4971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081  10551  Z= 0.246
  Angle     :  0.804  17.231  15181  Z= 0.430
  Chirality :  0.042   0.439   1833
  Planarity :  0.005   0.050   1279
  Dihedral  : 31.680 176.694   3121
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 21.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 43.92 %
    Favored  : 50.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.28), residues: 897
  helix:  0.84 (0.23), residues: 475
  sheet:  1.08 (0.47), residues: 122
  loop : -0.88 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP L  10 
 HIS   0.004   0.002   HIS G 113 
 PHE   0.047   0.002   PHE A  67 
 TYR   0.015   0.001   TYR H  72 
 ARG   0.015   0.001   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06662 (  651)
  hydrogen bonds       : angle       4.05498 ( 1667)
  covalent geometry    : bond        0.00548 (10551)
  covalent geometry    : angle       0.80427 (15181)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 1.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   63 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8650 (ttt-90)
REVERT: G  129 ARG cc_start: 0.9760 (ttt-90) cc_final: 0.9447 (mmm-85)
REVERT: H   92 ARG cc_start: 0.9167 (mtp-110) cc_final: 0.8895 (ttp80)
REVERT: H   93 GLN cc_start: 0.9516 (tp40) cc_final: 0.9281 (tp-100)
REVERT: E  120 MET cc_start: 0.9160 (mmm) cc_final: 0.7718 (mmt)
REVERT: F   39 ARG cc_start: 0.9664 (OUTLIER) cc_final: 0.9386 (tpp80)
REVERT: F   88 TYR cc_start: 0.9019 (m-80) cc_final: 0.8485 (m-80)
REVERT: C   55 GLN cc_start: 0.8577 (mt0) cc_final: 0.8279 (mp10)
REVERT: C   86 SER cc_start: 0.9694 (t) cc_final: 0.9458 (p)
REVERT: C   90 MET cc_start: 0.9138 (tpp) cc_final: 0.8766 (tpp)
REVERT: C  120 MET cc_start: 0.8853 (tpp) cc_final: 0.8400 (tpp)
REVERT: D   59 LYS cc_start: 0.9687 (mmmm) cc_final: 0.9106 (tppp)
REVERT: D   63 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8443 (mm-30)
REVERT: D   64 ASN cc_start: 0.9427 (m110) cc_final: 0.8911 (m110)
REVERT: D   67 ARG cc_start: 0.9182 (ttp80) cc_final: 0.8620 (ttm-80)
REVERT: D   75 HIS cc_start: 0.9371 (t-90) cc_final: 0.9063 (m-70)
REVERT: D   85 ASP cc_start: 0.8963 (m-30) cc_final: 0.8628 (t0)
REVERT: A   90 MET cc_start: 0.8393 (tmt) cc_final: 0.8125 (ppp)
REVERT: A   97 GLU cc_start: 0.9207 (pp20) cc_final: 0.8828 (pp20)
REVERT: B   55 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9033 (mmt90)
REVERT: B   67 ARG cc_start: 0.9663 (tpp-160) cc_final: 0.9154 (mmm160)
  outliers start: 23
  outliers final: 19
  residues processed: 155
  average time/residue: 0.2689
  time to fit residues: 55.4371
Evaluate side-chains
  156 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   63 ARG
Chi-restraints excluded: chain G residue   99 TYR
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   84 PHE
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  108 ASN
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   39 ARG
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   92 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 94 optimal weight:   30.0000
   chunk 28 optimal weight:   40.0000
   chunk 22 optimal weight:    0.7980
   chunk 100 optimal weight:   50.0000
   chunk 1 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0870
   chunk 59 optimal weight:    1.9990
   chunk 81 optimal weight:   30.0000
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.5764

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.052138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.036554 restraints weight = 73465.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.037649 restraints weight = 41700.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.038359 restraints weight = 29138.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10551  Z= 0.174
  Angle     :  0.795  16.074  15181  Z= 0.416
  Chirality :  0.042   0.450   1833
  Planarity :  0.004   0.059   1279
  Dihedral  : 31.550 177.207   3121
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 19.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 45.77 %
    Favored  : 49.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.28), residues: 897
  helix:  0.90 (0.24), residues: 475
  sheet:  1.08 (0.46), residues: 122
  loop : -0.84 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP L  10 
 HIS   0.005   0.002   HIS G 113 
 PHE   0.045   0.002   PHE A  67 
 TYR   0.016   0.001   TYR H  72 
 ARG   0.014   0.001   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05158 (  651)
  hydrogen bonds       : angle       3.88710 ( 1667)
  covalent geometry    : bond        0.00394 (10551)
  covalent geometry    : angle       0.79548 (15181)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3816.61 seconds
wall clock time: 66 minutes 22.66 seconds (3982.66 seconds total)