Starting phenix.real_space_refine
on Thu Jun 12 19:32:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn9_40617/06_2025/8sn9_40617.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn9_40617/06_2025/8sn9_40617.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn9_40617/06_2025/8sn9_40617.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn9_40617/06_2025/8sn9_40617.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn9_40617/06_2025/8sn9_40617.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn9_40617/06_2025/8sn9_40617.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      33      5.16       5
     C    8264      2.51       5
     N    2710      2.21       5
     O    3288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14591
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 682
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "M"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12296  SG  CYS K  31      53.370  71.554  45.709  1.00 90.47           S
  ATOM  12446  SG  CYS K  51      52.485  67.970  44.923  1.00 88.01           S
  ATOM  12470  SG  CYS K  54      52.408  70.634  42.129  1.00 89.07           S
  ATOM  12187  SG  CYS K  16      43.387  65.421  52.089  1.00 95.41           S
  ATOM  12205  SG  CYS K  19      43.026  62.019  53.804  1.00 88.88           S
  ATOM  12335  SG  CYS K  36      44.943  64.767  55.368  1.00 85.82           S
  ATOM  12357  SG  CYS K  39      46.383  62.853  52.270  1.00 90.71           S

  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY M  76 " occ=0.25
  Time building chain proxies: 10.03, per 1000 atoms: 0.69
  Number of scatterers: 14591
  At special positions: 0
  Unit cell: (130.144, 130.144, 124.832, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      33     16.00
     P     294     15.00
     O    3288      8.00
     N    2710      7.00
     C    8264      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
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 3.63
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
      Number of angles added : 9


  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2026

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 13 sheets defined
      61.6% alpha, 5.5% beta
      136 base pairs and 252 stacking pairs defined.
    Time for finding SS restraints: 7.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.817A  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 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.578A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.946A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.931A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.717A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.619A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.849A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.670A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.752A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.743A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.866A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.553A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS E  79 " --> pdb=" O   ALA E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.577A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.893A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 27 through 36
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.782A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.811A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.550A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
    Processing helix  chain 'K' and resid 58 through 68
      removed outlier: 3.806A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
    Processing helix  chain 'K' and resid 84 through 91
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 4.081A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.591A  pdb=" N   ASP L 111 " --> pdb=" O   ALA L 107 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ASP L 112 " --> pdb=" O   SER L 108 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.652A  pdb=" N   ALA L 124 " --> pdb=" O   VAL L 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 146
      removed outlier: 3.925A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 34
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.585A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.806A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.783A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.563A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.747A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24
    Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16

    492 hydrogen bonds defined for protein.
    1453 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      349 hydrogen bonds
      694 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      252 stacking parallelities
  Total time for adding SS restraints: 5.50

  Time building geometry restraints manager: 4.37 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: 3546
        1.34 -     1.46: 4319
        1.46 -     1.58: 6962
        1.58 -     1.70: 586
        1.70 -     1.82: 49
  Bond restraints: 15462
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.37e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.453 -0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" C4'  DT I -26 "
       pdb=" C3'  DT I -26 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.021 2.00e-02 2.50e+03 1.07e+00
  bond pdb=" C3'  DA J -73 "
       pdb=" C2'  DA J -73 "
    ideal  model  delta    sigma   weight residual
    1.525  1.545 -0.020 2.00e-02 2.50e+03 1.04e+00
  bond pdb=" CB  MET H  59 "
       pdb=" CG  MET H  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.490  0.030 3.00e-02 1.11e+03 9.68e-01
  ... (remaining 15457 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 21543
        1.53 -     3.07: 564
        3.07 -     4.60: 31
        4.60 -     6.13: 16
        6.13 -     7.67: 2
  Bond angle restraints: 22156
  Sorted by residual:
  angle pdb=" CB  MET H  59 "
        pdb=" CG  MET H  59 "
        pdb=" SD  MET H  59 "
      ideal   model   delta    sigma   weight residual
     112.70  105.03    7.67 3.00e+00 1.11e-01 6.53e+00
  angle pdb=" C   THR E  80 "
        pdb=" N   ASP E  81 "
        pdb=" CA  ASP E  81 "
      ideal   model   delta    sigma   weight residual
     122.46  126.05   -3.59 1.41e+00 5.03e-01 6.47e+00
  angle pdb=" C   ALA L  19 "
        pdb=" N   GLN L  20 "
        pdb=" CA  GLN L  20 "
      ideal   model   delta    sigma   weight residual
     121.54  126.31   -4.77 1.91e+00 2.74e-01 6.24e+00
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     113.18  118.86   -5.68 2.37e+00 1.78e-01 5.75e+00
  angle pdb=" CG  ARG L  15 "
        pdb=" CD  ARG L  15 "
        pdb=" NE  ARG L  15 "
      ideal   model   delta    sigma   weight residual
     112.00  116.98   -4.98 2.20e+00 2.07e-01 5.12e+00
  ... (remaining 22151 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    36.00: 7251
       36.00 -    71.99: 1335
       71.99 -   107.99: 14
      107.99 -   143.99: 0
      143.99 -   179.99: 2
  Dihedral angle restraints: 8602
    sinusoidal: 5466
      harmonic: 3136
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.01  179.99     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   70.83  149.17     1      3.50e+01 8.16e-04 1.46e+01
  dihedral pdb=" CG  ARG D  92 "
           pdb=" CD  ARG D  92 "
           pdb=" NE  ARG D  92 "
           pdb=" CZ  ARG D  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.58   44.42     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 8599 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1768
       0.032 -    0.064: 560
       0.064 -    0.096: 131
       0.096 -    0.128: 48
       0.128 -    0.160: 7
  Chirality restraints: 2514
  Sorted by residual:
  chirality pdb=" CB  VAL K  58 "
            pdb=" CA  VAL K  58 "
            pdb=" CG1 VAL K  58 "
            pdb=" CG2 VAL K  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  ASP E  81 "
            pdb=" N   ASP E  81 "
            pdb=" C   ASP E  81 "
            pdb=" CB  ASP E  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.81e-01
  ... (remaining 2511 not shown)

  Planarity restraints: 1794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  88 "   -0.009 2.00e-02 2.50e+03   1.38e-02 3.81e+00
        pdb=" CG  TYR F  88 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  88 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  88 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  88 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  88 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  88 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F  88 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.025 2.00e-02 2.50e+03   1.06e-02 3.07e+00
        pdb=" N9   DA I -35 "    0.021 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.005 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.024 2.00e-02 2.50e+03   9.63e-03 2.78e+00
        pdb=" N9   DG I  47 "    0.019 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.007 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1791 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 164
        2.63 -     3.20: 12082
        3.20 -     3.77: 25513
        3.77 -     4.33: 32901
        4.33 -     4.90: 48665
  Nonbonded interactions: 119325
  Sorted by model distance:
  nonbonded pdb=" OG  SER L  22 "
            pdb=" OG1 THR L  36 "
     model   vdw
     2.063 3.040
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.106 2.496
  nonbonded pdb=" NH2 ARG B  35 "
            pdb=" OP2  DG J   8 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" O   TYR G  39 "
            pdb=" OG  SER H  78 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER D  64 "
            pdb=" O   GLY F 101 "
     model   vdw
     2.226 3.040
  ... (remaining 119320 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'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.25 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:             15.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     45.490
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.120
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   64.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15472  Z= 0.159
  Angle     :  0.557   7.668  22171  Z= 0.322
  Chirality :  0.035   0.160   2514
  Planarity :  0.003   0.040   1792
  Dihedral  : 25.887 179.987   6570
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.26), residues: 1056
  helix:  2.33 (0.21), residues: 640
  sheet:  1.42 (0.81), residues: 48
  loop : -0.80 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP L  93 
 HIS   0.002   0.001   HIS D  82 
 PHE   0.010   0.001   PHE L  69 
 TYR   0.033   0.002   TYR F  88 
 ARG   0.014   0.000   ARG L  15 

Details of bonding type rmsd
  link_TRANS           : bond        0.00058 (    2)
  link_TRANS           : angle       0.24804 (    6)
  hydrogen bonds       : bond        0.10647 (  841)
  hydrogen bonds       : angle       3.84937 ( 2147)
  metal coordination   : bond        0.00697 (    8)
  metal coordination   : angle       3.45337 (    9)
  covalent geometry    : bond        0.00349 (15462)
  covalent geometry    : angle       0.55309 (22156)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   46 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8580 (tppt)
REVERT: D   83 TYR cc_start: 0.8301 (m-80) cc_final: 0.7966 (m-80)
REVERT: D  116 LYS cc_start: 0.9178 (ttpp) cc_final: 0.8815 (tttt)
REVERT: D  120 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8480 (tttp)
REVERT: G   30 VAL cc_start: 0.9252 (t) cc_final: 0.9023 (m)
REVERT: H   35 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8135 (mt-10)
REVERT: K   41 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7631 (mm-40)
REVERT: K   49 LEU cc_start: 0.8683 (tp) cc_final: 0.8430 (tp)
REVERT: K   57 ARG cc_start: 0.7490 (mtp-110) cc_final: 0.6992 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.3307
  time to fit residues: 84.3851
Evaluate side-chains
  150 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 97 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 101 optimal weight:    9.9990
   chunk 39 optimal weight:    0.0570
   chunk 61 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.9900

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  34 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.142269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.110047 restraints weight = 34476.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.111864 restraints weight = 82905.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.112785 restraints weight = 31138.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3294
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.0838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15472  Z= 0.177
  Angle     :  0.593  11.512  22171  Z= 0.335
  Chirality :  0.036   0.183   2514
  Planarity :  0.004   0.035   1792
  Dihedral  : 28.896 179.477   4410
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  9.99 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.26), residues: 1056
  helix:  2.39 (0.20), residues: 644
  sheet:  1.22 (0.80), residues: 48
  loop : -0.91 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 141 
 HIS   0.003   0.001   HIS L  32 
 PHE   0.008   0.001   PHE H  70 
 TYR   0.028   0.002   TYR H  83 
 ARG   0.008   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00133 (    2)
  link_TRANS           : angle       0.36561 (    6)
  hydrogen bonds       : bond        0.04997 (  841)
  hydrogen bonds       : angle       3.29374 ( 2147)
  metal coordination   : bond        0.00787 (    8)
  metal coordination   : angle       4.46612 (    9)
  covalent geometry    : bond        0.00400 (15462)
  covalent geometry    : angle       0.58618 (22156)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 159
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
REVERT: D   46 LYS cc_start: 0.9035 (mmtt) cc_final: 0.8672 (tptt)
REVERT: D   51 ASP cc_start: 0.7973 (t0) cc_final: 0.7698 (t0)
REVERT: D   83 TYR cc_start: 0.8574 (m-80) cc_final: 0.7933 (m-10)
REVERT: D  116 LYS cc_start: 0.9152 (ttpp) cc_final: 0.8782 (tttt)
REVERT: D  120 LYS cc_start: 0.8975 (ttpt) cc_final: 0.8418 (tttp)
REVERT: K   49 LEU cc_start: 0.8662 (tp) cc_final: 0.8454 (tp)
REVERT: L   97 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8286 (tp)
  outliers start: 6
  outliers final: 4
  residues processed: 160
  average time/residue: 0.3168
  time to fit residues: 73.0451
Evaluate side-chains
  159 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 154
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   97 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 114 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 73 optimal weight:    6.9990
   chunk 125 optimal weight:   40.0000
   chunk 6 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 121 optimal weight:    5.9990
   chunk 128 optimal weight:    6.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
** L  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  31 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.142977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.101021 restraints weight = 26978.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.100028 restraints weight = 42074.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.101226 restraints weight = 45229.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3141
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15472  Z= 0.159
  Angle     :  0.574  10.829  22171  Z= 0.325
  Chirality :  0.035   0.209   2514
  Planarity :  0.004   0.034   1792
  Dihedral  : 28.793 179.545   4410
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.05 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.26), residues: 1056
  helix:  2.45 (0.21), residues: 646
  sheet:  0.77 (0.78), residues: 48
  loop : -0.89 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L 141 
 HIS   0.002   0.001   HIS F  75 
 PHE   0.008   0.001   PHE D  65 
 TYR   0.025   0.002   TYR H  83 
 ARG   0.009   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00128 (    2)
  link_TRANS           : angle       0.29893 (    6)
  hydrogen bonds       : bond        0.04569 (  841)
  hydrogen bonds       : angle       3.11888 ( 2147)
  metal coordination   : bond        0.00593 (    8)
  metal coordination   : angle       3.64114 (    9)
  covalent geometry    : bond        0.00353 (15462)
  covalent geometry    : angle       0.56902 (22156)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 156
  time to evaluate  : 1.306 
Fit side-chains
   revert: symmetry clash
REVERT: D   46 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8755 (tptt)
REVERT: D   51 ASP cc_start: 0.7977 (t0) cc_final: 0.7636 (t0)
REVERT: D   83 TYR cc_start: 0.8602 (m-10) cc_final: 0.8039 (m-10)
REVERT: D  116 LYS cc_start: 0.9177 (ttpp) cc_final: 0.8807 (tttt)
REVERT: D  120 LYS cc_start: 0.8964 (ttpt) cc_final: 0.8759 (mtpt)
REVERT: H   51 ASP cc_start: 0.8649 (p0) cc_final: 0.8443 (p0)
  outliers start: 12
  outliers final: 7
  residues processed: 157
  average time/residue: 0.3183
  time to fit residues: 69.9066
Evaluate side-chains
  159 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 152
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain L residue   30 MET
Chi-restraints excluded: chain L residue   89 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9990
   chunk 91 optimal weight:    4.9990
   chunk 118 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 100 optimal weight:   30.0000
   chunk 19 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
K  41 GLN
** L  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.137857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.085757 restraints weight = 41778.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.083367 restraints weight = 32139.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.082651 restraints weight = 31039.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.057  15472  Z= 0.332
  Angle     :  0.697  11.413  22171  Z= 0.390
  Chirality :  0.042   0.208   2514
  Planarity :  0.004   0.035   1792
  Dihedral  : 29.073 178.650   4410
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.66 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1056
  helix:  2.00 (0.20), residues: 644
  sheet:  0.67 (0.81), residues: 48
  loop : -1.18 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L 141 
 HIS   0.005   0.001   HIS D  82 
 PHE   0.012   0.002   PHE L  62 
 TYR   0.024   0.002   TYR H  83 
 ARG   0.008   0.001   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00437 (    2)
  link_TRANS           : angle       0.42745 (    6)
  hydrogen bonds       : bond        0.06404 (  841)
  hydrogen bonds       : angle       3.71613 ( 2147)
  metal coordination   : bond        0.01013 (    8)
  metal coordination   : angle       3.82606 (    9)
  covalent geometry    : bond        0.00788 (15462)
  covalent geometry    : angle       0.69256 (22156)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 1.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.8547 (t0) cc_final: 0.8337 (t0)
REVERT: D   46 LYS cc_start: 0.9115 (mmtt) cc_final: 0.8802 (mptt)
REVERT: D  116 LYS cc_start: 0.9226 (ttpp) cc_final: 0.8855 (tttt)
REVERT: D  120 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8807 (mtpt)
REVERT: L   30 MET cc_start: 0.5533 (OUTLIER) cc_final: 0.5330 (mpp)
REVERT: L  147 MET cc_start: 0.6289 (ttm) cc_final: 0.3159 (pmm)
  outliers start: 18
  outliers final: 11
  residues processed: 156
  average time/residue: 0.3035
  time to fit residues: 66.7994
Evaluate side-chains
  156 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   30 MET
Chi-restraints excluded: chain L residue   37 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0570
   chunk 122 optimal weight:    8.9990
   chunk 10 optimal weight:    0.8980
   chunk 104 optimal weight:    8.9990
   chunk 65 optimal weight:    0.8980
   chunk 117 optimal weight:    5.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
** M  41 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 = 0.3815 r_free = 0.3815 target = 0.142515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.095082 restraints weight = 48362.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.090391 restraints weight = 40858.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.089275 restraints weight = 33677.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2952
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15472  Z= 0.156
  Angle     :  0.587  12.323  22171  Z= 0.330
  Chirality :  0.035   0.203   2514
  Planarity :  0.004   0.034   1792
  Dihedral  : 28.856 179.856   4410
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 15.74 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.26), residues: 1056
  helix:  2.34 (0.21), residues: 648
  sheet:  0.60 (0.78), residues: 48
  loop : -1.04 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L 141 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.015   0.001   PHE L  62 
 TYR   0.023   0.002   TYR H  83 
 ARG   0.006   0.000   ARG H  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00106 (    2)
  link_TRANS           : angle       0.26288 (    6)
  hydrogen bonds       : bond        0.04580 (  841)
  hydrogen bonds       : angle       3.11971 ( 2147)
  metal coordination   : bond        0.00630 (    8)
  metal coordination   : angle       3.80453 (    9)
  covalent geometry    : bond        0.00343 (15462)
  covalent geometry    : angle       0.58207 (22156)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 159
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   46 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8735 (mptt)
REVERT: D   51 ASP cc_start: 0.7771 (t0) cc_final: 0.7514 (t0)
REVERT: D   71 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7389 (tm-30)
REVERT: D   83 TYR cc_start: 0.8759 (m-10) cc_final: 0.8365 (m-10)
REVERT: D  116 LYS cc_start: 0.9142 (ttpp) cc_final: 0.8759 (tttt)
REVERT: D  120 LYS cc_start: 0.8942 (ttpt) cc_final: 0.8546 (tttt)
REVERT: K   49 LEU cc_start: 0.8446 (tp) cc_final: 0.8155 (tp)
REVERT: L  147 MET cc_start: 0.6176 (OUTLIER) cc_final: 0.3003 (pmm)
  outliers start: 10
  outliers final: 6
  residues processed: 161
  average time/residue: 0.3121
  time to fit residues: 70.9543
Evaluate side-chains
  158 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 151
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue  147 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 14 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 112 optimal weight:    0.0170
   chunk 36 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.1020

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
** M  41 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 = 0.3802 r_free = 0.3802 target = 0.141394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.093002 restraints weight = 54662.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.087914 restraints weight = 44569.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.087354 restraints weight = 35991.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2821
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15472  Z= 0.186
  Angle     :  0.603  12.711  22171  Z= 0.337
  Chirality :  0.036   0.217   2514
  Planarity :  0.004   0.032   1792
  Dihedral  : 28.903 179.576   4410
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.07 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.26), residues: 1056
  helix:  2.32 (0.20), residues: 650
  sheet:  0.74 (0.77), residues: 48
  loop : -1.05 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP K  61 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.014   0.001   PHE L  62 
 TYR   0.026   0.002   TYR H  83 
 ARG   0.007   0.000   ARG C  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00139 (    2)
  link_TRANS           : angle       0.50369 (    6)
  hydrogen bonds       : bond        0.04911 (  841)
  hydrogen bonds       : angle       3.22567 ( 2147)
  metal coordination   : bond        0.00644 (    8)
  metal coordination   : angle       3.53648 (    9)
  covalent geometry    : bond        0.00424 (15462)
  covalent geometry    : angle       0.59917 (22156)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 153
  time to evaluate  : 1.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   46 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8865 (mptt)
REVERT: D   51 ASP cc_start: 0.8006 (t0) cc_final: 0.7719 (t0)
REVERT: D   71 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7484 (tm-30)
REVERT: D  116 LYS cc_start: 0.9191 (ttpp) cc_final: 0.8803 (tttt)
REVERT: D  120 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8566 (tttt)
REVERT: F   84 MET cc_start: 0.8437 (mmm) cc_final: 0.7902 (mmm)
REVERT: H   33 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7533 (mtp-110)
REVERT: K   49 LEU cc_start: 0.8365 (tp) cc_final: 0.8026 (tp)
REVERT: L  147 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.3725 (pmm)
  outliers start: 12
  outliers final: 10
  residues processed: 158
  average time/residue: 0.3160
  time to fit residues: 70.3879
Evaluate side-chains
  159 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   30 MET
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue  147 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 125 optimal weight:    0.0870
   chunk 81 optimal weight:    4.9990
   chunk 116 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 113 optimal weight:    8.9990
   chunk 62 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.5960

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

Flipped N/Q/H residues before XYZ refinement:
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
** M  41 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 = 0.3825 r_free = 0.3825 target = 0.143332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.113106 restraints weight = 40624.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.115169 restraints weight = 83597.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.116492 restraints weight = 28143.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3330
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3330
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15472  Z= 0.147
  Angle     :  0.578  12.261  22171  Z= 0.324
  Chirality :  0.035   0.231   2514
  Planarity :  0.004   0.035   1792
  Dihedral  : 28.813 179.666   4410
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 15.96 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.26), residues: 1056
  helix:  2.37 (0.20), residues: 657
  sheet:  0.83 (0.79), residues: 48
  loop : -0.93 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP K  61 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.013   0.001   PHE L  62 
 TYR   0.023   0.001   TYR H  83 
 ARG   0.007   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00089 (    2)
  link_TRANS           : angle       0.57250 (    6)
  hydrogen bonds       : bond        0.04346 (  841)
  hydrogen bonds       : angle       3.04213 ( 2147)
  metal coordination   : bond        0.00544 (    8)
  metal coordination   : angle       3.12650 (    9)
  covalent geometry    : bond        0.00318 (15462)
  covalent geometry    : angle       0.57454 (22156)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 159
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
REVERT: D   46 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8734 (mptt)
REVERT: D   51 ASP cc_start: 0.7839 (t0) cc_final: 0.7552 (t0)
REVERT: D   71 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7688 (tm-30)
REVERT: D  116 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8744 (tttt)
REVERT: D  120 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8459 (tttt)
REVERT: H   33 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7533 (mtp-110)
REVERT: K   49 LEU cc_start: 0.8452 (tp) cc_final: 0.8132 (tp)
REVERT: L  147 MET cc_start: 0.4973 (OUTLIER) cc_final: 0.2763 (pmm)
  outliers start: 11
  outliers final: 8
  residues processed: 163
  average time/residue: 0.2895
  time to fit residues: 67.1169
Evaluate side-chains
  158 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   30 MET
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue   55 HIS
Chi-restraints excluded: chain L residue  147 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 103 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 125 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0570
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
** M  41 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 = 0.3826 r_free = 0.3826 target = 0.143265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.107940 restraints weight = 35236.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.111545 restraints weight = 77488.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.111947 restraints weight = 28581.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15472  Z= 0.150
  Angle     :  0.583  13.881  22171  Z= 0.325
  Chirality :  0.035   0.247   2514
  Planarity :  0.003   0.034   1792
  Dihedral  : 28.818 179.163   4410
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.83 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.26), residues: 1056
  helix:  2.35 (0.20), residues: 663
  sheet:  0.75 (0.79), residues: 48
  loop : -0.97 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP K  61 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.011   0.001   PHE L  62 
 TYR   0.027   0.002   TYR B  88 
 ARG   0.008   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00059 (    2)
  link_TRANS           : angle       0.57130 (    6)
  hydrogen bonds       : bond        0.04369 (  841)
  hydrogen bonds       : angle       3.03598 ( 2147)
  metal coordination   : bond        0.00512 (    8)
  metal coordination   : angle       3.02546 (    9)
  covalent geometry    : bond        0.00327 (15462)
  covalent geometry    : angle       0.58015 (22156)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 153
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   46 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8778 (mptt)
REVERT: D   51 ASP cc_start: 0.7892 (t0) cc_final: 0.7588 (t0)
REVERT: D   71 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7743 (tm-30)
REVERT: D  116 LYS cc_start: 0.9136 (ttpp) cc_final: 0.8775 (tttt)
REVERT: D  120 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8439 (tttt)
REVERT: E   59 GLU cc_start: 0.8730 (pm20) cc_final: 0.8321 (pm20)
REVERT: H   33 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7549 (mtp-110)
REVERT: K   49 LEU cc_start: 0.8442 (tp) cc_final: 0.8133 (tp)
REVERT: L  147 MET cc_start: 0.5203 (OUTLIER) cc_final: 0.2853 (pmm)
  outliers start: 12
  outliers final: 10
  residues processed: 158
  average time/residue: 0.3034
  time to fit residues: 67.6365
Evaluate side-chains
  162 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue  147 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 117 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 114 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   chunk 90 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN
L  77 ASN
** M  41 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 = 0.3824 r_free = 0.3824 target = 0.143102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112606 restraints weight = 40010.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.114513 restraints weight = 86366.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.115952 restraints weight = 29137.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3326
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3326
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15472  Z= 0.159
  Angle     :  0.586  13.301  22171  Z= 0.327
  Chirality :  0.035   0.230   2514
  Planarity :  0.004   0.045   1792
  Dihedral  : 28.823 178.855   4410
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.50 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.26), residues: 1056
  helix:  2.31 (0.20), residues: 663
  sheet:  0.73 (0.80), residues: 48
  loop : -0.97 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP K  61 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.001   PHE L  62 
 TYR   0.042   0.002   TYR D  83 
 ARG   0.010   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00059 (    2)
  link_TRANS           : angle       0.54349 (    6)
  hydrogen bonds       : bond        0.04440 (  841)
  hydrogen bonds       : angle       3.05317 ( 2147)
  metal coordination   : bond        0.00516 (    8)
  metal coordination   : angle       2.96731 (    9)
  covalent geometry    : bond        0.00351 (15462)
  covalent geometry    : angle       0.58351 (22156)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 151
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
REVERT: D   46 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8779 (mptt)
REVERT: D   51 ASP cc_start: 0.7960 (t0) cc_final: 0.7719 (t0)
REVERT: D   71 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7741 (tm-30)
REVERT: D  116 LYS cc_start: 0.9115 (ttpp) cc_final: 0.8759 (tttt)
REVERT: D  120 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8414 (tttt)
REVERT: E   59 GLU cc_start: 0.8720 (pm20) cc_final: 0.8274 (pm20)
REVERT: E   61 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8837 (mm)
REVERT: H   33 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7556 (mtp-110)
REVERT: K   49 LEU cc_start: 0.8455 (tp) cc_final: 0.8151 (tp)
REVERT: L  147 MET cc_start: 0.5016 (OUTLIER) cc_final: 0.2760 (pmm)
  outliers start: 14
  outliers final: 8
  residues processed: 157
  average time/residue: 0.2911
  time to fit residues: 65.0511
Evaluate side-chains
  161 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 151
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue  147 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 109 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.142369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.093566 restraints weight = 42198.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.089879 restraints weight = 36335.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.089507 restraints weight = 28804.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2951
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2951
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15472  Z= 0.175
  Angle     :  0.604  12.974  22171  Z= 0.335
  Chirality :  0.036   0.225   2514
  Planarity :  0.004   0.032   1792
  Dihedral  : 28.861 178.548   4410
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 17.16 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.26), residues: 1056
  helix:  2.24 (0.20), residues: 663
  sheet:  0.69 (0.78), residues: 48
  loop : -1.02 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP K  61 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.001   PHE L  62 
 TYR   0.045   0.002   TYR D  83 
 ARG   0.008   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00080 (    2)
  link_TRANS           : angle       0.50410 (    6)
  hydrogen bonds       : bond        0.04661 (  841)
  hydrogen bonds       : angle       3.14770 ( 2147)
  metal coordination   : bond        0.00540 (    8)
  metal coordination   : angle       3.00136 (    9)
  covalent geometry    : bond        0.00396 (15462)
  covalent geometry    : angle       0.60133 (22156)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 1.330 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8040 (mm-30)
REVERT: D   71 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7601 (tm-30)
REVERT: D  116 LYS cc_start: 0.9136 (ttpp) cc_final: 0.8747 (tttt)
REVERT: D  120 LYS cc_start: 0.8940 (ttpt) cc_final: 0.8483 (tttt)
REVERT: E   59 GLU cc_start: 0.8705 (pm20) cc_final: 0.8383 (pm20)
REVERT: E   61 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9021 (mm)
REVERT: F   88 TYR cc_start: 0.7036 (m-80) cc_final: 0.6166 (m-80)
REVERT: H   33 ARG cc_start: 0.7993 (mtp85) cc_final: 0.7494 (mtp-110)
REVERT: H   83 TYR cc_start: 0.7593 (m-80) cc_final: 0.6766 (m-80)
REVERT: L  147 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.3820 (pmm)
  outliers start: 11
  outliers final: 8
  residues processed: 158
  average time/residue: 0.2983
  time to fit residues: 67.0694
Evaluate side-chains
  159 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   37 ILE
Chi-restraints excluded: chain L residue  147 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 124 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   chunk 128 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 39 optimal weight:    0.4980
   chunk 69 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.143490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.108994 restraints weight = 36331.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.112158 restraints weight = 80946.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.112931 restraints weight = 28880.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3288
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3288 r_free = 0.3288    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3287
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15472  Z= 0.154
  Angle     :  0.606  18.501  22171  Z= 0.332
  Chirality :  0.035   0.241   2514
  Planarity :  0.004   0.034   1792
  Dihedral  : 28.829 178.866   4410
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 17.81 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.26), residues: 1056
  helix:  2.25 (0.20), residues: 663
  sheet:  0.70 (0.78), residues: 48
  loop : -0.98 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP K  61 
 HIS   0.002   0.001   HIS B  75 
 PHE   0.010   0.001   PHE L  62 
 TYR   0.036   0.002   TYR D  83 
 ARG   0.009   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00048 (    2)
  link_TRANS           : angle       0.56125 (    6)
  hydrogen bonds       : bond        0.04383 (  841)
  hydrogen bonds       : angle       3.06896 ( 2147)
  metal coordination   : bond        0.00506 (    8)
  metal coordination   : angle       2.85432 (    9)
  covalent geometry    : bond        0.00337 (15462)
  covalent geometry    : angle       0.60331 (22156)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4999.40 seconds
wall clock time: 88 minutes 48.27 seconds (5328.27 seconds total)