Starting phenix.real_space_refine
on Fri May 16 09:39:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sna_40618/05_2025/8sna_40618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sna_40618/05_2025/8sna_40618.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sna_40618/05_2025/8sna_40618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sna_40618/05_2025/8sna_40618.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sna_40618/05_2025/8sna_40618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sna_40618/05_2025/8sna_40618.cif"
  }
  resolution = 4.0
  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
     Zn      2      6.06       5
     P     294      5.49       5
     S      33      5.16       5
     C    8264      2.51       5
     N    2710      2.21       5
     O    3288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14591
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 682
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "M"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12296  SG  CYS K  31      52.091  72.096  45.471  1.00130.70           S
  ATOM  12446  SG  CYS K  51      50.512  68.670  45.375  1.00137.26           S
  ATOM  12470  SG  CYS K  54      52.924  69.743  42.642  1.00135.51           S
  ATOM  12187  SG  CYS K  16      41.580  66.180  52.218  1.00144.97           S
  ATOM  12205  SG  CYS K  19      40.762  63.036  54.186  1.00143.14           S
  ATOM  12335  SG  CYS K  36      43.515  65.426  55.432  1.00132.02           S
  ATOM  12357  SG  CYS K  39      43.985  63.037  52.593  1.00138.90           S

  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY M  76 " occ=0.25
  Time building chain proxies: 8.30, per 1000 atoms: 0.57
  Number of scatterers: 14591
  At special positions: 0
  Unit cell: (128.816, 130.144, 124.832, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      33     16.00
     P     294     15.00
     O    3288      8.00
     N    2710      7.00
     C    8264      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 3.32
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      Number of angles added : 9


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

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 11 sheets defined
      62.7% alpha, 5.4% beta
      135 base pairs and 239 stacking pairs defined.
    Time for finding SS restraints: 6.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.593A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.561A  pdb=" N   ARG A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.868A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.647A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.614A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.613A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.558A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.716A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.716A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.647A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.936A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.721A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.526A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.635A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.530A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'K' and resid 10 through 15
      removed outlier: 3.695A  pdb=" N   GLN K  15 " --> pdb=" O   LEU K  11 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 47
    Processing helix  chain 'K' and resid 58 through 68
      removed outlier: 3.533A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 4.279A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
      removed outlier: 3.596A  pdb=" N   ARG L   5 " --> pdb=" O   MET L   1 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.582A  pdb=" N   ALA L 124 " --> pdb=" O   VAL L 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 145
      removed outlier: 3.884A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing helix  chain 'M' and resid 37 through 39
      No H-bonds generated for 'chain 'M' and resid 37 through 39'
    Processing helix  chain 'M' and resid 56 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.796A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.784A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.362A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.520A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB1, first strand: chain 'L' and resid 21 through 24
    Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 16
      removed outlier: 3.559A  pdb=" N   HIS M  68 " --> pdb=" O   ILE M  44 " (cutoff:3.500A)

    499 hydrogen bonds defined for protein.
    1462 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      239 stacking parallelities
  Total time for adding SS restraints: 4.90

  Time building geometry restraints manager: 3.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3554
        1.34 -     1.46: 4330
        1.46 -     1.58: 6943
        1.58 -     1.70: 586
        1.70 -     1.82: 49
  Bond restraints: 15462
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.35e+00
  bond pdb=" CB  MET H  59 "
       pdb=" CG  MET H  59 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.22e+00
  bond pdb=" C3'  DA J -73 "
       pdb=" C2'  DA J -73 "
    ideal  model  delta    sigma   weight residual
    1.525  1.547 -0.022 2.00e-02 2.50e+03 1.20e+00
  bond pdb=" CA  ASP B  24 "
       pdb=" CB  ASP B  24 "
    ideal  model  delta    sigma   weight residual
    1.527  1.545 -0.018 1.70e-02 3.46e+03 1.15e+00
  bond pdb=" C4'  DT I -26 "
       pdb=" C3'  DT I -26 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.021 2.00e-02 2.50e+03 1.08e+00
  ... (remaining 15457 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 21726
        1.99 -     3.98: 400
        3.98 -     5.97: 27
        5.97 -     7.96: 1
        7.96 -     9.95: 2
  Bond angle restraints: 22156
  Sorted by residual:
  angle pdb=" C   TYR L  60 "
        pdb=" N   PRO L  61 "
        pdb=" CA  PRO L  61 "
      ideal   model   delta    sigma   weight residual
     127.00  136.95   -9.95 2.40e+00 1.74e-01 1.72e+01
  angle pdb=" C   TYR L  60 "
        pdb=" N   PRO L  61 "
        pdb=" CD  PRO L  61 "
      ideal   model   delta    sigma   weight residual
     120.60  112.27    8.33 2.20e+00 2.07e-01 1.43e+01
  angle pdb=" CA  ARG K  86 "
        pdb=" CB  ARG K  86 "
        pdb=" CG  ARG K  86 "
      ideal   model   delta    sigma   weight residual
     114.10  119.75   -5.65 2.00e+00 2.50e-01 7.99e+00
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     122.46  126.40   -3.94 1.41e+00 5.03e-01 7.80e+00
  angle pdb=" C3'  DG J -70 "
        pdb=" C2'  DG J -70 "
        pdb=" C1'  DG J -70 "
      ideal   model   delta    sigma   weight residual
     101.60  105.58   -3.98 1.50e+00 4.44e-01 7.05e+00
  ... (remaining 22151 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.45: 7269
       35.45 -    70.90: 1314
       70.90 -   106.36: 17
      106.36 -   141.81: 0
      141.81 -   177.26: 2
  Dihedral angle restraints: 8602
    sinusoidal: 5466
      harmonic: 3136
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   37.26 -177.26     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   72.91  147.09     1      3.50e+01 8.16e-04 1.44e+01
  dihedral pdb=" CG  ARG A 128 "
           pdb=" CD  ARG A 128 "
           pdb=" NE  ARG A 128 "
           pdb=" CZ  ARG A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.54   43.54     2      1.50e+01 4.44e-03 1.01e+01
  ... (remaining 8599 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1731
       0.030 -    0.061: 587
       0.061 -    0.091: 128
       0.091 -    0.121: 60
       0.121 -    0.151: 8
  Chirality restraints: 2514
  Sorted by residual:
  chirality pdb=" CA  ASP B  24 "
            pdb=" N   ASP B  24 "
            pdb=" C   ASP B  24 "
            pdb=" CB  ASP B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.74e-01
  chirality pdb=" CA  ARG L 136 "
            pdb=" N   ARG L 136 "
            pdb=" C   ARG L 136 "
            pdb=" CB  ARG L 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.01e-01
  chirality pdb=" CA  PRO E 121 "
            pdb=" N   PRO E 121 "
            pdb=" C   PRO E 121 "
            pdb=" CB  PRO E 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 2511 not shown)

  Planarity restraints: 1794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.025 2.00e-02 2.50e+03   1.05e-02 3.33e+00
        pdb=" N9   DG I  47 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.024 2.00e-02 2.50e+03   1.02e-02 2.84e+00
        pdb=" N9   DA I -35 "    0.020 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "   -0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO G  80 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1791 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 414
        2.68 -     3.24: 13010
        3.24 -     3.79: 26178
        3.79 -     4.35: 32343
        4.35 -     4.90: 47562
  Nonbonded interactions: 119507
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU K  45 "
            pdb=" NZ  LYS K  46 "
     model   vdw
     2.125 3.120
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.138 2.496
  nonbonded pdb=" OE2 GLU C  61 "
            pdb=" NH1 ARG K  63 "
     model   vdw
     2.194 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   PRO L  40 "
            pdb=" OG  SER L  43 "
     model   vdw
     2.222 3.040
  ... (remaining 119502 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.25 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     39.020
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15472  Z= 0.173
  Angle     :  0.591   9.951  22171  Z= 0.342
  Chirality :  0.035   0.151   2514
  Planarity :  0.004   0.058   1792
  Dihedral  : 25.679 177.259   6570
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.27), residues: 1056
  helix:  2.26 (0.21), residues: 639
  sheet:  0.73 (0.81), residues: 48
  loop : -0.45 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP L  33 
 HIS   0.004   0.001   HIS K  65 
 PHE   0.007   0.001   PHE L  62 
 TYR   0.023   0.002   TYR H  40 
 ARG   0.012   0.001   ARG K  86 

Details of bonding type rmsd
  link_TRANS           : bond        0.00231 (    2)
  link_TRANS           : angle       0.35621 (    6)
  hydrogen bonds       : bond        0.10479 (  846)
  hydrogen bonds       : angle       4.29032 ( 2152)
  metal coordination   : bond        0.00789 (    8)
  metal coordination   : angle       4.14638 (    9)
  covalent geometry    : bond        0.00384 (15462)
  covalent geometry    : angle       0.58555 (22156)

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

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   18 SER cc_start: 0.7819 (m) cc_final: 0.7514 (p)
REVERT: C   75 LYS cc_start: 0.9250 (mmtp) cc_final: 0.8951 (mmmm)
REVERT: C  111 ILE cc_start: 0.9141 (mt) cc_final: 0.8918 (tt)
REVERT: D   33 ARG cc_start: 0.8569 (ttm110) cc_final: 0.7930 (mtp-110)
REVERT: D   59 MET cc_start: 0.9391 (tpp) cc_final: 0.8980 (tpp)
REVERT: D  116 LYS cc_start: 0.9335 (tmtt) cc_final: 0.8991 (tttp)
REVERT: E   94 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7904 (mm-30)
REVERT: G   39 TYR cc_start: 0.8796 (m-80) cc_final: 0.8454 (m-80)
REVERT: G   56 GLU cc_start: 0.8353 (tt0) cc_final: 0.7968 (tt0)
REVERT: G   84 GLN cc_start: 0.9562 (tp-100) cc_final: 0.9354 (tp-100)
REVERT: H  120 LYS cc_start: 0.9184 (tttm) cc_final: 0.8906 (ttmt)
REVERT: K   39 CYS cc_start: 0.3631 (m) cc_final: 0.2810 (m)
REVERT: L   86 LEU cc_start: 0.8696 (tp) cc_final: 0.8403 (tp)
REVERT: L   97 LEU cc_start: 0.8363 (mt) cc_final: 0.8085 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.2901
  time to fit residues: 99.3270
Evaluate side-chains
  193 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 54 optimal weight:    0.3980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 101 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   chunk 117 optimal weight:   10.0000
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
E  68 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  62 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.119527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.078297 restraints weight = 43536.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.078283 restraints weight = 29112.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.078383 restraints weight = 32260.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  15472  Z= 0.168
  Angle     :  0.600  14.829  22171  Z= 0.338
  Chirality :  0.035   0.165   2514
  Planarity :  0.004   0.043   1792
  Dihedral  : 28.824 176.919   4410
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.05 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.27), residues: 1056
  helix:  2.31 (0.21), residues: 657
  sheet:  0.64 (0.83), residues: 47
  loop : -0.58 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  33 
 HIS   0.004   0.001   HIS K  65 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.021   0.002   TYR B  88 
 ARG   0.006   0.000   ARG D  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00111 (    2)
  link_TRANS           : angle       0.33346 (    6)
  hydrogen bonds       : bond        0.04534 (  846)
  hydrogen bonds       : angle       3.55051 ( 2152)
  metal coordination   : bond        0.00943 (    8)
  metal coordination   : angle       7.57857 (    9)
  covalent geometry    : bond        0.00375 (15462)
  covalent geometry    : angle       0.58026 (22156)

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

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 207
  time to evaluate  : 1.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8746 (tt0) cc_final: 0.8530 (tt0)
REVERT: C   18 SER cc_start: 0.7940 (m) cc_final: 0.7692 (p)
REVERT: C   75 LYS cc_start: 0.9224 (mmtp) cc_final: 0.8920 (mmmm)
REVERT: D   59 MET cc_start: 0.9379 (tpp) cc_final: 0.9077 (tpp)
REVERT: D  113 GLU cc_start: 0.8357 (tp30) cc_final: 0.7993 (tm-30)
REVERT: E   94 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8037 (mm-30)
REVERT: F   88 TYR cc_start: 0.7563 (m-80) cc_final: 0.7267 (m-10)
REVERT: G   56 GLU cc_start: 0.8324 (tt0) cc_final: 0.8054 (tt0)
REVERT: G   84 GLN cc_start: 0.9569 (tp-100) cc_final: 0.9245 (tp-100)
REVERT: H  120 LYS cc_start: 0.9108 (tttm) cc_final: 0.8827 (ttmt)
REVERT: K   35 LEU cc_start: 0.7127 (tp) cc_final: 0.6815 (mp)
REVERT: L   97 LEU cc_start: 0.8361 (mt) cc_final: 0.8075 (mt)
  outliers start: 12
  outliers final: 11
  residues processed: 212
  average time/residue: 0.2934
  time to fit residues: 86.5081
Evaluate side-chains
  198 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 187
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain M residue    5 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 102 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   chunk 125 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 121 optimal weight:    9.9990
   chunk 128 optimal weight:   20.0000
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
D  47 GLN
E  68 GLN
E 108 ASN
F  25 ASN
L   7 ASN
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.117765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.072899 restraints weight = 33886.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.072054 restraints weight = 28531.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.072541 restraints weight = 20868.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
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      :  0.005   0.055  15472  Z= 0.213
  Angle     :  0.616  12.020  22171  Z= 0.347
  Chirality :  0.036   0.164   2514
  Planarity :  0.004   0.057   1792
  Dihedral  : 28.900 176.447   4410
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.98 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.26), residues: 1056
  helix:  2.26 (0.21), residues: 650
  sheet:  0.48 (0.78), residues: 47
  loop : -0.65 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP L  33 
 HIS   0.004   0.001   HIS H  82 
 PHE   0.008   0.001   PHE H  70 
 TYR   0.034   0.002   TYR D  83 
 ARG   0.007   0.000   ARG D  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00181 (    2)
  link_TRANS           : angle       0.36803 (    6)
  hydrogen bonds       : bond        0.04773 (  846)
  hydrogen bonds       : angle       3.57738 ( 2152)
  metal coordination   : bond        0.02586 (    8)
  metal coordination   : angle       6.09963 (    9)
  covalent geometry    : bond        0.00487 (15462)
  covalent geometry    : angle       0.60427 (22156)

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

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 201
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8964 (tt0) cc_final: 0.8734 (tt0)
REVERT: B   59 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8667 (ttmm)
REVERT: B   88 TYR cc_start: 0.8229 (m-10) cc_final: 0.7059 (m-10)
REVERT: C   18 SER cc_start: 0.8380 (m) cc_final: 0.8061 (p)
REVERT: C   29 ARG cc_start: 0.8612 (ttm170) cc_final: 0.8076 (ttm170)
REVERT: D   35 GLU cc_start: 0.8445 (tp30) cc_final: 0.7737 (mm-30)
REVERT: D   59 MET cc_start: 0.9397 (tpp) cc_final: 0.9007 (tpp)
REVERT: D   83 TYR cc_start: 0.8354 (m-10) cc_final: 0.7898 (m-80)
REVERT: D  113 GLU cc_start: 0.8477 (tp30) cc_final: 0.7987 (tm-30)
REVERT: E   94 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8012 (mm-30)
REVERT: G   56 GLU cc_start: 0.8559 (tt0) cc_final: 0.8221 (tt0)
REVERT: G   84 GLN cc_start: 0.9547 (tp-100) cc_final: 0.9302 (tp-100)
REVERT: H  120 LYS cc_start: 0.9145 (tttm) cc_final: 0.8916 (ttmt)
REVERT: K   46 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7795 (mtmm)
REVERT: L   86 LEU cc_start: 0.8541 (tp) cc_final: 0.8270 (tt)
REVERT: L   97 LEU cc_start: 0.8521 (mt) cc_final: 0.8208 (mt)
REVERT: L  147 MET cc_start: 0.6999 (tpt) cc_final: 0.6348 (tpp)
  outliers start: 25
  outliers final: 14
  residues processed: 214
  average time/residue: 0.2895
  time to fit residues: 86.4738
Evaluate side-chains
  201 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 186
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   14 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 117 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 118 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
F  25 ASN
H  84 ASN
K  15 GLN
** L  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.114007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.064808 restraints weight = 52552.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.065533 restraints weight = 29654.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.065922 restraints weight = 19740.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.054  15472  Z= 0.347
  Angle     :  0.709  10.435  22171  Z= 0.395
  Chirality :  0.041   0.170   2514
  Planarity :  0.005   0.050   1792
  Dihedral  : 29.057 175.665   4410
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.18 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1056
  helix:  1.81 (0.21), residues: 655
  sheet:  0.30 (0.74), residues: 50
  loop : -0.85 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L  33 
 HIS   0.007   0.001   HIS H  82 
 PHE   0.011   0.002   PHE H  70 
 TYR   0.035   0.003   TYR D  83 
 ARG   0.009   0.001   ARG D  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00471 (    2)
  link_TRANS           : angle       0.63745 (    6)
  hydrogen bonds       : bond        0.05988 (  846)
  hydrogen bonds       : angle       4.06312 ( 2152)
  metal coordination   : bond        0.01323 (    8)
  metal coordination   : angle       4.90121 (    9)
  covalent geometry    : bond        0.00813 (15462)
  covalent geometry    : angle       0.70212 (22156)

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

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 180
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9109 (tt0) cc_final: 0.8872 (tt0)
REVERT: B   88 TYR cc_start: 0.8441 (m-10) cc_final: 0.7692 (m-10)
REVERT: D   35 GLU cc_start: 0.8630 (tp30) cc_final: 0.8053 (mm-30)
REVERT: D   59 MET cc_start: 0.9512 (tpp) cc_final: 0.9110 (tpp)
REVERT: E   68 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8668 (tt0)
REVERT: G   56 GLU cc_start: 0.8644 (tt0) cc_final: 0.8274 (tt0)
REVERT: G   95 LYS cc_start: 0.9137 (mtpp) cc_final: 0.8729 (ttmm)
REVERT: H   83 TYR cc_start: 0.7894 (m-80) cc_final: 0.7636 (m-80)
REVERT: H  120 LYS cc_start: 0.9180 (tttm) cc_final: 0.8936 (ttmt)
REVERT: K   46 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7384 (mtmm)
REVERT: K   68 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7435 (mtt180)
REVERT: L    5 ARG cc_start: 0.8523 (tmt-80) cc_final: 0.7889 (tmt170)
REVERT: L   97 LEU cc_start: 0.8052 (mt) cc_final: 0.7602 (mt)
  outliers start: 35
  outliers final: 22
  residues processed: 201
  average time/residue: 0.2793
  time to fit residues: 79.1462
Evaluate side-chains
  196 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 172
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   69 ASN
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   53 THR
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   14 THR
Chi-restraints excluded: chain M residue   52 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 122 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 104 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 117 optimal weight:    8.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
E  68 GLN
F  25 ASN
H  49 HIS
H  84 ASN
L  32 HIS
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  49 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.117833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.065774 restraints weight = 60644.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.067986 restraints weight = 30149.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.069414 restraints weight = 20294.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2806
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2806
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15472  Z= 0.177
  Angle     :  0.597  11.969  22171  Z= 0.340
  Chirality :  0.035   0.189   2514
  Planarity :  0.004   0.043   1792
  Dihedral  : 28.991 175.953   4410
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.81 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.26), residues: 1056
  helix:  2.18 (0.21), residues: 650
  sheet:  0.27 (0.73), residues: 50
  loop : -0.73 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP L  33 
 HIS   0.003   0.001   HIS K  65 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.022   0.002   TYR G  57 
 ARG   0.010   0.000   ARG D  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00082 (    2)
  link_TRANS           : angle       0.35447 (    6)
  hydrogen bonds       : bond        0.04473 (  846)
  hydrogen bonds       : angle       3.49726 ( 2152)
  metal coordination   : bond        0.01231 (    8)
  metal coordination   : angle       4.45327 (    9)
  covalent geometry    : bond        0.00398 (15462)
  covalent geometry    : angle       0.59072 (22156)

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

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9081 (tt0) cc_final: 0.8846 (tt0)
REVERT: B   88 TYR cc_start: 0.8360 (m-10) cc_final: 0.7573 (m-10)
REVERT: C   29 ARG cc_start: 0.8573 (ttm170) cc_final: 0.8289 (ttm110)
REVERT: D   35 GLU cc_start: 0.8517 (tp30) cc_final: 0.7986 (mm-30)
REVERT: D   59 MET cc_start: 0.9454 (tpp) cc_final: 0.9063 (tpp)
REVERT: D   85 LYS cc_start: 0.9301 (mtmm) cc_final: 0.9004 (mtmm)
REVERT: D  119 THR cc_start: 0.9222 (t) cc_final: 0.8998 (t)
REVERT: G   56 GLU cc_start: 0.8519 (tt0) cc_final: 0.8009 (tt0)
REVERT: G   95 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8578 (ttmm)
REVERT: H  120 LYS cc_start: 0.9039 (tttm) cc_final: 0.8792 (ttmt)
REVERT: K   46 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7319 (mtmm)
REVERT: K   68 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7428 (mtt180)
REVERT: L    5 ARG cc_start: 0.8572 (tmt-80) cc_final: 0.8012 (tmt170)
REVERT: L   86 LEU cc_start: 0.8452 (tp) cc_final: 0.8158 (tt)
REVERT: L   97 LEU cc_start: 0.7918 (mt) cc_final: 0.7554 (mt)
REVERT: M    6 LYS cc_start: 0.8972 (mptt) cc_final: 0.8756 (mptt)
REVERT: M   27 LYS cc_start: 0.9533 (ptmm) cc_final: 0.9286 (ptpp)
  outliers start: 25
  outliers final: 19
  residues processed: 217
  average time/residue: 0.2982
  time to fit residues: 90.5188
Evaluate side-chains
  211 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 191
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   14 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 93 optimal weight:    4.9990
   chunk 112 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
E  68 GLN
F  25 ASN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
L  46 GLN
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.115733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.066316 restraints weight = 68344.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.066892 restraints weight = 36360.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.067720 restraints weight = 24082.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  15472  Z= 0.275
  Angle     :  0.674  12.065  22171  Z= 0.372
  Chirality :  0.038   0.183   2514
  Planarity :  0.005   0.052   1792
  Dihedral  : 29.046 175.151   4410
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.89 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.26), residues: 1056
  helix:  2.06 (0.21), residues: 651
  sheet:  0.08 (0.71), residues: 50
  loop : -0.79 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP L  33 
 HIS   0.005   0.001   HIS H  82 
 PHE   0.011   0.002   PHE B  61 
 TYR   0.020   0.002   TYR H  83 
 ARG   0.010   0.001   ARG D  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00305 (    2)
  link_TRANS           : angle       0.51010 (    6)
  hydrogen bonds       : bond        0.05249 (  846)
  hydrogen bonds       : angle       3.79919 ( 2152)
  metal coordination   : bond        0.01339 (    8)
  metal coordination   : angle       6.25741 (    9)
  covalent geometry    : bond        0.00640 (15462)
  covalent geometry    : angle       0.66186 (22156)

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

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 188
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9118 (tt0) cc_final: 0.8880 (tt0)
REVERT: B   88 TYR cc_start: 0.8424 (m-10) cc_final: 0.7666 (m-10)
REVERT: C   29 ARG cc_start: 0.8780 (ttm170) cc_final: 0.8204 (ttm170)
REVERT: D   35 GLU cc_start: 0.8512 (tp30) cc_final: 0.7843 (mm-30)
REVERT: D   59 MET cc_start: 0.9492 (tpp) cc_final: 0.9096 (tpp)
REVERT: G   56 GLU cc_start: 0.8511 (tt0) cc_final: 0.8221 (tt0)
REVERT: G   95 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8657 (ttmm)
REVERT: H  120 LYS cc_start: 0.9084 (tttm) cc_final: 0.8819 (ttmt)
REVERT: K   20 MET cc_start: 0.8364 (mmp) cc_final: 0.8131 (mmp)
REVERT: K   22 ILE cc_start: 0.8088 (mm) cc_final: 0.7843 (mm)
REVERT: K   46 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7533 (mtmm)
REVERT: K   68 ARG cc_start: 0.7657 (mtt180) cc_final: 0.7441 (mtt180)
REVERT: L   52 LEU cc_start: 0.9294 (tt) cc_final: 0.8962 (tt)
REVERT: L   97 LEU cc_start: 0.8062 (mt) cc_final: 0.7813 (mt)
REVERT: M    6 LYS cc_start: 0.8947 (mptt) cc_final: 0.8724 (mptt)
REVERT: M   27 LYS cc_start: 0.9610 (ptmm) cc_final: 0.9371 (ptpp)
  outliers start: 28
  outliers final: 24
  residues processed: 204
  average time/residue: 0.2843
  time to fit residues: 81.8676
Evaluate side-chains
  209 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   69 ASN
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   53 THR
Chi-restraints excluded: chain L residue  109 LEU
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   14 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 125 optimal weight:   10.0000
   chunk 81 optimal weight:    4.9990
   chunk 116 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 113 optimal weight:    9.9990
   chunk 62 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  20 GLN
L  32 HIS
L  55 HIS
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.118273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.080119 restraints weight = 50531.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.080616 restraints weight = 42620.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.080272 restraints weight = 45881.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2977
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2976 r_free = 0.2976    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2976
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15472  Z= 0.173
  Angle     :  0.619  12.711  22171  Z= 0.344
  Chirality :  0.035   0.196   2514
  Planarity :  0.004   0.049   1792
  Dihedral  : 29.004 175.653   4410
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 20.20 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.26), residues: 1056
  helix:  2.23 (0.21), residues: 649
  sheet:  0.12 (0.70), residues: 50
  loop : -0.78 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP L  33 
 HIS   0.004   0.001   HIS K  65 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.020   0.002   TYR G  57 
 ARG   0.011   0.000   ARG D  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00073 (    2)
  link_TRANS           : angle       0.40303 (    6)
  hydrogen bonds       : bond        0.04332 (  846)
  hydrogen bonds       : angle       3.45811 ( 2152)
  metal coordination   : bond        0.00934 (    8)
  metal coordination   : angle       6.02676 (    9)
  covalent geometry    : bond        0.00393 (15462)
  covalent geometry    : angle       0.60712 (22156)

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

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 201
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9019 (tt0) cc_final: 0.8812 (tt0)
REVERT: B   88 TYR cc_start: 0.8204 (m-10) cc_final: 0.7486 (m-10)
REVERT: C   29 ARG cc_start: 0.8341 (ttm170) cc_final: 0.7537 (ttm170)
REVERT: D   35 GLU cc_start: 0.8491 (tp30) cc_final: 0.7848 (mm-30)
REVERT: D  119 THR cc_start: 0.9159 (t) cc_final: 0.8930 (t)
REVERT: G   56 GLU cc_start: 0.8537 (tt0) cc_final: 0.8031 (tt0)
REVERT: G   95 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8504 (ttmm)
REVERT: H  120 LYS cc_start: 0.9002 (tttm) cc_final: 0.8741 (ttmt)
REVERT: L   52 LEU cc_start: 0.8600 (tt) cc_final: 0.8253 (tt)
REVERT: M   24 GLU cc_start: 0.8717 (mp0) cc_final: 0.8515 (mp0)
  outliers start: 23
  outliers final: 19
  residues processed: 210
  average time/residue: 0.2917
  time to fit residues: 85.3605
Evaluate side-chains
  205 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 186
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain M residue    5 VAL
Chi-restraints excluded: chain M residue   52 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 60 optimal weight:    0.4980
   chunk 50 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0040
   chunk 14 optimal weight:    0.9980
   chunk 125 optimal weight:    0.0370
   chunk 19 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.4070

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
K  15 GLN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  20 GLN
L  32 HIS
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.120140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.079018 restraints weight = 44108.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.078502 restraints weight = 32547.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.078993 restraints weight = 35412.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  15472  Z= 0.149
  Angle     :  0.608  13.580  22171  Z= 0.338
  Chirality :  0.035   0.218   2514
  Planarity :  0.004   0.050   1792
  Dihedral  : 28.956 175.800   4410
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 21.61 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.26), residues: 1056
  helix:  2.25 (0.21), residues: 649
  sheet:  0.05 (0.68), residues: 43
  loop : -0.76 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  33 
 HIS   0.003   0.001   HIS K  65 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.022   0.001   TYR G  57 
 ARG   0.012   0.000   ARG D  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00053 (    2)
  link_TRANS           : angle       0.33802 (    6)
  hydrogen bonds       : bond        0.03948 (  846)
  hydrogen bonds       : angle       3.33231 ( 2152)
  metal coordination   : bond        0.02005 (    8)
  metal coordination   : angle       4.45086 (    9)
  covalent geometry    : bond        0.00326 (15462)
  covalent geometry    : angle       0.60154 (22156)

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

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 199
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8264 (m-10) cc_final: 0.7747 (m-10)
REVERT: C   29 ARG cc_start: 0.8424 (ttm170) cc_final: 0.7603 (ttm170)
REVERT: D   35 GLU cc_start: 0.8405 (tp30) cc_final: 0.7717 (mm-30)
REVERT: D   85 LYS cc_start: 0.9226 (mtmm) cc_final: 0.8931 (mtmm)
REVERT: D  119 THR cc_start: 0.9116 (t) cc_final: 0.8877 (t)
REVERT: G   56 GLU cc_start: 0.8465 (tt0) cc_final: 0.8233 (tt0)
REVERT: H  120 LYS cc_start: 0.9026 (tttm) cc_final: 0.8764 (ttmt)
REVERT: L   30 MET cc_start: 0.8226 (tpp) cc_final: 0.8023 (tpp)
REVERT: L   52 LEU cc_start: 0.8632 (tt) cc_final: 0.8275 (tt)
REVERT: L   86 LEU cc_start: 0.8570 (tp) cc_final: 0.8334 (tt)
  outliers start: 18
  outliers final: 12
  residues processed: 206
  average time/residue: 0.2982
  time to fit residues: 86.1188
Evaluate side-chains
  199 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 187
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain M residue    5 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 117 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 114 optimal weight:   10.0000
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.119006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.080999 restraints weight = 49885.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.080770 restraints weight = 44127.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.080873 restraints weight = 46536.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2987
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15472  Z= 0.182
  Angle     :  0.628  13.718  22171  Z= 0.348
  Chirality :  0.036   0.218   2514
  Planarity :  0.004   0.058   1792
  Dihedral  : 28.972 175.520   4410
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 22.37 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.26), residues: 1056
  helix:  2.20 (0.21), residues: 648
  sheet:  0.09 (0.70), residues: 43
  loop : -0.78 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  33 
 HIS   0.003   0.001   HIS K  65 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.025   0.002   TYR F  88 
 ARG   0.012   0.000   ARG D  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00100 (    2)
  link_TRANS           : angle       0.40615 (    6)
  hydrogen bonds       : bond        0.04351 (  846)
  hydrogen bonds       : angle       3.45350 ( 2152)
  metal coordination   : bond        0.01608 (    8)
  metal coordination   : angle       4.20792 (    9)
  covalent geometry    : bond        0.00415 (15462)
  covalent geometry    : angle       0.62288 (22156)

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

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 188
  time to evaluate  : 1.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8110 (m-10) cc_final: 0.7548 (m-10)
REVERT: C   29 ARG cc_start: 0.8398 (ttm170) cc_final: 0.7541 (ttm170)
REVERT: D   35 GLU cc_start: 0.8375 (tp30) cc_final: 0.7746 (mm-30)
REVERT: D   85 LYS cc_start: 0.9253 (mtmm) cc_final: 0.8948 (mtmm)
REVERT: F   88 TYR cc_start: 0.8201 (m-80) cc_final: 0.7955 (m-80)
REVERT: G   56 GLU cc_start: 0.8451 (tt0) cc_final: 0.7970 (tt0)
REVERT: H   59 MET cc_start: 0.8915 (tpt) cc_final: 0.8655 (tpp)
REVERT: H  120 LYS cc_start: 0.9023 (tttm) cc_final: 0.8756 (ttmt)
REVERT: L   52 LEU cc_start: 0.8536 (tt) cc_final: 0.8180 (tt)
REVERT: L   66 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8305 (mppt)
REVERT: L   86 LEU cc_start: 0.8566 (tp) cc_final: 0.8353 (tt)
  outliers start: 17
  outliers final: 16
  residues processed: 196
  average time/residue: 0.2885
  time to fit residues: 79.4832
Evaluate side-chains
  196 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 180
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain K residue   70 SER
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain M residue    5 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 82 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 59 optimal weight:    0.3980
   chunk 6 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 109 optimal weight:    8.9990
   chunk 55 optimal weight:    0.7980
   chunk 118 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
H  84 ASN
L  32 HIS
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.120170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.073655 restraints weight = 52768.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.073954 restraints weight = 32669.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.073858 restraints weight = 22865.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2875
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2875
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15472  Z= 0.156
  Angle     :  0.623  13.919  22171  Z= 0.345
  Chirality :  0.035   0.224   2514
  Planarity :  0.004   0.058   1792
  Dihedral  : 28.944 175.905   4410
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 22.91 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.26), residues: 1056
  helix:  2.23 (0.21), residues: 648
  sheet: -0.06 (0.71), residues: 42
  loop : -0.80 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L  33 
 HIS   0.004   0.001   HIS K  65 
 PHE   0.012   0.001   PHE A  67 
 TYR   0.024   0.002   TYR G  57 
 ARG   0.013   0.000   ARG D  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00015 (    2)
  link_TRANS           : angle       0.35829 (    6)
  hydrogen bonds       : bond        0.04076 (  846)
  hydrogen bonds       : angle       3.36452 ( 2152)
  metal coordination   : bond        0.01261 (    8)
  metal coordination   : angle       3.79727 (    9)
  covalent geometry    : bond        0.00347 (15462)
  covalent geometry    : angle       0.61849 (22156)

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

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 188
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8235 (m-10) cc_final: 0.7649 (m-10)
REVERT: C   29 ARG cc_start: 0.8573 (ttm170) cc_final: 0.7833 (ttm170)
REVERT: D   35 GLU cc_start: 0.8377 (tp30) cc_final: 0.7653 (mm-30)
REVERT: D   85 LYS cc_start: 0.9313 (mtmm) cc_final: 0.9003 (mtmm)
REVERT: D  119 THR cc_start: 0.9247 (t) cc_final: 0.9019 (t)
REVERT: G   56 GLU cc_start: 0.8491 (tt0) cc_final: 0.8073 (tt0)
REVERT: H  120 LYS cc_start: 0.9020 (tttm) cc_final: 0.8742 (ttmt)
REVERT: L   52 LEU cc_start: 0.8977 (tt) cc_final: 0.8590 (tt)
REVERT: L   66 LYS cc_start: 0.8774 (mtmm) cc_final: 0.8323 (mppt)
REVERT: L   86 LEU cc_start: 0.8618 (tp) cc_final: 0.8413 (tt)
  outliers start: 12
  outliers final: 12
  residues processed: 195
  average time/residue: 0.2800
  time to fit residues: 76.8958
Evaluate side-chains
  194 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 182
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   15 CYS
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   44 VAL
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain M residue    5 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 124 optimal weight:    9.9990
   chunk 59 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 128 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
L  32 HIS
** M  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.119147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.078383 restraints weight = 45247.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.078194 restraints weight = 34408.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.079055 restraints weight = 27899.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2970
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2970
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15472  Z= 0.185
  Angle     :  0.637  13.686  22171  Z= 0.353
  Chirality :  0.036   0.221   2514
  Planarity :  0.004   0.061   1792
  Dihedral  : 28.966 175.584   4410
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 22.48 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.26), residues: 1056
  helix:  2.22 (0.21), residues: 648
  sheet: -0.17 (0.70), residues: 43
  loop : -0.84 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  33 
 HIS   0.005   0.001   HIS H  82 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.031   0.002   TYR H  83 
 ARG   0.013   0.000   ARG D  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00098 (    2)
  link_TRANS           : angle       0.41214 (    6)
  hydrogen bonds       : bond        0.04338 (  846)
  hydrogen bonds       : angle       3.47952 ( 2152)
  metal coordination   : bond        0.01144 (    8)
  metal coordination   : angle       3.72010 (    9)
  covalent geometry    : bond        0.00420 (15462)
  covalent geometry    : angle       0.63319 (22156)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4535.02 seconds
wall clock time: 79 minutes 40.93 seconds (4780.93 seconds total)