Starting phenix.real_space_refine
on Fri Jun 27 21:50:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ypu_10869/06_2025/6ypu_10869.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ypu_10869/06_2025/6ypu_10869.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ypu_10869/06_2025/6ypu_10869.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ypu_10869/06_2025/6ypu_10869.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ypu_10869/06_2025/6ypu_10869.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ypu_10869/06_2025/6ypu_10869.cif"
  }
  resolution = 2.9
  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=   0.003
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
     P    1040      5.49       5
     Mg     59      5.21       5
     S      28      5.16       5
     C   16728      2.51       5
     N    6241      2.21       5
     O    9226      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 79 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 33322
  Number of models: 1
  Model: ""
    Number of chains: 17
    Chain: "2"
      Number of atoms: 19228
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 894, 19228
          Classifications: {'RNA': 894}
          Modifications used: {'rna2p_pur': 72, 'rna2p_pyr': 41, 'rna3p_pur': 457, 'rna3p_pyr': 324}
          Link IDs: {'rna2p': 113, 'rna3p': 780}
          Chain breaks: 3
    Chain: "4"
      Number of atoms: 3129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3129
          Classifications: {'RNA': 146}
          Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 73, 'rna3p_pyr': 59}
          Link IDs: {'rna2p': 14, 'rna3p': 131}
    Chain: "c"
      Number of atoms: 1079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1079
          Classifications: {'peptide': 219}
          Incomplete info: {'truncation_to_alanine': 179}
          Link IDs: {'PTRANS': 7, 'TRANS': 211}
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 669
          Unresolved non-hydrogen angles: 854
          Unresolved non-hydrogen dihedrals: 550
          Unresolved non-hydrogen chiralities: 60
          Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 9, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 372
    Chain: "e"
      Number of atoms: 1592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1592
          Classifications: {'peptide': 207}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 6, 'TRANS': 200}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "f"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1129
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 4, 'TRANS': 150}
    Chain: "g"
      Number of atoms: 858
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 858
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "i"
      Number of atoms: 984
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 984
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 4, 'TRANS': 125}
    Chain: "l"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 836
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 7, 'TRANS': 106}
    Chain: "m"
      Number of atoms: 945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 945
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 6, 'TRANS': 115}
    Chain: "p"
      Number of atoms: 704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 704
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "q"
      Number of atoms: 632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 632
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 3, 'TRANS': 76}
    Chain: "r"
      Number of atoms: 621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 621
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 2, 'TRANS': 76}
    Chain: "s"
      Number of atoms: 434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 434
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 2, 'TRANS': 50}
    Chain: "u"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 663
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
    Chain: "v"
      Number of atoms: 389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 389
          Classifications: {'peptide': 60}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 2, 'TRANS': 57}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 90
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 57
    Chain: "2"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 53
          Unusual residues: {' MG': 53}
          Classifications: {'undetermined': 53}
          Link IDs: {None: 52}
    Chain: "4"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 46
          Unusual residues: {' MG': 6, 'AKN': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 19.88, per 1000 atoms: 0.60
  Number of scatterers: 33322
  At special positions: 0
  Unit cell: (206.51, 159.43, 153.01, 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)
     S      28     16.00
     P    1040     15.00
     Mg     59     11.99
     O    9226      8.00
     N    6241      7.00
     C   16728      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 8.36
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2766

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 14 sheets defined
      40.4% alpha, 20.1% beta
      331 base pairs and 588 stacking pairs defined.
    Time for finding SS restraints: 16.93
  Creating SS restraints...
    Processing helix  chain 'c' and resid 26 through 30
      removed outlier: 3.647A  pdb=" N   ARG c  30 " --> pdb=" O   PRO c  27 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 44 through 64
      Proline residue:  c  50  - end of helix
      removed outlier: 3.752A  pdb=" N   ASN c  53 " --> pdb=" O   VAL c  49 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ASP c  54 " --> pdb=" O   PRO c  50 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   PHE c  58 " --> pdb=" O   ASP c  54 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ALA c  59 " --> pdb=" O   ALA c  55 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ASN c  60 " --> pdb=" O   LEU c  56 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 78 through 88
      removed outlier: 4.392A  pdb=" N   GLU c  84 " --> pdb=" O   ASN c  80 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA c  86 " --> pdb=" O   ILE c  82 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   GLN c  87 " --> pdb=" O   ARG c  83 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 105 through 122
      removed outlier: 4.704A  pdb=" N   GLN c 111 " --> pdb=" O   LYS c 107 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   SER c 112 " --> pdb=" O   THR c 108 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 132 through 149
      removed outlier: 4.222A  pdb=" N   SER c 149 " --> pdb=" O   LYS c 145 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 150 through 154
      removed outlier: 3.504A  pdb=" N   LYS c 154 " --> pdb=" O   GLY c 151 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 171 through 182
      removed outlier: 3.688A  pdb=" N   GLU c 177 " --> pdb=" O   ILE c 173 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 208 through 225
    Processing helix  chain 'e' and resid 9 through 16
      removed outlier: 3.615A  pdb=" N   ARG e  14 " --> pdb=" O   LYS e  10 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLU e  15 " --> pdb=" O   LEU e  11 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 53 through 68
    Processing helix  chain 'e' and resid 70 through 82
    Processing helix  chain 'e' and resid 87 through 98
      removed outlier: 3.576A  pdb=" N   ASN e  91 " --> pdb=" O   ALA e  87 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU e  92 " --> pdb=" O   THR e  88 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LEU e  93 " --> pdb=" O   GLY e  89 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 99 through 107
      removed outlier: 3.509A  pdb=" N   VAL e 103 " --> pdb=" O   ARG e  99 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 112 through 122
      removed outlier: 4.267A  pdb=" N   GLN e 118 " --> pdb=" O   ALA e 114 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 148 through 152
      removed outlier: 4.088A  pdb=" N   LYS e 152 " --> pdb=" O   GLU e 149 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 155 through 165
      removed outlier: 4.367A  pdb=" N   ASN e 159 " --> pdb=" O   LEU e 155 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ALA e 160 " --> pdb=" O   ARG e 156 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLU e 162 " --> pdb=" O   LYS e 158 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA e 165 " --> pdb=" O   ILE e 161 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 199 through 206
      removed outlier: 3.796A  pdb=" N   VAL e 203 " --> pdb=" O   GLU e 199 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU e 204 " --> pdb=" O   SER e 200 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 54 through 67
    Processing helix  chain 'f' and resid 108 through 116
      removed outlier: 3.648A  pdb=" N   ALA f 112 " --> pdb=" O   GLY f 108 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   VAL f 113 " --> pdb=" O   ALA f 109 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 131 through 145
    Processing helix  chain 'f' and resid 148 through 156
      removed outlier: 3.576A  pdb=" N   VAL f 152 " --> pdb=" O   SER f 148 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ALA f 153 " --> pdb=" O   PRO f 149 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 12 through 15
    Processing helix  chain 'g' and resid 18 through 32
      removed outlier: 4.155A  pdb=" N   ARG g  24 " --> pdb=" O   GLY g  20 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ALA g  32 " --> pdb=" O   GLN g  28 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 67 through 80
      removed outlier: 3.587A  pdb=" N   LEU g  71 " --> pdb=" O   GLY g  67 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 6 through 20
    Processing helix  chain 'i' and resid 30 through 43
    Processing helix  chain 'i' and resid 95 through 100
      removed outlier: 4.219A  pdb=" N   GLN i  98 " --> pdb=" O   SER i  95 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 114 through 121
      removed outlier: 3.646A  pdb=" N   ALA i 119 " --> pdb=" O   ARG i 115 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ALA i 120 " --> pdb=" O   ALA i 116 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 52 through 57
      removed outlier: 3.755A  pdb=" N   ARG l  55 " --> pdb=" O   ARG l  52 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 58 through 75
      removed outlier: 4.145A  pdb=" N   ASP l  75 " --> pdb=" O   LYS l  71 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 89 through 91
      No H-bonds generated for 'chain 'l' and resid 89 through 91'
    Processing helix  chain 'l' and resid 92 through 101
      removed outlier: 4.166A  pdb=" N   VAL l  96 " --> pdb=" O   ARG l  92 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 3 through 10
    Processing helix  chain 'm' and resid 21 through 25
      removed outlier: 3.537A  pdb=" N   LEU m  24 " --> pdb=" O   VAL m  21 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LYS m  25 " --> pdb=" O   PRO m  22 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'm' and resid 21 through 25'
    Processing helix  chain 'm' and resid 113 through 117
    Processing helix  chain 'p' and resid 4 through 16
      removed outlier: 3.505A  pdb=" N   ILE p  12 " --> pdb=" O   ARG p   8 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LYS p  14 " --> pdb=" O   GLU p  10 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 24 through 39
    Processing helix  chain 'p' and resid 39 through 44
    Processing helix  chain 'p' and resid 52 through 74
      removed outlier: 3.712A  pdb=" N   LYS p  65 " --> pdb=" O   ASN p  61 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLY p  72 " --> pdb=" O   ASP p  68 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 74 through 86
      removed outlier: 3.698A  pdb=" N   TYR p  78 " --> pdb=" O   ASP p  74 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 53 through 64
    Processing helix  chain 'q' and resid 70 through 78
      removed outlier: 3.557A  pdb=" N   ALA q  76 " --> pdb=" O   ALA q  72 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 25 through 30
      removed outlier: 3.680A  pdb=" N   LEU s  29 " --> pdb=" O   ASP s  25 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LYS s  30 " --> pdb=" O   ILE s  26 " (cutoff:3.500A)
      No H-bonds generated for 'chain 's' and resid 25 through 30'
    Processing helix  chain 's' and resid 31 through 33
      No H-bonds generated for 'chain 's' and resid 31 through 33'
    Processing helix  chain 's' and resid 41 through 46
      removed outlier: 3.635A  pdb=" N   THR s  45 " --> pdb=" O   PRO s  41 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 48 through 66
      removed outlier: 3.583A  pdb=" N   ARG s  53 " --> pdb=" O   ALA s  49 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLN s  54 " --> pdb=" O   ARG s  50 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   TYR s  64 " --> pdb=" O   LYS s  60 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 4 through 42
      removed outlier: 3.671A  pdb=" N   LYS u   8 " --> pdb=" O   SER u   4 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LYS u  16 " --> pdb=" O   ARG u  12 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   SER u  23 " --> pdb=" O   LYS u  19 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU u  24 " --> pdb=" O   HIS u  20 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLY u  41 " --> pdb=" O   SER u  37 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY u  42 " --> pdb=" O   ALA u  38 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 43 through 52
      removed outlier: 3.576A  pdb=" N   LYS u  52 " --> pdb=" O   THR u  48 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 54 through 64
    Processing helix  chain 'u' and resid 68 through 81
    Processing helix  chain 'v' and resid 15 through 23
      removed outlier: 3.844A  pdb=" N   ARG v  21 " --> pdb=" O   ARG v  17 " (cutoff:3.500A)
    Processing helix  chain 'v' and resid 40 through 56
      removed outlier: 3.526A  pdb=" N   ALA v  50 " --> pdb=" O   LYS v  46 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'c' and resid 18 through 21
      removed outlier: 5.141A  pdb=" N   HIS c  41 " --> pdb=" O   GLY c  19 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ILE c  40 " --> pdb=" O   ALA c  36 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ALA c  36 " --> pdb=" O   ILE c  40 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE c  42 " --> pdb=" O   PHE c  34 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'c' and resid 70 through 72
      removed outlier: 3.755A  pdb=" N   ILE c 188 " --> pdb=" O   VAL c 165 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   VAL c 185 " --> pdb=" O   TYR c 200 " (cutoff:3.500A)
      removed outlier: 7.515A  pdb=" N   ILE c 202 " --> pdb=" O   VAL c 185 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   GLY c 187 " --> pdb=" O   ILE c 202 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'e' and resid 126 through 127
    Processing sheet with id=AA4, first strand: chain 'f' and resid 11 through 23
      removed outlier: 6.577A  pdb=" N   LEU f  35 " --> pdb=" O   VAL f  15 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   VAL f  17 " --> pdb=" O   THR f  33 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   THR f  33 " --> pdb=" O   VAL f  17 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   ARG f  19 " --> pdb=" O   SER f  31 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   SER f  31 " --> pdb=" O   ARG f  19 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   ALA f  21 " --> pdb=" O   ILE f  29 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ILE f  29 " --> pdb=" O   ALA f  21 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'f' and resid 84 through 88
      removed outlier: 6.336A  pdb=" N   ILE f 105 " --> pdb=" O   ALA f 124 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   CYS f 126 " --> pdb=" O   ILE f 105 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'g' and resid 35 through 39
      removed outlier: 6.694A  pdb=" N   ASN g  63 " --> pdb=" O   HIS g  37 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   LEU g  39 " --> pdb=" O   LEU g  61 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   LEU g  61 " --> pdb=" O   LEU g  39 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   HIS g  55 " --> pdb=" O   LEU g  47 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'g' and resid 35 through 39
      removed outlier: 6.694A  pdb=" N   ASN g  63 " --> pdb=" O   HIS g  37 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   LEU g  39 " --> pdb=" O   LEU g  61 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   LEU g  61 " --> pdb=" O   LEU g  39 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE g   6 " --> pdb=" O   MET g  62 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   HIS g   3 " --> pdb=" O   ARG g  91 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   ARG g  91 " --> pdb=" O   HIS g   3 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   GLU g   5 " --> pdb=" O   ILE g  89 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ILE g  89 " --> pdb=" O   GLU g   5 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL g   7 " --> pdb=" O   ASN g  87 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ASN g  87 " --> pdb=" O   VAL g   7 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   LEU g   9 " --> pdb=" O   ILE g  85 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'i' and resid 24 through 28
      removed outlier: 3.772A  pdb=" N   ASN i  48 " --> pdb=" O   THR i  63 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'i' and resid 66 through 67
    Processing sheet with id=AB1, first strand: chain 'i' and resid 76 through 78
      removed outlier: 6.787A  pdb=" N   ILE i 104 " --> pdb=" O   ILE i 127 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   PHE i 129 " --> pdb=" O   ILE i 102 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   ILE i 102 " --> pdb=" O   PHE i 129 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'l' and resid 40 through 45
      removed outlier: 6.966A  pdb=" N   ILE l  33 " --> pdb=" O   LEU l  41 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   TRP l  43 " --> pdb=" O   VAL l  31 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   VAL l  31 " --> pdb=" O   TRP l  43 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   THR l  45 " --> pdb=" O   THR l  29 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   THR l  29 " --> pdb=" O   THR l  45 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   GLY l  18 " --> pdb=" O   ASP l  82 " (cutoff:3.500A)
      removed outlier: 8.335A  pdb=" N   LEU l  84 " --> pdb=" O   GLY l  18 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ALA l  20 " --> pdb=" O   LEU l  84 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   LYS l  86 " --> pdb=" O   ALA l  20 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   ILE l  22 " --> pdb=" O   LYS l  86 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   LEU l  81 " --> pdb=" O   ILE l 106 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   SER l 108 " --> pdb=" O   LEU l  81 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'm' and resid 30 through 40
      removed outlier: 6.379A  pdb=" N   ARG m  54 " --> pdb=" O   THR m  35 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   VAL m  37 " --> pdb=" O   VAL m  52 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   VAL m  52 " --> pdb=" O   VAL m  37 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   THR m  39 " --> pdb=" O   ARG m  50 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   ARG m  50 " --> pdb=" O   THR m  39 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   TYR m  95 " --> pdb=" O   SER m  64 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'q' and resid 50 through 52
      removed outlier: 6.085A  pdb=" N   ILE q  19 " --> pdb=" O   ILE q  36 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   PHE q  38 " --> pdb=" O   TYR q  17 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   TYR q  17 " --> pdb=" O   PHE q  38 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'r' and resid 8 through 18
      removed outlier: 16.880A  pdb=" N   THR r   8 " --> pdb=" O   ARG r  29 " (cutoff:3.500A)
      removed outlier: 13.372A  pdb=" N   ARG r  29 " --> pdb=" O   THR r   8 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   THR r  10 " --> pdb=" O   GLU r  27 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   GLU r  27 " --> pdb=" O   THR r  10 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   VAL r  23 " --> pdb=" O   VAL r  14 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   ASP r  16 " --> pdb=" O   SER r  21 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   SER r  21 " --> pdb=" O   ASP r  16 " (cutoff:3.500A)
      removed outlier: 9.170A  pdb=" N   LYS r  72 " --> pdb=" O   LYS r  44 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   HIS r  46 " --> pdb=" O   LYS r  72 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   TRP r  74 " --> pdb=" O   HIS r  46 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ALA r  73 " --> pdb=" O   SER r  65 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   THR r  61 " --> pdb=" O   VAL r  77 " (cutoff:3.500A)
      removed outlier: 5.142A  pdb=" N   VAL r  79 " --> pdb=" O   VAL r  59 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   VAL r  59 " --> pdb=" O   VAL r  79 " (cutoff:3.500A)

    475 hydrogen bonds defined for protein.
    1350 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      832 hydrogen bonds
      1280 hydrogen bond angles
      0 basepair planarities
      331 basepair parallelities
      588 stacking parallelities
  Total time for adding SS restraints: 27.79

  Time building geometry restraints manager: 10.15 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 3407
        1.30 -     1.43: 15692
        1.43 -     1.56: 14854
        1.56 -     1.68: 2075
        1.68 -     1.81: 48
  Bond restraints: 36076
  Sorted by residual:
  bond pdb=" C35 AKN 41607 "
       pdb=" N12 AKN 41607 "
    ideal  model  delta    sigma   weight residual
    1.339  1.471 -0.132 2.00e-02 2.50e+03 4.35e+01
  bond pdb=" C24 AKN 41607 "
       pdb=" C26 AKN 41607 "
    ideal  model  delta    sigma   weight residual
    1.532  1.450  0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" C7  AKN 41607 "
       pdb=" O8  AKN 41607 "
    ideal  model  delta    sigma   weight residual
    1.420  1.496 -0.076 2.00e-02 2.50e+03 1.46e+01
  bond pdb=" C28 AKN 41607 "
       pdb=" O29 AKN 41607 "
    ideal  model  delta    sigma   weight residual
    1.421  1.491 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" C4  AKN 41607 "
       pdb=" C5  AKN 41607 "
    ideal  model  delta    sigma   weight residual
    1.525  1.457  0.068 2.00e-02 2.50e+03 1.15e+01
  ... (remaining 36071 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 50883
        1.93 -     3.86: 2742
        3.86 -     5.79: 278
        5.79 -     7.72: 41
        7.72 -     9.65: 9
  Bond angle restraints: 53953
  Sorted by residual:
  angle pdb=" N   TYR e  53 "
        pdb=" CA  TYR e  53 "
        pdb=" C   TYR e  53 "
      ideal   model   delta    sigma   weight residual
     114.56  106.68    7.88 1.27e+00 6.20e-01 3.85e+01
  angle pdb=" N   VAL r  14 "
        pdb=" CA  VAL r  14 "
        pdb=" C   VAL r  14 "
      ideal   model   delta    sigma   weight residual
     113.71  109.26    4.45 9.50e-01 1.11e+00 2.20e+01
  angle pdb=" O4'   G 2 612 "
        pdb=" C1'   G 2 612 "
        pdb=" N9    G 2 612 "
      ideal   model   delta    sigma   weight residual
     108.20  114.93   -6.73 1.50e+00 4.44e-01 2.01e+01
  angle pdb=" C2'   A 2 360 "
        pdb=" C1'   A 2 360 "
        pdb=" N9    A 2 360 "
      ideal   model   delta    sigma   weight residual
     112.00  118.14   -6.14 1.50e+00 4.44e-01 1.67e+01
  angle pdb=" O3'   G 2 186 "
        pdb=" C3'   G 2 186 "
        pdb=" C2'   G 2 186 "
      ideal   model   delta    sigma   weight residual
     113.70  119.35   -5.65 1.50e+00 4.44e-01 1.42e+01
  ... (remaining 53948 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.76: 20342
       35.76 -    71.53: 2433
       71.53 -   107.29: 252
      107.29 -   143.05: 7
      143.05 -   178.82: 11
  Dihedral angle restraints: 23045
    sinusoidal: 18759
      harmonic: 4286
  Sorted by residual:
  dihedral pdb=" O4'   C 2 131 "
           pdb=" C1'   C 2 131 "
           pdb=" N1    C 2 131 "
           pdb=" C2    C 2 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   18.82 -178.82     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   C 2 172 "
           pdb=" C1'   C 2 172 "
           pdb=" N1    C 2 172 "
           pdb=" C2    C 2 172 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   24.73  175.27     1      1.50e+01 4.44e-03 8.52e+01
  dihedral pdb=" O4'   U 2 463 "
           pdb=" C1'   U 2 463 "
           pdb=" N1    U 2 463 "
           pdb=" C2    U 2 463 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   14.91 -174.91     1      1.50e+01 4.44e-03 8.52e+01
  ... (remaining 23042 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 5698
       0.072 -    0.145: 1095
       0.145 -    0.217: 123
       0.217 -    0.290: 15
       0.290 -    0.362: 4
  Chirality restraints: 6935
  Sorted by residual:
  chirality pdb=" C1'   U 2 361 "
            pdb=" O4'   U 2 361 "
            pdb=" C2'   U 2 361 "
            pdb=" N1    U 2 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.10    0.36 2.00e-01 2.50e+01 3.27e+00
  chirality pdb=" C3'   G 2 186 "
            pdb=" C4'   G 2 186 "
            pdb=" O3'   G 2 186 "
            pdb=" C2'   G 2 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.15   -0.32 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" C1'   G 41527 "
            pdb=" O4'   G 41527 "
            pdb=" C2'   G 41527 "
            pdb=" N9    G 41527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.14    0.32 2.00e-01 2.50e+01 2.49e+00
  ... (remaining 6932 not shown)

  Planarity restraints: 2985
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G 2 612 "    0.066 2.00e-02 2.50e+03   2.81e-02 2.38e+01
        pdb=" N9    G 2 612 "   -0.066 2.00e-02 2.50e+03
        pdb=" C8    G 2 612 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    G 2 612 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    G 2 612 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G 2 612 "    0.010 2.00e-02 2.50e+03
        pdb=" O6    G 2 612 "    0.013 2.00e-02 2.50e+03
        pdb=" N1    G 2 612 "    0.008 2.00e-02 2.50e+03
        pdb=" C2    G 2 612 "   -0.005 2.00e-02 2.50e+03
        pdb=" N2    G 2 612 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    G 2 612 "   -0.015 2.00e-02 2.50e+03
        pdb=" C4    G 2 612 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A 2 360 "   -0.060 2.00e-02 2.50e+03   2.82e-02 2.19e+01
        pdb=" N9    A 2 360 "    0.059 2.00e-02 2.50e+03
        pdb=" C8    A 2 360 "    0.013 2.00e-02 2.50e+03
        pdb=" N7    A 2 360 "   -0.017 2.00e-02 2.50e+03
        pdb=" C5    A 2 360 "    0.019 2.00e-02 2.50e+03
        pdb=" C6    A 2 360 "   -0.020 2.00e-02 2.50e+03
        pdb=" N6    A 2 360 "   -0.015 2.00e-02 2.50e+03
        pdb=" N1    A 2 360 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    A 2 360 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    A 2 360 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    A 2 360 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C 2 331 "    0.055 2.00e-02 2.50e+03   2.97e-02 1.99e+01
        pdb=" N1    C 2 331 "   -0.068 2.00e-02 2.50e+03
        pdb=" C2    C 2 331 "   -0.004 2.00e-02 2.50e+03
        pdb=" O2    C 2 331 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3    C 2 331 "    0.008 2.00e-02 2.50e+03
        pdb=" C4    C 2 331 "    0.006 2.00e-02 2.50e+03
        pdb=" N4    C 2 331 "    0.014 2.00e-02 2.50e+03
        pdb=" C5    C 2 331 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    C 2 331 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2982 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 123
        2.46 -     3.07: 19297
        3.07 -     3.68: 57171
        3.68 -     4.29: 94218
        4.29 -     4.90: 125210
  Nonbonded interactions: 296019
  Sorted by model distance:
  nonbonded pdb=" OP1   G 41502 "
            pdb="MG    MG 41602 "
     model   vdw
     1.849 2.170
  nonbonded pdb=" OP1   A 2 530 "
            pdb="MG    MG 21636 "
     model   vdw
     1.897 2.170
  nonbonded pdb=" O2    C 2 152 "
            pdb=" N2    G 2 161 "
     model   vdw
     1.931 2.496
  nonbonded pdb=" OP2   G 2 285 "
            pdb="MG    MG 21602 "
     model   vdw
     2.051 2.170
  nonbonded pdb=" OP2   A 2 191 "
            pdb="MG    MG 21629 "
     model   vdw
     2.056 2.170
  ... (remaining 296014 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.230
  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:          1.500
  Check model and map are aligned:         0.290
  Set scattering table:                    0.360
  Process input model:                     99.150
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.100
  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:11.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  117.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
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      :  0.012   0.132  36076  Z= 0.590
  Angle     :  0.989   9.647  53953  Z= 0.495
  Chirality :  0.057   0.362   6935
  Planarity :  0.007   0.065   2985
  Dihedral  : 23.552 178.817  20279
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.25 %
    Favored  : 90.54 %
  Rotamer:
    Outliers : 11.02 %
    Allowed  : 20.24 %
    Favored  : 68.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.96 (0.18), residues: 1470
  helix: -2.40 (0.17), residues: 558
  sheet: -1.23 (0.32), residues: 234
  loop : -3.35 (0.18), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP q  60 
 HIS   0.006   0.002   HIS f 120 
 PHE   0.021   0.003   PHE p  43 
 TYR   0.026   0.003   TYR m 117 
 ARG   0.007   0.001   ARG l 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13889 ( 1304)
  hydrogen bonds       : angle       5.08144 ( 2630)
  covalent geometry    : bond        0.01165 (36076)
  covalent geometry    : angle       0.98852 (53953)

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

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

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 110
    poor density    : 199
  time to evaluate  : 2.051 
Fit side-chains
   revert: symmetry clash
REVERT: e   41 GLN cc_start: 0.7417 (tt0) cc_final: 0.7170 (tt0)
REVERT: e   72 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7919 (ttt180)
REVERT: f   14 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8469 (tt)
REVERT: g   92 ARG cc_start: 0.8270 (mmt180) cc_final: 0.7930 (mmt180)
REVERT: l   33 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8331 (mm)
REVERT: p   58 ARG cc_start: 0.8467 (ttm170) cc_final: 0.8212 (ttp-170)
REVERT: p   71 ASN cc_start: 0.8955 (t0) cc_final: 0.8733 (t0)
REVERT: r   29 ARG cc_start: 0.7922 (ttm-80) cc_final: 0.7586 (ttm110)
REVERT: v   54 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7863 (tttt)
  outliers start: 110
  outliers final: 82
  residues processed: 295
  average time/residue: 1.4711
  time to fit residues: 517.8822
Evaluate side-chains
  269 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 184
  time to evaluate  : 1.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain e residue    5 ILE
Chi-restraints excluded: chain e residue   13 ARG
Chi-restraints excluded: chain e residue   17 THR
Chi-restraints excluded: chain e residue   42 HIS
Chi-restraints excluded: chain e residue   72 ARG
Chi-restraints excluded: chain e residue   75 SER
Chi-restraints excluded: chain e residue  103 VAL
Chi-restraints excluded: chain e residue  104 VAL
Chi-restraints excluded: chain e residue  121 SER
Chi-restraints excluded: chain e residue  130 ARG
Chi-restraints excluded: chain e residue  136 SER
Chi-restraints excluded: chain e residue  158 LYS
Chi-restraints excluded: chain e residue  175 VAL
Chi-restraints excluded: chain e residue  192 ASP
Chi-restraints excluded: chain e residue  193 LEU
Chi-restraints excluded: chain e residue  197 ILE
Chi-restraints excluded: chain e residue  200 SER
Chi-restraints excluded: chain e residue  207 SER
Chi-restraints excluded: chain f residue   14 LEU
Chi-restraints excluded: chain f residue   31 SER
Chi-restraints excluded: chain f residue   38 VAL
Chi-restraints excluded: chain f residue   72 THR
Chi-restraints excluded: chain f residue   73 VAL
Chi-restraints excluded: chain f residue   74 ASP
Chi-restraints excluded: chain f residue   79 THR
Chi-restraints excluded: chain f residue   91 SER
Chi-restraints excluded: chain f residue  102 THR
Chi-restraints excluded: chain f residue  129 SER
Chi-restraints excluded: chain f residue  130 THR
Chi-restraints excluded: chain f residue  159 SER
Chi-restraints excluded: chain f residue  162 GLU
Chi-restraints excluded: chain g residue    7 VAL
Chi-restraints excluded: chain g residue   10 VAL
Chi-restraints excluded: chain g residue   65 GLU
Chi-restraints excluded: chain g residue   66 CYS
Chi-restraints excluded: chain g residue   70 THR
Chi-restraints excluded: chain g residue   96 ILE
Chi-restraints excluded: chain i residue   24 THR
Chi-restraints excluded: chain i residue   56 THR
Chi-restraints excluded: chain i residue   59 THR
Chi-restraints excluded: chain i residue   80 SER
Chi-restraints excluded: chain i residue   95 SER
Chi-restraints excluded: chain i residue  107 THR
Chi-restraints excluded: chain i residue  108 SER
Chi-restraints excluded: chain i residue  131 SER
Chi-restraints excluded: chain l residue   17 GLU
Chi-restraints excluded: chain l residue   19 VAL
Chi-restraints excluded: chain l residue   32 THR
Chi-restraints excluded: chain l residue   33 ILE
Chi-restraints excluded: chain l residue   46 SER
Chi-restraints excluded: chain l residue   58 THR
Chi-restraints excluded: chain l residue   82 ASP
Chi-restraints excluded: chain l residue   84 LEU
Chi-restraints excluded: chain l residue  102 VAL
Chi-restraints excluded: chain l residue  106 ILE
Chi-restraints excluded: chain l residue  108 SER
Chi-restraints excluded: chain l residue  111 ASP
Chi-restraints excluded: chain l residue  113 THR
Chi-restraints excluded: chain l residue  118 ASN
Chi-restraints excluded: chain l residue  128 VAL
Chi-restraints excluded: chain m residue   12 ARG
Chi-restraints excluded: chain m residue   13 THR
Chi-restraints excluded: chain m residue   21 VAL
Chi-restraints excluded: chain m residue   40 THR
Chi-restraints excluded: chain m residue   41 THR
Chi-restraints excluded: chain m residue   52 VAL
Chi-restraints excluded: chain m residue   59 SER
Chi-restraints excluded: chain m residue   65 SER
Chi-restraints excluded: chain m residue   67 ILE
Chi-restraints excluded: chain m residue   82 ILE
Chi-restraints excluded: chain p residue   20 ASN
Chi-restraints excluded: chain p residue   22 THR
Chi-restraints excluded: chain p residue   33 THR
Chi-restraints excluded: chain p residue   52 SER
Chi-restraints excluded: chain p residue   82 ILE
Chi-restraints excluded: chain q residue   61 VAL
Chi-restraints excluded: chain q residue   73 SER
Chi-restraints excluded: chain r residue   30 VAL
Chi-restraints excluded: chain r residue   43 THR
Chi-restraints excluded: chain s residue   40 VAL
Chi-restraints excluded: chain s residue   47 THR
Chi-restraints excluded: chain s residue   71 THR
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain u residue   77 SER
Chi-restraints excluded: chain v residue   55 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 208 optimal weight:    0.6980
   chunk 187 optimal weight:    0.8980
   chunk 103 optimal weight:    7.9990
   chunk 63 optimal weight:    0.5980
   chunk 126 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9990
   chunk 193 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   chunk 117 optimal weight:    7.9990
   chunk 144 optimal weight:    3.9990
   chunk 224 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
e  56 GLN
e 122 HIS
e 177 HIS
f  88 HIS
f 120 HIS
f 137 ASN
g   3 HIS
g  58 HIS
g  63 ASN
i  16 ASN
i  42 GLN
l  49 GLN
l  63 GLN
m  96 HIS
m 111 ASN
p  42 HIS
p  62 GLN
q  26 ASN
q  44 GLN
r  32 HIS
s  52 GLN
u  13 GLN
u  20 HIS
u  68 HIS
u  70 ASN
u  75 HIS

Total number of N/Q/H flips: 26

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.141150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.125485 restraints weight = 37623.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 0.22
r_work: 0.3103 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  36076  Z= 0.137
  Angle     :  0.561   7.989  53953  Z= 0.295
  Chirality :  0.037   0.246   6935
  Planarity :  0.004   0.053   2985
  Dihedral  : 23.093 177.914  18049
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.63 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 24.25 %
    Favored  : 69.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.20), residues: 1470
  helix: -0.63 (0.21), residues: 567
  sheet: -0.69 (0.32), residues: 239
  loop : -2.78 (0.20), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP q  60 
 HIS   0.005   0.001   HIS r  32 
 PHE   0.012   0.001   PHE f 140 
 TYR   0.014   0.001   TYR m 117 
 ARG   0.003   0.000   ARG p   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05847 ( 1304)
  hydrogen bonds       : angle       3.38321 ( 2630)
  covalent geometry    : bond        0.00255 (36076)
  covalent geometry    : angle       0.56095 (53953)

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

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

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 197
  time to evaluate  : 2.052 
Fit side-chains
REVERT: e   41 GLN cc_start: 0.7436 (tt0) cc_final: 0.7204 (tt0)
REVERT: l   17 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6026 (mp0)
REVERT: p   61 ASN cc_start: 0.8210 (p0) cc_final: 0.7414 (m110)
REVERT: p   64 ARG cc_start: 0.8929 (tpp-160) cc_final: 0.8583 (tpm170)
REVERT: r   29 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7303 (ttm110)
REVERT: s   31 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8031 (mt0)
REVERT: v   40 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7906 (mtpt)
REVERT: v   54 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7824 (tttm)
REVERT: v   56 TYR cc_start: 0.8591 (t80) cc_final: 0.8375 (t80)
  outliers start: 64
  outliers final: 32
  residues processed: 244
  average time/residue: 1.5045
  time to fit residues: 438.2713
Evaluate side-chains
  206 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 171
  time to evaluate  : 2.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain e residue   17 THR
Chi-restraints excluded: chain e residue   42 HIS
Chi-restraints excluded: chain e residue  104 VAL
Chi-restraints excluded: chain e residue  130 ARG
Chi-restraints excluded: chain e residue  175 VAL
Chi-restraints excluded: chain e residue  178 SER
Chi-restraints excluded: chain f residue   73 VAL
Chi-restraints excluded: chain f residue   74 ASP
Chi-restraints excluded: chain f residue  102 THR
Chi-restraints excluded: chain f residue  130 THR
Chi-restraints excluded: chain g residue   10 VAL
Chi-restraints excluded: chain g residue   26 ILE
Chi-restraints excluded: chain g residue   69 SER
Chi-restraints excluded: chain g residue   70 THR
Chi-restraints excluded: chain g residue   94 HIS
Chi-restraints excluded: chain l residue   17 GLU
Chi-restraints excluded: chain l residue   19 VAL
Chi-restraints excluded: chain l residue  102 VAL
Chi-restraints excluded: chain l residue  113 THR
Chi-restraints excluded: chain l residue  128 VAL
Chi-restraints excluded: chain m residue   13 THR
Chi-restraints excluded: chain m residue   21 VAL
Chi-restraints excluded: chain m residue   40 THR
Chi-restraints excluded: chain m residue   41 THR
Chi-restraints excluded: chain m residue   82 ILE
Chi-restraints excluded: chain p residue   22 THR
Chi-restraints excluded: chain p residue   52 SER
Chi-restraints excluded: chain q residue   73 SER
Chi-restraints excluded: chain r residue   15 SER
Chi-restraints excluded: chain r residue   30 VAL
Chi-restraints excluded: chain s residue   31 GLN
Chi-restraints excluded: chain s residue   47 THR
Chi-restraints excluded: chain s residue   71 THR
Chi-restraints excluded: chain u residue   37 SER
Chi-restraints excluded: chain v residue   40 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 111 optimal weight:   20.0000
   chunk 166 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 204 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 199 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 135 optimal weight:    5.9990
   chunk 216 optimal weight:    2.9990
   chunk 138 optimal weight:    0.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
g  28 GLN
i  42 GLN
i  53 GLN
l  27 ASN
p  62 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.137359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.121616 restraints weight = 37497.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 0.25
r_work: 0.3048 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  36076  Z= 0.240
  Angle     :  0.630   8.404  53953  Z= 0.324
  Chirality :  0.040   0.270   6935
  Planarity :  0.005   0.054   2985
  Dihedral  : 23.057 179.828  17956
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.05 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  7.82 %
    Allowed  : 24.85 %
    Favored  : 67.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.21), residues: 1470
  helix: -0.10 (0.22), residues: 569
  sheet: -0.47 (0.32), residues: 239
  loop : -2.61 (0.21), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP q  60 
 HIS   0.004   0.001   HIS p  48 
 PHE   0.014   0.001   PHE f 140 
 TYR   0.019   0.002   TYR m 117 
 ARG   0.004   0.000   ARG g  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06594 ( 1304)
  hydrogen bonds       : angle       3.25557 ( 2630)
  covalent geometry    : bond        0.00471 (36076)
  covalent geometry    : angle       0.62994 (53953)

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

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

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 180
  time to evaluate  : 2.312 
Fit side-chains
REVERT: e  204 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7068 (mt-10)
REVERT: f  100 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7321 (tt0)
REVERT: g   14 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6617 (mt0)
REVERT: l  111 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7841 (t0)
REVERT: p   54 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7257 (mtt180)
REVERT: r   29 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.7258 (ttm110)
REVERT: v   54 LYS cc_start: 0.8241 (ttmm) cc_final: 0.7911 (tttm)
REVERT: v   56 TYR cc_start: 0.8672 (t80) cc_final: 0.8448 (t80)
  outliers start: 78
  outliers final: 46
  residues processed: 235
  average time/residue: 1.4947
  time to fit residues: 419.7660
Evaluate side-chains
  222 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 171
  time to evaluate  : 1.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain e residue   17 THR
Chi-restraints excluded: chain e residue   42 HIS
Chi-restraints excluded: chain e residue  104 VAL
Chi-restraints excluded: chain e residue  130 ARG
Chi-restraints excluded: chain e residue  175 VAL
Chi-restraints excluded: chain e residue  178 SER
Chi-restraints excluded: chain e residue  204 GLU
Chi-restraints excluded: chain e residue  205 LEU
Chi-restraints excluded: chain f residue   73 VAL
Chi-restraints excluded: chain f residue   74 ASP
Chi-restraints excluded: chain f residue  100 GLU
Chi-restraints excluded: chain f residue  102 THR
Chi-restraints excluded: chain f residue  130 THR
Chi-restraints excluded: chain g residue    7 VAL
Chi-restraints excluded: chain g residue   10 VAL
Chi-restraints excluded: chain g residue   14 GLN
Chi-restraints excluded: chain g residue   18 VAL
Chi-restraints excluded: chain g residue   26 ILE
Chi-restraints excluded: chain g residue   66 CYS
Chi-restraints excluded: chain g residue   69 SER
Chi-restraints excluded: chain g residue   70 THR
Chi-restraints excluded: chain g residue   94 HIS
Chi-restraints excluded: chain g residue   96 ILE
Chi-restraints excluded: chain l residue   19 VAL
Chi-restraints excluded: chain l residue  102 VAL
Chi-restraints excluded: chain l residue  106 ILE
Chi-restraints excluded: chain l residue  111 ASP
Chi-restraints excluded: chain l residue  118 ASN
Chi-restraints excluded: chain l residue  128 VAL
Chi-restraints excluded: chain m residue   13 THR
Chi-restraints excluded: chain m residue   16 VAL
Chi-restraints excluded: chain m residue   21 VAL
Chi-restraints excluded: chain m residue   40 THR
Chi-restraints excluded: chain m residue   41 THR
Chi-restraints excluded: chain m residue   47 SER
Chi-restraints excluded: chain m residue   82 ILE
Chi-restraints excluded: chain p residue   22 THR
Chi-restraints excluded: chain p residue   52 SER
Chi-restraints excluded: chain p residue   54 ARG
Chi-restraints excluded: chain q residue   20 VAL
Chi-restraints excluded: chain q residue   73 SER
Chi-restraints excluded: chain r residue   10 THR
Chi-restraints excluded: chain r residue   30 VAL
Chi-restraints excluded: chain r residue   43 THR
Chi-restraints excluded: chain s residue   47 THR
Chi-restraints excluded: chain s residue   68 ILE
Chi-restraints excluded: chain s residue   71 THR
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain u residue   37 SER
Chi-restraints excluded: chain u residue   74 ARG
Chi-restraints excluded: chain v residue   42 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 193 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 235 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 215 optimal weight:    4.9990
   chunk 157 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 140 optimal weight:   10.0000
   chunk 192 optimal weight:    0.0770
   chunk 218 optimal weight:    0.7980
   overall best weight:    1.5342

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

Flipped N/Q/H residues before XYZ refinement:
e  41 GLN
i  42 GLN
p  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.138488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.123634 restraints weight = 37498.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 0.49
r_work: 0.2951 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  36076  Z= 0.198
  Angle     :  0.589   8.101  53953  Z= 0.306
  Chirality :  0.038   0.259   6935
  Planarity :  0.004   0.053   2985
  Dihedral  : 23.000 179.435  17952
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 25.75 %
    Favored  : 66.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.21), residues: 1470
  helix:  0.27 (0.23), residues: 573
  sheet: -0.32 (0.33), residues: 239
  loop : -2.49 (0.21), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP q  60 
 HIS   0.003   0.001   HIS m  96 
 PHE   0.014   0.001   PHE f 140 
 TYR   0.016   0.002   TYR m 117 
 ARG   0.007   0.000   ARG e 106 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06156 ( 1304)
  hydrogen bonds       : angle       3.12763 ( 2630)
  covalent geometry    : bond        0.00386 (36076)
  covalent geometry    : angle       0.58931 (53953)

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

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

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 169
  time to evaluate  : 2.110 
Fit side-chains
REVERT: e   33 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6216 (tptt)
REVERT: e  193 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5481 (mt)
REVERT: e  204 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7177 (mt-10)
REVERT: g   14 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6739 (mt0)
REVERT: i  125 GLU cc_start: 0.8593 (tt0) cc_final: 0.8270 (tt0)
REVERT: l   17 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.6042 (mp0)
REVERT: l  111 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7958 (t0)
REVERT: q    1 MET cc_start: 0.8430 (ttm) cc_final: 0.8223 (ttm)
REVERT: r   29 ARG cc_start: 0.7587 (ttm-80) cc_final: 0.7247 (ttm110)
REVERT: u   34 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7640 (mtt90)
REVERT: v   54 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7808 (tttm)
  outliers start: 74
  outliers final: 41
  residues processed: 225
  average time/residue: 1.4534
  time to fit residues: 392.0787
Evaluate side-chains
  212 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 164
  time to evaluate  : 2.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain e residue   17 THR
Chi-restraints excluded: chain e residue   33 LYS
Chi-restraints excluded: chain e residue   42 HIS
Chi-restraints excluded: chain e residue  166 GLN
Chi-restraints excluded: chain e residue  175 VAL
Chi-restraints excluded: chain e residue  178 SER
Chi-restraints excluded: chain e residue  192 ASP
Chi-restraints excluded: chain e residue  193 LEU
Chi-restraints excluded: chain e residue  204 GLU
Chi-restraints excluded: chain e residue  205 LEU
Chi-restraints excluded: chain f residue   73 VAL
Chi-restraints excluded: chain f residue  102 THR
Chi-restraints excluded: chain f residue  130 THR
Chi-restraints excluded: chain g residue    7 VAL
Chi-restraints excluded: chain g residue   10 VAL
Chi-restraints excluded: chain g residue   14 GLN
Chi-restraints excluded: chain g residue   18 VAL
Chi-restraints excluded: chain g residue   26 ILE
Chi-restraints excluded: chain g residue   66 CYS
Chi-restraints excluded: chain g residue   70 THR
Chi-restraints excluded: chain g residue   94 HIS
Chi-restraints excluded: chain g residue   96 ILE
Chi-restraints excluded: chain l residue   17 GLU
Chi-restraints excluded: chain l residue   19 VAL
Chi-restraints excluded: chain l residue  106 ILE
Chi-restraints excluded: chain l residue  111 ASP
Chi-restraints excluded: chain l residue  118 ASN
Chi-restraints excluded: chain l residue  128 VAL
Chi-restraints excluded: chain m residue   12 ARG
Chi-restraints excluded: chain m residue   13 THR
Chi-restraints excluded: chain m residue   16 VAL
Chi-restraints excluded: chain m residue   21 VAL
Chi-restraints excluded: chain m residue   40 THR
Chi-restraints excluded: chain m residue   47 SER
Chi-restraints excluded: chain m residue   52 VAL
Chi-restraints excluded: chain m residue   67 ILE
Chi-restraints excluded: chain m residue   82 ILE
Chi-restraints excluded: chain p residue   22 THR
Chi-restraints excluded: chain p residue   52 SER
Chi-restraints excluded: chain q residue   73 SER
Chi-restraints excluded: chain r residue   30 VAL
Chi-restraints excluded: chain r residue   43 THR
Chi-restraints excluded: chain s residue   47 THR
Chi-restraints excluded: chain s residue   71 THR
Chi-restraints excluded: chain u residue   34 ARG
Chi-restraints excluded: chain u residue   37 SER
Chi-restraints excluded: chain u residue   74 ARG
Chi-restraints excluded: chain v residue   42 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 190 optimal weight:    0.9980
   chunk 92 optimal weight:    8.9990
   chunk 169 optimal weight:    0.7980
   chunk 198 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 189 optimal weight:    5.9990
   chunk 223 optimal weight:    5.9990
   chunk 43 optimal weight:    9.9990
   chunk 100 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 160 optimal weight:    0.7980
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
i  42 GLN
l  27 ASN
l  63 GLN
p  62 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.136871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.121353 restraints weight = 37282.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 0.27
r_work: 0.3037 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  36076  Z= 0.263
  Angle     :  0.647   8.168  53953  Z= 0.331
  Chirality :  0.041   0.274   6935
  Planarity :  0.005   0.054   2985
  Dihedral  : 23.007 179.939  17943
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.39 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  6.91 %
    Allowed  : 26.55 %
    Favored  : 66.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.21), residues: 1470
  helix:  0.33 (0.23), residues: 574
  sheet: -0.28 (0.34), residues: 228
  loop : -2.38 (0.21), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP q  60 
 HIS   0.004   0.001   HIS p  48 
 PHE   0.015   0.002   PHE f 140 
 TYR   0.019   0.002   TYR m 117 
 ARG   0.006   0.000   ARG g  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06794 ( 1304)
  hydrogen bonds       : angle       3.16444 ( 2630)
  covalent geometry    : bond        0.00516 (36076)
  covalent geometry    : angle       0.64687 (53953)

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

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

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 177
  time to evaluate  : 2.072 
Fit side-chains
REVERT: e   33 LYS cc_start: 0.6740 (OUTLIER) cc_final: 0.6242 (tptt)
REVERT: e  158 LYS cc_start: 0.4990 (OUTLIER) cc_final: 0.4712 (tmtt)
REVERT: e  193 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5294 (mt)
REVERT: e  204 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7222 (mt-10)
REVERT: g   14 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6643 (mt0)
REVERT: l   17 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6102 (mp0)
REVERT: l  111 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7899 (t0)
REVERT: p   54 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7281 (mtt180)
REVERT: q   55 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6875 (p0)
REVERT: r   29 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.7173 (ttm110)
REVERT: r   44 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7899 (mtpp)
REVERT: u   34 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7633 (mtt90)
REVERT: v   54 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7857 (tttm)
  outliers start: 69
  outliers final: 47
  residues processed: 230
  average time/residue: 1.4865
  time to fit residues: 406.9019
Evaluate side-chains
  226 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 168
  time to evaluate  : 1.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain e residue   17 THR
Chi-restraints excluded: chain e residue   33 LYS
Chi-restraints excluded: chain e residue   42 HIS
Chi-restraints excluded: chain e residue  103 VAL
Chi-restraints excluded: chain e residue  158 LYS
Chi-restraints excluded: chain e residue  166 GLN
Chi-restraints excluded: chain e residue  178 SER
Chi-restraints excluded: chain e residue  192 ASP
Chi-restraints excluded: chain e residue  193 LEU
Chi-restraints excluded: chain e residue  204 GLU
Chi-restraints excluded: chain f residue   25 LYS
Chi-restraints excluded: chain f residue   73 VAL
Chi-restraints excluded: chain f residue   74 ASP
Chi-restraints excluded: chain f residue  102 THR
Chi-restraints excluded: chain f residue  130 THR
Chi-restraints excluded: chain g residue    7 VAL
Chi-restraints excluded: chain g residue   10 VAL
Chi-restraints excluded: chain g residue   14 GLN
Chi-restraints excluded: chain g residue   18 VAL
Chi-restraints excluded: chain g residue   26 ILE
Chi-restraints excluded: chain g residue   56 LYS
Chi-restraints excluded: chain g residue   66 CYS
Chi-restraints excluded: chain g residue   69 SER
Chi-restraints excluded: chain g residue   70 THR
Chi-restraints excluded: chain g residue   94 HIS
Chi-restraints excluded: chain g residue   96 ILE
Chi-restraints excluded: chain l residue   17 GLU
Chi-restraints excluded: chain l residue   19 VAL
Chi-restraints excluded: chain l residue  106 ILE
Chi-restraints excluded: chain l residue  108 SER
Chi-restraints excluded: chain l residue  111 ASP
Chi-restraints excluded: chain l residue  118 ASN
Chi-restraints excluded: chain l residue  128 VAL
Chi-restraints excluded: chain m residue   12 ARG
Chi-restraints excluded: chain m residue   13 THR
Chi-restraints excluded: chain m residue   16 VAL
Chi-restraints excluded: chain m residue   21 VAL
Chi-restraints excluded: chain m residue   40 THR
Chi-restraints excluded: chain m residue   41 THR
Chi-restraints excluded: chain m residue   47 SER
Chi-restraints excluded: chain m residue   52 VAL
Chi-restraints excluded: chain m residue   67 ILE
Chi-restraints excluded: chain m residue   82 ILE
Chi-restraints excluded: chain p residue   22 THR
Chi-restraints excluded: chain p residue   54 ARG
Chi-restraints excluded: chain q residue   55 ASP
Chi-restraints excluded: chain q residue   73 SER
Chi-restraints excluded: chain r residue   10 THR
Chi-restraints excluded: chain r residue   30 VAL
Chi-restraints excluded: chain r residue   43 THR
Chi-restraints excluded: chain r residue   44 LYS
Chi-restraints excluded: chain s residue   47 THR
Chi-restraints excluded: chain s residue   71 THR
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain u residue   34 ARG
Chi-restraints excluded: chain u residue   37 SER
Chi-restraints excluded: chain u residue   74 ARG
Chi-restraints excluded: chain v residue   42 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 113 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 179 optimal weight:    0.7980
   chunk 126 optimal weight:    0.5980
   chunk 17 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9990
   chunk 217 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 151 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
e  41 GLN
i  42 GLN
i  53 GLN
p  62 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.138357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.122153 restraints weight = 37563.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 0.23
r_work: 0.3047 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  36076  Z= 0.171
  Angle     :  0.591   8.114  53953  Z= 0.307
  Chirality :  0.037   0.264   6935
  Planarity :  0.004   0.054   2985
  Dihedral  : 23.008 179.542  17941
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  6.81 %
    Allowed  : 27.15 %
    Favored  : 66.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.22), residues: 1470
  helix:  0.49 (0.23), residues: 573
  sheet: -0.22 (0.33), residues: 237
  loop : -2.30 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP q  60 
 HIS   0.004   0.001   HIS p  48 
 PHE   0.014   0.001   PHE f 140 
 TYR   0.016   0.001   TYR m 117 
 ARG   0.008   0.000   ARG g  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06193 ( 1304)
  hydrogen bonds       : angle       3.09881 ( 2630)
  covalent geometry    : bond        0.00334 (36076)
  covalent geometry    : angle       0.59054 (53953)

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

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

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 173
  time to evaluate  : 1.831 
Fit side-chains
REVERT: e   33 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6266 (tptt)
REVERT: e  158 LYS cc_start: 0.4977 (OUTLIER) cc_final: 0.4706 (tmtt)
REVERT: e  204 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7209 (mt-10)
REVERT: g   14 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.6655 (mt0)
REVERT: l   17 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6168 (mp0)
REVERT: l  111 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7893 (t0)
REVERT: p   54 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7290 (mtt180)
REVERT: q    1 MET cc_start: 0.8384 (ttm) cc_final: 0.8161 (ttm)
REVERT: r   29 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7157 (ttm110)
REVERT: u   34 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7627 (mtt90)
REVERT: v   54 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7846 (tttm)
  outliers start: 68
  outliers final: 49
  residues processed: 229
  average time/residue: 1.5573
  time to fit residues: 423.5535
Evaluate side-chains
  227 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 170
  time to evaluate  : 2.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain e residue   17 THR
Chi-restraints excluded: chain e residue   33 LYS
Chi-restraints excluded: chain e residue   42 HIS
Chi-restraints excluded: chain e residue  104 VAL
Chi-restraints excluded: chain e residue  158 LYS
Chi-restraints excluded: chain e residue  166 GLN
Chi-restraints excluded: chain e residue  175 VAL
Chi-restraints excluded: chain e residue  178 SER
Chi-restraints excluded: chain e residue  192 ASP
Chi-restraints excluded: chain e residue  204 GLU
Chi-restraints excluded: chain e residue  205 LEU
Chi-restraints excluded: chain f residue   73 VAL
Chi-restraints excluded: chain f residue   74 ASP
Chi-restraints excluded: chain f residue  102 THR
Chi-restraints excluded: chain f residue  130 THR
Chi-restraints excluded: chain g residue    7 VAL
Chi-restraints excluded: chain g residue   10 VAL
Chi-restraints excluded: chain g residue   14 GLN
Chi-restraints excluded: chain g residue   18 VAL
Chi-restraints excluded: chain g residue   26 ILE
Chi-restraints excluded: chain g residue   56 LYS
Chi-restraints excluded: chain g residue   66 CYS
Chi-restraints excluded: chain g residue   69 SER
Chi-restraints excluded: chain g residue   70 THR
Chi-restraints excluded: chain g residue   94 HIS
Chi-restraints excluded: chain g residue   96 ILE
Chi-restraints excluded: chain l residue   17 GLU
Chi-restraints excluded: chain l residue   19 VAL
Chi-restraints excluded: chain l residue  106 ILE
Chi-restraints excluded: chain l residue  108 SER
Chi-restraints excluded: chain l residue  111 ASP
Chi-restraints excluded: chain l residue  113 THR
Chi-restraints excluded: chain l residue  118 ASN
Chi-restraints excluded: chain l residue  128 VAL
Chi-restraints excluded: chain m residue   12 ARG
Chi-restraints excluded: chain m residue   13 THR
Chi-restraints excluded: chain m residue   16 VAL
Chi-restraints excluded: chain m residue   21 VAL
Chi-restraints excluded: chain m residue   40 THR
Chi-restraints excluded: chain m residue   41 THR
Chi-restraints excluded: chain m residue   47 SER
Chi-restraints excluded: chain m residue   52 VAL
Chi-restraints excluded: chain m residue   67 ILE
Chi-restraints excluded: chain m residue   82 ILE
Chi-restraints excluded: chain p residue   22 THR
Chi-restraints excluded: chain p residue   54 ARG
Chi-restraints excluded: chain q residue   73 SER
Chi-restraints excluded: chain r residue   10 THR
Chi-restraints excluded: chain r residue   30 VAL
Chi-restraints excluded: chain r residue   43 THR
Chi-restraints excluded: chain s residue   47 THR
Chi-restraints excluded: chain s residue   71 THR
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain u residue   34 ARG
Chi-restraints excluded: chain u residue   37 SER
Chi-restraints excluded: chain u residue   74 ARG
Chi-restraints excluded: chain v residue   42 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 148 optimal weight:    2.9990
   chunk 211 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 121 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 207 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 108 optimal weight:    0.8980
   chunk 195 optimal weight:    0.6980
   chunk 94 optimal weight:   10.0000
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
e  41 GLN
i  42 GLN
l  63 GLN
p  62 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.137473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.122041 restraints weight = 37550.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 0.25
r_work: 0.3052 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  36076  Z= 0.241
  Angle     :  0.625  10.466  53953  Z= 0.321
  Chirality :  0.040   0.267   6935
  Planarity :  0.005   0.054   2985
  Dihedral  : 22.972 179.820  17941
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.99 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  7.11 %
    Allowed  : 27.35 %
    Favored  : 65.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.22), residues: 1470
  helix:  0.48 (0.23), residues: 578
  sheet: -0.30 (0.33), residues: 237
  loop : -2.24 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP q  60 
 HIS   0.004   0.001   HIS m  96 
 PHE   0.014   0.002   PHE f 140 
 TYR   0.017   0.002   TYR m 117 
 ARG   0.007   0.000   ARG g  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06538 ( 1304)
  hydrogen bonds       : angle       3.09943 ( 2630)
  covalent geometry    : bond        0.00472 (36076)
  covalent geometry    : angle       0.62547 (53953)

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

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

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 172
  time to evaluate  : 1.871 
Fit side-chains
REVERT: e   33 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6224 (tptt)
REVERT: e  158 LYS cc_start: 0.4803 (OUTLIER) cc_final: 0.4535 (tmtt)
REVERT: e  193 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5176 (mt)
REVERT: e  204 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7184 (mt-10)
REVERT: g   14 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6624 (mt0)
REVERT: i  125 GLU cc_start: 0.8489 (tt0) cc_final: 0.8227 (tt0)
REVERT: l   17 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6155 (mp0)
REVERT: p   54 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7289 (mtt180)
REVERT: q    1 MET cc_start: 0.8355 (ttm) cc_final: 0.8136 (ttm)
REVERT: r   29 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.7146 (ttm110)
REVERT: u   34 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7615 (mtt90)
REVERT: v   54 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7886 (tttm)
  outliers start: 71
  outliers final: 48
  residues processed: 228
  average time/residue: 1.5397
  time to fit residues: 417.3197
Evaluate side-chains
  226 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 170
  time to evaluate  : 1.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain e residue   17 THR
Chi-restraints excluded: chain e residue   33 LYS
Chi-restraints excluded: chain e residue   42 HIS
Chi-restraints excluded: chain e residue  103 VAL
Chi-restraints excluded: chain e residue  104 VAL
Chi-restraints excluded: chain e residue  158 LYS
Chi-restraints excluded: chain e residue  166 GLN
Chi-restraints excluded: chain e residue  175 VAL
Chi-restraints excluded: chain e residue  178 SER
Chi-restraints excluded: chain e residue  192 ASP
Chi-restraints excluded: chain e residue  193 LEU
Chi-restraints excluded: chain e residue  204 GLU
Chi-restraints excluded: chain e residue  205 LEU
Chi-restraints excluded: chain f residue   73 VAL
Chi-restraints excluded: chain f residue   74 ASP
Chi-restraints excluded: chain f residue  102 THR
Chi-restraints excluded: chain f residue  130 THR
Chi-restraints excluded: chain g residue    7 VAL
Chi-restraints excluded: chain g residue   10 VAL
Chi-restraints excluded: chain g residue   14 GLN
Chi-restraints excluded: chain g residue   18 VAL
Chi-restraints excluded: chain g residue   26 ILE
Chi-restraints excluded: chain g residue   56 LYS
Chi-restraints excluded: chain g residue   66 CYS
Chi-restraints excluded: chain g residue   69 SER
Chi-restraints excluded: chain g residue   70 THR
Chi-restraints excluded: chain g residue   94 HIS
Chi-restraints excluded: chain g residue   96 ILE
Chi-restraints excluded: chain l residue   17 GLU
Chi-restraints excluded: chain l residue   19 VAL
Chi-restraints excluded: chain l residue  106 ILE
Chi-restraints excluded: chain l residue  113 THR
Chi-restraints excluded: chain l residue  118 ASN
Chi-restraints excluded: chain l residue  128 VAL
Chi-restraints excluded: chain m residue   12 ARG
Chi-restraints excluded: chain m residue   13 THR
Chi-restraints excluded: chain m residue   16 VAL
Chi-restraints excluded: chain m residue   21 VAL
Chi-restraints excluded: chain m residue   40 THR
Chi-restraints excluded: chain m residue   41 THR
Chi-restraints excluded: chain m residue   47 SER
Chi-restraints excluded: chain m residue   52 VAL
Chi-restraints excluded: chain m residue   67 ILE
Chi-restraints excluded: chain m residue   82 ILE
Chi-restraints excluded: chain p residue   22 THR
Chi-restraints excluded: chain p residue   54 ARG
Chi-restraints excluded: chain q residue   73 SER
Chi-restraints excluded: chain r residue   10 THR
Chi-restraints excluded: chain r residue   43 THR
Chi-restraints excluded: chain s residue   47 THR
Chi-restraints excluded: chain s residue   71 THR
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain u residue   34 ARG
Chi-restraints excluded: chain u residue   37 SER
Chi-restraints excluded: chain u residue   74 ARG
Chi-restraints excluded: chain v residue   42 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 193 optimal weight:    0.9990
   chunk 220 optimal weight:    0.7980
   chunk 244 optimal weight:    4.9990
   chunk 167 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 207 optimal weight:    0.5980
   chunk 143 optimal weight:    3.9990
   chunk 178 optimal weight:    1.9990
   chunk 227 optimal weight:    0.9990
   chunk 218 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
e  41 GLN
i  42 GLN
l  27 ASN
l  63 GLN
p  62 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.138552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.123145 restraints weight = 37413.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 0.22
r_work: 0.3063 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  36076  Z= 0.155
  Angle     :  0.584   9.757  53953  Z= 0.304
  Chirality :  0.036   0.259   6935
  Planarity :  0.004   0.053   2985
  Dihedral  : 22.979 179.668  17940
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 27.96 %
    Favored  : 65.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.22), residues: 1470
  helix:  0.59 (0.23), residues: 577
  sheet: -0.20 (0.33), residues: 233
  loop : -2.19 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP q  60 
 HIS   0.003   0.001   HIS p  48 
 PHE   0.013   0.001   PHE f 140 
 TYR   0.016   0.001   TYR m 117 
 ARG   0.009   0.000   ARG g  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06116 ( 1304)
  hydrogen bonds       : angle       3.05755 ( 2630)
  covalent geometry    : bond        0.00299 (36076)
  covalent geometry    : angle       0.58362 (53953)

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

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

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 171
  time to evaluate  : 1.860 
Fit side-chains
REVERT: e   20 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7296 (mt0)
REVERT: e   33 LYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6262 (tptt)
REVERT: e  158 LYS cc_start: 0.4780 (OUTLIER) cc_final: 0.4497 (tmtt)
REVERT: e  204 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7077 (mt-10)
REVERT: g   14 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6604 (mt0)
REVERT: i  125 GLU cc_start: 0.8497 (tt0) cc_final: 0.8238 (tt0)
REVERT: l   17 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6175 (mp0)
REVERT: l   41 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7767 (mt)
REVERT: l  111 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7791 (t0)
REVERT: p   54 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7269 (mtt180)
REVERT: q    1 MET cc_start: 0.8354 (ttm) cc_final: 0.8125 (ttm)
REVERT: r   29 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.7128 (ttm110)
REVERT: r   78 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8011 (pt0)
REVERT: s   31 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.8038 (mt0)
REVERT: u   34 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7600 (mtt90)
REVERT: v   54 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7834 (tttm)
  outliers start: 67
  outliers final: 49
  residues processed: 223
  average time/residue: 1.9865
  time to fit residues: 525.9624
Evaluate side-chains
  230 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 169
  time to evaluate  : 4.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain e residue   17 THR
Chi-restraints excluded: chain e residue   20 GLN
Chi-restraints excluded: chain e residue   33 LYS
Chi-restraints excluded: chain e residue   42 HIS
Chi-restraints excluded: chain e residue  103 VAL
Chi-restraints excluded: chain e residue  104 VAL
Chi-restraints excluded: chain e residue  130 ARG
Chi-restraints excluded: chain e residue  158 LYS
Chi-restraints excluded: chain e residue  166 GLN
Chi-restraints excluded: chain e residue  175 VAL
Chi-restraints excluded: chain e residue  178 SER
Chi-restraints excluded: chain e residue  192 ASP
Chi-restraints excluded: chain e residue  204 GLU
Chi-restraints excluded: chain e residue  205 LEU
Chi-restraints excluded: chain f residue   73 VAL
Chi-restraints excluded: chain f residue   74 ASP
Chi-restraints excluded: chain f residue  102 THR
Chi-restraints excluded: chain f residue  130 THR
Chi-restraints excluded: chain g residue    7 VAL
Chi-restraints excluded: chain g residue   10 VAL
Chi-restraints excluded: chain g residue   14 GLN
Chi-restraints excluded: chain g residue   18 VAL
Chi-restraints excluded: chain g residue   26 ILE
Chi-restraints excluded: chain g residue   56 LYS
Chi-restraints excluded: chain g residue   66 CYS
Chi-restraints excluded: chain g residue   69 SER
Chi-restraints excluded: chain g residue   70 THR
Chi-restraints excluded: chain g residue   77 LEU
Chi-restraints excluded: chain g residue   94 HIS
Chi-restraints excluded: chain g residue   96 ILE
Chi-restraints excluded: chain l residue   17 GLU
Chi-restraints excluded: chain l residue   41 LEU
Chi-restraints excluded: chain l residue  106 ILE
Chi-restraints excluded: chain l residue  108 SER
Chi-restraints excluded: chain l residue  111 ASP
Chi-restraints excluded: chain l residue  118 ASN
Chi-restraints excluded: chain l residue  128 VAL
Chi-restraints excluded: chain m residue   13 THR
Chi-restraints excluded: chain m residue   16 VAL
Chi-restraints excluded: chain m residue   21 VAL
Chi-restraints excluded: chain m residue   40 THR
Chi-restraints excluded: chain m residue   41 THR
Chi-restraints excluded: chain m residue   47 SER
Chi-restraints excluded: chain m residue   52 VAL
Chi-restraints excluded: chain m residue   67 ILE
Chi-restraints excluded: chain m residue   82 ILE
Chi-restraints excluded: chain p residue   22 THR
Chi-restraints excluded: chain p residue   54 ARG
Chi-restraints excluded: chain q residue   73 SER
Chi-restraints excluded: chain r residue   10 THR
Chi-restraints excluded: chain r residue   30 VAL
Chi-restraints excluded: chain r residue   43 THR
Chi-restraints excluded: chain r residue   78 GLU
Chi-restraints excluded: chain s residue   31 GLN
Chi-restraints excluded: chain s residue   47 THR
Chi-restraints excluded: chain s residue   71 THR
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain u residue   34 ARG
Chi-restraints excluded: chain u residue   37 SER
Chi-restraints excluded: chain u residue   74 ARG
Chi-restraints excluded: chain v residue   42 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 247
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 180 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 201 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 236 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 173 optimal weight:    0.0470
   chunk 239 optimal weight:    1.9990
   overall best weight:    1.7684

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

Flipped N/Q/H residues before XYZ refinement:
e  41 GLN
i  42 GLN
l  27 ASN
l  63 GLN
p  62 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.137873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.123000 restraints weight = 37353.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 0.50
r_work: 0.2955 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  36076  Z= 0.224
  Angle     :  0.608   8.269  53953  Z= 0.314
  Chirality :  0.039   0.265   6935
  Planarity :  0.005   0.053   2985
  Dihedral  : 22.953 179.691  17939
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  6.81 %
    Allowed  : 28.06 %
    Favored  : 65.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.22), residues: 1470
  helix:  0.61 (0.23), residues: 577
  sheet: -0.26 (0.33), residues: 237
  loop : -2.15 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP q  60 
 HIS   0.004   0.001   HIS m  96 
 PHE   0.014   0.001   PHE f 140 
 TYR   0.016   0.002   TYR m 117 
 ARG   0.008   0.000   ARG g  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06377 ( 1304)
  hydrogen bonds       : angle       3.06336 ( 2630)
  covalent geometry    : bond        0.00440 (36076)
  covalent geometry    : angle       0.60829 (53953)

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

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

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2940 Ramachandran restraints generated.
    1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 170
  time to evaluate  : 2.001 
Fit side-chains
REVERT: e   20 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7391 (mt0)
REVERT: e   33 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6200 (tptt)
REVERT: e  158 LYS cc_start: 0.4904 (OUTLIER) cc_final: 0.4599 (tmtt)
REVERT: e  193 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5318 (mt)
REVERT: e  204 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7193 (mt-10)
REVERT: f  110 MET cc_start: 0.8416 (mtm) cc_final: 0.7896 (mtt)
REVERT: i  125 GLU cc_start: 0.8576 (tt0) cc_final: 0.8310 (tt0)
REVERT: l   41 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7827 (mt)
REVERT: p   54 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7286 (mtt180)
REVERT: r   78 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8162 (pt0)
REVERT: u   34 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7643 (mtt90)
REVERT: v   54 LYS cc_start: 0.8243 (ttmm) cc_final: 0.7842 (tttm)
  outliers start: 68
  outliers final: 47
  residues processed: 223
  average time/residue: 1.5880
  time to fit residues: 420.0901
Evaluate side-chains
  225 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 169
  time to evaluate  : 1.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain e residue   17 THR
Chi-restraints excluded: chain e residue   20 GLN
Chi-restraints excluded: chain e residue   33 LYS
Chi-restraints excluded: chain e residue   42 HIS
Chi-restraints excluded: chain e residue  103 VAL
Chi-restraints excluded: chain e residue  104 VAL
Chi-restraints excluded: chain e residue  130 ARG
Chi-restraints excluded: chain e residue  158 LYS
Chi-restraints excluded: chain e residue  166 GLN
Chi-restraints excluded: chain e residue  175 VAL
Chi-restraints excluded: chain e residue  178 SER
Chi-restraints excluded: chain e residue  192 ASP
Chi-restraints excluded: chain e residue  193 LEU
Chi-restraints excluded: chain e residue  204 GLU
Chi-restraints excluded: chain e residue  205 LEU
Chi-restraints excluded: chain f residue   73 VAL
Chi-restraints excluded: chain f residue   74 ASP
Chi-restraints excluded: chain f residue  102 THR
Chi-restraints excluded: chain f residue  130 THR
Chi-restraints excluded: chain g residue    7 VAL
Chi-restraints excluded: chain g residue   10 VAL
Chi-restraints excluded: chain g residue   18 VAL
Chi-restraints excluded: chain g residue   26 ILE
Chi-restraints excluded: chain g residue   56 LYS
Chi-restraints excluded: chain g residue   66 CYS
Chi-restraints excluded: chain g residue   69 SER
Chi-restraints excluded: chain g residue   70 THR
Chi-restraints excluded: chain g residue   94 HIS
Chi-restraints excluded: chain g residue   96 ILE
Chi-restraints excluded: chain l residue   41 LEU
Chi-restraints excluded: chain l residue  106 ILE
Chi-restraints excluded: chain l residue  108 SER
Chi-restraints excluded: chain l residue  118 ASN
Chi-restraints excluded: chain l residue  128 VAL
Chi-restraints excluded: chain m residue   13 THR
Chi-restraints excluded: chain m residue   16 VAL
Chi-restraints excluded: chain m residue   21 VAL
Chi-restraints excluded: chain m residue   40 THR
Chi-restraints excluded: chain m residue   41 THR
Chi-restraints excluded: chain m residue   47 SER
Chi-restraints excluded: chain m residue   52 VAL
Chi-restraints excluded: chain m residue   67 ILE
Chi-restraints excluded: chain m residue   82 ILE
Chi-restraints excluded: chain p residue   22 THR
Chi-restraints excluded: chain p residue   54 ARG
Chi-restraints excluded: chain q residue   73 SER
Chi-restraints excluded: chain r residue   10 THR
Chi-restraints excluded: chain r residue   43 THR
Chi-restraints excluded: chain r residue   78 GLU
Chi-restraints excluded: chain s residue   47 THR
Chi-restraints excluded: chain s residue   71 THR
Chi-restraints excluded: chain u residue   32 ILE
Chi-restraints excluded: chain u residue   34 ARG
Chi-restraints excluded: chain u residue   37 SER
Chi-restraints excluded: chain u residue   74 ARG
Chi-restraints excluded: chain v residue   42 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 56.9494 > 50:
  distance: 11 - 15:   8.314
  distance: 15 - 16:  13.687
  distance: 15 - 21:  28.459
  distance: 16 - 17:  19.280
  distance: 16 - 19:  13.945
  distance: 17 - 18:   4.636
  distance: 17 - 22:  16.449
  distance: 19 - 20:  14.537
  distance: 20 - 21:  17.616
  distance: 22 - 23:  16.464
  distance: 23 - 24:   3.962
  distance: 23 - 26:  25.927
  distance: 24 - 25:  10.310
  distance: 24 - 31:  21.878
  distance: 25 - 52:  13.281
  distance: 31 - 32:  14.789
  distance: 32 - 33:  15.048
  distance: 32 - 35:  11.144
  distance: 33 - 34:  13.008
  distance: 33 - 40:  17.236
  distance: 34 - 57:  18.385
  distance: 35 - 36:  14.124
  distance: 36 - 37:   6.136
  distance: 37 - 38:  21.053
  distance: 38 - 39:  14.197
  distance: 40 - 41:  14.072
  distance: 41 - 42:  20.194
  distance: 41 - 44:   6.335
  distance: 42 - 43:  24.685
  distance: 42 - 47:  14.311
  distance: 43 - 66:  26.051
  distance: 44 - 46:  16.581
  distance: 47 - 48:  15.595
  distance: 48 - 49:  31.641
  distance: 48 - 51:  19.412
  distance: 49 - 50:  25.773
  distance: 49 - 52:  43.253
  distance: 53 - 54:  17.991
  distance: 53 - 56:  10.355
  distance: 54 - 55:  23.933
  distance: 54 - 57:  26.770
  distance: 57 - 58:   9.884
  distance: 58 - 59:   6.331
  distance: 58 - 61:   9.225
  distance: 59 - 60:   6.575
  distance: 59 - 66:   7.042
  distance: 61 - 62:  11.767
  distance: 62 - 63:  16.712
  distance: 63 - 64:   9.867
  distance: 64 - 65:  14.698
  distance: 66 - 67:   8.217
  distance: 67 - 68:  12.212
  distance: 67 - 70:   7.243
  distance: 68 - 69:  10.373
  distance: 68 - 77:   7.382
  distance: 70 - 71:   7.146
  distance: 71 - 72:  10.062
  distance: 72 - 73:   5.749
  distance: 74 - 75:   8.287
  distance: 74 - 76:  11.980
  distance: 77 - 78:   9.334
  distance: 78 - 79:  18.110
  distance: 79 - 80:  17.456
  distance: 79 - 81:  13.239
  distance: 81 - 82:   3.215
  distance: 82 - 83:  15.800
  distance: 82 - 85:  11.506
  distance: 83 - 84:  22.807
  distance: 85 - 86:  20.200
  distance: 86 - 87:   3.558
  distance: 87 - 88:  12.237
  distance: 88 - 89:  12.971