Starting phenix.real_space_refine
on Thu Aug  6 07:47:39 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn7_40615/08_2026/8sn7_40615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn7_40615/08_2026/8sn7_40615.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn7_40615/08_2026/8sn7_40615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn7_40615/08_2026/8sn7_40615.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn7_40615/08_2026/8sn7_40615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn7_40615/08_2026/8sn7_40615.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8sn7_40615/08_2026/8sn7_40615.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8sn7_40615/08_2026/8sn7_40615.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      33      5.16       5
     C    8269      2.51       5
     N    2713      2.21       5
     O    3289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14600
  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: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    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      33.174  72.290  48.380  1.00 72.35           S
  ATOM  12446  SG  CYS K  51      31.114  69.178  47.704  1.00 73.71           S
  ATOM  12470  SG  CYS K  54      32.901  70.989  44.890  1.00 79.16           S
  ATOM  12187  SG  CYS K  16      22.600  66.502  53.978  1.00 79.23           S
  ATOM  12205  SG  CYS K  19      20.009  64.339  55.691  1.00 76.33           S
  ATOM  12335  SG  CYS K  36      23.168  65.453  57.650  1.00 74.99           S
  ATOM  12357  SG  CYS K  39      23.514  62.918  55.146  1.00 76.41           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: 2.99, per 1000 atoms: 0.20
  Number of scatterers: 14600
  At special positions: 0
  Unit cell: (110.224, 131.472, 127.488, 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    3289      8.00
     N    2713      7.00
     C    8269      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 124 " - " SER D 123 "
      " SER G-102 " - " SER H 123 "
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 405.0 milliseconds
  
  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  54 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
      pdb="  ZN K 302 "
        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  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
      Number of angles added : 9


  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 12 sheets defined
      62.9% alpha, 4.5% beta
      136 base pairs and 244 stacking pairs defined.
    Time for finding SS restraints: 1.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.543A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.683A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.919A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.675A  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 129 through 134
      removed outlier: 3.864A  pdb=" N   ALA C 134 " --> pdb=" O   ARG C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 150
    Processing helix  chain 'C' and resid 159 through 186
      removed outlier: 3.548A  pdb=" N   LEU C 178 " --> pdb=" O   GLU C 174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 202
    Processing helix  chain 'C' and resid 203 through 210
    Processing helix  chain 'C' and resid 225 through 229
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.795A  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: 3.602A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.504A  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: 3.697A  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
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 4.006A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.833A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.635A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid -97 through -92
    Processing helix  chain 'G' and resid -86 through -76
    Processing helix  chain 'G' and resid -67 through -40
    Processing helix  chain 'G' and resid -34 through -23
      removed outlier: 3.658A  pdb=" N   ASP G -23 " --> pdb=" O   ALA G -27 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid -22 through -16
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.549A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.650A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.730A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 10 through 15
      removed outlier: 3.895A  pdb=" N   GLN K  15 " --> pdb=" O   LEU K  11 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 36 through 47
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 3.861A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 4.025A  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 90
      removed outlier: 3.567A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
      removed outlier: 3.676A  pdb=" N   ARG L   5 " --> pdb=" O   MET L   1 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASP L  16 " --> pdb=" O   ASP L  12 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 4.132A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 3.575A  pdb=" N   ASP L 130 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 143
      removed outlier: 3.968A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 34
    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: 7.099A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 155 through 156
      removed outlier: 8.078A  pdb=" N   ARG C 155 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 190 through 191
    Processing sheet with id=AA6, first strand: chain 'C' and resid 214 through 215
      removed outlier: 7.013A  pdb=" N   THR C 214 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.205A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid -71 through -70
      removed outlier: 7.725A  pdb=" N   ARG G -71 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 28
      removed outlier: 3.558A  pdb=" N   LEU K  35 " --> pdb=" O   VAL K  27 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24
    Processing sheet with id=AB3, first strand: chain 'M' and resid 5 through 6

    491 hydrogen bonds defined for protein.
    1437 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      349 hydrogen bonds
      694 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      244 stacking parallelities
  Total time for adding SS restraints: 2.33

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3222
        1.33 -     1.45: 4431
        1.45 -     1.57: 7184
        1.57 -     1.69: 586
        1.69 -     1.81: 49
  Bond restraints: 15472
  Sorted by residual:
  bond pdb=" C3'  DA J -73 "
       pdb=" C2'  DA J -73 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.28e+01
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.09e+01
  bond pdb=" C3'  DT J -17 "
       pdb=" C2'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.06e+01
  bond pdb=" C3'  DA I -22 "
       pdb=" C2'  DA I -22 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.22e+00
  bond pdb=" C3'  DC I   0 "
       pdb=" C2'  DC I   0 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.12e+00
  ... (remaining 15467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 20986
        1.56 -     3.12: 1122
        3.12 -     4.68: 41
        4.68 -     6.24: 15
        6.24 -     7.80: 7
  Bond angle restraints: 22171
  Sorted by residual:
  angle pdb=" O4'  DT I -26 "
        pdb=" C4'  DT I -26 "
        pdb=" C3'  DT I -26 "
      ideal   model   delta    sigma   weight residual
     106.00  102.92    3.08 6.00e-01 2.78e+00 2.63e+01
  angle pdb=" O4'  DC J -71 "
        pdb=" C4'  DC J -71 "
        pdb=" C3'  DC J -71 "
      ideal   model   delta    sigma   weight residual
     106.00  103.04    2.96 6.00e-01 2.78e+00 2.43e+01
  angle pdb=" N3   DT J   9 "
        pdb=" C4   DT J   9 "
        pdb=" O4   DT J   9 "
      ideal   model   delta    sigma   weight residual
     119.90  122.68   -2.78 6.00e-01 2.78e+00 2.14e+01
  angle pdb=" N3   DT I  38 "
        pdb=" C4   DT I  38 "
        pdb=" O4   DT I  38 "
      ideal   model   delta    sigma   weight residual
     119.90  122.55   -2.65 6.00e-01 2.78e+00 1.95e+01
  angle pdb=" N3   DT I -17 "
        pdb=" C4   DT I -17 "
        pdb=" O4   DT I -17 "
      ideal   model   delta    sigma   weight residual
     119.90  122.53   -2.63 6.00e-01 2.78e+00 1.91e+01
  ... (remaining 22166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.74: 7274
       35.74 -    71.48: 1319
       71.48 -   107.22: 16
      107.22 -   142.96: 0
      142.96 -   178.70: 2
  Dihedral angle restraints: 8611
    sinusoidal: 5471
      harmonic: 3140
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   41.30  178.70     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   70.18  149.82     1      3.50e+01 8.16e-04 1.46e+01
  dihedral pdb=" CB  GLU D 105 "
           pdb=" CG  GLU D 105 "
           pdb=" CD  GLU D 105 "
           pdb=" OE1 GLU D 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.83  -89.83     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 8608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1478
       0.032 -    0.065: 670
       0.065 -    0.097: 240
       0.097 -    0.129: 120
       0.129 -    0.162: 8
  Chirality restraints: 2516
  Sorted by residual:
  chirality pdb=" CG  LEU F  62 "
            pdb=" CB  LEU F  62 "
            pdb=" CD1 LEU F  62 "
            pdb=" CD2 LEU F  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.54e-01
  chirality pdb=" C3'  DT J -17 "
            pdb=" C4'  DT J -17 "
            pdb=" O3'  DT J -17 "
            pdb=" C2'  DT J -17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.58   -0.15 2.00e-01 2.50e+01 5.79e-01
  chirality pdb=" CA  ASN K  32 "
            pdb=" N   ASN K  32 "
            pdb=" C   ASN K  32 "
            pdb=" CB  ASN K  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.24e-01
  ... (remaining 2513 not shown)

  Planarity restraints: 1796
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L  60 "   -0.048 5.00e-02 4.00e+02   7.34e-02 8.63e+00
        pdb=" N   PRO L  61 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO L  61 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO L  61 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS K  37 "    0.034 5.00e-02 4.00e+02   5.12e-02 4.20e+00
        pdb=" N   PRO K  38 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO K  38 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO K  38 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.027 2.00e-02 2.50e+03   1.15e-02 3.66e+00
        pdb=" N9   DA I -35 "    0.024 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1793 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1637
        2.75 -     3.29: 13071
        3.29 -     3.82: 27060
        3.82 -     4.36: 31252
        4.36 -     4.90: 46874
  Nonbonded interactions: 119894
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.210 2.496
  nonbonded pdb=" OG  SER L 138 "
            pdb=" NH1 ARG L 139 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" O   PRO L  40 "
            pdb=" OG  SER L  43 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   TYR C 152 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   ARG L 125 "
            pdb=" OG1 THR L 129 "
     model   vdw
     2.300 3.040
  ... (remaining 119889 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 -102 through 5)
}
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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.730
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
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      :  0.006   0.048  15482  Z= 0.477
  Angle     :  0.718   8.823  22186  Z= 0.609
  Chirality :  0.045   0.162   2516
  Planarity :  0.004   0.073   1794
  Dihedral  : 25.759 178.704   6577
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.26), residues: 1057
  helix:  2.34 (0.21), residues: 627
  sheet: -1.13 (0.72), residues: 41
  loop : -0.41 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 125 
 TYR   0.025   0.002   TYR M  59 
 PHE   0.008   0.001   PHE E  78 
 TRP   0.007   0.001   TRP K  77 
 HIS   0.004   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00554 /  0.48 (15472)
  covalent geometry    : angle       0.71384 /  0.61 (22171)
  hydrogen bonds       : bond        0.10596 /  6.66 (  840)
  hydrogen bonds       : angle       4.21654 /  2.94 ( 2131)
  metal coordination   : bond        0.00765 /  0.37 (    8)
  metal coordination   : angle       3.87919 /  1.75 (    9)
  link_TRANS           : bond        0.00083 /  0.04 (    2)
  link_TRANS           : angle       0.23139 /  0.12 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  116 LYS cc_start: 0.8814 (ttpp) cc_final: 0.8564 (ttmm)
REVERT: E   76 GLN cc_start: 0.8261 (pp30) cc_final: 0.8002 (pp30)
REVERT: H   86 ARG cc_start: 0.8111 (mmt90) cc_final: 0.7803 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8569 (ttpp)
REVERT: L   63 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8253 (mttt)
REVERT: L  114 ASN cc_start: 0.7881 (t0) cc_final: 0.7666 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1269
  time to fit residues: 39.5773
Evaluate side-chains
  189 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
F  25 ASN
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
** M  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  40 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 = 0.3707 r_free = 0.3707 target = 0.136264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.084739 restraints weight = 42249.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.086729 restraints weight = 23448.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.086699 restraints weight = 17121.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.086944 restraints weight = 15426.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.087191 restraints weight = 15286.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2825
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2825 r_free = 0.2825    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (11 function evaluations)
r_final: 0.2823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.0785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15482  Z= 0.172
  Angle     :  0.658  11.859  22186  Z= 0.372
  Chirality :  0.044   0.249   2516
  Planarity :  0.005   0.062   1794
  Dihedral  : 28.998 179.521   4413
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.17 %
    Favored  : 88.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.26), residues: 1057
  helix:  2.34 (0.21), residues: 644
  sheet: -1.47 (0.70), residues: 42
  loop : -0.53 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  92 
 TYR   0.036   0.002   TYR L 134 
 PHE   0.013   0.001   PHE L  62 
 TRP   0.020   0.002   TRP L  33 
 HIS   0.004   0.001   HIS L  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.17 (15472)
  covalent geometry    : angle       0.65047 /  0.37 (22171)
  hydrogen bonds       : bond        0.05627 /  3.75 (  840)
  hydrogen bonds       : angle       3.76823 /  2.61 ( 2131)
  metal coordination   : bond        0.00550 /  0.24 (    8)
  metal coordination   : angle       4.86933 /  2.07 (    9)
  link_TRANS           : bond        0.00146 /  0.07 (    2)
  link_TRANS           : angle       0.49991 /  0.24 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 194
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  116 LYS cc_start: 0.8877 (ttpp) cc_final: 0.8436 (ttmm)
REVERT: E   76 GLN cc_start: 0.8307 (pp30) cc_final: 0.7974 (pp30)
REVERT: E  120 MET cc_start: 0.8389 (mtp) cc_final: 0.8117 (mtt)
REVERT: H   86 ARG cc_start: 0.8220 (mmt90) cc_final: 0.7950 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9105 (ttpt) cc_final: 0.8519 (ttpt)
REVERT: L    8 LYS cc_start: 0.9410 (mmtm) cc_final: 0.9195 (mmtt)
REVERT: L   63 LYS cc_start: 0.8378 (mmtp) cc_final: 0.8019 (mttt)
REVERT: L   92 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7743 (mm-40)
REVERT: L  127 TYR cc_start: 0.7976 (t80) cc_final: 0.7266 (t80)
REVERT: L  133 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8353 (mmmt)
REVERT: L  136 ARG cc_start: 0.9409 (pmt-80) cc_final: 0.8909 (pmt-80)
  outliers start: 10
  outliers final: 7
  residues processed: 197
  average time/residue: 0.1301
  time to fit residues: 36.1380
Evaluate side-chains
  194 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 187
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain M residue   13 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0980
   chunk 39 optimal weight:    0.9980
   chunk 101 optimal weight:    6.9990
   chunk 77 optimal weight:    9.9990
   chunk 35 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  20 GLN
** 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 = 0.3708 r_free = 0.3708 target = 0.136357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.084047 restraints weight = 37634.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.085670 restraints weight = 26274.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.086710 restraints weight = 17402.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.087065 restraints weight = 14043.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.087281 restraints weight = 15031.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2825
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2825 r_free = 0.2825    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2825 r_free = 0.2825    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (8 function evaluations)
r_final: 0.2825
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.1075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  15482  Z= 0.146
  Angle     :  0.615  12.673  22186  Z= 0.351
  Chirality :  0.042   0.249   2516
  Planarity :  0.005   0.076   1794
  Dihedral  : 29.153 179.481   4413
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.69 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.27), residues: 1057
  helix:  2.42 (0.21), residues: 651
  sheet: -1.37 (0.72), residues: 39
  loop : -0.63 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  92 
 TYR   0.019   0.002   TYR K  84 
 PHE   0.011   0.001   PHE L  50 
 TRP   0.038   0.003   TRP L  33 
 HIS   0.004   0.001   HIS L  55 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.15 (15472)
  covalent geometry    : angle       0.60612 /  0.35 (22171)
  hydrogen bonds       : bond        0.05024 /  3.35 (  840)
  hydrogen bonds       : angle       3.56678 /  2.47 ( 2131)
  metal coordination   : bond        0.00700 /  0.37 (    8)
  metal coordination   : angle       5.20874 /  2.28 (    9)
  link_TRANS           : bond        0.00052 /  0.03 (    2)
  link_TRANS           : angle       0.43864 /  0.21 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 191
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 GLU cc_start: 0.8464 (pm20) cc_final: 0.8235 (pm20)
REVERT: E   76 GLN cc_start: 0.8265 (pp30) cc_final: 0.7852 (pp30)
REVERT: E  120 MET cc_start: 0.8291 (mtp) cc_final: 0.8072 (mtt)
REVERT: F   25 ASN cc_start: 0.9390 (OUTLIER) cc_final: 0.9158 (t0)
REVERT: H   86 ARG cc_start: 0.8158 (mmt90) cc_final: 0.7885 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9081 (ttpt) cc_final: 0.8527 (ttpt)
REVERT: L   63 LYS cc_start: 0.8531 (mmtp) cc_final: 0.8150 (mttt)
REVERT: L  127 TYR cc_start: 0.7811 (t80) cc_final: 0.7560 (t80)
REVERT: L  147 MET cc_start: 0.8352 (mpp) cc_final: 0.8004 (mpp)
  outliers start: 18
  outliers final: 11
  residues processed: 199
  average time/residue: 0.1399
  time to fit residues: 39.5935
Evaluate side-chains
  198 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 186
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain M residue   13 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 73 optimal weight:   20.0000
   chunk 7 optimal weight:    0.9980
   chunk 102 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
L  92 GLN
** 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 = 0.3712 r_free = 0.3712 target = 0.136632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.084393 restraints weight = 48655.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.086283 restraints weight = 25839.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.086971 restraints weight = 18425.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.087232 restraints weight = 15886.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.087528 restraints weight = 15204.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2807
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.2807
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15482  Z= 0.152
  Angle     :  0.630  16.122  22186  Z= 0.351
  Chirality :  0.042   0.264   2516
  Planarity :  0.005   0.058   1794
  Dihedral  : 29.294 178.729   4413
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.10 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.27), residues: 1057
  helix:  2.49 (0.21), residues: 645
  sheet: -1.17 (0.72), residues: 38
  loop : -0.59 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  72 
 TYR   0.023   0.002   TYR K  84 
 PHE   0.021   0.002   PHE L  62 
 TRP   0.035   0.003   TRP L  33 
 HIS   0.003   0.001   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.15 (15472)
  covalent geometry    : angle       0.61719 /  0.35 (22171)
  hydrogen bonds       : bond        0.05018 /  3.35 (  840)
  hydrogen bonds       : angle       3.55234 /  2.46 ( 2131)
  metal coordination   : bond        0.00744 /  0.34 (    8)
  metal coordination   : angle       6.25064 /  2.75 (    9)
  link_TRANS           : bond        0.00091 /  0.05 (    2)
  link_TRANS           : angle       0.40764 /  0.20 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 189
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 GLU cc_start: 0.8482 (pm20) cc_final: 0.8156 (pm20)
REVERT: E   76 GLN cc_start: 0.8369 (pp30) cc_final: 0.7937 (pp30)
REVERT: E  120 MET cc_start: 0.8333 (mtp) cc_final: 0.8109 (mtt)
REVERT: H   86 ARG cc_start: 0.8214 (mmt90) cc_final: 0.7947 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9044 (ttpt) cc_final: 0.8464 (ttpt)
REVERT: L   63 LYS cc_start: 0.8496 (mmtp) cc_final: 0.8138 (mttt)
REVERT: L  101 LYS cc_start: 0.9259 (mmmm) cc_final: 0.9057 (mmmm)
REVERT: L  127 TYR cc_start: 0.7785 (t80) cc_final: 0.7506 (t80)
REVERT: L  136 ARG cc_start: 0.9390 (pmt-80) cc_final: 0.9100 (pmt-80)
REVERT: L  147 MET cc_start: 0.8683 (mpp) cc_final: 0.8414 (mpp)
  outliers start: 15
  outliers final: 13
  residues processed: 194
  average time/residue: 0.1392
  time to fit residues: 38.3390
Evaluate side-chains
  199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 186
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 78 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 87 optimal weight:   20.0000
   chunk 98 optimal weight:   10.0000
   chunk 54 optimal weight:    0.4980
   chunk 126 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0970
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
F  25 ASN
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
L  92 GLN
** 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 = 0.3638 r_free = 0.3638 target = 0.130287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.075152 restraints weight = 42111.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.077830 restraints weight = 20527.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.079540 restraints weight = 13699.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.080572 restraints weight = 11047.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.080789 restraints weight = 9907.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15482  Z= 0.151
  Angle     :  0.627  14.123  22186  Z= 0.349
  Chirality :  0.042   0.251   2516
  Planarity :  0.004   0.061   1794
  Dihedral  : 29.382 178.726   4413
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.96 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.27), residues: 1057
  helix:  2.46 (0.21), residues: 647
  sheet: -1.15 (0.79), residues: 33
  loop : -0.58 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 125 
 TYR   0.016   0.001   TYR A  54 
 PHE   0.013   0.001   PHE L  51 
 TRP   0.025   0.002   TRP L  33 
 HIS   0.003   0.001   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.15 (15472)
  covalent geometry    : angle       0.61657 /  0.35 (22171)
  hydrogen bonds       : bond        0.04968 /  3.31 (  840)
  hydrogen bonds       : angle       3.49994 /  2.41 ( 2131)
  metal coordination   : bond        0.00588 /  0.26 (    8)
  metal coordination   : angle       5.65908 /  2.50 (    9)
  link_TRANS           : bond        0.00098 /  0.05 (    2)
  link_TRANS           : angle       0.42321 /  0.21 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 191
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8786 (pm20) cc_final: 0.8311 (pm20)
REVERT: C  205 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8236 (mm-30)
REVERT: E   59 GLU cc_start: 0.8601 (pm20) cc_final: 0.8209 (pm20)
REVERT: E   76 GLN cc_start: 0.8421 (pp30) cc_final: 0.7988 (pp30)
REVERT: E  120 MET cc_start: 0.8365 (mtp) cc_final: 0.8143 (mtt)
REVERT: H   86 ARG cc_start: 0.8261 (mmt90) cc_final: 0.8008 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8436 (ttpt)
REVERT: L   63 LYS cc_start: 0.8379 (mmtp) cc_final: 0.8012 (mttt)
REVERT: L  127 TYR cc_start: 0.7873 (t80) cc_final: 0.7558 (t80)
REVERT: L  136 ARG cc_start: 0.9380 (pmt-80) cc_final: 0.9145 (pmt-80)
REVERT: L  147 MET cc_start: 0.8734 (mpp) cc_final: 0.8491 (mpp)
  outliers start: 20
  outliers final: 15
  residues processed: 194
  average time/residue: 0.1227
  time to fit residues: 34.1233
Evaluate side-chains
  203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 188
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  231 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain G residue  -13 VAL
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 122 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 110 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
L  41 ASN
** 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 = 0.3669 r_free = 0.3669 target = 0.132929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.080278 restraints weight = 41692.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.081702 restraints weight = 23249.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.082237 restraints weight = 15808.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.082330 restraints weight = 14868.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.082628 restraints weight = 14403.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2828
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2828
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15482  Z= 0.154
  Angle     :  0.631  13.932  22186  Z= 0.349
  Chirality :  0.042   0.252   2516
  Planarity :  0.005   0.061   1794
  Dihedral  : 29.463 178.469   4413
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.29 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.27), residues: 1057
  helix:  2.43 (0.21), residues: 646
  sheet: -0.98 (0.76), residues: 38
  loop : -0.51 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 125 
 TYR   0.028   0.002   TYR L 134 
 PHE   0.022   0.002   PHE L  62 
 TRP   0.028   0.002   TRP L  33 
 HIS   0.003   0.001   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.15 (15472)
  covalent geometry    : angle       0.62123 /  0.35 (22171)
  hydrogen bonds       : bond        0.04992 /  3.32 (  840)
  hydrogen bonds       : angle       3.47919 /  2.40 ( 2131)
  metal coordination   : bond        0.00704 /  0.33 (    8)
  metal coordination   : angle       5.58460 /  2.46 (    9)
  link_TRANS           : bond        0.00099 /  0.05 (    2)
  link_TRANS           : angle       0.40772 /  0.20 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 190
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8752 (pm20) cc_final: 0.8294 (pm20)
REVERT: E   59 GLU cc_start: 0.8551 (pm20) cc_final: 0.8179 (pm20)
REVERT: E   76 GLN cc_start: 0.8483 (pp30) cc_final: 0.8094 (pp30)
REVERT: E   94 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8446 (mm-30)
REVERT: H   86 ARG cc_start: 0.8252 (mmt90) cc_final: 0.7988 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9039 (ttpt) cc_final: 0.8451 (ttpt)
REVERT: L  125 ARG cc_start: 0.8936 (mtm110) cc_final: 0.8555 (ptt-90)
REVERT: L  136 ARG cc_start: 0.9407 (pmt-80) cc_final: 0.9160 (pmt-80)
REVERT: L  147 MET cc_start: 0.8726 (mpp) cc_final: 0.8493 (mpp)
  outliers start: 24
  outliers final: 18
  residues processed: 200
  average time/residue: 0.1252
  time to fit residues: 35.6390
Evaluate side-chains
  205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 187
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  231 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain G residue  -13 VAL
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue   67 VAL
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 94 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 62 optimal weight:    0.3980
   chunk 23 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
L  46 GLN
L  92 GLN
** 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 = 0.3680 r_free = 0.3680 target = 0.133773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.081817 restraints weight = 43458.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.083036 restraints weight = 26059.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.083466 restraints weight = 19383.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.083755 restraints weight = 16640.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.083950 restraints weight = 16406.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15482  Z= 0.137
  Angle     :  0.617  12.731  22186  Z= 0.343
  Chirality :  0.041   0.248   2516
  Planarity :  0.004   0.059   1794
  Dihedral  : 29.451 178.316   4413
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.69 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.26), residues: 1057
  helix:  2.46 (0.21), residues: 648
  sheet: -1.24 (0.71), residues: 38
  loop : -0.49 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L   5 
 TYR   0.020   0.001   TYR L 134 
 PHE   0.015   0.001   PHE L  51 
 TRP   0.031   0.003   TRP L  33 
 HIS   0.003   0.001   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.14 (15472)
  covalent geometry    : angle       0.60824 /  0.34 (22171)
  hydrogen bonds       : bond        0.04745 /  3.15 (  840)
  hydrogen bonds       : angle       3.39783 /  2.34 ( 2131)
  metal coordination   : bond        0.00626 /  0.30 (    8)
  metal coordination   : angle       5.22681 /  2.30 (    9)
  link_TRANS           : bond        0.00060 /  0.03 (    2)
  link_TRANS           : angle       0.36101 /  0.18 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 190
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8705 (pm20) cc_final: 0.8282 (pm20)
REVERT: E   59 GLU cc_start: 0.8506 (pm20) cc_final: 0.8137 (pm20)
REVERT: E   76 GLN cc_start: 0.8518 (pp30) cc_final: 0.8077 (pp30)
REVERT: E   94 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8418 (mm-30)
REVERT: H   86 ARG cc_start: 0.8192 (mmt90) cc_final: 0.7937 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8468 (ttpt)
REVERT: L    5 ARG cc_start: 0.9151 (ttt-90) cc_final: 0.8728 (ttt-90)
REVERT: L   33 TRP cc_start: 0.8069 (m100) cc_final: 0.7360 (m100)
REVERT: L  140 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8591 (pm20)
REVERT: L  147 MET cc_start: 0.8734 (mpp) cc_final: 0.8512 (mpp)
  outliers start: 23
  outliers final: 18
  residues processed: 198
  average time/residue: 0.1339
  time to fit residues: 37.5724
Evaluate side-chains
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  128 CYS
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  231 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain G residue  -13 VAL
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain L residue  140 GLU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 103 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9980
   chunk 116 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 127 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 94 optimal weight:   10.0000
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  32 HIS
L  46 GLN
** 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 = 0.3674 r_free = 0.3674 target = 0.133343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.081061 restraints weight = 47049.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.082567 restraints weight = 24154.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.082736 restraints weight = 15828.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.083104 restraints weight = 17032.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.083272 restraints weight = 15007.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2873
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8743
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15482  Z= 0.151
  Angle     :  0.631  12.494  22186  Z= 0.348
  Chirality :  0.042   0.252   2516
  Planarity :  0.005   0.059   1794
  Dihedral  : 29.489 178.143   4413
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.13 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.26), residues: 1057
  helix:  2.45 (0.21), residues: 647
  sheet: -1.44 (0.70), residues: 38
  loop : -0.49 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L   5 
 TYR   0.018   0.001   TYR L 134 
 PHE   0.030   0.002   PHE L  50 
 TRP   0.025   0.003   TRP L  33 
 HIS   0.003   0.001   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.15 (15472)
  covalent geometry    : angle       0.62325 /  0.35 (22171)
  hydrogen bonds       : bond        0.04851 /  3.23 (  840)
  hydrogen bonds       : angle       3.42005 /  2.35 ( 2131)
  metal coordination   : bond        0.00624 /  0.31 (    8)
  metal coordination   : angle       5.09457 /  2.24 (    9)
  link_TRANS           : bond        0.00090 /  0.05 (    2)
  link_TRANS           : angle       0.38982 /  0.19 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8735 (pm20) cc_final: 0.8253 (pm20)
REVERT: E   59 GLU cc_start: 0.8563 (pm20) cc_final: 0.8228 (pm20)
REVERT: E   76 GLN cc_start: 0.8562 (pp30) cc_final: 0.8119 (pp30)
REVERT: E   94 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8423 (mm-30)
REVERT: H   86 ARG cc_start: 0.8239 (mmt90) cc_final: 0.7986 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9024 (ttpt) cc_final: 0.8435 (ttpt)
REVERT: K   42 SER cc_start: 0.7746 (p) cc_final: 0.7380 (p)
REVERT: L    5 ARG cc_start: 0.9136 (ttt-90) cc_final: 0.8720 (ttt-90)
REVERT: L   33 TRP cc_start: 0.8262 (m100) cc_final: 0.7603 (m100)
REVERT: L  140 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8642 (pm20)
REVERT: L  147 MET cc_start: 0.8838 (mpp) cc_final: 0.8632 (mpp)
  outliers start: 19
  outliers final: 16
  residues processed: 192
  average time/residue: 0.1409
  time to fit residues: 38.5188
Evaluate side-chains
  201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 184
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  231 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain G residue  -13 VAL
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain L residue  140 GLU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 87 optimal weight:   20.0000
   chunk 13 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.133556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.090780 restraints weight = 36594.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.089784 restraints weight = 26924.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.090896 restraints weight = 23682.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.091655 restraints weight = 17856.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.091805 restraints weight = 17709.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2997
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2997
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15482  Z= 0.147
  Angle     :  0.638  13.308  22186  Z= 0.349
  Chirality :  0.041   0.251   2516
  Planarity :  0.005   0.079   1794
  Dihedral  : 29.516 178.049   4413
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.88 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.94 (0.27), residues: 1057
  helix:  2.44 (0.21), residues: 647
  sheet: -1.42 (0.77), residues: 33
  loop : -0.54 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  92 
 TYR   0.024   0.001   TYR L  45 
 PHE   0.034   0.002   PHE L  62 
 TRP   0.028   0.003   TRP L 141 
 HIS   0.003   0.001   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.15 (15472)
  covalent geometry    : angle       0.62862 /  0.35 (22171)
  hydrogen bonds       : bond        0.04837 /  3.22 (  840)
  hydrogen bonds       : angle       3.40419 /  2.35 ( 2131)
  metal coordination   : bond        0.00617 /  0.30 (    8)
  metal coordination   : angle       5.38250 /  2.36 (    9)
  link_TRANS           : bond        0.00081 /  0.04 (    2)
  link_TRANS           : angle       0.37713 /  0.19 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 184
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8697 (pm20) cc_final: 0.8216 (pm20)
REVERT: E   59 GLU cc_start: 0.8508 (pm20) cc_final: 0.8231 (pm20)
REVERT: E   76 GLN cc_start: 0.8520 (pp30) cc_final: 0.8081 (pp30)
REVERT: E   94 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8412 (mm-30)
REVERT: H   86 ARG cc_start: 0.8224 (mmt90) cc_final: 0.7959 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9025 (ttpt) cc_final: 0.8524 (ttpt)
REVERT: L   33 TRP cc_start: 0.7682 (m100) cc_final: 0.7276 (m100)
REVERT: L  140 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7966 (pm20)
  outliers start: 18
  outliers final: 15
  residues processed: 192
  average time/residue: 0.1209
  time to fit residues: 33.5080
Evaluate side-chains
  196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 180
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  231 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain G residue  -13 VAL
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain L residue  140 GLU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 112 optimal weight:    0.0770
   chunk 18 optimal weight:    0.5980
   chunk 81 optimal weight:   10.0000
   chunk 97 optimal weight:    9.9990
   chunk 111 optimal weight:    5.9990
   chunk 104 optimal weight:    6.9990
   chunk 114 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 121 optimal weight:    1.9990
   chunk 86 optimal weight:   10.0000
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.8742

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  25 ASN
L  32 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.133481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.081337 restraints weight = 49414.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.082824 restraints weight = 24766.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.083774 restraints weight = 16089.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.084015 restraints weight = 16824.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.083873 restraints weight = 14629.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2811
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2811 r_free = 0.2811    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2811
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15482  Z= 0.152
  Angle     :  0.648  13.450  22186  Z= 0.353
  Chirality :  0.042   0.444   2516
  Planarity :  0.005   0.074   1794
  Dihedral  : 29.540 177.959   4413
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.21 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.26), residues: 1057
  helix:  2.43 (0.21), residues: 647
  sheet: -1.42 (0.79), residues: 33
  loop : -0.56 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  35 
 TYR   0.017   0.001   TYR L 134 
 PHE   0.027   0.002   PHE L  50 
 TRP   0.027   0.003   TRP L 141 
 HIS   0.003   0.001   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.15 (15472)
  covalent geometry    : angle       0.63832 /  0.35 (22171)
  hydrogen bonds       : bond        0.04905 /  3.27 (  840)
  hydrogen bonds       : angle       3.41297 /  2.37 ( 2131)
  metal coordination   : bond        0.00657 /  0.31 (    8)
  metal coordination   : angle       5.50691 /  2.41 (    9)
  link_TRANS           : bond        0.00087 /  0.05 (    2)
  link_TRANS           : angle       0.36972 /  0.18 (    6)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 182
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8723 (pm20) cc_final: 0.8228 (pm20)
REVERT: C  174 GLU cc_start: 0.8518 (tp30) cc_final: 0.8236 (tp30)
REVERT: E   59 GLU cc_start: 0.8556 (pm20) cc_final: 0.8222 (pm20)
REVERT: E   94 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8435 (mm-30)
REVERT: H   86 ARG cc_start: 0.8248 (mmt90) cc_final: 0.8001 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9023 (ttpt) cc_final: 0.8437 (ttpt)
REVERT: L    5 ARG cc_start: 0.9129 (ttt-90) cc_final: 0.8911 (ttt-90)
REVERT: L   33 TRP cc_start: 0.8234 (m100) cc_final: 0.7706 (m100)
REVERT: L  140 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8487 (pm20)
  outliers start: 17
  outliers final: 16
  residues processed: 188
  average time/residue: 0.1284
  time to fit residues: 34.2636
Evaluate side-chains
  197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 180
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  231 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
Chi-restraints excluded: chain G residue  -13 VAL
Chi-restraints excluded: chain L residue   69 PHE
Chi-restraints excluded: chain L residue   86 LEU
Chi-restraints excluded: chain L residue  140 GLU
Chi-restraints excluded: chain L residue  143 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 103 optimal weight:    8.9990
   chunk 128 optimal weight:    9.9990
   chunk 49 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 113 optimal weight:    6.9990
   chunk 24 optimal weight:    0.1980
   chunk 87 optimal weight:   20.0000
   chunk 123 optimal weight:    7.9990
   chunk 127 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   overall best weight:    2.1584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN
L  32 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.130082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.077393 restraints weight = 43063.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.078138 restraints weight = 23488.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.078730 restraints weight = 16916.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.079091 restraints weight = 15103.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.079261 restraints weight = 14583.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2717 r_free = 0.2717    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2717 r_free = 0.2717    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  15482  Z= 0.255
  Angle     :  0.733  15.841  22186  Z= 0.388
  Chirality :  0.046   0.325   2516
  Planarity :  0.005   0.062   1794
  Dihedral  : 29.764 178.144   4413
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.86 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.26), residues: 1057
  helix:  2.17 (0.21), residues: 647
  sheet: -1.65 (0.76), residues: 34
  loop : -0.69 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  40 
 TYR   0.028   0.003   TYR B  88 
 PHE   0.023   0.002   PHE L  50 
 TRP   0.027   0.003   TRP L  33 
 HIS   0.007   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00586 /  0.26 (15472)
  covalent geometry    : angle       0.72118 /  0.39 (22171)
  hydrogen bonds       : bond        0.06058 /  4.04 (  840)
  hydrogen bonds       : angle       3.72642 /  2.61 ( 2131)
  metal coordination   : bond        0.00989 /  0.49 (    8)
  metal coordination   : angle       6.45894 /  2.86 (    9)
  link_TRANS           : bond        0.00230 /  0.12 (    2)
  link_TRANS           : angle       0.57816 /  0.28 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2410.00 seconds
wall clock time: 42 minutes 8.23 seconds (2528.23 seconds total)