Starting phenix.real_space_refine
on Fri May 16 09:16:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sn7_40615/05_2025/8sn7_40615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sn7_40615/05_2025/8sn7_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sn7_40615/05_2025/8sn7_40615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sn7_40615/05_2025/8sn7_40615.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sn7_40615/05_2025/8sn7_40615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sn7_40615/05_2025/8sn7_40615.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      33      5.16       5
     C    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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.28, per 1000 atoms: 0.64
  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: 3.66
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  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: 6.62
  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: 5.89

  Time building geometry restraints manager: 4.28 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=" CG  LEU M  50 "
       pdb=" CD1 LEU M  50 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.08e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.33e+00
  bond pdb=" CB  GLU C 174 "
       pdb=" CG  GLU C 174 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.09e+00
  bond pdb=" CB  CYS E  96 "
       pdb=" SG  CYS E  96 "
    ideal  model  delta    sigma   weight residual
    1.808  1.775  0.033 3.30e-02 9.18e+02 1.02e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.452 -0.030 3.00e-02 1.11e+03 1.02e+00
  ... (remaining 15467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 21582
        1.56 -     3.12: 539
        3.12 -     4.68: 28
        4.68 -     6.24: 15
        6.24 -     7.80: 7
  Bond angle restraints: 22171
  Sorted by residual:
  angle pdb=" C   CYS K  31 "
        pdb=" N   ASN K  32 "
        pdb=" CA  ASN K  32 "
      ideal   model   delta    sigma   weight residual
     121.54  128.11   -6.57 1.91e+00 2.74e-01 1.18e+01
  angle pdb=" C3'  DG J -70 "
        pdb=" C2'  DG J -70 "
        pdb=" C1'  DG J -70 "
      ideal   model   delta    sigma   weight residual
     101.60  105.65   -4.05 1.50e+00 4.44e-01 7.31e+00
  angle pdb=" CB  MET L  38 "
        pdb=" CG  MET L  38 "
        pdb=" SD  MET L  38 "
      ideal   model   delta    sigma   weight residual
     112.70  120.02   -7.32 3.00e+00 1.11e-01 5.95e+00
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     122.46  125.89   -3.43 1.41e+00 5.03e-01 5.93e+00
  angle pdb=" CB  MET H  59 "
        pdb=" CG  MET H  59 "
        pdb=" SD  MET H  59 "
      ideal   model   delta    sigma   weight residual
     112.70  105.40    7.30 3.00e+00 1.11e-01 5.92e+00
  ... (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: 1777
       0.032 -    0.065: 559
       0.065 -    0.097: 128
       0.097 -    0.129: 46
       0.129 -    0.162: 6
  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=" 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
  chirality pdb=" CA  ILE L  54 "
            pdb=" N   ILE L  54 "
            pdb=" C   ILE L  54 "
            pdb=" CB  ILE L  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.12e-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:             0.890
  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:          0.570
  Check model and map are aligned:         0.120
  Set scattering table:                    0.140
  Process input model:                     42.520
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15482  Z= 0.165
  Angle     :  0.572   8.823  22186  Z= 0.329
  Chirality :  0.035   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (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
 TRP   0.007   0.001   TRP K  77 
 HIS   0.004   0.001   HIS D  82 
 PHE   0.008   0.001   PHE E  78 
 TYR   0.025   0.002   TYR M  59 
 ARG   0.005   0.000   ARG L 125 

Details of bonding type rmsd
  link_TRANS           : bond        0.00083 (    2)
  link_TRANS           : angle       0.23139 (    6)
  hydrogen bonds       : bond        0.10596 (  840)
  hydrogen bonds       : angle       4.21654 ( 2131)
  metal coordination   : bond        0.00765 (    8)
  metal coordination   : angle       3.87919 (    9)
  covalent geometry    : bond        0.00369 (15472)
  covalent geometry    : angle       0.56729 (22171)

*********************** 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  : 1.287 
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   34 LYS cc_start: 0.9132 (mtmm) cc_final: 0.8899 (mtmm)
REVERT: H   86 ARG cc_start: 0.8111 (mmt90) cc_final: 0.7804 (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: 0.7667 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.3268
  time to fit residues: 100.6119
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  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0770
   chunk 39 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    1.1142

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G -29 GLN
** 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 = 0.3702 r_free = 0.3702 target = 0.135839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.095582 restraints weight = 30561.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.094882 restraints weight = 35934.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.096507 restraints weight = 27434.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.0896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15482  Z= 0.192
  Angle     :  0.608  12.262  22186  Z= 0.343
  Chirality :  0.037   0.165   2516
  Planarity :  0.005   0.050   1794
  Dihedral  : 28.887 179.690   4413
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 10.39 %
    Favored  : 88.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.27), residues: 1057
  helix:  2.30 (0.21), residues: 649
  sheet: -1.11 (0.79), residues: 34
  loop : -0.67 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP L  33 
 HIS   0.004   0.001   HIS E  39 
 PHE   0.011   0.001   PHE L  62 
 TYR   0.023   0.002   TYR D  83 
 ARG   0.009   0.000   ARG H  92 

Details of bonding type rmsd
  link_TRANS           : bond        0.00201 (    2)
  link_TRANS           : angle       0.52959 (    6)
  hydrogen bonds       : bond        0.04987 (  840)
  hydrogen bonds       : angle       3.67547 ( 2131)
  metal coordination   : bond        0.00542 (    8)
  metal coordination   : angle       5.09397 (    9)
  covalent geometry    : bond        0.00441 (15472)
  covalent geometry    : angle       0.59940 (22171)

*********************** 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
  206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 195
  time to evaluate  : 1.270 
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: 0.8498 (pm20) cc_final: 0.8294 (pm20)
REVERT: E   76 GLN cc_start: 0.8352 (pp30) cc_final: 0.8051 (pp30)
REVERT: H   34 LYS cc_start: 0.9155 (mtmm) cc_final: 0.8880 (mtmm)
REVERT: H   86 ARG cc_start: 0.8225 (mmt90) cc_final: 0.7932 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9086 (ttpt) cc_final: 0.8570 (ttpt)
REVERT: L   63 LYS cc_start: 0.8807 (mmtp) cc_final: 0.8533 (mttt)
REVERT: L  114 ASN cc_start: 0.7874 (t0) cc_final: 0.7649 (m-40)
REVERT: L  127 TYR cc_start: 0.7754 (t80) cc_final: 0.7414 (t80)
REVERT: L  135 ASN cc_start: 0.8549 (m-40) cc_final: 0.8320 (m-40)
REVERT: L  147 MET cc_start: 0.7188 (mpp) cc_final: 0.6940 (mpp)
  outliers start: 11
  outliers final: 9
  residues processed: 198
  average time/residue: 0.3270
  time to fit residues: 89.5719
Evaluate side-chains
  194 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 185
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
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   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 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 121 optimal weight:    0.9990
   chunk 128 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 126 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 104 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  20 GLN
L  32 HIS
L  92 GLN
M  40 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.134860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.081776 restraints weight = 50064.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.083865 restraints weight = 26752.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.086018 restraints weight = 18251.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15482  Z= 0.189
  Angle     :  0.599  15.364  22186  Z= 0.338
  Chirality :  0.036   0.169   2516
  Planarity :  0.004   0.050   1794
  Dihedral  : 29.023 179.830   4413
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.12 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.27), residues: 1057
  helix:  2.30 (0.21), residues: 651
  sheet: -1.63 (0.73), residues: 33
  loop : -0.64 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP L  33 
 HIS   0.004   0.001   HIS E  39 
 PHE   0.009   0.001   PHE E  78 
 TYR   0.021   0.002   TYR L 134 
 ARG   0.005   0.000   ARG H  92 

Details of bonding type rmsd
  link_TRANS           : bond        0.00166 (    2)
  link_TRANS           : angle       0.48765 (    6)
  hydrogen bonds       : bond        0.04916 (  840)
  hydrogen bonds       : angle       3.60850 ( 2131)
  metal coordination   : bond        0.01292 (    8)
  metal coordination   : angle       6.24122 (    9)
  covalent geometry    : bond        0.00432 (15472)
  covalent geometry    : angle       0.58602 (22171)

*********************** 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
  215 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 195
  time to evaluate  : 1.234 
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: 0.8508 (pm20) cc_final: 0.8252 (pm20)
REVERT: E   76 GLN cc_start: 0.8609 (pp30) cc_final: 0.8151 (pp30)
REVERT: E   94 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8471 (mm-30)
REVERT: H   34 LYS cc_start: 0.9222 (mtmm) cc_final: 0.8942 (mtmm)
REVERT: H   86 ARG cc_start: 0.8218 (mmt90) cc_final: 0.7935 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8536 (ttpt)
REVERT: L   63 LYS cc_start: 0.8680 (mmtp) cc_final: 0.8414 (mttt)
REVERT: L  101 LYS cc_start: 0.9268 (mmmt) cc_final: 0.9047 (mmmm)
REVERT: L  127 TYR cc_start: 0.7843 (t80) cc_final: 0.7502 (t80)
REVERT: L  135 ASN cc_start: 0.9072 (m-40) cc_final: 0.8746 (m-40)
REVERT: L  147 MET cc_start: 0.8529 (mpp) cc_final: 0.8032 (mpp)
  outliers start: 20
  outliers final: 14
  residues processed: 201
  average time/residue: 0.3080
  time to fit residues: 86.1850
Evaluate side-chains
  202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 188
  time to evaluate  : 1.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 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 F residue   82 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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   chunk 90 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 98 optimal weight:    4.9990
   chunk 121 optimal weight:    0.8980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS
L  41 ASN
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 = 0.3688 r_free = 0.3688 target = 0.134678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.081251 restraints weight = 44275.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.084105 restraints weight = 24388.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.085017 restraints weight = 17332.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.2799
-------------------------------------------------------------------------------
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:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15482  Z= 0.184
  Angle     :  0.602  15.923  22186  Z= 0.337
  Chirality :  0.036   0.157   2516
  Planarity :  0.004   0.049   1794
  Dihedral  : 29.086 179.570   4413
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.85 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.26), residues: 1057
  helix:  2.38 (0.21), residues: 645
  sheet: -1.59 (0.70), residues: 33
  loop : -0.63 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP L  33 
 HIS   0.004   0.001   HIS E  39 
 PHE   0.019   0.002   PHE L  62 
 TYR   0.020   0.002   TYR K  84 
 ARG   0.005   0.000   ARG L   5 

Details of bonding type rmsd
  link_TRANS           : bond        0.00141 (    2)
  link_TRANS           : angle       0.46923 (    6)
  hydrogen bonds       : bond        0.04844 (  840)
  hydrogen bonds       : angle       3.56409 ( 2131)
  metal coordination   : bond        0.00786 (    8)
  metal coordination   : angle       6.29582 (    9)
  covalent geometry    : bond        0.00423 (15472)
  covalent geometry    : angle       0.58891 (22171)

*********************** 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
  209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 189
  time to evaluate  : 1.284 
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: 0.8477 (pm20) cc_final: 0.8250 (pm20)
REVERT: E   94 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8468 (mm-30)
REVERT: H   34 LYS cc_start: 0.9222 (mtmm) cc_final: 0.8950 (mtmm)
REVERT: H   86 ARG cc_start: 0.8206 (mmt90) cc_final: 0.7923 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9065 (ttpt) cc_final: 0.8524 (ttpt)
REVERT: L    0 HIS cc_start: 0.8393 (t-90) cc_final: 0.7842 (t-90)
REVERT: L    1 MET cc_start: 0.8274 (mmm) cc_final: 0.7896 (mmm)
REVERT: L  101 LYS cc_start: 0.9315 (mmmt) cc_final: 0.9090 (mmmm)
REVERT: L  136 ARG cc_start: 0.9429 (pmt-80) cc_final: 0.9138 (pmt-80)
REVERT: L  147 MET cc_start: 0.8773 (mpp) cc_final: 0.8289 (mpp)
  outliers start: 20
  outliers final: 15
  residues processed: 195
  average time/residue: 0.3232
  time to fit residues: 87.1964
Evaluate side-chains
  202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 187
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
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 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 F residue   82 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 125 optimal weight:    0.0050
   chunk 47 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0050
   chunk 2 optimal weight:    2.9990
   chunk 112 optimal weight:    9.9990
   chunk 45 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.4408

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

Flipped N/Q/H residues before XYZ refinement:
D  49 HIS
F  25 ASN
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 = 0.3690 r_free = 0.3690 target = 0.134520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.082255 restraints weight = 41685.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.084363 restraints weight = 25939.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.084747 restraints weight = 17893.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    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 = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.1616

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= 0.142
  Angle     :  0.572  13.026  22186  Z= 0.323
  Chirality :  0.034   0.161   2516
  Planarity :  0.004   0.062   1794
  Dihedral  : 29.026 179.614   4413
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.72 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.27), residues: 1057
  helix:  2.51 (0.21), residues: 648
  sheet: -1.45 (0.75), residues: 33
  loop : -0.55 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP L  33 
 HIS   0.003   0.000   HIS E  39 
 PHE   0.016   0.001   PHE L  51 
 TYR   0.016   0.001   TYR L 134 
 ARG   0.004   0.000   ARG L   5 

Details of bonding type rmsd
  link_TRANS           : bond        0.00067 (    2)
  link_TRANS           : angle       0.31793 (    6)
  hydrogen bonds       : bond        0.04138 (  840)
  hydrogen bonds       : angle       3.34558 ( 2131)
  metal coordination   : bond        0.00519 (    8)
  metal coordination   : angle       5.32898 (    9)
  covalent geometry    : bond        0.00308 (15472)
  covalent geometry    : angle       0.56201 (22171)

*********************** 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
  218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 199
  time to evaluate  : 1.221 
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: 0.8704 (pm20) cc_final: 0.8382 (pm20)
REVERT: E   59 GLU cc_start: 0.8467 (pm20) cc_final: 0.8185 (pm20)
REVERT: E   76 GLN cc_start: 0.8396 (pp30) cc_final: 0.8006 (pp30)
REVERT: H   34 LYS cc_start: 0.9258 (mtmm) cc_final: 0.8945 (mtmm)
REVERT: H   86 ARG cc_start: 0.8130 (mmt90) cc_final: 0.7873 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9013 (ttpt) cc_final: 0.8476 (ttpt)
REVERT: L    0 HIS cc_start: 0.8529 (t-90) cc_final: 0.8023 (t-90)
REVERT: L    1 MET cc_start: 0.8524 (mmm) cc_final: 0.8298 (mmm)
REVERT: L    5 ARG cc_start: 0.9219 (ttt-90) cc_final: 0.9010 (ttt-90)
REVERT: L   72 ARG cc_start: 0.6810 (ttt180) cc_final: 0.6480 (ttt180)
REVERT: L   92 GLN cc_start: 0.8089 (mm110) cc_final: 0.7236 (mm-40)
REVERT: L  127 TYR cc_start: 0.7680 (t80) cc_final: 0.7446 (t80)
REVERT: L  136 ARG cc_start: 0.9451 (pmt-80) cc_final: 0.9218 (pmt-80)
REVERT: L  147 MET cc_start: 0.8899 (mpp) cc_final: 0.8452 (mpp)
  outliers start: 19
  outliers final: 13
  residues processed: 205
  average time/residue: 0.3219
  time to fit residues: 91.3024
Evaluate side-chains
  200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 187
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
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   50 ILE
Chi-restraints excluded: chain C residue  128 CYS
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue -102 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 99 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 120 optimal weight:    4.9990
   chunk 124 optimal weight:   10.0000
   chunk 85 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3654 r_free = 0.3654 target = 0.131850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.077560 restraints weight = 43494.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.080614 restraints weight = 25253.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.080916 restraints weight = 16786.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2812
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    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 = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  15482  Z= 0.202
  Angle     :  0.615  14.630  22186  Z= 0.343
  Chirality :  0.037   0.373   2516
  Planarity :  0.004   0.050   1794
  Dihedral  : 29.184 178.783   4413
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.80 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.27), residues: 1057
  helix:  2.40 (0.21), residues: 648
  sheet: -1.58 (0.74), residues: 33
  loop : -0.59 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP L 141 
 HIS   0.004   0.001   HIS E  39 
 PHE   0.021   0.002   PHE L  62 
 TYR   0.024   0.002   TYR L 134 
 ARG   0.004   0.000   ARG H  92 

Details of bonding type rmsd
  link_TRANS           : bond        0.00162 (    2)
  link_TRANS           : angle       0.47672 (    6)
  hydrogen bonds       : bond        0.04957 (  840)
  hydrogen bonds       : angle       3.53461 ( 2131)
  metal coordination   : bond        0.00843 (    8)
  metal coordination   : angle       5.89765 (    9)
  covalent geometry    : bond        0.00471 (15472)
  covalent geometry    : angle       0.60369 (22171)

*********************** 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
  207 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 1.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8774 (pm20) cc_final: 0.8360 (pm20)
REVERT: E   59 GLU cc_start: 0.8551 (pm20) cc_final: 0.8249 (pm20)
REVERT: E   94 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8517 (mm-30)
REVERT: H   34 LYS cc_start: 0.9286 (mtmm) cc_final: 0.8973 (mtmm)
REVERT: H   86 ARG cc_start: 0.8267 (mmt90) cc_final: 0.7991 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8442 (ttpt)
REVERT: L    0 HIS cc_start: 0.8584 (t-90) cc_final: 0.7832 (t-90)
REVERT: L    1 MET cc_start: 0.8559 (mmm) cc_final: 0.8259 (mmm)
REVERT: L    5 ARG cc_start: 0.9272 (ttt-90) cc_final: 0.8997 (ttt-90)
REVERT: L   72 ARG cc_start: 0.6499 (ttt180) cc_final: 0.6291 (ttt180)
REVERT: L  147 MET cc_start: 0.8892 (mpp) cc_final: 0.8525 (mpp)
  outliers start: 22
  outliers final: 18
  residues processed: 195
  average time/residue: 0.3070
  time to fit residues: 83.1701
Evaluate side-chains
  199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 181
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
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   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 E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 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  143 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 123 optimal weight:   40.0000
   chunk 52 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9980
   chunk 73 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 118 optimal weight:    0.7980
   chunk 111 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
F  25 ASN
L  32 HIS
L  46 GLN
L  92 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.132704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.080568 restraints weight = 46258.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.082045 restraints weight = 23622.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.082701 restraints weight = 15464.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2805
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    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 = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2805
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15482  Z= 0.173
  Angle     :  0.595  13.543  22186  Z= 0.334
  Chirality :  0.035   0.249   2516
  Planarity :  0.004   0.049   1794
  Dihedral  : 29.192 179.236   4413
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.88 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.27), residues: 1057
  helix:  2.39 (0.21), residues: 648
  sheet: -1.53 (0.75), residues: 33
  loop : -0.58 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP L 141 
 HIS   0.003   0.001   HIS E  39 
 PHE   0.014   0.001   PHE L  51 
 TYR   0.018   0.001   TYR L 134 
 ARG   0.004   0.000   ARG H  92 

Details of bonding type rmsd
  link_TRANS           : bond        0.00111 (    2)
  link_TRANS           : angle       0.40864 (    6)
  hydrogen bonds       : bond        0.04655 (  840)
  hydrogen bonds       : angle       3.43818 ( 2131)
  metal coordination   : bond        0.00764 (    8)
  metal coordination   : angle       5.57275 (    9)
  covalent geometry    : bond        0.00393 (15472)
  covalent geometry    : angle       0.58407 (22171)

*********************** 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
  203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 182
  time to evaluate  : 1.269 
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: 0.8745 (pm20) cc_final: 0.8345 (pm20)
REVERT: E   59 GLU cc_start: 0.8509 (pm20) cc_final: 0.8216 (pm20)
REVERT: E   94 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8472 (mm-30)
REVERT: H   34 LYS cc_start: 0.9268 (mtmm) cc_final: 0.8947 (mtmm)
REVERT: H   86 ARG cc_start: 0.8235 (mmt90) cc_final: 0.7987 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8475 (ttpt)
REVERT: L    0 HIS cc_start: 0.8479 (t-90) cc_final: 0.7649 (t-90)
REVERT: L    1 MET cc_start: 0.8384 (mmm) cc_final: 0.8172 (mmm)
REVERT: L    5 ARG cc_start: 0.9183 (ttt-90) cc_final: 0.8922 (ttt-90)
REVERT: L   72 ARG cc_start: 0.6800 (ttt180) cc_final: 0.6408 (ttt180)
REVERT: L  140 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8522 (pm20)
REVERT: L  147 MET cc_start: 0.8670 (mpp) cc_final: 0.8290 (mpp)
  outliers start: 21
  outliers final: 16
  residues processed: 191
  average time/residue: 0.3141
  time to fit residues: 83.7624
Evaluate side-chains
  198 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 181
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
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   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 E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue -102 SER
Chi-restraints excluded: chain G residue  -95 SER
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 19 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 123 optimal weight:   30.0000
   chunk 42 optimal weight:    0.5980
   chunk 126 optimal weight:    0.9990
   chunk 109 optimal weight:    6.9990
   chunk 115 optimal weight:    7.9990
   chunk 25 optimal weight:    0.5980
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.7382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.133288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.081336 restraints weight = 44942.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.081761 restraints weight = 25032.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.083430 restraints weight = 17039.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2865
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    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 = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2865
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15482  Z= 0.158
  Angle     :  0.589  12.968  22186  Z= 0.330
  Chirality :  0.035   0.185   2516
  Planarity :  0.004   0.048   1794
  Dihedral  : 29.183 179.302   4413
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.42 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.27), residues: 1057
  helix:  2.43 (0.21), residues: 649
  sheet: -1.52 (0.73), residues: 33
  loop : -0.56 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP L 141 
 HIS   0.003   0.001   HIS E  39 
 PHE   0.021   0.001   PHE L  62 
 TYR   0.018   0.001   TYR L 134 
 ARG   0.009   0.000   ARG L 125 

Details of bonding type rmsd
  link_TRANS           : bond        0.00081 (    2)
  link_TRANS           : angle       0.36419 (    6)
  hydrogen bonds       : bond        0.04494 (  840)
  hydrogen bonds       : angle       3.36834 ( 2131)
  metal coordination   : bond        0.00691 (    8)
  metal coordination   : angle       5.32544 (    9)
  covalent geometry    : bond        0.00356 (15472)
  covalent geometry    : angle       0.57944 (22171)

*********************** 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
  200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 183
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8714 (pm20) cc_final: 0.8298 (pm20)
REVERT: E   59 GLU cc_start: 0.8489 (pm20) cc_final: 0.8180 (pm20)
REVERT: E   94 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8426 (mm-30)
REVERT: H   34 LYS cc_start: 0.9256 (mtmm) cc_final: 0.8953 (mtmm)
REVERT: H   86 ARG cc_start: 0.8198 (mmt90) cc_final: 0.7943 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8452 (ttpt)
REVERT: L    0 HIS cc_start: 0.8447 (t-90) cc_final: 0.7844 (t-90)
REVERT: L    1 MET cc_start: 0.8350 (mmm) cc_final: 0.8116 (mmm)
REVERT: L    5 ARG cc_start: 0.9140 (ttt-90) cc_final: 0.8854 (ttt-90)
REVERT: L   72 ARG cc_start: 0.6811 (ttt180) cc_final: 0.6407 (ttt180)
REVERT: L  140 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8431 (pm20)
REVERT: L  147 MET cc_start: 0.8626 (mpp) cc_final: 0.8248 (mpp)
  outliers start: 17
  outliers final: 15
  residues processed: 191
  average time/residue: 0.3045
  time to fit residues: 81.3316
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  : 1.212 
-------------------------------------------------------------------------------
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   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 F residue   82 THR
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
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 82 optimal weight:    4.9990
   chunk 117 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
L  46 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.129767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.085710 restraints weight = 34798.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.085140 restraints weight = 25562.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.085933 restraints weight = 23584.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  15482  Z= 0.269
  Angle     :  0.664  16.154  22186  Z= 0.367
  Chirality :  0.039   0.169   2516
  Planarity :  0.005   0.049   1794
  Dihedral  : 29.424 178.727   4413
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.64 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.27), residues: 1057
  helix:  2.15 (0.21), residues: 653
  sheet: -1.72 (0.72), residues: 39
  loop : -0.60 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L 141 
 HIS   0.004   0.001   HIS E  39 
 PHE   0.015   0.002   PHE L  51 
 TYR   0.018   0.002   TYR L 134 
 ARG   0.008   0.001   ARG L 125 

Details of bonding type rmsd
  link_TRANS           : bond        0.00318 (    2)
  link_TRANS           : angle       0.57742 (    6)
  hydrogen bonds       : bond        0.05751 (  840)
  hydrogen bonds       : angle       3.69917 ( 2131)
  metal coordination   : bond        0.01014 (    8)
  metal coordination   : angle       6.57595 (    9)
  covalent geometry    : bond        0.00637 (15472)
  covalent geometry    : angle       0.65034 (22171)

*********************** 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
  205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 184
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8765 (pm20) cc_final: 0.8318 (pm20)
REVERT: D  105 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7986 (mm-30)
REVERT: E   59 GLU cc_start: 0.8521 (pm20) cc_final: 0.8256 (pm20)
REVERT: E   61 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8998 (mm)
REVERT: H   34 LYS cc_start: 0.9309 (mtmm) cc_final: 0.9083 (mtmm)
REVERT: H   86 ARG cc_start: 0.8303 (mmt90) cc_final: 0.8032 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8530 (ttpp)
REVERT: K   42 SER cc_start: 0.7689 (p) cc_final: 0.7366 (p)
REVERT: L    0 HIS cc_start: 0.7975 (t-90) cc_final: 0.7470 (t-90)
REVERT: L  140 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7878 (pm20)
REVERT: L  147 MET cc_start: 0.7594 (mpp) cc_final: 0.7218 (mpp)
  outliers start: 21
  outliers final: 16
  residues processed: 193
  average time/residue: 0.3104
  time to fit residues: 82.9151
Evaluate side-chains
  200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 182
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
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   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 E residue   61 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   82 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 101 optimal weight:    0.2980
   chunk 115 optimal weight:    6.9990
   chunk 33 optimal weight:    0.5980
   chunk 120 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
L  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.133225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.088496 restraints weight = 33854.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.088320 restraints weight = 23948.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.089040 restraints weight = 22128.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    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 = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15482  Z= 0.153
  Angle     :  0.606  13.203  22186  Z= 0.337
  Chirality :  0.035   0.196   2516
  Planarity :  0.004   0.052   1794
  Dihedral  : 29.281 179.509   4413
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 18.40 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.27), residues: 1057
  helix:  2.38 (0.21), residues: 651
  sheet: -1.62 (0.73), residues: 38
  loop : -0.42 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L 141 
 HIS   0.003   0.001   HIS E  39 
 PHE   0.023   0.001   PHE L  62 
 TYR   0.020   0.001   TYR L 134 
 ARG   0.007   0.000   ARG L 125 

Details of bonding type rmsd
  link_TRANS           : bond        0.00082 (    2)
  link_TRANS           : angle       0.32910 (    6)
  hydrogen bonds       : bond        0.04563 (  840)
  hydrogen bonds       : angle       3.35467 ( 2131)
  metal coordination   : bond        0.00708 (    8)
  metal coordination   : angle       5.47407 (    9)
  covalent geometry    : bond        0.00341 (15472)
  covalent geometry    : angle       0.59642 (22171)

********************** 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
  204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 187
  time to evaluate  : 1.330 
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: 0.8716 (pm20) cc_final: 0.8264 (pm20)
REVERT: E   59 GLU cc_start: 0.8492 (pm20) cc_final: 0.8208 (pm20)
REVERT: E   94 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8469 (mm-30)
REVERT: H   34 LYS cc_start: 0.9239 (mtmm) cc_final: 0.8970 (mtmm)
REVERT: H   86 ARG cc_start: 0.8169 (mmt90) cc_final: 0.7930 (mmt-90)
REVERT: H  120 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8514 (ttpt)
REVERT: L    1 MET cc_start: 0.7834 (mmm) cc_final: 0.7479 (mmm)
REVERT: L    8 LYS cc_start: 0.9201 (mmtm) cc_final: 0.8990 (mmtm)
REVERT: L   92 GLN cc_start: 0.7601 (mm110) cc_final: 0.7205 (tp40)
REVERT: L  140 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7851 (pm20)
REVERT: L  147 MET cc_start: 0.7519 (mpp) cc_final: 0.7146 (mpp)
  outliers start: 17
  outliers final: 16
  residues processed: 194
  average time/residue: 0.3076
  time to fit residues: 83.7746
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  : 1.239 
-------------------------------------------------------------------------------
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   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 F residue   82 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
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 50 optimal weight:    2.9990
   chunk 110 optimal weight:    7.9990
   chunk 111 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.130774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.075505 restraints weight = 54020.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.078282 restraints weight = 28666.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.079424 restraints weight = 18866.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2818
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    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 = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2818
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  15482  Z= 0.223
  Angle     :  0.641  14.948  22186  Z= 0.355
  Chirality :  0.037   0.178   2516
  Planarity :  0.005   0.047   1794
  Dihedral  : 29.405 178.812   4413
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.61 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.27), residues: 1057
  helix:  2.23 (0.21), residues: 655
  sheet: -1.87 (0.69), residues: 39
  loop : -0.55 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L 141 
 HIS   0.007   0.001   HIS L   0 
 PHE   0.023   0.002   PHE L  51 
 TYR   0.019   0.002   TYR K  64 
 ARG   0.006   0.000   ARG L 125 

Details of bonding type rmsd
  link_TRANS           : bond        0.00208 (    2)
  link_TRANS           : angle       0.48401 (    6)
  hydrogen bonds       : bond        0.05301 (  840)
  hydrogen bonds       : angle       3.56990 ( 2131)
  metal coordination   : bond        0.00909 (    8)
  metal coordination   : angle       6.20989 (    9)
  covalent geometry    : bond        0.00522 (15472)
  covalent geometry    : angle       0.62834 (22171)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4803.84 seconds
wall clock time: 84 minutes 17.23 seconds (5057.23 seconds total)